Starting phenix.real_space_refine on Thu Sep 26 15:36:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x6k_22076/09_2024/6x6k_22076.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x6k_22076/09_2024/6x6k_22076.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x6k_22076/09_2024/6x6k_22076.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x6k_22076/09_2024/6x6k_22076.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x6k_22076/09_2024/6x6k_22076.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x6k_22076/09_2024/6x6k_22076.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 196 5.16 5 C 39060 2.51 5 N 10332 2.21 5 O 11382 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 252 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 60970 Number of models: 1 Model: "" Number of chains: 42 Chain: "AT" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1502 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 5, 'TRANS': 173} Chain breaks: 3 Chain: "AX" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1275 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "AY" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1578 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain breaks: 1 Chain: "BT" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1502 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 5, 'TRANS': 173} Chain breaks: 3 Chain: "BX" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1275 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "BY" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1578 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain breaks: 1 Chain: "CT" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1502 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 5, 'TRANS': 173} Chain breaks: 3 Chain: "CX" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1275 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "CY" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1578 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain breaks: 1 Chain: "DT" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1502 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 5, 'TRANS': 173} Chain breaks: 3 Chain: "DX" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1275 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "DY" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1578 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain breaks: 1 Chain: "ET" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1502 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 5, 'TRANS': 173} Chain breaks: 3 Chain: "EX" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1275 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "EY" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1578 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain breaks: 1 Chain: "FT" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1502 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 5, 'TRANS': 173} Chain breaks: 3 Chain: "FX" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1275 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "FY" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1578 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain breaks: 1 Chain: "GT" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1502 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 5, 'TRANS': 173} Chain breaks: 3 Chain: "GX" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1275 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "GY" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1578 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain breaks: 1 Chain: "HT" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1502 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 5, 'TRANS': 173} Chain breaks: 3 Chain: "HX" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1275 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "HY" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1578 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain breaks: 1 Chain: "IT" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1502 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 5, 'TRANS': 173} Chain breaks: 3 Chain: "IX" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1275 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "IY" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1578 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain breaks: 1 Chain: "JT" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1502 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 5, 'TRANS': 173} Chain breaks: 3 Chain: "JX" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1275 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "JY" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1578 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain breaks: 1 Chain: "KT" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1502 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 5, 'TRANS': 173} Chain breaks: 3 Chain: "KX" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1275 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "KY" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1578 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain breaks: 1 Chain: "LT" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1502 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 5, 'TRANS': 173} Chain breaks: 3 Chain: "LX" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1275 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "LY" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1578 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain breaks: 1 Chain: "MT" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1502 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 5, 'TRANS': 173} Chain breaks: 3 Chain: "MX" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1275 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "MY" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1578 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain breaks: 1 Chain: "NT" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1502 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 5, 'TRANS': 173} Chain breaks: 3 Chain: "NX" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1275 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "NY" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1578 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain breaks: 1 Time building chain proxies: 25.17, per 1000 atoms: 0.41 Number of scatterers: 60970 At special positions: 0 Unit cell: (231, 231, 141, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 196 16.00 O 11382 8.00 N 10332 7.00 C 39060 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: 11.20 Conformation dependent library (CDL) restraints added in 5.8 seconds 14812 Ramachandran restraints generated. 7406 Oldfield, 0 Emsley, 7406 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14392 Finding SS restraints... Secondary structure from input PDB file: 154 helices and 126 sheets defined 33.0% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.55 Creating SS restraints... Processing helix chain 'AT' and resid 79 through 90 Processing helix chain 'AT' and resid 98 through 113 Processing helix chain 'AT' and resid 191 through 221 removed outlier: 4.423A pdb=" N ILEAT 195 " --> pdb=" O GLNAT 191 " (cutoff:3.500A) Processing helix chain 'AT' and resid 287 through 307 removed outlier: 3.859A pdb=" N TYRAT 297 " --> pdb=" O ARGAT 293 " (cutoff:3.500A) Processing helix chain 'AX' and resid 362 through 393 removed outlier: 4.015A pdb=" N LYSAX 393 " --> pdb=" O HISAX 389 " (cutoff:3.500A) Processing helix chain 'AX' and resid 411 through 415 removed outlier: 3.550A pdb=" N ILEAX 414 " --> pdb=" O SERAX 411 " (cutoff:3.500A) Processing helix chain 'AX' and resid 460 through 464 Processing helix chain 'AY' and resid 1793 through 1798 Processing helix chain 'AY' and resid 1798 through 1821 Proline residue: AY1815 - end of helix Processing helix chain 'AY' and resid 1850 through 1863 Processing helix chain 'AY' and resid 1897 through 1909 Processing helix chain 'BT' and resid 79 through 90 Processing helix chain 'BT' and resid 98 through 113 Processing helix chain 'BT' and resid 191 through 221 removed outlier: 4.423A pdb=" N ILEBT 195 " --> pdb=" O GLNBT 191 " (cutoff:3.500A) Processing helix chain 'BT' and resid 287 through 307 removed outlier: 3.859A pdb=" N TYRBT 297 " --> pdb=" O ARGBT 293 " (cutoff:3.500A) Processing helix chain 'BX' and resid 362 through 393 removed outlier: 4.015A pdb=" N LYSBX 393 " --> pdb=" O HISBX 389 " (cutoff:3.500A) Processing helix chain 'BX' and resid 411 through 415 removed outlier: 3.551A pdb=" N ILEBX 414 " --> pdb=" O SERBX 411 " (cutoff:3.500A) Processing helix chain 'BX' and resid 460 through 464 Processing helix chain 'BY' and resid 1793 through 1798 Processing helix chain 'BY' and resid 1798 through 1821 Proline residue: BY1815 - end of helix Processing helix chain 'BY' and resid 1850 through 1863 Processing helix chain 'BY' and resid 1897 through 1909 Processing helix chain 'CT' and resid 79 through 90 Processing helix chain 'CT' and resid 98 through 113 Processing helix chain 'CT' and resid 191 through 221 removed outlier: 4.423A pdb=" N ILECT 195 " --> pdb=" O GLNCT 191 " (cutoff:3.500A) Processing helix chain 'CT' and resid 287 through 307 removed outlier: 3.859A pdb=" N TYRCT 297 " --> pdb=" O ARGCT 293 " (cutoff:3.500A) Processing helix chain 'CX' and resid 362 through 393 removed outlier: 4.014A pdb=" N LYSCX 393 " --> pdb=" O HISCX 389 " (cutoff:3.500A) Processing helix chain 'CX' and resid 411 through 415 removed outlier: 3.550A pdb=" N ILECX 414 " --> pdb=" O SERCX 411 " (cutoff:3.500A) Processing helix chain 'CX' and resid 460 through 464 Processing helix chain 'CY' and resid 1793 through 1798 Processing helix chain 'CY' and resid 1798 through 1821 Proline residue: CY1815 - end of helix Processing helix chain 'CY' and resid 1850 through 1863 Processing helix chain 'CY' and resid 1897 through 1909 Processing helix chain 'DT' and resid 79 through 90 Processing helix chain 'DT' and resid 98 through 113 Processing helix chain 'DT' and resid 191 through 221 removed outlier: 4.423A pdb=" N ILEDT 195 " --> pdb=" O GLNDT 191 " (cutoff:3.500A) Processing helix chain 'DT' and resid 287 through 307 removed outlier: 3.857A pdb=" N TYRDT 297 " --> pdb=" O ARGDT 293 " (cutoff:3.500A) Processing helix chain 'DX' and resid 362 through 393 removed outlier: 4.014A pdb=" N LYSDX 393 " --> pdb=" O HISDX 389 " (cutoff:3.500A) Processing helix chain 'DX' and resid 411 through 415 removed outlier: 3.550A pdb=" N ILEDX 414 " --> pdb=" O SERDX 411 " (cutoff:3.500A) Processing helix chain 'DX' and resid 460 through 464 Processing helix chain 'DY' and resid 1793 through 1798 Processing helix chain 'DY' and resid 1798 through 1821 Proline residue: DY1815 - end of helix Processing helix chain 'DY' and resid 1850 through 1863 Processing helix chain 'DY' and resid 1897 through 1909 Processing helix chain 'ET' and resid 79 through 90 Processing helix chain 'ET' and resid 98 through 113 Processing helix chain 'ET' and resid 191 through 221 removed outlier: 4.423A pdb=" N ILEET 195 " --> pdb=" O GLNET 191 " (cutoff:3.500A) Processing helix chain 'ET' and resid 287 through 307 removed outlier: 3.858A pdb=" N TYRET 297 " --> pdb=" O ARGET 293 " (cutoff:3.500A) Processing helix chain 'EX' and resid 362 through 393 removed outlier: 4.015A pdb=" N LYSEX 393 " --> pdb=" O HISEX 389 " (cutoff:3.500A) Processing helix chain 'EX' and resid 411 through 415 removed outlier: 3.550A pdb=" N ILEEX 414 " --> pdb=" O SEREX 411 " (cutoff:3.500A) Processing helix chain 'EX' and resid 460 through 464 Processing helix chain 'EY' and resid 1793 through 1798 Processing helix chain 'EY' and resid 1798 through 1821 Proline residue: EY1815 - end of helix Processing helix chain 'EY' and resid 1850 through 1863 Processing helix chain 'EY' and resid 1897 through 1909 Processing helix chain 'FT' and resid 79 through 90 Processing helix chain 'FT' and resid 98 through 113 Processing helix chain 'FT' and resid 191 through 221 removed outlier: 4.423A pdb=" N ILEFT 195 " --> pdb=" O GLNFT 191 " (cutoff:3.500A) Processing helix chain 'FT' and resid 287 through 307 removed outlier: 3.858A pdb=" N TYRFT 297 " --> pdb=" O ARGFT 293 " (cutoff:3.500A) Processing helix chain 'FX' and resid 362 through 393 removed outlier: 4.015A pdb=" N LYSFX 393 " --> pdb=" O HISFX 389 " (cutoff:3.500A) Processing helix chain 'FX' and resid 411 through 415 removed outlier: 3.551A pdb=" N ILEFX 414 " --> pdb=" O SERFX 411 " (cutoff:3.500A) Processing helix chain 'FX' and resid 460 through 464 Processing helix chain 'FY' and resid 1793 through 1798 Processing helix chain 'FY' and resid 1798 through 1821 Proline residue: FY1815 - end of helix Processing helix chain 'FY' and resid 1850 through 1863 Processing helix chain 'FY' and resid 1897 through 1909 Processing helix chain 'GT' and resid 79 through 90 Processing helix chain 'GT' and resid 98 through 113 Processing helix chain 'GT' and resid 191 through 221 removed outlier: 4.422A pdb=" N ILEGT 195 " --> pdb=" O GLNGT 191 " (cutoff:3.500A) Processing helix chain 'GT' and resid 287 through 307 removed outlier: 3.858A pdb=" N TYRGT 297 " --> pdb=" O ARGGT 293 " (cutoff:3.500A) Processing helix chain 'GX' and resid 362 through 393 removed outlier: 4.014A pdb=" N LYSGX 393 " --> pdb=" O HISGX 389 " (cutoff:3.500A) Processing helix chain 'GX' and resid 411 through 415 removed outlier: 3.550A pdb=" N ILEGX 414 " --> pdb=" O SERGX 411 " (cutoff:3.500A) Processing helix chain 'GX' and resid 460 through 464 Processing helix chain 'GY' and resid 1793 through 1798 Processing helix chain 'GY' and resid 1798 through 1821 Proline residue: GY1815 - end of helix Processing helix chain 'GY' and resid 1850 through 1863 Processing helix chain 'GY' and resid 1897 through 1909 Processing helix chain 'HT' and resid 79 through 90 Processing helix chain 'HT' and resid 98 through 113 Processing helix chain 'HT' and resid 191 through 221 removed outlier: 4.423A pdb=" N ILEHT 195 " --> pdb=" O GLNHT 191 " (cutoff:3.500A) Processing helix chain 'HT' and resid 287 through 307 removed outlier: 3.858A pdb=" N TYRHT 297 " --> pdb=" O ARGHT 293 " (cutoff:3.500A) Processing helix chain 'HX' and resid 362 through 393 removed outlier: 4.015A pdb=" N LYSHX 393 " --> pdb=" O HISHX 389 " (cutoff:3.500A) Processing helix chain 'HX' and resid 411 through 415 removed outlier: 3.550A pdb=" N ILEHX 414 " --> pdb=" O SERHX 411 " (cutoff:3.500A) Processing helix chain 'HX' and resid 460 through 464 Processing helix chain 'HY' and resid 1793 through 1798 Processing helix chain 'HY' and resid 1798 through 1821 Proline residue: HY1815 - end of helix Processing helix chain 'HY' and resid 1850 through 1863 Processing helix chain 'HY' and resid 1897 through 1909 Processing helix chain 'IT' and resid 79 through 90 Processing helix chain 'IT' and resid 98 through 113 Processing helix chain 'IT' and resid 191 through 221 removed outlier: 4.423A pdb=" N ILEIT 195 " --> pdb=" O GLNIT 191 " (cutoff:3.500A) Processing helix chain 'IT' and resid 287 through 307 removed outlier: 3.858A pdb=" N TYRIT 297 " --> pdb=" O ARGIT 293 " (cutoff:3.500A) Processing helix chain 'IX' and resid 362 through 393 removed outlier: 4.015A pdb=" N LYSIX 393 " --> pdb=" O HISIX 389 " (cutoff:3.500A) Processing helix chain 'IX' and resid 411 through 415 removed outlier: 3.550A pdb=" N ILEIX 414 " --> pdb=" O SERIX 411 " (cutoff:3.500A) Processing helix chain 'IX' and resid 460 through 464 Processing helix chain 'IY' and resid 1793 through 1798 Processing helix chain 'IY' and resid 1798 through 1821 Proline residue: IY1815 - end of helix Processing helix chain 'IY' and resid 1850 through 1863 Processing helix chain 'IY' and resid 1897 through 1909 Processing helix chain 'JT' and resid 79 through 90 Processing helix chain 'JT' and resid 98 through 113 Processing helix chain 'JT' and resid 191 through 221 removed outlier: 4.423A pdb=" N ILEJT 195 " --> pdb=" O GLNJT 191 " (cutoff:3.500A) Processing helix chain 'JT' and resid 287 through 307 removed outlier: 3.859A pdb=" N TYRJT 297 " --> pdb=" O ARGJT 293 " (cutoff:3.500A) Processing helix chain 'JX' and resid 362 through 393 removed outlier: 4.014A pdb=" N LYSJX 393 " --> pdb=" O HISJX 389 " (cutoff:3.500A) Processing helix chain 'JX' and resid 411 through 415 removed outlier: 3.550A pdb=" N ILEJX 414 " --> pdb=" O SERJX 411 " (cutoff:3.500A) Processing helix chain 'JX' and resid 460 through 464 Processing helix chain 'JY' and resid 1793 through 1798 Processing helix chain 'JY' and resid 1798 through 1821 Proline residue: JY1815 - end of helix Processing helix chain 'JY' and resid 1850 through 1863 Processing helix chain 'JY' and resid 1897 through 1909 Processing helix chain 'KT' and resid 79 through 90 Processing helix chain 'KT' and resid 98 through 113 Processing helix chain 'KT' and resid 191 through 221 removed outlier: 4.423A pdb=" N ILEKT 195 " --> pdb=" O GLNKT 191 " (cutoff:3.500A) Processing helix chain 'KT' and resid 287 through 307 removed outlier: 3.859A pdb=" N TYRKT 297 " --> pdb=" O ARGKT 293 " (cutoff:3.500A) Processing helix chain 'KX' and resid 362 through 393 removed outlier: 4.014A pdb=" N LYSKX 393 " --> pdb=" O HISKX 389 " (cutoff:3.500A) Processing helix chain 'KX' and resid 411 through 415 removed outlier: 3.551A pdb=" N ILEKX 414 " --> pdb=" O SERKX 411 " (cutoff:3.500A) Processing helix chain 'KX' and resid 460 through 464 Processing helix chain 'KY' and resid 1793 through 1798 Processing helix chain 'KY' and resid 1798 through 1821 Proline residue: KY1815 - end of helix Processing helix chain 'KY' and resid 1850 through 1863 Processing helix chain 'KY' and resid 1897 through 1909 Processing helix chain 'LT' and resid 79 through 90 Processing helix chain 'LT' and resid 98 through 113 Processing helix chain 'LT' and resid 191 through 221 removed outlier: 4.422A pdb=" N ILELT 195 " --> pdb=" O GLNLT 191 " (cutoff:3.500A) Processing helix chain 'LT' and resid 287 through 307 removed outlier: 3.858A pdb=" N TYRLT 297 " --> pdb=" O ARGLT 293 " (cutoff:3.500A) Processing helix chain 'LX' and resid 362 through 393 removed outlier: 4.015A pdb=" N LYSLX 393 " --> pdb=" O HISLX 389 " (cutoff:3.500A) Processing helix chain 'LX' and resid 411 through 415 removed outlier: 3.550A pdb=" N ILELX 414 " --> pdb=" O SERLX 411 " (cutoff:3.500A) Processing helix chain 'LX' and resid 460 through 464 Processing helix chain 'LY' and resid 1793 through 1798 Processing helix chain 'LY' and resid 1798 through 1821 Proline residue: LY1815 - end of helix Processing helix chain 'LY' and resid 1850 through 1863 Processing helix chain 'LY' and resid 1897 through 1909 Processing helix chain 'MT' and resid 79 through 90 Processing helix chain 'MT' and resid 98 through 113 Processing helix chain 'MT' and resid 191 through 221 removed outlier: 4.424A pdb=" N ILEMT 195 " --> pdb=" O GLNMT 191 " (cutoff:3.500A) Processing helix chain 'MT' and resid 287 through 307 removed outlier: 3.858A pdb=" N TYRMT 297 " --> pdb=" O ARGMT 293 " (cutoff:3.500A) Processing helix chain 'MX' and resid 362 through 393 removed outlier: 4.014A pdb=" N LYSMX 393 " --> pdb=" O HISMX 389 " (cutoff:3.500A) Processing helix chain 'MX' and resid 411 through 415 removed outlier: 3.551A pdb=" N ILEMX 414 " --> pdb=" O SERMX 411 " (cutoff:3.500A) Processing helix chain 'MX' and resid 460 through 464 Processing helix chain 'MY' and resid 1793 through 1798 Processing helix chain 'MY' and resid 1798 through 1821 Proline residue: MY1815 - end of helix Processing helix chain 'MY' and resid 1850 through 1863 Processing helix chain 'MY' and resid 1897 through 1909 Processing helix chain 'NT' and resid 79 through 90 Processing helix chain 'NT' and resid 98 through 113 Processing helix chain 'NT' and resid 191 through 221 removed outlier: 4.423A pdb=" N ILENT 195 " --> pdb=" O GLNNT 191 " (cutoff:3.500A) Processing helix chain 'NT' and resid 287 through 307 removed outlier: 3.859A pdb=" N TYRNT 297 " --> pdb=" O ARGNT 293 " (cutoff:3.500A) Processing helix chain 'NX' and resid 362 through 393 removed outlier: 4.015A pdb=" N LYSNX 393 " --> pdb=" O HISNX 389 " (cutoff:3.500A) Processing helix chain 'NX' and resid 411 through 415 removed outlier: 3.551A pdb=" N ILENX 414 " --> pdb=" O SERNX 411 " (cutoff:3.500A) Processing helix chain 'NX' and resid 460 through 464 Processing helix chain 'NY' and resid 1793 through 1798 Processing helix chain 'NY' and resid 1798 through 1821 Proline residue: NY1815 - end of helix Processing helix chain 'NY' and resid 1850 through 1863 Processing helix chain 'NY' and resid 1897 through 1909 Processing sheet with id=AA1, first strand: chain 'AT' and resid 37 through 38 removed outlier: 4.986A pdb=" N LYSBX 475 " --> pdb=" O VALBX 442 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'AT' and resid 61 through 67 removed outlier: 6.432A pdb=" N ILEAT 93 " --> pdb=" O TYRAT 121 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLNAT 123 " --> pdb=" O ILEAT 93 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEUAT 95 " --> pdb=" O GLNAT 123 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'AX' and resid 448 through 450 removed outlier: 4.986A pdb=" N LYSAX 475 " --> pdb=" O VALAX 442 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'AX' and resid 418 through 421 Processing sheet with id=AA5, first strand: chain 'AX' and resid 509 through 513 Processing sheet with id=AA6, first strand: chain 'AY' and resid 1682 through 1683 removed outlier: 5.799A pdb=" N ILENY1757 " --> pdb=" O ALANY1777 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THRNY1696 " --> pdb=" O THRNY1881 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LYSNY1737 " --> pdb=" O ALANY1762 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ALANY1762 " --> pdb=" O LYSNY1737 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TYRNY1739 " --> pdb=" O THRNY1760 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'AY' and resid 1691 through 1692 Processing sheet with id=AA8, first strand: chain 'BY' and resid 1682 through 1683 removed outlier: 5.800A pdb=" N ILEAY1757 " --> pdb=" O ALAAY1777 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N THRAY1696 " --> pdb=" O THRAY1881 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LYSAY1737 " --> pdb=" O ALAAY1762 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ALAAY1762 " --> pdb=" O LYSAY1737 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TYRAY1739 " --> pdb=" O THRAY1760 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'AY' and resid 1706 through 1707 Processing sheet with id=AB1, first strand: chain 'AY' and resid 1722 through 1723 Processing sheet with id=AB2, first strand: chain 'AY' and resid 1754 through 1755 Processing sheet with id=AB3, first strand: chain 'AY' and resid 1891 through 1895 Processing sheet with id=AB4, first strand: chain 'BT' and resid 37 through 38 removed outlier: 4.986A pdb=" N LYSCX 475 " --> pdb=" O VALCX 442 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'BT' and resid 61 through 67 removed outlier: 6.432A pdb=" N ILEBT 93 " --> pdb=" O TYRBT 121 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLNBT 123 " --> pdb=" O ILEBT 93 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEUBT 95 " --> pdb=" O GLNBT 123 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'BX' and resid 418 through 421 Processing sheet with id=AB7, first strand: chain 'BX' and resid 509 through 513 Processing sheet with id=AB8, first strand: chain 'BY' and resid 1691 through 1692 Processing sheet with id=AB9, first strand: chain 'CY' and resid 1682 through 1683 removed outlier: 5.800A pdb=" N ILEBY1757 " --> pdb=" O ALABY1777 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THRBY1696 " --> pdb=" O THRBY1881 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LYSBY1737 " --> pdb=" O ALABY1762 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ALABY1762 " --> pdb=" O LYSBY1737 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TYRBY1739 " --> pdb=" O THRBY1760 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'BY' and resid 1706 through 1707 Processing sheet with id=AC2, first strand: chain 'BY' and resid 1722 through 1723 Processing sheet with id=AC3, first strand: chain 'BY' and resid 1754 through 1755 Processing sheet with id=AC4, first strand: chain 'CT' and resid 37 through 38 removed outlier: 4.986A pdb=" N LYSDX 475 " --> pdb=" O VALDX 442 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'CT' and resid 61 through 67 removed outlier: 6.432A pdb=" N ILECT 93 " --> pdb=" O TYRCT 121 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLNCT 123 " --> pdb=" O ILECT 93 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEUCT 95 " --> pdb=" O GLNCT 123 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'CX' and resid 418 through 421 Processing sheet with id=AC7, first strand: chain 'CX' and resid 509 through 513 Processing sheet with id=AC8, first strand: chain 'CY' and resid 1691 through 1692 Processing sheet with id=AC9, first strand: chain 'DY' and resid 1682 through 1683 removed outlier: 5.800A pdb=" N ILECY1757 " --> pdb=" O ALACY1777 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THRCY1696 " --> pdb=" O THRCY1881 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LYSCY1737 " --> pdb=" O ALACY1762 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ALACY1762 " --> pdb=" O LYSCY1737 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TYRCY1739 " --> pdb=" O THRCY1760 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'CY' and resid 1706 through 1707 Processing sheet with id=AD2, first strand: chain 'CY' and resid 1722 through 1723 Processing sheet with id=AD3, first strand: chain 'CY' and resid 1754 through 1755 Processing sheet with id=AD4, first strand: chain 'DT' and resid 37 through 38 removed outlier: 4.985A pdb=" N LYSEX 475 " --> pdb=" O VALEX 442 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'DT' and resid 61 through 67 removed outlier: 6.432A pdb=" N ILEDT 93 " --> pdb=" O TYRDT 121 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLNDT 123 " --> pdb=" O ILEDT 93 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEUDT 95 " --> pdb=" O GLNDT 123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'DX' and resid 418 through 421 Processing sheet with id=AD7, first strand: chain 'DX' and resid 509 through 513 Processing sheet with id=AD8, first strand: chain 'DY' and resid 1691 through 1692 Processing sheet with id=AD9, first strand: chain 'EY' and resid 1682 through 1683 removed outlier: 5.800A pdb=" N ILEDY1757 " --> pdb=" O ALADY1777 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THRDY1696 " --> pdb=" O THRDY1881 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LYSDY1737 " --> pdb=" O ALADY1762 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ALADY1762 " --> pdb=" O LYSDY1737 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TYRDY1739 " --> pdb=" O THRDY1760 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'DY' and resid 1706 through 1707 Processing sheet with id=AE2, first strand: chain 'DY' and resid 1722 through 1723 Processing sheet with id=AE3, first strand: chain 'DY' and resid 1754 through 1755 Processing sheet with id=AE4, first strand: chain 'ET' and resid 37 through 38 removed outlier: 4.986A pdb=" N LYSFX 475 " --> pdb=" O VALFX 442 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'ET' and resid 61 through 67 removed outlier: 6.433A pdb=" N ILEET 93 " --> pdb=" O TYRET 121 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLNET 123 " --> pdb=" O ILEET 93 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEUET 95 " --> pdb=" O GLNET 123 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'EX' and resid 418 through 421 Processing sheet with id=AE7, first strand: chain 'EX' and resid 509 through 513 Processing sheet with id=AE8, first strand: chain 'EY' and resid 1691 through 1692 Processing sheet with id=AE9, first strand: chain 'FY' and resid 1682 through 1683 removed outlier: 5.800A pdb=" N ILEEY1757 " --> pdb=" O ALAEY1777 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THREY1696 " --> pdb=" O THREY1881 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LYSEY1737 " --> pdb=" O ALAEY1762 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ALAEY1762 " --> pdb=" O LYSEY1737 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TYREY1739 " --> pdb=" O THREY1760 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'EY' and resid 1706 through 1707 Processing sheet with id=AF2, first strand: chain 'EY' and resid 1722 through 1723 Processing sheet with id=AF3, first strand: chain 'EY' and resid 1754 through 1755 Processing sheet with id=AF4, first strand: chain 'FT' and resid 37 through 38 removed outlier: 4.986A pdb=" N LYSGX 475 " --> pdb=" O VALGX 442 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'FT' and resid 61 through 67 removed outlier: 6.432A pdb=" N ILEFT 93 " --> pdb=" O TYRFT 121 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLNFT 123 " --> pdb=" O ILEFT 93 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEUFT 95 " --> pdb=" O GLNFT 123 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'FX' and resid 418 through 421 Processing sheet with id=AF7, first strand: chain 'FX' and resid 509 through 513 Processing sheet with id=AF8, first strand: chain 'FY' and resid 1691 through 1692 Processing sheet with id=AF9, first strand: chain 'GY' and resid 1682 through 1683 removed outlier: 5.799A pdb=" N ILEFY1757 " --> pdb=" O ALAFY1777 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N THRFY1696 " --> pdb=" O THRFY1881 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LYSFY1737 " --> pdb=" O ALAFY1762 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ALAFY1762 " --> pdb=" O LYSFY1737 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TYRFY1739 " --> pdb=" O THRFY1760 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'FY' and resid 1706 through 1707 Processing sheet with id=AG2, first strand: chain 'FY' and resid 1722 through 1723 Processing sheet with id=AG3, first strand: chain 'FY' and resid 1754 through 1755 Processing sheet with id=AG4, first strand: chain 'GT' and resid 37 through 38 removed outlier: 4.985A pdb=" N LYSHX 475 " --> pdb=" O VALHX 442 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'GT' and resid 61 through 67 removed outlier: 6.432A pdb=" N ILEGT 93 " --> pdb=" O TYRGT 121 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLNGT 123 " --> pdb=" O ILEGT 93 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEUGT 95 " --> pdb=" O GLNGT 123 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'GX' and resid 418 through 421 Processing sheet with id=AG7, first strand: chain 'GX' and resid 509 through 513 Processing sheet with id=AG8, first strand: chain 'GY' and resid 1691 through 1692 Processing sheet with id=AG9, first strand: chain 'HY' and resid 1682 through 1683 removed outlier: 5.800A pdb=" N ILEGY1757 " --> pdb=" O ALAGY1777 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THRGY1696 " --> pdb=" O THRGY1881 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LYSGY1737 " --> pdb=" O ALAGY1762 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ALAGY1762 " --> pdb=" O LYSGY1737 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TYRGY1739 " --> pdb=" O THRGY1760 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'GY' and resid 1706 through 1707 Processing sheet with id=AH2, first strand: chain 'GY' and resid 1722 through 1723 Processing sheet with id=AH3, first strand: chain 'GY' and resid 1754 through 1755 Processing sheet with id=AH4, first strand: chain 'HT' and resid 37 through 38 removed outlier: 4.986A pdb=" N LYSIX 475 " --> pdb=" O VALIX 442 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'HT' and resid 61 through 67 removed outlier: 6.432A pdb=" N ILEHT 93 " --> pdb=" O TYRHT 121 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLNHT 123 " --> pdb=" O ILEHT 93 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEUHT 95 " --> pdb=" O GLNHT 123 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'HX' and resid 418 through 421 Processing sheet with id=AH7, first strand: chain 'HX' and resid 509 through 513 Processing sheet with id=AH8, first strand: chain 'HY' and resid 1691 through 1692 Processing sheet with id=AH9, first strand: chain 'IY' and resid 1682 through 1683 removed outlier: 5.799A pdb=" N ILEHY1757 " --> pdb=" O ALAHY1777 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THRHY1696 " --> pdb=" O THRHY1881 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LYSHY1737 " --> pdb=" O ALAHY1762 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ALAHY1762 " --> pdb=" O LYSHY1737 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TYRHY1739 " --> pdb=" O THRHY1760 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'HY' and resid 1706 through 1707 Processing sheet with id=AI2, first strand: chain 'HY' and resid 1722 through 1723 Processing sheet with id=AI3, first strand: chain 'HY' and resid 1754 through 1755 Processing sheet with id=AI4, first strand: chain 'IT' and resid 37 through 38 removed outlier: 4.986A pdb=" N LYSJX 475 " --> pdb=" O VALJX 442 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'IT' and resid 61 through 67 removed outlier: 6.432A pdb=" N ILEIT 93 " --> pdb=" O TYRIT 121 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLNIT 123 " --> pdb=" O ILEIT 93 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEUIT 95 " --> pdb=" O GLNIT 123 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'IX' and resid 418 through 421 Processing sheet with id=AI7, first strand: chain 'IX' and resid 509 through 513 Processing sheet with id=AI8, first strand: chain 'IY' and resid 1691 through 1692 Processing sheet with id=AI9, first strand: chain 'JY' and resid 1682 through 1683 removed outlier: 5.799A pdb=" N ILEIY1757 " --> pdb=" O ALAIY1777 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THRIY1696 " --> pdb=" O THRIY1881 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LYSIY1737 " --> pdb=" O ALAIY1762 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ALAIY1762 " --> pdb=" O LYSIY1737 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TYRIY1739 " --> pdb=" O THRIY1760 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'IY' and resid 1706 through 1707 Processing sheet with id=AJ2, first strand: chain 'IY' and resid 1722 through 1723 Processing sheet with id=AJ3, first strand: chain 'IY' and resid 1754 through 1755 Processing sheet with id=AJ4, first strand: chain 'JT' and resid 37 through 38 removed outlier: 4.985A pdb=" N LYSKX 475 " --> pdb=" O VALKX 442 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'JT' and resid 61 through 67 removed outlier: 6.431A pdb=" N ILEJT 93 " --> pdb=" O TYRJT 121 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLNJT 123 " --> pdb=" O ILEJT 93 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEUJT 95 " --> pdb=" O GLNJT 123 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'JX' and resid 418 through 421 Processing sheet with id=AJ7, first strand: chain 'JX' and resid 509 through 513 Processing sheet with id=AJ8, first strand: chain 'JY' and resid 1691 through 1692 Processing sheet with id=AJ9, first strand: chain 'KY' and resid 1682 through 1683 removed outlier: 5.800A pdb=" N ILEJY1757 " --> pdb=" O ALAJY1777 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N THRJY1696 " --> pdb=" O THRJY1881 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LYSJY1737 " --> pdb=" O ALAJY1762 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ALAJY1762 " --> pdb=" O LYSJY1737 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TYRJY1739 " --> pdb=" O THRJY1760 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'JY' and resid 1706 through 1707 Processing sheet with id=AK2, first strand: chain 'JY' and resid 1722 through 1723 Processing sheet with id=AK3, first strand: chain 'JY' and resid 1754 through 1755 Processing sheet with id=AK4, first strand: chain 'KT' and resid 37 through 38 removed outlier: 4.986A pdb=" N LYSLX 475 " --> pdb=" O VALLX 442 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'KT' and resid 61 through 67 removed outlier: 6.433A pdb=" N ILEKT 93 " --> pdb=" O TYRKT 121 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLNKT 123 " --> pdb=" O ILEKT 93 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEUKT 95 " --> pdb=" O GLNKT 123 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'KX' and resid 418 through 421 Processing sheet with id=AK7, first strand: chain 'KX' and resid 509 through 513 Processing sheet with id=AK8, first strand: chain 'KY' and resid 1691 through 1692 Processing sheet with id=AK9, first strand: chain 'LY' and resid 1682 through 1683 removed outlier: 5.799A pdb=" N ILEKY1757 " --> pdb=" O ALAKY1777 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THRKY1696 " --> pdb=" O THRKY1881 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LYSKY1737 " --> pdb=" O ALAKY1762 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ALAKY1762 " --> pdb=" O LYSKY1737 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TYRKY1739 " --> pdb=" O THRKY1760 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'KY' and resid 1706 through 1707 Processing sheet with id=AL2, first strand: chain 'KY' and resid 1722 through 1723 Processing sheet with id=AL3, first strand: chain 'KY' and resid 1754 through 1755 Processing sheet with id=AL4, first strand: chain 'LT' and resid 37 through 38 removed outlier: 4.985A pdb=" N LYSMX 475 " --> pdb=" O VALMX 442 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'LT' and resid 61 through 67 removed outlier: 6.432A pdb=" N ILELT 93 " --> pdb=" O TYRLT 121 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLNLT 123 " --> pdb=" O ILELT 93 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEULT 95 " --> pdb=" O GLNLT 123 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'LX' and resid 418 through 421 Processing sheet with id=AL7, first strand: chain 'LX' and resid 509 through 513 Processing sheet with id=AL8, first strand: chain 'LY' and resid 1691 through 1692 Processing sheet with id=AL9, first strand: chain 'MY' and resid 1682 through 1683 removed outlier: 5.800A pdb=" N ILELY1757 " --> pdb=" O ALALY1777 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THRLY1696 " --> pdb=" O THRLY1881 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LYSLY1737 " --> pdb=" O ALALY1762 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ALALY1762 " --> pdb=" O LYSLY1737 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TYRLY1739 " --> pdb=" O THRLY1760 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'LY' and resid 1706 through 1707 Processing sheet with id=AM2, first strand: chain 'LY' and resid 1722 through 1723 Processing sheet with id=AM3, first strand: chain 'LY' and resid 1754 through 1755 Processing sheet with id=AM4, first strand: chain 'MT' and resid 37 through 38 removed outlier: 4.986A pdb=" N LYSNX 475 " --> pdb=" O VALNX 442 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'MT' and resid 61 through 67 removed outlier: 6.432A pdb=" N ILEMT 93 " --> pdb=" O TYRMT 121 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N GLNMT 123 " --> pdb=" O ILEMT 93 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEUMT 95 " --> pdb=" O GLNMT 123 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'MX' and resid 418 through 421 Processing sheet with id=AM7, first strand: chain 'MX' and resid 509 through 513 Processing sheet with id=AM8, first strand: chain 'MY' and resid 1691 through 1692 Processing sheet with id=AM9, first strand: chain 'NY' and resid 1682 through 1683 removed outlier: 5.799A pdb=" N ILEMY1757 " --> pdb=" O ALAMY1777 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N THRMY1696 " --> pdb=" O THRMY1881 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LYSMY1737 " --> pdb=" O ALAMY1762 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ALAMY1762 " --> pdb=" O LYSMY1737 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TYRMY1739 " --> pdb=" O THRMY1760 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'MY' and resid 1706 through 1707 Processing sheet with id=AN2, first strand: chain 'MY' and resid 1722 through 1723 Processing sheet with id=AN3, first strand: chain 'MY' and resid 1754 through 1755 Processing sheet with id=AN4, first strand: chain 'NT' and resid 61 through 67 removed outlier: 6.432A pdb=" N ILENT 93 " --> pdb=" O TYRNT 121 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLNNT 123 " --> pdb=" O ILENT 93 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEUNT 95 " --> pdb=" O GLNNT 123 " (cutoff:3.500A) Processing sheet with id=AN5, first strand: chain 'NX' and resid 418 through 421 Processing sheet with id=AN6, first strand: chain 'NY' and resid 1691 through 1692 Processing sheet with id=AN7, first strand: chain 'NY' and resid 1706 through 1707 Processing sheet with id=AN8, first strand: chain 'NY' and resid 1722 through 1723 Processing sheet with id=AN9, first strand: chain 'NY' and resid 1754 through 1755 3054 hydrogen bonds defined for protein. 8280 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 30.86 Time building geometry restraints manager: 13.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 10583 1.32 - 1.44: 14905 1.44 - 1.56: 36112 1.56 - 1.69: 0 1.69 - 1.81: 392 Bond restraints: 61992 Sorted by residual: bond pdb=" C PHECX 440 " pdb=" N VALCX 441 " ideal model delta sigma weight residual 1.334 1.286 0.048 1.24e-02 6.50e+03 1.49e+01 bond pdb=" C PHEGX 440 " pdb=" N VALGX 441 " ideal model delta sigma weight residual 1.334 1.286 0.048 1.24e-02 6.50e+03 1.49e+01 bond pdb=" C PHENX 440 " pdb=" N VALNX 441 " ideal model delta sigma weight residual 1.334 1.286 0.048 1.24e-02 6.50e+03 1.48e+01 bond pdb=" C PHEMX 440 " pdb=" N VALMX 441 " ideal model delta sigma weight residual 1.334 1.286 0.048 1.24e-02 6.50e+03 1.47e+01 bond pdb=" C PHEHX 440 " pdb=" N VALHX 441 " ideal model delta sigma weight residual 1.334 1.286 0.048 1.24e-02 6.50e+03 1.47e+01 ... (remaining 61987 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.38: 81523 3.38 - 6.77: 1749 6.77 - 10.15: 266 10.15 - 13.53: 28 13.53 - 16.92: 28 Bond angle restraints: 83594 Sorted by residual: angle pdb=" N GLNDT 197 " pdb=" CA GLNDT 197 " pdb=" CB GLNDT 197 " ideal model delta sigma weight residual 110.40 119.59 -9.19 1.63e+00 3.76e-01 3.18e+01 angle pdb=" N GLNGT 197 " pdb=" CA GLNGT 197 " pdb=" CB GLNGT 197 " ideal model delta sigma weight residual 110.40 119.58 -9.18 1.63e+00 3.76e-01 3.17e+01 angle pdb=" N GLNNT 197 " pdb=" CA GLNNT 197 " pdb=" CB GLNNT 197 " ideal model delta sigma weight residual 110.40 119.58 -9.18 1.63e+00 3.76e-01 3.17e+01 angle pdb=" N GLNFT 197 " pdb=" CA GLNFT 197 " pdb=" CB GLNFT 197 " ideal model delta sigma weight residual 110.40 119.56 -9.16 1.63e+00 3.76e-01 3.16e+01 angle pdb=" N GLNLT 197 " pdb=" CA GLNLT 197 " pdb=" CB GLNLT 197 " ideal model delta sigma weight residual 110.40 119.55 -9.15 1.63e+00 3.76e-01 3.15e+01 ... (remaining 83589 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.07: 33464 15.07 - 30.14: 3705 30.14 - 45.22: 729 45.22 - 60.29: 70 60.29 - 75.36: 140 Dihedral angle restraints: 38108 sinusoidal: 15806 harmonic: 22302 Sorted by residual: dihedral pdb=" CA ILEAX 479 " pdb=" C ILEAX 479 " pdb=" N LYSAX 480 " pdb=" CA LYSAX 480 " ideal model delta harmonic sigma weight residual 180.00 146.08 33.92 0 5.00e+00 4.00e-02 4.60e+01 dihedral pdb=" CA ILEDX 479 " pdb=" C ILEDX 479 " pdb=" N LYSDX 480 " pdb=" CA LYSDX 480 " ideal model delta harmonic sigma weight residual 180.00 146.12 33.88 0 5.00e+00 4.00e-02 4.59e+01 dihedral pdb=" CA ILECX 479 " pdb=" C ILECX 479 " pdb=" N LYSCX 480 " pdb=" CA LYSCX 480 " ideal model delta harmonic sigma weight residual 180.00 146.13 33.87 0 5.00e+00 4.00e-02 4.59e+01 ... (remaining 38105 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 6428 0.063 - 0.127: 2426 0.127 - 0.190: 546 0.190 - 0.253: 78 0.253 - 0.317: 42 Chirality restraints: 9520 Sorted by residual: chirality pdb=" CB VALIY1786 " pdb=" CA VALIY1786 " pdb=" CG1 VALIY1786 " pdb=" CG2 VALIY1786 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CB VALMY1786 " pdb=" CA VALMY1786 " pdb=" CG1 VALMY1786 " pdb=" CG2 VALMY1786 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" CB VALAY1786 " pdb=" CA VALAY1786 " pdb=" CG1 VALAY1786 " pdb=" CG2 VALAY1786 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.47e+00 ... (remaining 9517 not shown) Planarity restraints: 10598 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYRBY1739 " -0.013 2.00e-02 2.50e+03 2.15e-02 9.23e+00 pdb=" CG TYRBY1739 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TYRBY1739 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TYRBY1739 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 TYRBY1739 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYRBY1739 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYRBY1739 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYRBY1739 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYRIY1739 " -0.013 2.00e-02 2.50e+03 2.14e-02 9.18e+00 pdb=" CG TYRIY1739 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TYRIY1739 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TYRIY1739 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 TYRIY1739 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYRIY1739 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYRIY1739 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYRIY1739 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYRCY1739 " -0.013 2.00e-02 2.50e+03 2.14e-02 9.17e+00 pdb=" CG TYRCY1739 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TYRCY1739 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TYRCY1739 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 TYRCY1739 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYRCY1739 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYRCY1739 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYRCY1739 " 0.003 2.00e-02 2.50e+03 ... (remaining 10595 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 8435 2.75 - 3.29: 59590 3.29 - 3.82: 108013 3.82 - 4.36: 129045 4.36 - 4.90: 217400 Nonbonded interactions: 522483 Sorted by model distance: nonbonded pdb=" O PROHX 444 " pdb=" NH1 ARGIX 410 " model vdw 2.210 3.120 nonbonded pdb=" O PROBX 444 " pdb=" NH1 ARGCX 410 " model vdw 2.222 3.120 nonbonded pdb=" OG SERBT 48 " pdb=" O GLYCT 170 " model vdw 2.222 3.040 nonbonded pdb=" OD2 ASPFT 54 " pdb=" OH TYRFX 404 " model vdw 2.263 3.040 nonbonded pdb=" OD2 ASPLT 54 " pdb=" OH TYRLX 404 " model vdw 2.269 3.040 ... (remaining 522478 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 'AT' selection = chain 'BT' selection = chain 'CT' selection = chain 'DT' selection = chain 'ET' selection = chain 'FT' selection = chain 'GT' selection = chain 'HT' selection = chain 'IT' selection = chain 'JT' selection = chain 'KT' selection = chain 'LT' selection = chain 'MT' selection = chain 'NT' } ncs_group { reference = chain 'AX' selection = chain 'BX' selection = chain 'CX' selection = chain 'DX' selection = chain 'EX' selection = chain 'FX' selection = chain 'GX' selection = chain 'HX' selection = chain 'IX' selection = chain 'JX' selection = chain 'KX' selection = chain 'LX' selection = chain 'MX' selection = chain 'NX' } ncs_group { reference = chain 'AY' selection = chain 'BY' selection = chain 'CY' selection = chain 'DY' selection = chain 'EY' selection = chain 'FY' selection = chain 'GY' selection = chain 'HY' selection = chain 'IY' selection = chain 'JY' selection = chain 'KY' selection = chain 'LY' selection = chain 'MY' selection = chain 'NY' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 1.770 Check model and map are aligned: 0.350 Set scattering table: 0.430 Process input model: 115.790 Find NCS groups from input model: 2.370 Set up NCS constraints: 0.750 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 132.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 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 : 0.011 0.140 61992 Z= 0.696 Angle : 1.233 16.918 83594 Z= 0.650 Chirality : 0.070 0.317 9520 Planarity : 0.007 0.070 10598 Dihedral : 13.772 75.362 23716 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.94 (0.09), residues: 7406 helix: -1.37 (0.09), residues: 2212 sheet: -1.16 (0.12), residues: 1624 loop : -1.16 (0.10), residues: 3570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.003 TRPNY1723 HIS 0.007 0.002 HISET 169 PHE 0.019 0.003 PHENY1682 TYR 0.051 0.004 TYRBY1739 ARG 0.033 0.002 ARGBX 394 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14812 Ramachandran restraints generated. 7406 Oldfield, 0 Emsley, 7406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14812 Ramachandran restraints generated. 7406 Oldfield, 0 Emsley, 7406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2063 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2063 time to evaluate : 5.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AT 64 GLN cc_start: 0.8176 (tt0) cc_final: 0.7538 (mt0) REVERT: AT 194 LYS cc_start: 0.7823 (pttm) cc_final: 0.7573 (tptp) REVERT: AT 197 GLN cc_start: 0.8069 (pm20) cc_final: 0.7850 (tp40) REVERT: AT 201 THR cc_start: 0.8293 (p) cc_final: 0.8010 (p) REVERT: AT 300 ASN cc_start: 0.7020 (m-40) cc_final: 0.6730 (m-40) REVERT: AX 386 GLN cc_start: 0.8217 (tm-30) cc_final: 0.7773 (tp40) REVERT: AX 389 HIS cc_start: 0.7688 (t70) cc_final: 0.7479 (m90) REVERT: AX 405 GLN cc_start: 0.7969 (pt0) cc_final: 0.7244 (pt0) REVERT: AX 459 MET cc_start: 0.8907 (mtp) cc_final: 0.8688 (mtt) REVERT: AY 1715 SER cc_start: 0.8255 (p) cc_final: 0.8029 (p) REVERT: AY 1780 MET cc_start: 0.8451 (mmm) cc_final: 0.8195 (mmt) REVERT: AY 1884 ASP cc_start: 0.7762 (m-30) cc_final: 0.7534 (m-30) REVERT: AY 1907 GLN cc_start: 0.8339 (tm-30) cc_final: 0.7879 (tm-30) REVERT: BT 39 VAL cc_start: 0.9215 (t) cc_final: 0.8996 (t) REVERT: BT 49 GLU cc_start: 0.7392 (mp0) cc_final: 0.7181 (mp0) REVERT: BT 64 GLN cc_start: 0.7931 (tt0) cc_final: 0.7399 (mt0) REVERT: BT 194 LYS cc_start: 0.7933 (pttm) cc_final: 0.7581 (tptp) REVERT: BT 197 GLN cc_start: 0.8081 (pm20) cc_final: 0.7840 (tp-100) REVERT: BT 209 GLU cc_start: 0.7305 (tm-30) cc_final: 0.6847 (tp30) REVERT: BT 210 TYR cc_start: 0.8250 (t80) cc_final: 0.7811 (t80) REVERT: BT 216 ASN cc_start: 0.7559 (m110) cc_final: 0.7158 (m110) REVERT: BX 386 GLN cc_start: 0.8387 (tm-30) cc_final: 0.7987 (tp40) REVERT: BX 389 HIS cc_start: 0.7823 (t-90) cc_final: 0.7580 (m-70) REVERT: BX 405 GLN cc_start: 0.8069 (pt0) cc_final: 0.7580 (pt0) REVERT: BY 1685 LYS cc_start: 0.6911 (mmtm) cc_final: 0.6674 (mmtm) REVERT: BY 1817 ILE cc_start: 0.8746 (mm) cc_final: 0.8419 (mt) REVERT: CT 45 GLU cc_start: 0.7416 (pp20) cc_final: 0.6620 (pp20) REVERT: CT 194 LYS cc_start: 0.8117 (pttm) cc_final: 0.7658 (tptp) REVERT: CT 197 GLN cc_start: 0.8077 (pm20) cc_final: 0.7770 (tp-100) REVERT: CT 201 THR cc_start: 0.8131 (p) cc_final: 0.7887 (p) REVERT: CX 378 ASP cc_start: 0.8085 (m-30) cc_final: 0.7843 (m-30) REVERT: CX 386 GLN cc_start: 0.8376 (tm-30) cc_final: 0.7834 (tp40) REVERT: CX 387 TYR cc_start: 0.8636 (t80) cc_final: 0.8392 (t80) REVERT: CX 389 HIS cc_start: 0.7846 (t70) cc_final: 0.7513 (m90) REVERT: CX 405 GLN cc_start: 0.8044 (pt0) cc_final: 0.7629 (pt0) REVERT: CX 484 LEU cc_start: 0.9156 (tp) cc_final: 0.8937 (tp) REVERT: CY 1685 LYS cc_start: 0.7368 (mmtm) cc_final: 0.7163 (mmtt) REVERT: CY 1817 ILE cc_start: 0.8687 (mm) cc_final: 0.8347 (mt) REVERT: CY 1907 GLN cc_start: 0.8484 (tm-30) cc_final: 0.7939 (tm-30) REVERT: DT 64 GLN cc_start: 0.7971 (tt0) cc_final: 0.7281 (mt0) REVERT: DT 194 LYS cc_start: 0.8097 (pttm) cc_final: 0.7703 (tptp) REVERT: DT 197 GLN cc_start: 0.7972 (pm20) cc_final: 0.7693 (tp-100) REVERT: DT 201 THR cc_start: 0.8416 (p) cc_final: 0.8195 (p) REVERT: DX 386 GLN cc_start: 0.8276 (tm-30) cc_final: 0.7782 (tp40) REVERT: DX 389 HIS cc_start: 0.7862 (t-90) cc_final: 0.7612 (m90) REVERT: DX 405 GLN cc_start: 0.7992 (pt0) cc_final: 0.7792 (pt0) REVERT: DY 1739 TYR cc_start: 0.8929 (m-80) cc_final: 0.8625 (m-80) REVERT: DY 1774 ASN cc_start: 0.8878 (p0) cc_final: 0.8633 (p0) REVERT: DY 1817 ILE cc_start: 0.8653 (mm) cc_final: 0.8347 (mt) REVERT: ET 27 LYS cc_start: 0.7499 (mmtt) cc_final: 0.7244 (mmtm) REVERT: ET 194 LYS cc_start: 0.7809 (pttm) cc_final: 0.7576 (tptp) REVERT: ET 197 GLN cc_start: 0.8004 (pm20) cc_final: 0.7731 (tp40) REVERT: ET 201 THR cc_start: 0.8258 (p) cc_final: 0.7845 (p) REVERT: ET 210 TYR cc_start: 0.8340 (t80) cc_final: 0.8009 (t80) REVERT: ET 215 ASN cc_start: 0.7952 (m-40) cc_final: 0.7575 (m-40) REVERT: ET 290 GLN cc_start: 0.7165 (tp-100) cc_final: 0.6923 (mp10) REVERT: EX 378 ASP cc_start: 0.8037 (m-30) cc_final: 0.7731 (t0) REVERT: EX 386 GLN cc_start: 0.8302 (tm-30) cc_final: 0.8056 (tp40) REVERT: EY 1884 ASP cc_start: 0.7708 (m-30) cc_final: 0.7504 (m-30) REVERT: FT 27 LYS cc_start: 0.7564 (mmtt) cc_final: 0.7335 (mmtm) REVERT: FT 64 GLN cc_start: 0.7935 (tt0) cc_final: 0.7344 (mt0) REVERT: FT 194 LYS cc_start: 0.7746 (pttm) cc_final: 0.7516 (tptp) REVERT: FT 197 GLN cc_start: 0.8209 (pm20) cc_final: 0.7934 (tp40) REVERT: FT 201 THR cc_start: 0.8498 (p) cc_final: 0.8166 (p) REVERT: FT 213 ARG cc_start: 0.6907 (ttp80) cc_final: 0.6670 (ptt180) REVERT: FT 216 ASN cc_start: 0.7616 (m110) cc_final: 0.7225 (m110) REVERT: FX 386 GLN cc_start: 0.8315 (tm-30) cc_final: 0.7768 (tp40) REVERT: FX 405 GLN cc_start: 0.8113 (pt0) cc_final: 0.7892 (pt0) REVERT: FY 1685 LYS cc_start: 0.6991 (mmtm) cc_final: 0.6452 (mmtm) REVERT: FY 1856 ASN cc_start: 0.8249 (t0) cc_final: 0.8029 (t0) REVERT: GT 27 LYS cc_start: 0.7439 (mmtt) cc_final: 0.7235 (mmtt) REVERT: GT 197 GLN cc_start: 0.8098 (pm20) cc_final: 0.7691 (tp40) REVERT: GT 201 THR cc_start: 0.8258 (p) cc_final: 0.7887 (p) REVERT: GT 210 TYR cc_start: 0.8392 (t80) cc_final: 0.7961 (t80) REVERT: GT 216 ASN cc_start: 0.7782 (m110) cc_final: 0.7412 (m-40) REVERT: GX 386 GLN cc_start: 0.8388 (tm-30) cc_final: 0.7857 (tp40) REVERT: GY 1685 LYS cc_start: 0.7133 (mmtm) cc_final: 0.6868 (mmtt) REVERT: GY 1739 TYR cc_start: 0.8957 (m-80) cc_final: 0.8686 (m-80) REVERT: GY 1891 TYR cc_start: 0.8743 (m-80) cc_final: 0.8540 (m-80) REVERT: HT 27 LYS cc_start: 0.7415 (mmtt) cc_final: 0.7183 (mmtm) REVERT: HT 49 GLU cc_start: 0.7278 (mp0) cc_final: 0.7076 (mp0) REVERT: HT 64 GLN cc_start: 0.8185 (tt0) cc_final: 0.7538 (mt0) REVERT: HT 194 LYS cc_start: 0.7841 (pttm) cc_final: 0.7589 (tptp) REVERT: HT 197 GLN cc_start: 0.8086 (pm20) cc_final: 0.7852 (tp40) REVERT: HT 201 THR cc_start: 0.8315 (p) cc_final: 0.8033 (p) REVERT: HT 300 ASN cc_start: 0.7099 (m-40) cc_final: 0.6807 (m-40) REVERT: HX 386 GLN cc_start: 0.8220 (tm-30) cc_final: 0.7780 (tp40) REVERT: HX 405 GLN cc_start: 0.7974 (pt0) cc_final: 0.7259 (pt0) REVERT: HX 459 MET cc_start: 0.8905 (mtp) cc_final: 0.8682 (mtt) REVERT: HY 1715 SER cc_start: 0.8260 (p) cc_final: 0.8034 (p) REVERT: HY 1780 MET cc_start: 0.8460 (mmm) cc_final: 0.8209 (mmt) REVERT: HY 1884 ASP cc_start: 0.7746 (m-30) cc_final: 0.7503 (m-30) REVERT: HY 1907 GLN cc_start: 0.8303 (tm-30) cc_final: 0.7829 (tm-30) REVERT: IT 49 GLU cc_start: 0.7446 (mp0) cc_final: 0.7206 (mp0) REVERT: IT 194 LYS cc_start: 0.7847 (pttm) cc_final: 0.7538 (tptp) REVERT: IT 197 GLN cc_start: 0.8078 (pm20) cc_final: 0.7817 (tp40) REVERT: IT 198 TYR cc_start: 0.8017 (t80) cc_final: 0.7624 (t80) REVERT: IT 209 GLU cc_start: 0.7194 (tm-30) cc_final: 0.6694 (tp30) REVERT: IX 386 GLN cc_start: 0.8310 (tm-30) cc_final: 0.7922 (tp40) REVERT: IX 389 HIS cc_start: 0.7735 (t70) cc_final: 0.7491 (m-70) REVERT: IX 405 GLN cc_start: 0.8108 (pt0) cc_final: 0.7587 (pt0) REVERT: IY 1685 LYS cc_start: 0.6775 (mmtm) cc_final: 0.6535 (mmtm) REVERT: IY 1817 ILE cc_start: 0.8746 (mm) cc_final: 0.8421 (mt) REVERT: JT 45 GLU cc_start: 0.7332 (pp20) cc_final: 0.6439 (pp20) REVERT: JT 64 GLN cc_start: 0.7837 (tt0) cc_final: 0.7478 (mp10) REVERT: JT 194 LYS cc_start: 0.8134 (pttm) cc_final: 0.7733 (tptp) REVERT: JT 197 GLN cc_start: 0.8067 (pm20) cc_final: 0.7812 (tp-100) REVERT: JT 201 THR cc_start: 0.7887 (p) cc_final: 0.7678 (p) REVERT: JT 296 GLU cc_start: 0.7425 (tm-30) cc_final: 0.7190 (tm-30) REVERT: JT 300 ASN cc_start: 0.7047 (m-40) cc_final: 0.6752 (m-40) REVERT: JX 378 ASP cc_start: 0.8146 (m-30) cc_final: 0.7894 (m-30) REVERT: JX 386 GLN cc_start: 0.8330 (tm-30) cc_final: 0.7918 (tp40) REVERT: JX 389 HIS cc_start: 0.7925 (t70) cc_final: 0.7572 (m90) REVERT: JX 405 GLN cc_start: 0.8016 (pt0) cc_final: 0.7515 (pt0) REVERT: JX 484 LEU cc_start: 0.9189 (tp) cc_final: 0.8988 (tp) REVERT: JY 1685 LYS cc_start: 0.7368 (mmtm) cc_final: 0.7166 (mmtt) REVERT: JY 1817 ILE cc_start: 0.8692 (mm) cc_final: 0.8354 (mt) REVERT: KT 64 GLN cc_start: 0.8021 (tt0) cc_final: 0.7276 (mt0) REVERT: KT 194 LYS cc_start: 0.8035 (pttm) cc_final: 0.7692 (tptp) REVERT: KT 197 GLN cc_start: 0.8191 (pm20) cc_final: 0.7852 (tp40) REVERT: KT 210 TYR cc_start: 0.8229 (t80) cc_final: 0.7885 (t80) REVERT: KT 216 ASN cc_start: 0.7696 (m110) cc_final: 0.7314 (m110) REVERT: KX 386 GLN cc_start: 0.8453 (tm-30) cc_final: 0.7959 (tp40) REVERT: KX 389 HIS cc_start: 0.7856 (t-90) cc_final: 0.7631 (m-70) REVERT: KY 1739 TYR cc_start: 0.8924 (m-80) cc_final: 0.8602 (m-80) REVERT: KY 1774 ASN cc_start: 0.8878 (p0) cc_final: 0.8630 (p0) REVERT: KY 1817 ILE cc_start: 0.8648 (mm) cc_final: 0.8348 (mt) REVERT: LT 194 LYS cc_start: 0.7832 (pttm) cc_final: 0.7620 (tptp) REVERT: LT 197 GLN cc_start: 0.8040 (pm20) cc_final: 0.7741 (tp40) REVERT: LT 201 THR cc_start: 0.8296 (p) cc_final: 0.7916 (t) REVERT: LT 210 TYR cc_start: 0.8122 (t80) cc_final: 0.7915 (t80) REVERT: LT 215 ASN cc_start: 0.7967 (m-40) cc_final: 0.7616 (m-40) REVERT: LX 378 ASP cc_start: 0.8057 (m-30) cc_final: 0.7738 (t0) REVERT: LX 386 GLN cc_start: 0.8313 (tm-30) cc_final: 0.8056 (tp40) REVERT: LY 1884 ASP cc_start: 0.7669 (m-30) cc_final: 0.7453 (m-30) REVERT: MT 27 LYS cc_start: 0.7539 (mmtt) cc_final: 0.7310 (mmtm) REVERT: MT 45 GLU cc_start: 0.7388 (pp20) cc_final: 0.7162 (pp20) REVERT: MT 194 LYS cc_start: 0.7712 (pttm) cc_final: 0.7481 (tptp) REVERT: MT 197 GLN cc_start: 0.8174 (pm20) cc_final: 0.7931 (tp40) REVERT: MT 201 THR cc_start: 0.8473 (p) cc_final: 0.8188 (p) REVERT: MX 386 GLN cc_start: 0.8318 (tm-30) cc_final: 0.7774 (tp40) REVERT: MX 405 GLN cc_start: 0.8075 (pt0) cc_final: 0.7813 (pt0) REVERT: MY 1685 LYS cc_start: 0.6986 (mmtm) cc_final: 0.6437 (mmtm) REVERT: MY 1856 ASN cc_start: 0.8254 (t0) cc_final: 0.8034 (t0) REVERT: NT 197 GLN cc_start: 0.8040 (pm20) cc_final: 0.7733 (tp40) REVERT: NT 210 TYR cc_start: 0.8519 (t80) cc_final: 0.7939 (t80) REVERT: NT 216 ASN cc_start: 0.7617 (m110) cc_final: 0.7224 (m-40) REVERT: NX 386 GLN cc_start: 0.8400 (tm-30) cc_final: 0.7864 (tm-30) REVERT: NY 1685 LYS cc_start: 0.7125 (mmtm) cc_final: 0.6859 (mmtt) REVERT: NY 1739 TYR cc_start: 0.8955 (m-80) cc_final: 0.8673 (m-80) outliers start: 0 outliers final: 0 residues processed: 2063 average time/residue: 0.5972 time to fit residues: 2053.3321 Evaluate side-chains 1573 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1573 time to evaluate : 5.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 614 optimal weight: 1.9990 chunk 551 optimal weight: 0.5980 chunk 306 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 chunk 372 optimal weight: 1.9990 chunk 294 optimal weight: 0.9980 chunk 570 optimal weight: 0.6980 chunk 220 optimal weight: 4.9990 chunk 346 optimal weight: 0.7980 chunk 424 optimal weight: 0.9980 chunk 661 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AT 204 GLN AX 413 HIS AY1856 ASN BT 204 GLN BX 373 GLN BX 389 HIS BX 413 HIS BY1726 ASN BY1856 ASN CT 64 GLN CT 204 GLN CX 373 GLN CX 413 HIS CY1856 ASN DT 204 GLN DX 373 GLN DX 389 HIS DX 413 HIS ** DY1856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ET 301 GLN EX 373 GLN EX 405 GLN ** EX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** EY1856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** FT 204 GLN GT 301 GLN ** GX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** GY1856 ASN HT 204 GLN HX 373 GLN HX 413 HIS HY1856 ASN HY1857 GLN IX 373 GLN IX 413 HIS IY1726 ASN IY1856 ASN JT 204 GLN JX 373 GLN ** JX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** JY1856 ASN KT 204 GLN KX 389 HIS KX 413 HIS ** KY1856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LT 301 GLN LX 373 GLN LX 405 GLN ** LX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LY1856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** MT 33 ASN MX 373 GLN NX 373 GLN ** NX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NY1856 ASN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 61992 Z= 0.217 Angle : 0.650 7.923 83594 Z= 0.347 Chirality : 0.046 0.165 9520 Planarity : 0.005 0.055 10598 Dihedral : 5.777 30.785 8134 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.31 % Allowed : 9.56 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 7406 helix: 0.17 (0.10), residues: 2212 sheet: -1.23 (0.12), residues: 1638 loop : -0.97 (0.10), residues: 3556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRPLX 466 HIS 0.002 0.001 HISNX 413 PHE 0.013 0.001 PHEDT 84 TYR 0.019 0.001 TYRIT 210 ARG 0.007 0.001 ARGEX 410 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14812 Ramachandran restraints generated. 7406 Oldfield, 0 Emsley, 7406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14812 Ramachandran restraints generated. 7406 Oldfield, 0 Emsley, 7406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1909 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 1820 time to evaluate : 5.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AT 49 GLU cc_start: 0.7340 (mp0) cc_final: 0.7033 (mp0) REVERT: AT 64 GLN cc_start: 0.8104 (tt0) cc_final: 0.7470 (mt0) REVERT: AT 193 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7369 (mt-10) REVERT: AT 194 LYS cc_start: 0.7809 (pttm) cc_final: 0.7443 (tptp) REVERT: AT 196 ASN cc_start: 0.7750 (m-40) cc_final: 0.7497 (m-40) REVERT: AT 208 GLN cc_start: 0.7710 (tp40) cc_final: 0.7508 (tp40) REVERT: AT 216 ASN cc_start: 0.7616 (m110) cc_final: 0.7253 (m-40) REVERT: AT 292 GLU cc_start: 0.8066 (tp30) cc_final: 0.7836 (tp30) REVERT: AX 378 ASP cc_start: 0.7925 (m-30) cc_final: 0.7710 (t0) REVERT: AX 386 GLN cc_start: 0.8325 (tm-30) cc_final: 0.7939 (tp40) REVERT: AX 415 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.7811 (mmm) REVERT: AX 447 LYS cc_start: 0.8662 (mmtm) cc_final: 0.8444 (mmtm) REVERT: AX 450 MET cc_start: 0.9056 (OUTLIER) cc_final: 0.8823 (ptm) REVERT: AX 467 TYR cc_start: 0.9128 (t80) cc_final: 0.8759 (t80) REVERT: AY 1884 ASP cc_start: 0.7766 (m-30) cc_final: 0.7542 (m-30) REVERT: AY 1907 GLN cc_start: 0.8166 (tm-30) cc_final: 0.7929 (tt0) REVERT: BT 49 GLU cc_start: 0.7312 (mp0) cc_final: 0.7057 (mp0) REVERT: BT 64 GLN cc_start: 0.7916 (tt0) cc_final: 0.7423 (mt0) REVERT: BT 194 LYS cc_start: 0.7914 (pttm) cc_final: 0.7542 (tptp) REVERT: BT 209 GLU cc_start: 0.7113 (tm-30) cc_final: 0.6614 (tp30) REVERT: BT 216 ASN cc_start: 0.7730 (m110) cc_final: 0.7341 (m110) REVERT: BX 371 GLU cc_start: 0.7754 (tm-30) cc_final: 0.7548 (tm-30) REVERT: BX 386 GLN cc_start: 0.8427 (tm-30) cc_final: 0.8023 (tp40) REVERT: BX 508 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8265 (mt-10) REVERT: BY 1715 SER cc_start: 0.8480 (p) cc_final: 0.8254 (p) REVERT: CT 45 GLU cc_start: 0.7247 (pp20) cc_final: 0.6994 (pp20) REVERT: CT 49 GLU cc_start: 0.7356 (mp0) cc_final: 0.7065 (mp0) REVERT: CT 194 LYS cc_start: 0.7823 (pttm) cc_final: 0.7438 (tptp) REVERT: CT 214 LYS cc_start: 0.7570 (pptt) cc_final: 0.7190 (pptt) REVERT: CT 216 ASN cc_start: 0.7715 (m110) cc_final: 0.7390 (m110) REVERT: CX 371 GLU cc_start: 0.7703 (tm-30) cc_final: 0.7501 (tm-30) REVERT: CX 378 ASP cc_start: 0.8024 (m-30) cc_final: 0.7782 (m-30) REVERT: CX 386 GLN cc_start: 0.8441 (tm-30) cc_final: 0.8035 (tp40) REVERT: CX 387 TYR cc_start: 0.8739 (t80) cc_final: 0.8458 (t80) REVERT: CX 389 HIS cc_start: 0.7710 (t70) cc_final: 0.7469 (m90) REVERT: CX 450 MET cc_start: 0.9072 (OUTLIER) cc_final: 0.8739 (ptm) REVERT: CX 474 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7523 (mm-30) REVERT: CY 1715 SER cc_start: 0.8459 (p) cc_final: 0.8242 (p) REVERT: CY 1817 ILE cc_start: 0.8631 (mm) cc_final: 0.8319 (mt) REVERT: DT 49 GLU cc_start: 0.7273 (mp0) cc_final: 0.6940 (mp0) REVERT: DT 193 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7362 (mt-10) REVERT: DT 194 LYS cc_start: 0.7800 (pttm) cc_final: 0.7443 (tptp) REVERT: DT 296 GLU cc_start: 0.7595 (tm-30) cc_final: 0.7297 (tm-30) REVERT: DT 300 ASN cc_start: 0.7325 (m-40) cc_final: 0.7106 (m-40) REVERT: DX 386 GLN cc_start: 0.8395 (tm-30) cc_final: 0.7996 (tp40) REVERT: DY 1739 TYR cc_start: 0.8845 (m-80) cc_final: 0.8546 (m-80) REVERT: DY 1903 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8154 (tm-30) REVERT: DY 1904 ILE cc_start: 0.8464 (mt) cc_final: 0.8032 (mt) REVERT: ET 27 LYS cc_start: 0.7530 (mmtt) cc_final: 0.7281 (mmtm) REVERT: ET 64 GLN cc_start: 0.7918 (tt0) cc_final: 0.7402 (mt0) REVERT: ET 105 TYR cc_start: 0.8629 (m-80) cc_final: 0.8284 (m-80) REVERT: ET 194 LYS cc_start: 0.7722 (pttm) cc_final: 0.7416 (tptp) REVERT: ET 209 GLU cc_start: 0.7381 (tm-30) cc_final: 0.6334 (tp30) REVERT: ET 210 TYR cc_start: 0.8196 (t80) cc_final: 0.7845 (t80) REVERT: ET 290 GLN cc_start: 0.7238 (tp-100) cc_final: 0.7011 (mp10) REVERT: EX 378 ASP cc_start: 0.7991 (m-30) cc_final: 0.7618 (t0) REVERT: EX 386 GLN cc_start: 0.8404 (tm-30) cc_final: 0.8175 (tp40) REVERT: EX 403 TYR cc_start: 0.8592 (m-80) cc_final: 0.8360 (m-80) REVERT: EX 405 GLN cc_start: 0.7566 (pt0) cc_final: 0.6856 (pt0) REVERT: EX 410 ARG cc_start: 0.7393 (mtm110) cc_final: 0.7022 (mtm110) REVERT: EX 421 ASP cc_start: 0.8658 (p0) cc_final: 0.8422 (p0) REVERT: EY 1715 SER cc_start: 0.8569 (p) cc_final: 0.8337 (p) REVERT: EY 1884 ASP cc_start: 0.7754 (m-30) cc_final: 0.7528 (m-30) REVERT: EY 1907 GLN cc_start: 0.8335 (tm-30) cc_final: 0.7915 (tm-30) REVERT: FT 27 LYS cc_start: 0.7487 (mmtt) cc_final: 0.7242 (mmtm) REVERT: FT 64 GLN cc_start: 0.7872 (tt0) cc_final: 0.7322 (mt0) REVERT: FT 194 LYS cc_start: 0.7805 (pttm) cc_final: 0.7437 (tptp) REVERT: FT 197 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7875 (tp-100) REVERT: FT 216 ASN cc_start: 0.7634 (m110) cc_final: 0.7272 (m110) REVERT: FT 296 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7545 (tm-30) REVERT: FX 378 ASP cc_start: 0.8281 (m-30) cc_final: 0.7702 (t0) REVERT: FX 386 GLN cc_start: 0.8481 (tm-30) cc_final: 0.8061 (tp40) REVERT: FX 405 GLN cc_start: 0.7710 (pt0) cc_final: 0.7474 (pt0) REVERT: FX 415 MET cc_start: 0.8382 (mmm) cc_final: 0.7917 (mmm) REVERT: FX 450 MET cc_start: 0.8982 (ttp) cc_final: 0.8723 (ptm) REVERT: FX 474 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7447 (mm-30) REVERT: GT 64 GLN cc_start: 0.7916 (tt0) cc_final: 0.7342 (mt0) REVERT: GT 209 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7623 (tp30) REVERT: GT 216 ASN cc_start: 0.7643 (m110) cc_final: 0.7276 (m110) REVERT: GX 386 GLN cc_start: 0.8421 (tm-30) cc_final: 0.8035 (tp40) REVERT: GX 410 ARG cc_start: 0.7400 (mtm110) cc_final: 0.7099 (mtm110) REVERT: GY 1685 LYS cc_start: 0.7116 (mmtm) cc_final: 0.6894 (mmtt) REVERT: HT 27 LYS cc_start: 0.7327 (mmtt) cc_final: 0.7096 (mmtm) REVERT: HT 49 GLU cc_start: 0.7314 (mp0) cc_final: 0.7044 (mp0) REVERT: HT 64 GLN cc_start: 0.8076 (tt0) cc_final: 0.7456 (mt0) REVERT: HT 193 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7406 (mt-10) REVERT: HT 194 LYS cc_start: 0.7802 (pttm) cc_final: 0.7451 (tptp) REVERT: HT 216 ASN cc_start: 0.7622 (m110) cc_final: 0.7252 (m-40) REVERT: HT 296 GLU cc_start: 0.7626 (tm-30) cc_final: 0.7383 (tm-30) REVERT: HT 300 ASN cc_start: 0.7104 (m-40) cc_final: 0.6873 (m-40) REVERT: HX 386 GLN cc_start: 0.8308 (tm-30) cc_final: 0.7906 (tp40) REVERT: HX 415 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.7803 (mmm) REVERT: HX 447 LYS cc_start: 0.8680 (mmtm) cc_final: 0.8455 (mmtm) REVERT: HX 450 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.8840 (ptm) REVERT: HY 1884 ASP cc_start: 0.7752 (m-30) cc_final: 0.7515 (m-30) REVERT: IT 49 GLU cc_start: 0.7326 (mp0) cc_final: 0.7050 (mp0) REVERT: IT 64 GLN cc_start: 0.7968 (tt0) cc_final: 0.7415 (mt0) REVERT: IT 194 LYS cc_start: 0.7802 (pttm) cc_final: 0.7470 (tptp) REVERT: IT 198 TYR cc_start: 0.7925 (t80) cc_final: 0.7660 (t80) REVERT: IT 208 GLN cc_start: 0.7718 (tp40) cc_final: 0.7516 (tp40) REVERT: IT 209 GLU cc_start: 0.7044 (tm-30) cc_final: 0.6545 (tp30) REVERT: IT 287 GLU cc_start: 0.6235 (pm20) cc_final: 0.5822 (pm20) REVERT: IT 290 GLN cc_start: 0.6979 (tp40) cc_final: 0.6581 (mp10) REVERT: IT 296 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7544 (tm-30) REVERT: IX 386 GLN cc_start: 0.8384 (tm-30) cc_final: 0.8036 (tp40) REVERT: IX 474 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7392 (mm-30) REVERT: IY 1715 SER cc_start: 0.8469 (p) cc_final: 0.8242 (p) REVERT: JT 45 GLU cc_start: 0.7129 (pp20) cc_final: 0.6826 (pp20) REVERT: JT 64 GLN cc_start: 0.7767 (tt0) cc_final: 0.7402 (mp10) REVERT: JT 193 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7319 (mt-10) REVERT: JT 194 LYS cc_start: 0.7902 (pttm) cc_final: 0.7500 (tptp) REVERT: JT 197 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7800 (tp40) REVERT: JT 201 THR cc_start: 0.7950 (p) cc_final: 0.7750 (p) REVERT: JT 210 TYR cc_start: 0.8254 (t80) cc_final: 0.7835 (t80) REVERT: JX 386 GLN cc_start: 0.8383 (tm-30) cc_final: 0.8042 (tp40) REVERT: JX 389 HIS cc_start: 0.7775 (t70) cc_final: 0.7495 (m90) REVERT: JX 450 MET cc_start: 0.9115 (ttp) cc_final: 0.8804 (ptm) REVERT: JX 484 LEU cc_start: 0.9141 (tp) cc_final: 0.8931 (tp) REVERT: JY 1715 SER cc_start: 0.8459 (p) cc_final: 0.8254 (p) REVERT: JY 1817 ILE cc_start: 0.8636 (mm) cc_final: 0.8324 (mt) REVERT: KT 49 GLU cc_start: 0.7322 (mp0) cc_final: 0.6958 (mp0) REVERT: KT 194 LYS cc_start: 0.7871 (pttm) cc_final: 0.7477 (tptp) REVERT: KT 197 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.7945 (tp-100) REVERT: KT 209 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7698 (tp30) REVERT: KT 210 TYR cc_start: 0.8172 (t80) cc_final: 0.7934 (t80) REVERT: KT 216 ASN cc_start: 0.7673 (m110) cc_final: 0.7336 (m110) REVERT: KT 292 GLU cc_start: 0.7982 (tp30) cc_final: 0.6835 (mt-10) REVERT: KX 371 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7552 (tm-30) REVERT: KX 378 ASP cc_start: 0.8247 (m-30) cc_final: 0.7906 (m-30) REVERT: KX 386 GLN cc_start: 0.8434 (tm-30) cc_final: 0.8123 (tp40) REVERT: KX 389 HIS cc_start: 0.7776 (t70) cc_final: 0.7542 (m-70) REVERT: KY 1739 TYR cc_start: 0.8840 (m-80) cc_final: 0.8550 (m-80) REVERT: KY 1817 ILE cc_start: 0.8555 (mm) cc_final: 0.8232 (mt) REVERT: KY 1903 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8154 (tm-30) REVERT: KY 1904 ILE cc_start: 0.8496 (mt) cc_final: 0.8074 (mt) REVERT: LT 49 GLU cc_start: 0.7465 (mp0) cc_final: 0.7158 (mp0) REVERT: LT 64 GLN cc_start: 0.7886 (tt0) cc_final: 0.7374 (mt0) REVERT: LT 194 LYS cc_start: 0.7683 (pttm) cc_final: 0.7183 (tptp) REVERT: LT 209 GLU cc_start: 0.7412 (tm-30) cc_final: 0.6395 (tp30) REVERT: LT 210 TYR cc_start: 0.8124 (t80) cc_final: 0.7731 (t80) REVERT: LT 216 ASN cc_start: 0.7675 (m110) cc_final: 0.7222 (m110) REVERT: LX 378 ASP cc_start: 0.8002 (m-30) cc_final: 0.7626 (t0) REVERT: LX 386 GLN cc_start: 0.8464 (tm-30) cc_final: 0.8215 (tp40) REVERT: LX 403 TYR cc_start: 0.8594 (m-80) cc_final: 0.8358 (m-80) REVERT: LX 405 GLN cc_start: 0.7561 (pt0) cc_final: 0.5642 (pt0) REVERT: LX 410 ARG cc_start: 0.7377 (mtm110) cc_final: 0.7014 (mtm110) REVERT: LX 421 ASP cc_start: 0.8664 (p0) cc_final: 0.8420 (p0) REVERT: LY 1715 SER cc_start: 0.8534 (p) cc_final: 0.8295 (p) REVERT: LY 1721 ASP cc_start: 0.7904 (m-30) cc_final: 0.7638 (m-30) REVERT: LY 1884 ASP cc_start: 0.7757 (m-30) cc_final: 0.7534 (m-30) REVERT: MT 49 GLU cc_start: 0.7353 (mp0) cc_final: 0.6964 (mp0) REVERT: MT 194 LYS cc_start: 0.7703 (pttm) cc_final: 0.7375 (tptp) REVERT: MT 209 GLU cc_start: 0.7474 (tm-30) cc_final: 0.6448 (tp30) REVERT: MT 216 ASN cc_start: 0.7331 (m110) cc_final: 0.6948 (m110) REVERT: MT 296 GLU cc_start: 0.7739 (tm-30) cc_final: 0.7481 (tm-30) REVERT: MX 378 ASP cc_start: 0.8288 (m-30) cc_final: 0.7701 (t0) REVERT: MX 386 GLN cc_start: 0.8479 (tm-30) cc_final: 0.8068 (tp40) REVERT: MX 405 GLN cc_start: 0.7862 (pt0) cc_final: 0.7640 (pt0) REVERT: MX 415 MET cc_start: 0.8349 (mmm) cc_final: 0.7921 (mmm) REVERT: MX 450 MET cc_start: 0.8983 (ttp) cc_final: 0.8727 (ptm) REVERT: NT 64 GLN cc_start: 0.7852 (tt0) cc_final: 0.7343 (mt0) REVERT: NT 209 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7610 (tp30) REVERT: NT 216 ASN cc_start: 0.7676 (m110) cc_final: 0.7337 (m-40) REVERT: NX 386 GLN cc_start: 0.8416 (tm-30) cc_final: 0.8029 (tp40) REVERT: NY 1685 LYS cc_start: 0.7140 (mmtm) cc_final: 0.6916 (mmtt) outliers start: 89 outliers final: 52 residues processed: 1856 average time/residue: 0.6255 time to fit residues: 1956.5751 Evaluate side-chains 1656 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 1594 time to evaluate : 5.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AT residue 136 SER Chi-restraints excluded: chain AX residue 411 SER Chi-restraints excluded: chain AX residue 415 MET Chi-restraints excluded: chain AX residue 450 MET Chi-restraints excluded: chain AY residue 1713 ILE Chi-restraints excluded: chain AY residue 1752 MET Chi-restraints excluded: chain BT residue 29 VAL Chi-restraints excluded: chain BT residue 136 SER Chi-restraints excluded: chain BX residue 377 LEU Chi-restraints excluded: chain BX residue 415 MET Chi-restraints excluded: chain CT residue 29 VAL Chi-restraints excluded: chain CT residue 136 SER Chi-restraints excluded: chain CT residue 204 GLN Chi-restraints excluded: chain CX residue 377 LEU Chi-restraints excluded: chain CX residue 415 MET Chi-restraints excluded: chain CX residue 424 THR Chi-restraints excluded: chain CX residue 450 MET Chi-restraints excluded: chain DT residue 29 VAL Chi-restraints excluded: chain DT residue 30 LYS Chi-restraints excluded: chain DT residue 136 SER Chi-restraints excluded: chain DT residue 173 VAL Chi-restraints excluded: chain DX residue 415 MET Chi-restraints excluded: chain DY residue 1879 ILE Chi-restraints excluded: chain DY residue 1903 GLU Chi-restraints excluded: chain ET residue 136 SER Chi-restraints excluded: chain EX residue 377 LEU Chi-restraints excluded: chain EX residue 411 SER Chi-restraints excluded: chain EY residue 1713 ILE Chi-restraints excluded: chain EY residue 1752 MET Chi-restraints excluded: chain FT residue 136 SER Chi-restraints excluded: chain FT residue 197 GLN Chi-restraints excluded: chain FY residue 1752 MET Chi-restraints excluded: chain HT residue 136 SER Chi-restraints excluded: chain HX residue 411 SER Chi-restraints excluded: chain HX residue 415 MET Chi-restraints excluded: chain HX residue 450 MET Chi-restraints excluded: chain HY residue 1713 ILE Chi-restraints excluded: chain HY residue 1752 MET Chi-restraints excluded: chain IT residue 136 SER Chi-restraints excluded: chain IX residue 377 LEU Chi-restraints excluded: chain IX residue 383 LEU Chi-restraints excluded: chain IX residue 415 MET Chi-restraints excluded: chain JT residue 29 VAL Chi-restraints excluded: chain JT residue 82 LEU Chi-restraints excluded: chain JT residue 136 SER Chi-restraints excluded: chain JT residue 173 VAL Chi-restraints excluded: chain JT residue 197 GLN Chi-restraints excluded: chain JX residue 377 LEU Chi-restraints excluded: chain JX residue 424 THR Chi-restraints excluded: chain KT residue 30 LYS Chi-restraints excluded: chain KT residue 173 VAL Chi-restraints excluded: chain KT residue 197 GLN Chi-restraints excluded: chain KX residue 377 LEU Chi-restraints excluded: chain KY residue 1879 ILE Chi-restraints excluded: chain KY residue 1903 GLU Chi-restraints excluded: chain LT residue 136 SER Chi-restraints excluded: chain LX residue 377 LEU Chi-restraints excluded: chain LX residue 411 SER Chi-restraints excluded: chain LY residue 1713 ILE Chi-restraints excluded: chain MT residue 136 SER Chi-restraints excluded: chain MY residue 1752 MET Chi-restraints excluded: chain NT residue 136 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 367 optimal weight: 4.9990 chunk 205 optimal weight: 2.9990 chunk 550 optimal weight: 4.9990 chunk 450 optimal weight: 0.5980 chunk 182 optimal weight: 1.9990 chunk 662 optimal weight: 2.9990 chunk 715 optimal weight: 2.9990 chunk 589 optimal weight: 9.9990 chunk 656 optimal weight: 4.9990 chunk 225 optimal weight: 5.9990 chunk 531 optimal weight: 6.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AY1856 ASN ** BT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BX 443 GLN ** BY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CT 197 GLN CT 204 GLN CY1856 ASN ** EX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** EY1856 ASN EY1857 GLN ** FT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** FT 41 ASN GX 373 GLN GX 413 HIS ** GY1856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** GY1857 GLN HT 33 ASN HY1694 GLN HY1856 ASN ** IY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** JT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** JT 204 GLN JX 413 HIS JY1856 ASN LT 33 ASN LT 301 GLN ** LX 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LY1856 ASN LY1857 GLN MT 41 ASN NT 33 ASN NX 413 HIS ** NY1856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NY1857 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 61992 Z= 0.375 Angle : 0.654 6.675 83594 Z= 0.351 Chirality : 0.048 0.173 9520 Planarity : 0.004 0.049 10598 Dihedral : 5.455 29.341 8134 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.97 % Allowed : 12.37 % Favored : 84.65 % 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: -0.75 (0.09), residues: 7406 helix: 0.80 (0.11), residues: 2212 sheet: -1.11 (0.12), residues: 1652 loop : -0.95 (0.10), residues: 3542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRPDX 466 HIS 0.002 0.001 HISAX 413 PHE 0.012 0.002 PHEFY1682 TYR 0.016 0.002 TYRGX 401 ARG 0.007 0.000 ARGAX 410 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14812 Ramachandran restraints generated. 7406 Oldfield, 0 Emsley, 7406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14812 Ramachandran restraints generated. 7406 Oldfield, 0 Emsley, 7406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1889 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 1687 time to evaluate : 5.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AT 49 GLU cc_start: 0.7490 (mp0) cc_final: 0.7053 (mp0) REVERT: AT 64 GLN cc_start: 0.8110 (tt0) cc_final: 0.7449 (mt0) REVERT: AT 194 LYS cc_start: 0.7939 (pttm) cc_final: 0.7307 (tptp) REVERT: AT 208 GLN cc_start: 0.7579 (tp40) cc_final: 0.7307 (tp40) REVERT: AT 216 ASN cc_start: 0.7667 (m110) cc_final: 0.7334 (m110) REVERT: AX 378 ASP cc_start: 0.8144 (m-30) cc_final: 0.7830 (t0) REVERT: AX 386 GLN cc_start: 0.8373 (tm-30) cc_final: 0.7984 (tp40) REVERT: AX 405 GLN cc_start: 0.7894 (pt0) cc_final: 0.7492 (pt0) REVERT: AX 415 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.8141 (mmm) REVERT: BT 64 GLN cc_start: 0.8019 (tt0) cc_final: 0.7500 (mt0) REVERT: BT 194 LYS cc_start: 0.8021 (pttm) cc_final: 0.7429 (tptp) REVERT: BT 209 GLU cc_start: 0.7139 (tm-30) cc_final: 0.6611 (tp30) REVERT: BT 216 ASN cc_start: 0.7617 (m110) cc_final: 0.7201 (m110) REVERT: BX 371 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7427 (tm-30) REVERT: BX 386 GLN cc_start: 0.8482 (tm-30) cc_final: 0.8105 (tp40) REVERT: BX 410 ARG cc_start: 0.7787 (ptp-170) cc_final: 0.7495 (mtm110) REVERT: BY 1873 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8055 (pm20) REVERT: CT 49 GLU cc_start: 0.7460 (mp0) cc_final: 0.7253 (mp0) REVERT: CT 194 LYS cc_start: 0.8087 (pttm) cc_final: 0.7409 (tptp) REVERT: CT 209 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7697 (tp30) REVERT: CT 210 TYR cc_start: 0.8203 (t80) cc_final: 0.7894 (t80) REVERT: CT 216 ASN cc_start: 0.7737 (m110) cc_final: 0.7420 (m110) REVERT: CX 371 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7252 (tm-30) REVERT: CX 378 ASP cc_start: 0.8062 (m-30) cc_final: 0.7771 (m-30) REVERT: CX 386 GLN cc_start: 0.8463 (tm-30) cc_final: 0.8112 (tp40) REVERT: CX 387 TYR cc_start: 0.8685 (t80) cc_final: 0.8353 (t80) REVERT: CX 389 HIS cc_start: 0.7799 (t70) cc_final: 0.7554 (m90) REVERT: CX 450 MET cc_start: 0.9128 (ttp) cc_final: 0.8828 (ptm) REVERT: DT 49 GLU cc_start: 0.7443 (mp0) cc_final: 0.7243 (mp0) REVERT: DT 194 LYS cc_start: 0.7873 (pttm) cc_final: 0.7234 (tptp) REVERT: DT 208 GLN cc_start: 0.7716 (tp40) cc_final: 0.7484 (tp40) REVERT: DT 296 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7336 (tm-30) REVERT: DT 300 ASN cc_start: 0.7304 (m-40) cc_final: 0.6979 (m-40) REVERT: DX 374 LYS cc_start: 0.7950 (ptmm) cc_final: 0.7456 (ptpp) REVERT: DX 386 GLN cc_start: 0.8504 (tm-30) cc_final: 0.8114 (tp40) REVERT: DY 1685 LYS cc_start: 0.7187 (mmtm) cc_final: 0.6786 (mmtm) REVERT: DY 1772 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8140 (pp) REVERT: DY 1903 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8132 (tm-30) REVERT: DY 1904 ILE cc_start: 0.8464 (mt) cc_final: 0.8052 (mt) REVERT: ET 49 GLU cc_start: 0.7424 (mp0) cc_final: 0.7203 (mp0) REVERT: ET 64 GLN cc_start: 0.8020 (tt0) cc_final: 0.7467 (mt0) REVERT: ET 105 TYR cc_start: 0.8649 (m-80) cc_final: 0.8285 (m-80) REVERT: ET 194 LYS cc_start: 0.7838 (pttm) cc_final: 0.7310 (tptp) REVERT: ET 209 GLU cc_start: 0.7336 (tm-30) cc_final: 0.6288 (tp30) REVERT: ET 301 GLN cc_start: 0.7566 (tp40) cc_final: 0.7311 (tp-100) REVERT: EX 378 ASP cc_start: 0.8160 (m-30) cc_final: 0.7701 (t0) REVERT: EX 386 GLN cc_start: 0.8493 (tm-30) cc_final: 0.8287 (tp40) REVERT: FT 27 LYS cc_start: 0.7605 (mmtt) cc_final: 0.7342 (mmtm) REVERT: FT 194 LYS cc_start: 0.7855 (pttm) cc_final: 0.7481 (tptp) REVERT: FT 216 ASN cc_start: 0.7577 (m110) cc_final: 0.7188 (m110) REVERT: FT 296 GLU cc_start: 0.7751 (tm-30) cc_final: 0.7544 (tm-30) REVERT: FX 378 ASP cc_start: 0.8313 (m-30) cc_final: 0.7586 (t0) REVERT: FX 386 GLN cc_start: 0.8512 (tm-30) cc_final: 0.8096 (tp40) REVERT: FX 415 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.8034 (mmm) REVERT: FY 1685 LYS cc_start: 0.7179 (mmtm) cc_final: 0.6669 (mmtm) REVERT: GT 209 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7593 (tp30) REVERT: GT 216 ASN cc_start: 0.7669 (m110) cc_final: 0.7274 (m110) REVERT: GX 374 LYS cc_start: 0.7829 (ptmm) cc_final: 0.7486 (ptpp) REVERT: GX 386 GLN cc_start: 0.8418 (tm-30) cc_final: 0.8125 (tp40) REVERT: GY 1685 LYS cc_start: 0.7037 (mmtm) cc_final: 0.6745 (mmtt) REVERT: HT 49 GLU cc_start: 0.7455 (mp0) cc_final: 0.7131 (mp0) REVERT: HT 64 GLN cc_start: 0.8125 (tt0) cc_final: 0.7477 (mt0) REVERT: HT 194 LYS cc_start: 0.7940 (pttm) cc_final: 0.7355 (tptp) REVERT: HT 216 ASN cc_start: 0.7647 (m110) cc_final: 0.7286 (m-40) REVERT: HT 296 GLU cc_start: 0.7652 (tm-30) cc_final: 0.7348 (tm-30) REVERT: HT 300 ASN cc_start: 0.7027 (m-40) cc_final: 0.6748 (m-40) REVERT: HX 386 GLN cc_start: 0.8417 (tm-30) cc_final: 0.8005 (tp40) REVERT: HX 405 GLN cc_start: 0.7875 (pt0) cc_final: 0.7636 (pt0) REVERT: HY 1884 ASP cc_start: 0.7748 (m-30) cc_final: 0.7528 (m-30) REVERT: IT 64 GLN cc_start: 0.8030 (tt0) cc_final: 0.7458 (mt0) REVERT: IT 192 LEU cc_start: 0.7086 (mm) cc_final: 0.6332 (tp) REVERT: IT 194 LYS cc_start: 0.7961 (pttm) cc_final: 0.7375 (tptp) REVERT: IT 196 ASN cc_start: 0.7509 (m-40) cc_final: 0.6954 (m-40) REVERT: IT 208 GLN cc_start: 0.7719 (tp40) cc_final: 0.7447 (tp40) REVERT: IT 209 GLU cc_start: 0.7127 (tm-30) cc_final: 0.6648 (tp30) REVERT: IT 292 GLU cc_start: 0.8012 (tp30) cc_final: 0.7593 (tp30) REVERT: IT 296 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7452 (tm-30) REVERT: IX 378 ASP cc_start: 0.8282 (m-30) cc_final: 0.7969 (m-30) REVERT: IX 386 GLN cc_start: 0.8465 (tm-30) cc_final: 0.7932 (tp40) REVERT: IX 410 ARG cc_start: 0.7925 (ptp-170) cc_final: 0.7647 (mtm110) REVERT: IY 1699 GLU cc_start: 0.7844 (tt0) cc_final: 0.7610 (tt0) REVERT: IY 1873 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8030 (pm20) REVERT: JT 194 LYS cc_start: 0.7860 (pttm) cc_final: 0.7485 (tptp) REVERT: JT 216 ASN cc_start: 0.7662 (m110) cc_final: 0.7361 (m110) REVERT: JT 300 ASN cc_start: 0.6770 (m-40) cc_final: 0.6535 (p0) REVERT: JX 386 GLN cc_start: 0.8456 (tm-30) cc_final: 0.8139 (tp40) REVERT: JX 389 HIS cc_start: 0.7892 (t70) cc_final: 0.7672 (m90) REVERT: JX 450 MET cc_start: 0.9132 (ttp) cc_final: 0.8835 (ptm) REVERT: JX 484 LEU cc_start: 0.9162 (tp) cc_final: 0.8961 (tp) REVERT: KT 49 GLU cc_start: 0.7491 (mp0) cc_final: 0.7274 (mp0) REVERT: KT 59 THR cc_start: 0.8840 (m) cc_final: 0.8583 (m) REVERT: KT 194 LYS cc_start: 0.7933 (pttm) cc_final: 0.7539 (tptp) REVERT: KT 197 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.8247 (tp-100) REVERT: KT 208 GLN cc_start: 0.7660 (tp40) cc_final: 0.7452 (tp40) REVERT: KT 209 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7788 (tp30) REVERT: KT 216 ASN cc_start: 0.7681 (m110) cc_final: 0.7383 (m110) REVERT: KX 378 ASP cc_start: 0.8387 (m-30) cc_final: 0.7828 (t0) REVERT: KX 386 GLN cc_start: 0.8471 (tm-30) cc_final: 0.8171 (tp40) REVERT: KX 389 HIS cc_start: 0.7885 (t70) cc_final: 0.7600 (m-70) REVERT: KY 1685 LYS cc_start: 0.7225 (mmtm) cc_final: 0.6821 (mmtm) REVERT: KY 1739 TYR cc_start: 0.9005 (m-80) cc_final: 0.8764 (m-80) REVERT: KY 1772 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8193 (pp) REVERT: KY 1903 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8073 (tm-30) REVERT: KY 1904 ILE cc_start: 0.8509 (mt) cc_final: 0.8106 (mt) REVERT: LT 49 GLU cc_start: 0.7468 (mp0) cc_final: 0.7128 (mp0) REVERT: LT 64 GLN cc_start: 0.7981 (tt0) cc_final: 0.7484 (mt0) REVERT: LT 105 TYR cc_start: 0.8662 (m-80) cc_final: 0.8308 (m-80) REVERT: LT 194 LYS cc_start: 0.7858 (pttm) cc_final: 0.7325 (tptp) REVERT: LT 201 THR cc_start: 0.8347 (p) cc_final: 0.7860 (t) REVERT: LT 209 GLU cc_start: 0.7466 (tm-30) cc_final: 0.6387 (tp30) REVERT: LT 216 ASN cc_start: 0.7702 (m110) cc_final: 0.7274 (m110) REVERT: LX 378 ASP cc_start: 0.8167 (m-30) cc_final: 0.7699 (t0) REVERT: LX 386 GLN cc_start: 0.8488 (tm-30) cc_final: 0.8280 (tp40) REVERT: LY 1907 GLN cc_start: 0.8343 (tm-30) cc_final: 0.7600 (tm-30) REVERT: MT 45 GLU cc_start: 0.7515 (pm20) cc_final: 0.7209 (pt0) REVERT: MT 49 GLU cc_start: 0.7469 (mp0) cc_final: 0.7181 (mp0) REVERT: MT 194 LYS cc_start: 0.7893 (pttm) cc_final: 0.7267 (tptp) REVERT: MT 209 GLU cc_start: 0.7485 (tm-30) cc_final: 0.6425 (tp30) REVERT: MT 216 ASN cc_start: 0.7437 (m110) cc_final: 0.7173 (m110) REVERT: MX 378 ASP cc_start: 0.8275 (m-30) cc_final: 0.7572 (t0) REVERT: MX 386 GLN cc_start: 0.8510 (tm-30) cc_final: 0.8084 (tp40) REVERT: MX 405 GLN cc_start: 0.7909 (pt0) cc_final: 0.7337 (pt0) REVERT: MX 415 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.7894 (mmm) REVERT: MX 474 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7757 (tp30) REVERT: MY 1685 LYS cc_start: 0.7183 (mmtm) cc_final: 0.6624 (mmtm) REVERT: NT 64 GLN cc_start: 0.7954 (tt0) cc_final: 0.7431 (mt0) REVERT: NT 209 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7563 (tp30) REVERT: NT 216 ASN cc_start: 0.7706 (m110) cc_final: 0.7374 (m-40) REVERT: NX 374 LYS cc_start: 0.7829 (ptmm) cc_final: 0.7482 (ptpp) REVERT: NX 386 GLN cc_start: 0.8440 (tm-30) cc_final: 0.8150 (tp40) REVERT: NX 410 ARG cc_start: 0.7074 (mtm110) cc_final: 0.6802 (mtm110) REVERT: NY 1685 LYS cc_start: 0.7041 (mmtm) cc_final: 0.6743 (mmtt) outliers start: 202 outliers final: 113 residues processed: 1812 average time/residue: 0.5683 time to fit residues: 1737.9815 Evaluate side-chains 1649 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 1526 time to evaluate : 5.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AT residue 80 VAL Chi-restraints excluded: chain AT residue 136 SER Chi-restraints excluded: chain AT residue 173 VAL Chi-restraints excluded: chain AX residue 411 SER Chi-restraints excluded: chain AX residue 415 MET Chi-restraints excluded: chain AX residue 424 THR Chi-restraints excluded: chain AY residue 1713 ILE Chi-restraints excluded: chain AY residue 1725 MET Chi-restraints excluded: chain AY residue 1751 ILE Chi-restraints excluded: chain AY residue 1873 GLU Chi-restraints excluded: chain BT residue 29 VAL Chi-restraints excluded: chain BT residue 35 VAL Chi-restraints excluded: chain BT residue 80 VAL Chi-restraints excluded: chain BT residue 136 SER Chi-restraints excluded: chain BT residue 173 VAL Chi-restraints excluded: chain BX residue 415 MET Chi-restraints excluded: chain BY residue 1751 ILE Chi-restraints excluded: chain BY residue 1809 SER Chi-restraints excluded: chain BY residue 1873 GLU Chi-restraints excluded: chain CT residue 29 VAL Chi-restraints excluded: chain CT residue 80 VAL Chi-restraints excluded: chain CT residue 82 LEU Chi-restraints excluded: chain CT residue 136 SER Chi-restraints excluded: chain CT residue 173 VAL Chi-restraints excluded: chain CX residue 383 LEU Chi-restraints excluded: chain CX residue 415 MET Chi-restraints excluded: chain CX residue 424 THR Chi-restraints excluded: chain CX residue 509 LEU Chi-restraints excluded: chain CY residue 1873 GLU Chi-restraints excluded: chain DT residue 29 VAL Chi-restraints excluded: chain DT residue 30 LYS Chi-restraints excluded: chain DT residue 35 VAL Chi-restraints excluded: chain DT residue 80 VAL Chi-restraints excluded: chain DT residue 136 SER Chi-restraints excluded: chain DT residue 173 VAL Chi-restraints excluded: chain DX residue 383 LEU Chi-restraints excluded: chain DX residue 415 MET Chi-restraints excluded: chain DX residue 417 SER Chi-restraints excluded: chain DY residue 1772 LEU Chi-restraints excluded: chain DY residue 1809 SER Chi-restraints excluded: chain DY residue 1873 GLU Chi-restraints excluded: chain DY residue 1879 ILE Chi-restraints excluded: chain DY residue 1903 GLU Chi-restraints excluded: chain ET residue 80 VAL Chi-restraints excluded: chain ET residue 136 SER Chi-restraints excluded: chain ET residue 173 VAL Chi-restraints excluded: chain EX residue 383 LEU Chi-restraints excluded: chain EX residue 424 THR Chi-restraints excluded: chain EY residue 1752 MET Chi-restraints excluded: chain EY residue 1873 GLU Chi-restraints excluded: chain FT residue 136 SER Chi-restraints excluded: chain FT residue 173 VAL Chi-restraints excluded: chain FX residue 383 LEU Chi-restraints excluded: chain FX residue 415 MET Chi-restraints excluded: chain FY residue 1713 ILE Chi-restraints excluded: chain FY residue 1751 ILE Chi-restraints excluded: chain FY residue 1752 MET Chi-restraints excluded: chain FY residue 1809 SER Chi-restraints excluded: chain GT residue 80 VAL Chi-restraints excluded: chain GT residue 136 SER Chi-restraints excluded: chain GT residue 173 VAL Chi-restraints excluded: chain GX residue 377 LEU Chi-restraints excluded: chain HT residue 35 VAL Chi-restraints excluded: chain HT residue 80 VAL Chi-restraints excluded: chain HT residue 136 SER Chi-restraints excluded: chain HT residue 173 VAL Chi-restraints excluded: chain HX residue 383 LEU Chi-restraints excluded: chain HX residue 411 SER Chi-restraints excluded: chain HX residue 415 MET Chi-restraints excluded: chain HX residue 424 THR Chi-restraints excluded: chain HY residue 1713 ILE Chi-restraints excluded: chain HY residue 1751 ILE Chi-restraints excluded: chain HY residue 1873 GLU Chi-restraints excluded: chain IT residue 35 VAL Chi-restraints excluded: chain IT residue 80 VAL Chi-restraints excluded: chain IT residue 136 SER Chi-restraints excluded: chain IT residue 173 VAL Chi-restraints excluded: chain IX residue 383 LEU Chi-restraints excluded: chain IX residue 415 MET Chi-restraints excluded: chain IX residue 509 LEU Chi-restraints excluded: chain IY residue 1751 ILE Chi-restraints excluded: chain IY residue 1809 SER Chi-restraints excluded: chain IY residue 1873 GLU Chi-restraints excluded: chain JT residue 29 VAL Chi-restraints excluded: chain JT residue 80 VAL Chi-restraints excluded: chain JT residue 82 LEU Chi-restraints excluded: chain JT residue 136 SER Chi-restraints excluded: chain JT residue 173 VAL Chi-restraints excluded: chain JT residue 204 GLN Chi-restraints excluded: chain JX residue 415 MET Chi-restraints excluded: chain JX residue 424 THR Chi-restraints excluded: chain JY residue 1873 GLU Chi-restraints excluded: chain KT residue 30 LYS Chi-restraints excluded: chain KT residue 35 VAL Chi-restraints excluded: chain KT residue 80 VAL Chi-restraints excluded: chain KT residue 136 SER Chi-restraints excluded: chain KT residue 173 VAL Chi-restraints excluded: chain KT residue 197 GLN Chi-restraints excluded: chain KX residue 415 MET Chi-restraints excluded: chain KY residue 1772 LEU Chi-restraints excluded: chain KY residue 1873 GLU Chi-restraints excluded: chain KY residue 1879 ILE Chi-restraints excluded: chain KY residue 1903 GLU Chi-restraints excluded: chain LT residue 80 VAL Chi-restraints excluded: chain LT residue 136 SER Chi-restraints excluded: chain LT residue 173 VAL Chi-restraints excluded: chain LX residue 383 LEU Chi-restraints excluded: chain LX residue 424 THR Chi-restraints excluded: chain LY residue 1752 MET Chi-restraints excluded: chain LY residue 1862 LEU Chi-restraints excluded: chain LY residue 1873 GLU Chi-restraints excluded: chain MT residue 136 SER Chi-restraints excluded: chain MT residue 173 VAL Chi-restraints excluded: chain MX residue 383 LEU Chi-restraints excluded: chain MX residue 415 MET Chi-restraints excluded: chain MY residue 1713 ILE Chi-restraints excluded: chain MY residue 1751 ILE Chi-restraints excluded: chain MY residue 1752 MET Chi-restraints excluded: chain MY residue 1809 SER Chi-restraints excluded: chain NT residue 80 VAL Chi-restraints excluded: chain NT residue 136 SER Chi-restraints excluded: chain NT residue 173 VAL Chi-restraints excluded: chain NX residue 377 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 654 optimal weight: 1.9990 chunk 497 optimal weight: 0.6980 chunk 343 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 316 optimal weight: 5.9990 chunk 444 optimal weight: 0.6980 chunk 664 optimal weight: 0.7980 chunk 703 optimal weight: 0.7980 chunk 347 optimal weight: 1.9990 chunk 629 optimal weight: 0.5980 chunk 189 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AT 33 ASN AY1857 GLN BT 33 ASN ** BY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CT 204 GLN CY1856 ASN DX 432 ASN ** EX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** EX 432 ASN EX 443 GLN EY1907 GLN FT 33 ASN FT 208 GLN ** FY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** FY1856 ASN GT 169 HIS GT 301 GLN GX 432 ASN GY1907 GLN HX 373 GLN HY1857 GLN IX 443 GLN ** IY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** IY1907 GLN JT 64 GLN JT 197 GLN JY1856 ASN ** KY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** KY1907 GLN LT 301 GLN ** LX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LX 443 GLN ** MX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** MY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** MY1856 ASN NT 196 ASN NT 301 GLN NX 432 ASN NY1907 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 61992 Z= 0.198 Angle : 0.584 10.107 83594 Z= 0.312 Chirality : 0.045 0.169 9520 Planarity : 0.004 0.045 10598 Dihedral : 5.132 27.420 8134 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.55 % Allowed : 14.52 % Favored : 82.93 % 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: -0.48 (0.10), residues: 7406 helix: 1.25 (0.11), residues: 2212 sheet: -1.03 (0.12), residues: 1624 loop : -0.92 (0.10), residues: 3570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRPLY1723 HIS 0.002 0.000 HISFT 88 PHE 0.009 0.001 PHEHY1682 TYR 0.021 0.001 TYRIT 210 ARG 0.004 0.000 ARGJX 410 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14812 Ramachandran restraints generated. 7406 Oldfield, 0 Emsley, 7406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14812 Ramachandran restraints generated. 7406 Oldfield, 0 Emsley, 7406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1933 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 1760 time to evaluate : 5.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: AT 49 GLU cc_start: 0.7384 (mp0) cc_final: 0.6935 (mp0) REVERT: AT 64 GLN cc_start: 0.8077 (tt0) cc_final: 0.7433 (mt0) REVERT: AT 194 LYS cc_start: 0.7847 (pttm) cc_final: 0.7363 (tptp) REVERT: AT 216 ASN cc_start: 0.7628 (m110) cc_final: 0.7337 (m110) REVERT: AT 292 GLU cc_start: 0.8005 (tp30) cc_final: 0.6989 (mt-10) REVERT: AT 300 ASN cc_start: 0.6947 (m-40) cc_final: 0.6563 (m-40) REVERT: AX 378 ASP cc_start: 0.8158 (m-30) cc_final: 0.7864 (t0) REVERT: AX 386 GLN cc_start: 0.8368 (tm-30) cc_final: 0.8017 (tp40) REVERT: AX 405 GLN cc_start: 0.7809 (pt0) cc_final: 0.7584 (pt0) REVERT: AX 415 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.7797 (mmm) REVERT: AX 508 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8255 (mt-10) REVERT: BT 49 GLU cc_start: 0.7386 (mp0) cc_final: 0.7081 (mp0) REVERT: BT 64 GLN cc_start: 0.7981 (tt0) cc_final: 0.7472 (mt0) REVERT: BT 194 LYS cc_start: 0.7938 (pttm) cc_final: 0.7516 (tptp) REVERT: BT 209 GLU cc_start: 0.7185 (tm-30) cc_final: 0.6607 (tp30) REVERT: BT 216 ASN cc_start: 0.7767 (m110) cc_final: 0.7386 (m110) REVERT: BX 371 GLU cc_start: 0.7689 (tm-30) cc_final: 0.7349 (tm-30) REVERT: BX 401 TYR cc_start: 0.8961 (m-80) cc_final: 0.8602 (m-80) REVERT: BX 410 ARG cc_start: 0.7751 (ptp-170) cc_final: 0.7340 (mtm110) REVERT: BY 1739 TYR cc_start: 0.9026 (m-80) cc_final: 0.8772 (m-80) REVERT: BY 1873 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7806 (pm20) REVERT: CT 49 GLU cc_start: 0.7400 (mp0) cc_final: 0.7134 (mp0) REVERT: CT 194 LYS cc_start: 0.8018 (pttm) cc_final: 0.7457 (tptp) REVERT: CT 209 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7691 (tp30) REVERT: CT 210 TYR cc_start: 0.8195 (t80) cc_final: 0.7764 (t80) REVERT: CT 214 LYS cc_start: 0.7465 (pptt) cc_final: 0.7102 (pptt) REVERT: CT 216 ASN cc_start: 0.7721 (m110) cc_final: 0.7399 (m110) REVERT: CT 292 GLU cc_start: 0.8176 (tp30) cc_final: 0.7072 (mt-10) REVERT: CT 296 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7438 (tm-30) REVERT: CT 300 ASN cc_start: 0.6669 (m-40) cc_final: 0.6300 (m-40) REVERT: CT 301 GLN cc_start: 0.7164 (tp-100) cc_final: 0.6879 (mm110) REVERT: CX 371 GLU cc_start: 0.7653 (tm-30) cc_final: 0.7306 (tm-30) REVERT: CX 386 GLN cc_start: 0.8473 (tm-30) cc_final: 0.8200 (tp40) REVERT: CX 387 TYR cc_start: 0.8607 (t80) cc_final: 0.8216 (t80) REVERT: CY 1715 SER cc_start: 0.8560 (p) cc_final: 0.8339 (p) REVERT: CY 1783 GLU cc_start: 0.8862 (pm20) cc_final: 0.8577 (pm20) REVERT: DT 49 GLU cc_start: 0.7426 (mp0) cc_final: 0.7096 (mp0) REVERT: DT 194 LYS cc_start: 0.7735 (pttm) cc_final: 0.7275 (tptp) REVERT: DT 208 GLN cc_start: 0.7689 (tp40) cc_final: 0.7437 (tp40) REVERT: DT 296 GLU cc_start: 0.7811 (tm-30) cc_final: 0.6991 (tm-30) REVERT: DT 300 ASN cc_start: 0.7241 (m-40) cc_final: 0.6891 (m-40) REVERT: DX 386 GLN cc_start: 0.8496 (tm-30) cc_final: 0.8182 (tp40) REVERT: DY 1772 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.8059 (pp) REVERT: DY 1903 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.8053 (tm-30) REVERT: DY 1904 ILE cc_start: 0.8330 (mt) cc_final: 0.7998 (mt) REVERT: ET 30 LYS cc_start: 0.7594 (OUTLIER) cc_final: 0.7328 (ptmt) REVERT: ET 49 GLU cc_start: 0.7377 (mp0) cc_final: 0.7154 (mp0) REVERT: ET 64 GLN cc_start: 0.7982 (tt0) cc_final: 0.7415 (mt0) REVERT: ET 105 TYR cc_start: 0.8643 (m-80) cc_final: 0.8288 (m-80) REVERT: ET 194 LYS cc_start: 0.7764 (pttm) cc_final: 0.7374 (tptp) REVERT: ET 210 TYR cc_start: 0.8082 (t80) cc_final: 0.7764 (t80) REVERT: ET 296 GLU cc_start: 0.7567 (tm-30) cc_final: 0.7337 (tm-30) REVERT: ET 300 ASN cc_start: 0.6923 (m-40) cc_final: 0.6689 (m-40) REVERT: EX 378 ASP cc_start: 0.8154 (m-30) cc_final: 0.7669 (t0) REVERT: EY 1685 LYS cc_start: 0.7555 (mmtt) cc_final: 0.7314 (mmtt) REVERT: FT 27 LYS cc_start: 0.7508 (mmtt) cc_final: 0.7297 (mmtm) REVERT: FT 194 LYS cc_start: 0.7763 (pttm) cc_final: 0.7151 (tptp) REVERT: FT 216 ASN cc_start: 0.7820 (m110) cc_final: 0.7612 (m110) REVERT: FT 292 GLU cc_start: 0.7892 (tp30) cc_final: 0.6930 (mt-10) REVERT: FT 296 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7496 (tm-30) REVERT: FT 300 ASN cc_start: 0.6562 (m-40) cc_final: 0.5937 (m-40) REVERT: FX 378 ASP cc_start: 0.8193 (m-30) cc_final: 0.7592 (t0) REVERT: FX 386 GLN cc_start: 0.8440 (tm-30) cc_final: 0.8135 (tp40) REVERT: FX 405 GLN cc_start: 0.7692 (pt0) cc_final: 0.7262 (pt0) REVERT: FX 410 ARG cc_start: 0.7944 (ttp-110) cc_final: 0.7255 (ptt-90) REVERT: FX 415 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.7867 (mmm) REVERT: FY 1685 LYS cc_start: 0.7186 (mmtm) cc_final: 0.6804 (mmtm) REVERT: FY 1903 GLU cc_start: 0.8219 (tm-30) cc_final: 0.8011 (tm-30) REVERT: GT 209 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7561 (tp30) REVERT: GT 216 ASN cc_start: 0.7763 (m110) cc_final: 0.7398 (m110) REVERT: GT 292 GLU cc_start: 0.8044 (tp30) cc_final: 0.7034 (mt-10) REVERT: GT 296 GLU cc_start: 0.7753 (tm-30) cc_final: 0.7519 (tm-30) REVERT: GT 300 ASN cc_start: 0.6934 (m-40) cc_final: 0.6706 (m-40) REVERT: GX 369 ARG cc_start: 0.6798 (mtt180) cc_final: 0.6592 (mtt-85) REVERT: GX 386 GLN cc_start: 0.8461 (tm-30) cc_final: 0.8241 (tp40) REVERT: GX 409 LYS cc_start: 0.7424 (ttmt) cc_final: 0.7179 (ttmt) REVERT: GX 410 ARG cc_start: 0.7390 (mtm110) cc_final: 0.6971 (mtm110) REVERT: GY 1685 LYS cc_start: 0.7020 (mmtm) cc_final: 0.6758 (mmtt) REVERT: HT 49 GLU cc_start: 0.7454 (mp0) cc_final: 0.7131 (mp0) REVERT: HT 64 GLN cc_start: 0.8074 (tt0) cc_final: 0.7460 (mt0) REVERT: HT 194 LYS cc_start: 0.7837 (pttm) cc_final: 0.7363 (tptp) REVERT: HT 201 THR cc_start: 0.8277 (p) cc_final: 0.7911 (t) REVERT: HT 208 GLN cc_start: 0.7632 (tp40) cc_final: 0.7373 (tp40) REVERT: HT 216 ASN cc_start: 0.7655 (m110) cc_final: 0.7345 (m-40) REVERT: HT 292 GLU cc_start: 0.7878 (tp30) cc_final: 0.6861 (mt-10) REVERT: HT 296 GLU cc_start: 0.7712 (tm-30) cc_final: 0.7302 (tm-30) REVERT: HT 300 ASN cc_start: 0.7022 (m-40) cc_final: 0.6748 (m-40) REVERT: HX 374 LYS cc_start: 0.8105 (ptmm) cc_final: 0.7544 (ptpp) REVERT: HX 386 GLN cc_start: 0.8355 (tm-30) cc_final: 0.8002 (tp40) REVERT: HX 415 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.7834 (mmm) REVERT: HX 508 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8257 (mt-10) REVERT: IT 49 GLU cc_start: 0.7349 (mp0) cc_final: 0.7066 (mp0) REVERT: IT 194 LYS cc_start: 0.7890 (pttm) cc_final: 0.7427 (tptp) REVERT: IT 208 GLN cc_start: 0.7678 (tp40) cc_final: 0.7407 (tp40) REVERT: IT 209 GLU cc_start: 0.7193 (tm-30) cc_final: 0.6643 (tp30) REVERT: IT 296 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7155 (tm-30) REVERT: IT 297 TYR cc_start: 0.7602 (t80) cc_final: 0.7391 (t80) REVERT: IT 300 ASN cc_start: 0.6880 (m-40) cc_final: 0.6303 (m-40) REVERT: IX 371 GLU cc_start: 0.7692 (tm-30) cc_final: 0.7232 (tm-30) REVERT: IX 384 GLU cc_start: 0.8301 (tt0) cc_final: 0.7914 (tt0) REVERT: IX 386 GLN cc_start: 0.8444 (tm-30) cc_final: 0.8226 (tp40) REVERT: IX 410 ARG cc_start: 0.7693 (ptp-170) cc_final: 0.7132 (mtm110) REVERT: IY 1715 SER cc_start: 0.8590 (p) cc_final: 0.8371 (p) REVERT: IY 1873 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7862 (pm20) REVERT: JT 64 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7528 (mt0) REVERT: JT 194 LYS cc_start: 0.7911 (pttm) cc_final: 0.7415 (tptp) REVERT: JT 204 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.8016 (mt0) REVERT: JT 210 TYR cc_start: 0.8256 (t80) cc_final: 0.8024 (t80) REVERT: JT 216 ASN cc_start: 0.7818 (m110) cc_final: 0.7549 (m110) REVERT: JT 296 GLU cc_start: 0.7638 (tm-30) cc_final: 0.7240 (tm-30) REVERT: JT 300 ASN cc_start: 0.6544 (m-40) cc_final: 0.6285 (m-40) REVERT: JX 378 ASP cc_start: 0.8071 (m-30) cc_final: 0.7715 (t0) REVERT: JX 386 GLN cc_start: 0.8483 (tm-30) cc_final: 0.8185 (tp40) REVERT: JX 450 MET cc_start: 0.9007 (ttp) cc_final: 0.8772 (ptm) REVERT: JY 1715 SER cc_start: 0.8555 (p) cc_final: 0.8344 (p) REVERT: JY 1783 GLU cc_start: 0.8865 (pm20) cc_final: 0.8574 (pm20) REVERT: KT 49 GLU cc_start: 0.7423 (mp0) cc_final: 0.7178 (mp0) REVERT: KT 194 LYS cc_start: 0.7807 (pttm) cc_final: 0.7423 (tptp) REVERT: KT 208 GLN cc_start: 0.7687 (tp40) cc_final: 0.7454 (tp-100) REVERT: KT 209 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7747 (tp30) REVERT: KT 216 ASN cc_start: 0.7685 (m110) cc_final: 0.7336 (m110) REVERT: KT 292 GLU cc_start: 0.8079 (tp30) cc_final: 0.7007 (mt-10) REVERT: KT 296 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7275 (tm-30) REVERT: KT 300 ASN cc_start: 0.7021 (m-40) cc_final: 0.6682 (m110) REVERT: KX 371 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7396 (tm-30) REVERT: KX 378 ASP cc_start: 0.8309 (m-30) cc_final: 0.7762 (t0) REVERT: KX 386 GLN cc_start: 0.8476 (tm-30) cc_final: 0.8183 (tp40) REVERT: KY 1739 TYR cc_start: 0.8969 (m-80) cc_final: 0.8719 (m-80) REVERT: KY 1772 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.8074 (pp) REVERT: KY 1904 ILE cc_start: 0.8350 (mt) cc_final: 0.7988 (mt) REVERT: LT 49 GLU cc_start: 0.7456 (mp0) cc_final: 0.7073 (mp0) REVERT: LT 64 GLN cc_start: 0.7940 (tt0) cc_final: 0.7438 (mt0) REVERT: LT 105 TYR cc_start: 0.8642 (m-80) cc_final: 0.8319 (m-80) REVERT: LT 194 LYS cc_start: 0.7808 (pttm) cc_final: 0.7416 (tptp) REVERT: LT 201 THR cc_start: 0.8159 (p) cc_final: 0.7781 (t) REVERT: LT 210 TYR cc_start: 0.8186 (t80) cc_final: 0.7848 (t80) REVERT: LT 216 ASN cc_start: 0.7714 (m110) cc_final: 0.7373 (m110) REVERT: LT 292 GLU cc_start: 0.7909 (tp30) cc_final: 0.7029 (mt-10) REVERT: LT 296 GLU cc_start: 0.7633 (tm-30) cc_final: 0.7296 (tm-30) REVERT: LT 300 ASN cc_start: 0.6974 (m-40) cc_final: 0.6725 (m-40) REVERT: LX 378 ASP cc_start: 0.8136 (m-30) cc_final: 0.7702 (t0) REVERT: LY 1685 LYS cc_start: 0.7561 (mmtt) cc_final: 0.7319 (mmtt) REVERT: LY 1739 TYR cc_start: 0.8958 (m-80) cc_final: 0.8703 (m-80) REVERT: MT 49 GLU cc_start: 0.7431 (mp0) cc_final: 0.7145 (mp0) REVERT: MT 194 LYS cc_start: 0.7716 (pttm) cc_final: 0.7208 (tptp) REVERT: MT 209 GLU cc_start: 0.7457 (tm-30) cc_final: 0.6365 (tp30) REVERT: MT 216 ASN cc_start: 0.7502 (m110) cc_final: 0.7225 (m110) REVERT: MT 300 ASN cc_start: 0.6687 (m-40) cc_final: 0.6435 (m-40) REVERT: MX 378 ASP cc_start: 0.8184 (m-30) cc_final: 0.7596 (t0) REVERT: MX 386 GLN cc_start: 0.8443 (tm-30) cc_final: 0.8141 (tp40) REVERT: MX 405 GLN cc_start: 0.7833 (pt0) cc_final: 0.7537 (pt0) REVERT: MX 410 ARG cc_start: 0.7973 (ttp-110) cc_final: 0.7262 (ptt-90) REVERT: MX 415 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.7882 (mmm) REVERT: MY 1685 LYS cc_start: 0.7237 (mmtm) cc_final: 0.6814 (mmtm) REVERT: MY 1721 ASP cc_start: 0.7663 (m-30) cc_final: 0.7453 (m-30) REVERT: MY 1903 GLU cc_start: 0.8178 (tm-30) cc_final: 0.7923 (tm-30) REVERT: NT 64 GLN cc_start: 0.7949 (tt0) cc_final: 0.7451 (mt0) REVERT: NT 209 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7541 (tp30) REVERT: NT 216 ASN cc_start: 0.7692 (m110) cc_final: 0.7374 (m-40) REVERT: NT 296 GLU cc_start: 0.7612 (tm-30) cc_final: 0.7395 (tm-30) REVERT: NX 369 ARG cc_start: 0.6804 (mtt180) cc_final: 0.6594 (mtt-85) REVERT: NX 386 GLN cc_start: 0.8471 (tm-30) cc_final: 0.8250 (tp40) REVERT: NX 506 TYR cc_start: 0.9135 (p90) cc_final: 0.8928 (p90) REVERT: NY 1685 LYS cc_start: 0.7001 (mmtm) cc_final: 0.6740 (mmtt) outliers start: 173 outliers final: 86 residues processed: 1843 average time/residue: 0.5963 time to fit residues: 1843.5495 Evaluate side-chains 1709 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 1611 time to evaluate : 5.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AT residue 35 VAL Chi-restraints excluded: chain AT residue 67 LEU Chi-restraints excluded: chain AT residue 136 SER Chi-restraints excluded: chain AT residue 173 VAL Chi-restraints excluded: chain AX residue 415 MET Chi-restraints excluded: chain AY residue 1713 ILE Chi-restraints excluded: chain AY residue 1751 ILE Chi-restraints excluded: chain AY residue 1752 MET Chi-restraints excluded: chain BT residue 29 VAL Chi-restraints excluded: chain BT residue 35 VAL Chi-restraints excluded: chain BT residue 80 VAL Chi-restraints excluded: chain BT residue 136 SER Chi-restraints excluded: chain BT residue 173 VAL Chi-restraints excluded: chain BX residue 415 MET Chi-restraints excluded: chain BY residue 1751 ILE Chi-restraints excluded: chain BY residue 1809 SER Chi-restraints excluded: chain BY residue 1873 GLU Chi-restraints excluded: chain CT residue 29 VAL Chi-restraints excluded: chain CT residue 80 VAL Chi-restraints excluded: chain CT residue 136 SER Chi-restraints excluded: chain CT residue 173 VAL Chi-restraints excluded: chain CY residue 1873 GLU Chi-restraints excluded: chain DT residue 29 VAL Chi-restraints excluded: chain DT residue 35 VAL Chi-restraints excluded: chain DT residue 80 VAL Chi-restraints excluded: chain DT residue 136 SER Chi-restraints excluded: chain DT residue 173 VAL Chi-restraints excluded: chain DX residue 415 MET Chi-restraints excluded: chain DY residue 1772 LEU Chi-restraints excluded: chain DY residue 1809 SER Chi-restraints excluded: chain DY residue 1879 ILE Chi-restraints excluded: chain DY residue 1903 GLU Chi-restraints excluded: chain ET residue 30 LYS Chi-restraints excluded: chain ET residue 80 VAL Chi-restraints excluded: chain ET residue 136 SER Chi-restraints excluded: chain ET residue 173 VAL Chi-restraints excluded: chain EY residue 1713 ILE Chi-restraints excluded: chain EY residue 1752 MET Chi-restraints excluded: chain EY residue 1862 LEU Chi-restraints excluded: chain EY residue 1873 GLU Chi-restraints excluded: chain FT residue 136 SER Chi-restraints excluded: chain FT residue 173 VAL Chi-restraints excluded: chain FX residue 415 MET Chi-restraints excluded: chain FX residue 459 MET Chi-restraints excluded: chain FY residue 1713 ILE Chi-restraints excluded: chain FY residue 1752 MET Chi-restraints excluded: chain FY residue 1809 SER Chi-restraints excluded: chain GT residue 80 VAL Chi-restraints excluded: chain GT residue 136 SER Chi-restraints excluded: chain GT residue 173 VAL Chi-restraints excluded: chain GX residue 383 LEU Chi-restraints excluded: chain HT residue 136 SER Chi-restraints excluded: chain HT residue 173 VAL Chi-restraints excluded: chain HX residue 415 MET Chi-restraints excluded: chain HY residue 1713 ILE Chi-restraints excluded: chain HY residue 1752 MET Chi-restraints excluded: chain IT residue 35 VAL Chi-restraints excluded: chain IT residue 80 VAL Chi-restraints excluded: chain IT residue 136 SER Chi-restraints excluded: chain IT residue 173 VAL Chi-restraints excluded: chain IX residue 383 LEU Chi-restraints excluded: chain IX residue 415 MET Chi-restraints excluded: chain IX residue 459 MET Chi-restraints excluded: chain IY residue 1751 ILE Chi-restraints excluded: chain IY residue 1809 SER Chi-restraints excluded: chain IY residue 1873 GLU Chi-restraints excluded: chain JT residue 29 VAL Chi-restraints excluded: chain JT residue 64 GLN Chi-restraints excluded: chain JT residue 80 VAL Chi-restraints excluded: chain JT residue 136 SER Chi-restraints excluded: chain JT residue 173 VAL Chi-restraints excluded: chain JT residue 204 GLN Chi-restraints excluded: chain JX residue 508 GLU Chi-restraints excluded: chain JY residue 1873 GLU Chi-restraints excluded: chain KT residue 80 VAL Chi-restraints excluded: chain KT residue 136 SER Chi-restraints excluded: chain KT residue 173 VAL Chi-restraints excluded: chain KX residue 415 MET Chi-restraints excluded: chain KX residue 418 GLU Chi-restraints excluded: chain KY residue 1772 LEU Chi-restraints excluded: chain KY residue 1879 ILE Chi-restraints excluded: chain LT residue 67 LEU Chi-restraints excluded: chain LT residue 80 VAL Chi-restraints excluded: chain LT residue 136 SER Chi-restraints excluded: chain LT residue 173 VAL Chi-restraints excluded: chain LY residue 1713 ILE Chi-restraints excluded: chain LY residue 1752 MET Chi-restraints excluded: chain LY residue 1873 GLU Chi-restraints excluded: chain MT residue 136 SER Chi-restraints excluded: chain MT residue 173 VAL Chi-restraints excluded: chain MX residue 415 MET Chi-restraints excluded: chain MY residue 1713 ILE Chi-restraints excluded: chain MY residue 1752 MET Chi-restraints excluded: chain MY residue 1809 SER Chi-restraints excluded: chain NT residue 80 VAL Chi-restraints excluded: chain NT residue 136 SER Chi-restraints excluded: chain NT residue 173 VAL Chi-restraints excluded: chain NX residue 415 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 586 optimal weight: 5.9990 chunk 399 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 523 optimal weight: 0.9980 chunk 290 optimal weight: 6.9990 chunk 600 optimal weight: 4.9990 chunk 486 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 359 optimal weight: 5.9990 chunk 631 optimal weight: 5.9990 chunk 177 optimal weight: 5.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AT 197 GLN AY1694 GLN BT 33 ASN BX 443 GLN BY1694 GLN ** BY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CT 33 ASN CT 204 GLN CX 432 ASN CY1694 GLN CY1856 ASN DT 33 ASN DX 443 GLN DY1694 GLN ET 33 ASN ** EX 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EX 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** EX 432 ASN EX 443 GLN EY1694 GLN ** EY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** FT 33 ASN FX 443 GLN FY1856 ASN ** FY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** GT 33 ASN ** GT 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GY1856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** HT 196 ASN HT 301 GLN ** IT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** IX 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** IY1694 GLN ** IY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** JT 33 ASN ** JT 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** JT 204 GLN JX 432 ASN ** JX 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** JY1694 GLN JY1856 ASN KT 33 ASN KX 432 ASN KX 443 GLN KY1694 GLN ** KY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LX 443 GLN LY1694 GLN ** MX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** MX 443 GLN MY1856 ASN ** NY1856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 61992 Z= 0.352 Angle : 0.648 13.334 83594 Z= 0.342 Chirality : 0.047 0.173 9520 Planarity : 0.004 0.046 10598 Dihedral : 5.175 27.404 8134 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.96 % Allowed : 16.07 % Favored : 80.97 % 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: -0.44 (0.10), residues: 7406 helix: 1.26 (0.11), residues: 2226 sheet: -1.03 (0.12), residues: 1624 loop : -0.87 (0.10), residues: 3556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPCX 466 HIS 0.003 0.001 HISNT 169 PHE 0.011 0.002 PHEHY1682 TYR 0.027 0.002 TYRET 210 ARG 0.007 0.000 ARGET 213 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14812 Ramachandran restraints generated. 7406 Oldfield, 0 Emsley, 7406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14812 Ramachandran restraints generated. 7406 Oldfield, 0 Emsley, 7406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1806 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 1605 time to evaluate : 5.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: AT 49 GLU cc_start: 0.7491 (mp0) cc_final: 0.7089 (mp0) REVERT: AT 64 GLN cc_start: 0.8160 (tt0) cc_final: 0.7471 (mt0) REVERT: AT 194 LYS cc_start: 0.7882 (pttm) cc_final: 0.7396 (tptp) REVERT: AT 208 GLN cc_start: 0.7632 (tp-100) cc_final: 0.7385 (tp40) REVERT: AT 216 ASN cc_start: 0.7628 (m110) cc_final: 0.7355 (m110) REVERT: AT 296 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7213 (tm-30) REVERT: AT 300 ASN cc_start: 0.6782 (m-40) cc_final: 0.6414 (m-40) REVERT: AX 374 LYS cc_start: 0.8054 (ptmm) cc_final: 0.7552 (ptpp) REVERT: AX 386 GLN cc_start: 0.8458 (tm-30) cc_final: 0.8114 (tp40) REVERT: AX 474 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7735 (tp30) REVERT: BT 64 GLN cc_start: 0.8042 (tt0) cc_final: 0.7509 (mt0) REVERT: BT 67 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9103 (mt) REVERT: BT 194 LYS cc_start: 0.7993 (pttm) cc_final: 0.7547 (tptp) REVERT: BT 209 GLU cc_start: 0.7236 (tm-30) cc_final: 0.6631 (tp30) REVERT: BT 216 ASN cc_start: 0.7667 (m110) cc_final: 0.7243 (m110) REVERT: BX 371 GLU cc_start: 0.7750 (tm-30) cc_final: 0.7342 (tm-30) REVERT: BX 410 ARG cc_start: 0.7754 (ptp-170) cc_final: 0.7392 (mtm110) REVERT: BY 1739 TYR cc_start: 0.9063 (m-80) cc_final: 0.8778 (m-80) REVERT: BY 1873 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8058 (pm20) REVERT: CT 49 GLU cc_start: 0.7434 (mp0) cc_final: 0.7164 (mp0) REVERT: CT 209 GLU cc_start: 0.8336 (mm-30) cc_final: 0.7753 (tp30) REVERT: CT 214 LYS cc_start: 0.7494 (pptt) cc_final: 0.7139 (pptt) REVERT: CT 216 ASN cc_start: 0.7743 (m110) cc_final: 0.7432 (m110) REVERT: CT 296 GLU cc_start: 0.7914 (tm-30) cc_final: 0.7349 (tm-30) REVERT: CT 300 ASN cc_start: 0.6551 (m-40) cc_final: 0.6109 (m-40) REVERT: CX 371 GLU cc_start: 0.7636 (tm-30) cc_final: 0.7200 (tm-30) REVERT: CX 378 ASP cc_start: 0.8128 (m-30) cc_final: 0.7881 (m-30) REVERT: CX 386 GLN cc_start: 0.8522 (tm-30) cc_final: 0.8210 (tp40) REVERT: CY 1783 GLU cc_start: 0.8877 (pm20) cc_final: 0.8588 (pm20) REVERT: DT 49 GLU cc_start: 0.7530 (mp0) cc_final: 0.7288 (mp0) REVERT: DT 194 LYS cc_start: 0.7799 (pttm) cc_final: 0.7351 (tptp) REVERT: DT 208 GLN cc_start: 0.7704 (tp40) cc_final: 0.7434 (tp40) REVERT: DT 296 GLU cc_start: 0.7775 (tm-30) cc_final: 0.6936 (tm-30) REVERT: DT 300 ASN cc_start: 0.7175 (m-40) cc_final: 0.6786 (m-40) REVERT: DX 378 ASP cc_start: 0.8338 (m-30) cc_final: 0.7776 (t0) REVERT: DX 386 GLN cc_start: 0.8505 (tm-30) cc_final: 0.8245 (tp40) REVERT: DY 1772 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8130 (pp) REVERT: DY 1903 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.8069 (tm-30) REVERT: DY 1904 ILE cc_start: 0.8403 (mt) cc_final: 0.8049 (mt) REVERT: ET 49 GLU cc_start: 0.7396 (mp0) cc_final: 0.7142 (mp0) REVERT: ET 64 GLN cc_start: 0.8007 (tt0) cc_final: 0.7472 (mt0) REVERT: ET 105 TYR cc_start: 0.8623 (m-80) cc_final: 0.8292 (m-80) REVERT: ET 194 LYS cc_start: 0.7809 (pttm) cc_final: 0.7434 (tptp) REVERT: ET 209 GLU cc_start: 0.7296 (tm-30) cc_final: 0.6333 (tp30) REVERT: ET 210 TYR cc_start: 0.8081 (t80) cc_final: 0.7872 (t80) REVERT: ET 296 GLU cc_start: 0.7635 (tm-30) cc_final: 0.7378 (tm-30) REVERT: ET 300 ASN cc_start: 0.6866 (m-40) cc_final: 0.6516 (m110) REVERT: EX 378 ASP cc_start: 0.8234 (m-30) cc_final: 0.7679 (t0) REVERT: EY 1685 LYS cc_start: 0.7583 (mmtt) cc_final: 0.7360 (mmtt) REVERT: EY 1694 GLN cc_start: 0.8888 (OUTLIER) cc_final: 0.8683 (tt0) REVERT: EY 1739 TYR cc_start: 0.9027 (m-80) cc_final: 0.8764 (m-80) REVERT: FT 194 LYS cc_start: 0.7848 (pttm) cc_final: 0.7333 (tptp) REVERT: FT 216 ASN cc_start: 0.7829 (m110) cc_final: 0.7610 (m110) REVERT: FX 386 GLN cc_start: 0.8422 (tm-30) cc_final: 0.8194 (tp40) REVERT: FX 410 ARG cc_start: 0.7969 (ttp-110) cc_final: 0.7276 (ptt-90) REVERT: FX 415 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.8038 (mmm) REVERT: FY 1685 LYS cc_start: 0.7259 (mmtm) cc_final: 0.6902 (mmtm) REVERT: GT 201 THR cc_start: 0.8298 (p) cc_final: 0.7900 (t) REVERT: GT 216 ASN cc_start: 0.7711 (m110) cc_final: 0.7322 (m110) REVERT: GT 296 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7280 (tm-30) REVERT: GT 300 ASN cc_start: 0.6718 (m-40) cc_final: 0.6394 (m-40) REVERT: GX 374 LYS cc_start: 0.7827 (ptmm) cc_final: 0.7464 (ptpp) REVERT: GX 410 ARG cc_start: 0.7384 (mtm110) cc_final: 0.7010 (mtm110) REVERT: GX 459 MET cc_start: 0.8788 (mtp) cc_final: 0.8481 (mtp) REVERT: GY 1685 LYS cc_start: 0.7005 (mmtm) cc_final: 0.6688 (mmtt) REVERT: HT 49 GLU cc_start: 0.7518 (mp0) cc_final: 0.7163 (mp0) REVERT: HT 64 GLN cc_start: 0.8148 (tt0) cc_final: 0.7555 (mt0) REVERT: HT 194 LYS cc_start: 0.7791 (pttm) cc_final: 0.7315 (tptp) REVERT: HT 216 ASN cc_start: 0.7666 (m110) cc_final: 0.7325 (m110) REVERT: HT 292 GLU cc_start: 0.7944 (tp30) cc_final: 0.6995 (mt-10) REVERT: HT 296 GLU cc_start: 0.7759 (tm-30) cc_final: 0.7391 (tm-30) REVERT: HT 300 ASN cc_start: 0.7019 (m-40) cc_final: 0.6724 (m-40) REVERT: HT 301 GLN cc_start: 0.7399 (tp40) cc_final: 0.7160 (tp-100) REVERT: HX 374 LYS cc_start: 0.8092 (ptmm) cc_final: 0.7552 (ptpp) REVERT: HX 386 GLN cc_start: 0.8443 (tm-30) cc_final: 0.8079 (tp40) REVERT: HX 474 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7747 (tp30) REVERT: IT 64 GLN cc_start: 0.8025 (tt0) cc_final: 0.7462 (mt0) REVERT: IT 67 LEU cc_start: 0.9433 (OUTLIER) cc_final: 0.9123 (mt) REVERT: IT 194 LYS cc_start: 0.7995 (pttm) cc_final: 0.7524 (tptp) REVERT: IT 209 GLU cc_start: 0.7267 (tm-30) cc_final: 0.6686 (tp30) REVERT: IT 296 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7155 (tm-30) REVERT: IT 300 ASN cc_start: 0.6911 (m-40) cc_final: 0.6300 (m-40) REVERT: IX 371 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7212 (tm-30) REVERT: IX 384 GLU cc_start: 0.8325 (tt0) cc_final: 0.7935 (tt0) REVERT: IX 410 ARG cc_start: 0.7736 (ptp-170) cc_final: 0.7212 (mtm110) REVERT: IY 1873 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8014 (pm20) REVERT: IY 1907 GLN cc_start: 0.7367 (tt0) cc_final: 0.7015 (tt0) REVERT: JT 194 LYS cc_start: 0.7970 (pttm) cc_final: 0.7342 (tptp) REVERT: JT 216 ASN cc_start: 0.7832 (m110) cc_final: 0.7562 (m110) REVERT: JT 296 GLU cc_start: 0.7689 (tm-30) cc_final: 0.7128 (tm-30) REVERT: JT 300 ASN cc_start: 0.6399 (m-40) cc_final: 0.6064 (m-40) REVERT: JX 386 GLN cc_start: 0.8515 (tm-30) cc_final: 0.8200 (tp40) REVERT: JX 484 LEU cc_start: 0.9108 (tp) cc_final: 0.8906 (tp) REVERT: JY 1783 GLU cc_start: 0.8854 (pm20) cc_final: 0.8569 (pm20) REVERT: KT 49 GLU cc_start: 0.7495 (mp0) cc_final: 0.7184 (mp0) REVERT: KT 59 THR cc_start: 0.8823 (m) cc_final: 0.8564 (m) REVERT: KT 194 LYS cc_start: 0.7924 (pttm) cc_final: 0.7224 (tptp) REVERT: KT 208 GLN cc_start: 0.7574 (tp40) cc_final: 0.7331 (tp40) REVERT: KT 209 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7815 (tp30) REVERT: KT 216 ASN cc_start: 0.7673 (m110) cc_final: 0.7337 (m110) REVERT: KT 292 GLU cc_start: 0.8037 (tp30) cc_final: 0.7002 (mt-10) REVERT: KT 296 GLU cc_start: 0.7724 (tm-30) cc_final: 0.6848 (tm-30) REVERT: KT 300 ASN cc_start: 0.6851 (m-40) cc_final: 0.6490 (m110) REVERT: KX 371 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7405 (tm-30) REVERT: KX 378 ASP cc_start: 0.8358 (m-30) cc_final: 0.7755 (t0) REVERT: KX 386 GLN cc_start: 0.8559 (tm-30) cc_final: 0.8229 (tp40) REVERT: KX 410 ARG cc_start: 0.7484 (mtm110) cc_final: 0.7278 (mtm110) REVERT: KY 1739 TYR cc_start: 0.9068 (m-80) cc_final: 0.8765 (m-80) REVERT: KY 1772 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8161 (pp) REVERT: KY 1903 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7884 (tm-30) REVERT: LT 49 GLU cc_start: 0.7490 (mp0) cc_final: 0.7198 (mp0) REVERT: LT 105 TYR cc_start: 0.8658 (m-80) cc_final: 0.8308 (m-80) REVERT: LT 194 LYS cc_start: 0.7854 (pttm) cc_final: 0.7449 (tptp) REVERT: LT 201 THR cc_start: 0.8057 (p) cc_final: 0.7684 (t) REVERT: LT 210 TYR cc_start: 0.8226 (t80) cc_final: 0.7867 (t80) REVERT: LT 216 ASN cc_start: 0.7750 (m110) cc_final: 0.7409 (m110) REVERT: LT 296 GLU cc_start: 0.7653 (tm-30) cc_final: 0.7087 (tm-30) REVERT: LT 300 ASN cc_start: 0.6908 (m-40) cc_final: 0.6526 (m-40) REVERT: LT 301 GLN cc_start: 0.7562 (tp40) cc_final: 0.7321 (tp-100) REVERT: LX 378 ASP cc_start: 0.8208 (m-30) cc_final: 0.7635 (t0) REVERT: LY 1685 LYS cc_start: 0.7589 (mmtt) cc_final: 0.7364 (mmtt) REVERT: LY 1739 TYR cc_start: 0.9028 (m-80) cc_final: 0.8769 (m-80) REVERT: MT 49 GLU cc_start: 0.7480 (mp0) cc_final: 0.7198 (mp0) REVERT: MT 194 LYS cc_start: 0.7758 (pttm) cc_final: 0.7282 (tptp) REVERT: MT 209 GLU cc_start: 0.7464 (tm-30) cc_final: 0.6343 (tp30) REVERT: MT 216 ASN cc_start: 0.7526 (m110) cc_final: 0.7290 (m110) REVERT: MT 296 GLU cc_start: 0.7615 (tm-30) cc_final: 0.7388 (tm-30) REVERT: MT 300 ASN cc_start: 0.6755 (m-40) cc_final: 0.6453 (m110) REVERT: MX 378 ASP cc_start: 0.8234 (m-30) cc_final: 0.7592 (t0) REVERT: MX 386 GLN cc_start: 0.8396 (tm-30) cc_final: 0.8159 (tp40) REVERT: MX 405 GLN cc_start: 0.7912 (pt0) cc_final: 0.7322 (pt0) REVERT: MX 410 ARG cc_start: 0.8027 (ttp-110) cc_final: 0.7327 (ptt-90) REVERT: MX 415 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.7932 (mmm) REVERT: MY 1685 LYS cc_start: 0.7255 (mmtm) cc_final: 0.6899 (mmtm) REVERT: NT 216 ASN cc_start: 0.7716 (m110) cc_final: 0.7358 (m-40) REVERT: NX 374 LYS cc_start: 0.7855 (ptmm) cc_final: 0.7486 (ptpp) REVERT: NX 459 MET cc_start: 0.8786 (mtp) cc_final: 0.8451 (mtp) REVERT: NY 1685 LYS cc_start: 0.7022 (mmtm) cc_final: 0.6684 (mmtt) outliers start: 201 outliers final: 126 residues processed: 1727 average time/residue: 0.6558 time to fit residues: 1926.1419 Evaluate side-chains 1661 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 1525 time to evaluate : 5.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AT residue 35 VAL Chi-restraints excluded: chain AT residue 80 VAL Chi-restraints excluded: chain AT residue 136 SER Chi-restraints excluded: chain AT residue 173 VAL Chi-restraints excluded: chain AX residue 411 SER Chi-restraints excluded: chain AY residue 1713 ILE Chi-restraints excluded: chain AY residue 1725 MET Chi-restraints excluded: chain AY residue 1751 ILE Chi-restraints excluded: chain AY residue 1752 MET Chi-restraints excluded: chain AY residue 1873 GLU Chi-restraints excluded: chain BT residue 29 VAL Chi-restraints excluded: chain BT residue 35 VAL Chi-restraints excluded: chain BT residue 67 LEU Chi-restraints excluded: chain BT residue 80 VAL Chi-restraints excluded: chain BT residue 136 SER Chi-restraints excluded: chain BT residue 173 VAL Chi-restraints excluded: chain BX residue 415 MET Chi-restraints excluded: chain BX residue 459 MET Chi-restraints excluded: chain BY residue 1725 MET Chi-restraints excluded: chain BY residue 1751 ILE Chi-restraints excluded: chain BY residue 1809 SER Chi-restraints excluded: chain BY residue 1873 GLU Chi-restraints excluded: chain CT residue 29 VAL Chi-restraints excluded: chain CT residue 80 VAL Chi-restraints excluded: chain CT residue 82 LEU Chi-restraints excluded: chain CT residue 136 SER Chi-restraints excluded: chain CT residue 173 VAL Chi-restraints excluded: chain CX residue 383 LEU Chi-restraints excluded: chain CX residue 415 MET Chi-restraints excluded: chain CX residue 424 THR Chi-restraints excluded: chain CY residue 1729 MET Chi-restraints excluded: chain CY residue 1746 LYS Chi-restraints excluded: chain CY residue 1873 GLU Chi-restraints excluded: chain DT residue 29 VAL Chi-restraints excluded: chain DT residue 80 VAL Chi-restraints excluded: chain DT residue 136 SER Chi-restraints excluded: chain DT residue 173 VAL Chi-restraints excluded: chain DX residue 415 MET Chi-restraints excluded: chain DX residue 418 GLU Chi-restraints excluded: chain DY residue 1772 LEU Chi-restraints excluded: chain DY residue 1809 SER Chi-restraints excluded: chain DY residue 1873 GLU Chi-restraints excluded: chain DY residue 1879 ILE Chi-restraints excluded: chain DY residue 1903 GLU Chi-restraints excluded: chain ET residue 80 VAL Chi-restraints excluded: chain ET residue 136 SER Chi-restraints excluded: chain ET residue 173 VAL Chi-restraints excluded: chain EX residue 385 THR Chi-restraints excluded: chain EX residue 508 GLU Chi-restraints excluded: chain EY residue 1694 GLN Chi-restraints excluded: chain EY residue 1713 ILE Chi-restraints excluded: chain EY residue 1752 MET Chi-restraints excluded: chain EY residue 1873 GLU Chi-restraints excluded: chain FT residue 80 VAL Chi-restraints excluded: chain FT residue 136 SER Chi-restraints excluded: chain FT residue 173 VAL Chi-restraints excluded: chain FX residue 383 LEU Chi-restraints excluded: chain FX residue 415 MET Chi-restraints excluded: chain FX residue 508 GLU Chi-restraints excluded: chain FY residue 1713 ILE Chi-restraints excluded: chain FY residue 1752 MET Chi-restraints excluded: chain FY residue 1809 SER Chi-restraints excluded: chain GT residue 80 VAL Chi-restraints excluded: chain GT residue 136 SER Chi-restraints excluded: chain GT residue 173 VAL Chi-restraints excluded: chain GX residue 383 LEU Chi-restraints excluded: chain GX residue 415 MET Chi-restraints excluded: chain GY residue 1711 THR Chi-restraints excluded: chain HT residue 35 VAL Chi-restraints excluded: chain HT residue 80 VAL Chi-restraints excluded: chain HT residue 136 SER Chi-restraints excluded: chain HT residue 173 VAL Chi-restraints excluded: chain HX residue 383 LEU Chi-restraints excluded: chain HX residue 411 SER Chi-restraints excluded: chain HX residue 415 MET Chi-restraints excluded: chain HY residue 1713 ILE Chi-restraints excluded: chain HY residue 1751 ILE Chi-restraints excluded: chain HY residue 1752 MET Chi-restraints excluded: chain HY residue 1873 GLU Chi-restraints excluded: chain IT residue 35 VAL Chi-restraints excluded: chain IT residue 67 LEU Chi-restraints excluded: chain IT residue 80 VAL Chi-restraints excluded: chain IT residue 136 SER Chi-restraints excluded: chain IT residue 173 VAL Chi-restraints excluded: chain IX residue 383 LEU Chi-restraints excluded: chain IX residue 415 MET Chi-restraints excluded: chain IX residue 459 MET Chi-restraints excluded: chain IY residue 1725 MET Chi-restraints excluded: chain IY residue 1751 ILE Chi-restraints excluded: chain IY residue 1809 SER Chi-restraints excluded: chain IY residue 1873 GLU Chi-restraints excluded: chain JT residue 29 VAL Chi-restraints excluded: chain JT residue 80 VAL Chi-restraints excluded: chain JT residue 82 LEU Chi-restraints excluded: chain JT residue 136 SER Chi-restraints excluded: chain JT residue 173 VAL Chi-restraints excluded: chain JT residue 204 GLN Chi-restraints excluded: chain JX residue 424 THR Chi-restraints excluded: chain JX residue 508 GLU Chi-restraints excluded: chain JY residue 1711 THR Chi-restraints excluded: chain JY residue 1746 LYS Chi-restraints excluded: chain JY residue 1873 GLU Chi-restraints excluded: chain KT residue 35 VAL Chi-restraints excluded: chain KT residue 80 VAL Chi-restraints excluded: chain KT residue 136 SER Chi-restraints excluded: chain KT residue 173 VAL Chi-restraints excluded: chain KX residue 415 MET Chi-restraints excluded: chain KX residue 418 GLU Chi-restraints excluded: chain KX residue 497 LEU Chi-restraints excluded: chain KX residue 508 GLU Chi-restraints excluded: chain KY residue 1772 LEU Chi-restraints excluded: chain KY residue 1873 GLU Chi-restraints excluded: chain KY residue 1879 ILE Chi-restraints excluded: chain LT residue 67 LEU Chi-restraints excluded: chain LT residue 80 VAL Chi-restraints excluded: chain LT residue 136 SER Chi-restraints excluded: chain LT residue 173 VAL Chi-restraints excluded: chain LX residue 383 LEU Chi-restraints excluded: chain LX residue 508 GLU Chi-restraints excluded: chain LY residue 1713 ILE Chi-restraints excluded: chain LY residue 1752 MET Chi-restraints excluded: chain MT residue 80 VAL Chi-restraints excluded: chain MT residue 136 SER Chi-restraints excluded: chain MT residue 173 VAL Chi-restraints excluded: chain MX residue 383 LEU Chi-restraints excluded: chain MX residue 415 MET Chi-restraints excluded: chain MX residue 508 GLU Chi-restraints excluded: chain MY residue 1713 ILE Chi-restraints excluded: chain MY residue 1751 ILE Chi-restraints excluded: chain MY residue 1752 MET Chi-restraints excluded: chain MY residue 1809 SER Chi-restraints excluded: chain NT residue 80 VAL Chi-restraints excluded: chain NT residue 136 SER Chi-restraints excluded: chain NT residue 173 VAL Chi-restraints excluded: chain NX residue 415 MET Chi-restraints excluded: chain NY residue 1711 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 236 optimal weight: 2.9990 chunk 633 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 chunk 413 optimal weight: 0.5980 chunk 173 optimal weight: 10.0000 chunk 704 optimal weight: 0.9980 chunk 584 optimal weight: 7.9990 chunk 326 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 232 optimal weight: 0.5980 chunk 369 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AT 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AT 301 GLN ** AY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BX 443 GLN ** BY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CY1856 ASN DT 301 GLN ** EX 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** EX 432 ASN EX 443 GLN FT 208 GLN FX 413 HIS FX 443 GLN ** FY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** FY1856 ASN GT 33 ASN GX 386 GLN HT 197 GLN IT 33 ASN ** IX 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** IX 443 GLN ** IY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** JT 64 GLN JT 204 GLN JT 208 GLN ** JX 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** JY1856 ASN KX 432 ASN ** KY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LX 443 GLN ** MX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** MX 443 GLN ** MY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** MY1856 ASN NT 64 GLN NX 386 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 61992 Z= 0.211 Angle : 0.606 12.131 83594 Z= 0.320 Chirality : 0.045 0.172 9520 Planarity : 0.004 0.043 10598 Dihedral : 5.004 26.326 8134 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.87 % Allowed : 16.88 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.10), residues: 7406 helix: 1.41 (0.11), residues: 2226 sheet: -1.23 (0.12), residues: 1666 loop : -0.73 (0.11), residues: 3514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRPEY1723 HIS 0.002 0.000 HISNT 89 PHE 0.010 0.001 PHEAX 420 TYR 0.024 0.001 TYRET 210 ARG 0.004 0.000 ARGJT 213 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14812 Ramachandran restraints generated. 7406 Oldfield, 0 Emsley, 7406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14812 Ramachandran restraints generated. 7406 Oldfield, 0 Emsley, 7406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1846 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 1651 time to evaluate : 5.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AT 49 GLU cc_start: 0.7447 (mp0) cc_final: 0.7084 (mp0) REVERT: AT 64 GLN cc_start: 0.8134 (tt0) cc_final: 0.7455 (mt0) REVERT: AT 194 LYS cc_start: 0.7742 (pttm) cc_final: 0.7282 (tptp) REVERT: AT 208 GLN cc_start: 0.7729 (tp-100) cc_final: 0.7516 (tp40) REVERT: AT 292 GLU cc_start: 0.7980 (tp30) cc_final: 0.6961 (mt-10) REVERT: AT 296 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7298 (tm-30) REVERT: AT 300 ASN cc_start: 0.6671 (m-40) cc_final: 0.6371 (m-40) REVERT: AX 378 ASP cc_start: 0.8177 (m-30) cc_final: 0.7802 (t0) REVERT: AX 386 GLN cc_start: 0.8376 (tm-30) cc_final: 0.8094 (tp40) REVERT: AX 415 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.8264 (mmm) REVERT: BT 49 GLU cc_start: 0.7397 (mp0) cc_final: 0.7167 (mp0) REVERT: BT 64 GLN cc_start: 0.8010 (tt0) cc_final: 0.7422 (mt0) REVERT: BT 67 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9071 (mt) REVERT: BT 194 LYS cc_start: 0.7987 (pttm) cc_final: 0.7574 (tptp) REVERT: BT 216 ASN cc_start: 0.7855 (m110) cc_final: 0.7450 (m110) REVERT: BT 292 GLU cc_start: 0.8028 (tp30) cc_final: 0.7010 (mt-10) REVERT: BT 296 GLU cc_start: 0.7624 (tm-30) cc_final: 0.7397 (tm-30) REVERT: BT 300 ASN cc_start: 0.6929 (m-40) cc_final: 0.6619 (m110) REVERT: BX 371 GLU cc_start: 0.7714 (tm-30) cc_final: 0.7316 (tm-30) REVERT: BX 384 GLU cc_start: 0.8263 (tt0) cc_final: 0.7879 (tt0) REVERT: BX 401 TYR cc_start: 0.8994 (m-80) cc_final: 0.8553 (m-80) REVERT: BX 410 ARG cc_start: 0.7727 (ptp-170) cc_final: 0.7383 (mtm110) REVERT: BY 1739 TYR cc_start: 0.9016 (m-80) cc_final: 0.8750 (m-80) REVERT: BY 1873 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7816 (pm20) REVERT: CT 49 GLU cc_start: 0.7379 (mp0) cc_final: 0.7098 (mp0) REVERT: CT 209 GLU cc_start: 0.8319 (mm-30) cc_final: 0.8069 (tm-30) REVERT: CT 213 ARG cc_start: 0.6002 (ptt180) cc_final: 0.5778 (ptt180) REVERT: CT 214 LYS cc_start: 0.7625 (pptt) cc_final: 0.7271 (pptt) REVERT: CT 216 ASN cc_start: 0.7638 (m110) cc_final: 0.7226 (m110) REVERT: CT 296 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7385 (tm-30) REVERT: CT 300 ASN cc_start: 0.6624 (m-40) cc_final: 0.6212 (m-40) REVERT: CX 371 GLU cc_start: 0.7568 (tm-30) cc_final: 0.7173 (tm-30) REVERT: CX 378 ASP cc_start: 0.8082 (m-30) cc_final: 0.7880 (m-30) REVERT: CX 386 GLN cc_start: 0.8575 (tm-30) cc_final: 0.8320 (tp40) REVERT: CX 387 TYR cc_start: 0.8525 (t80) cc_final: 0.8183 (t80) REVERT: CY 1739 TYR cc_start: 0.8951 (m-80) cc_final: 0.8671 (m-80) REVERT: CY 1783 GLU cc_start: 0.8810 (pm20) cc_final: 0.8576 (pm20) REVERT: DT 49 GLU cc_start: 0.7448 (mp0) cc_final: 0.7076 (mp0) REVERT: DT 194 LYS cc_start: 0.7835 (pttm) cc_final: 0.7341 (tptp) REVERT: DT 208 GLN cc_start: 0.7651 (tp40) cc_final: 0.7393 (tp40) REVERT: DT 296 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7050 (tm-30) REVERT: DT 300 ASN cc_start: 0.7076 (m-40) cc_final: 0.6728 (m-40) REVERT: DT 301 GLN cc_start: 0.7443 (tp40) cc_final: 0.7201 (tp-100) REVERT: DX 378 ASP cc_start: 0.8292 (m-30) cc_final: 0.7740 (t0) REVERT: DX 410 ARG cc_start: 0.7371 (mtm110) cc_final: 0.7168 (mtm110) REVERT: DY 1772 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.8065 (pp) REVERT: DY 1903 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.8078 (tm-30) REVERT: DY 1904 ILE cc_start: 0.8287 (mt) cc_final: 0.7978 (mt) REVERT: ET 49 GLU cc_start: 0.7334 (mp0) cc_final: 0.7073 (mp0) REVERT: ET 64 GLN cc_start: 0.7972 (tt0) cc_final: 0.7442 (mt0) REVERT: ET 194 LYS cc_start: 0.7768 (pttm) cc_final: 0.7379 (tptp) REVERT: ET 209 GLU cc_start: 0.7252 (tm-30) cc_final: 0.6291 (tp30) REVERT: ET 210 TYR cc_start: 0.7979 (t80) cc_final: 0.7723 (t80) REVERT: ET 292 GLU cc_start: 0.7778 (tp30) cc_final: 0.6854 (mt-10) REVERT: ET 296 GLU cc_start: 0.7659 (tm-30) cc_final: 0.7327 (tm-30) REVERT: ET 300 ASN cc_start: 0.6784 (m-40) cc_final: 0.6417 (m110) REVERT: EX 378 ASP cc_start: 0.8210 (m-30) cc_final: 0.7733 (t0) REVERT: EY 1694 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.8207 (tt0) REVERT: EY 1739 TYR cc_start: 0.9000 (m-80) cc_final: 0.8705 (m-80) REVERT: FT 194 LYS cc_start: 0.7782 (pttm) cc_final: 0.7285 (tptp) REVERT: FT 208 GLN cc_start: 0.7399 (tp40) cc_final: 0.7188 (tp40) REVERT: FT 292 GLU cc_start: 0.7743 (tp30) cc_final: 0.6848 (mt-10) REVERT: FT 296 GLU cc_start: 0.7696 (tm-30) cc_final: 0.7053 (tm-30) REVERT: FT 300 ASN cc_start: 0.7047 (m-40) cc_final: 0.6745 (m-40) REVERT: FT 301 GLN cc_start: 0.7526 (tp40) cc_final: 0.7009 (mm110) REVERT: FX 378 ASP cc_start: 0.8238 (m-30) cc_final: 0.7650 (t0) REVERT: FX 386 GLN cc_start: 0.8408 (tm-30) cc_final: 0.8205 (tp40) REVERT: FX 410 ARG cc_start: 0.7712 (ttp-110) cc_final: 0.7064 (ptt-90) REVERT: FY 1685 LYS cc_start: 0.7080 (mmtm) cc_final: 0.6733 (mmtm) REVERT: GT 216 ASN cc_start: 0.7762 (m110) cc_final: 0.7480 (m110) REVERT: GT 292 GLU cc_start: 0.7719 (tp30) cc_final: 0.6982 (mt-10) REVERT: GT 296 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7436 (tm-30) REVERT: GT 300 ASN cc_start: 0.6747 (m-40) cc_final: 0.6337 (m110) REVERT: GT 301 GLN cc_start: 0.7195 (tp40) cc_final: 0.6713 (mm110) REVERT: GX 374 LYS cc_start: 0.7805 (ptmm) cc_final: 0.7436 (ptpp) REVERT: GX 409 LYS cc_start: 0.7364 (ttmt) cc_final: 0.6863 (ttpt) REVERT: GX 410 ARG cc_start: 0.7254 (mtm110) cc_final: 0.6942 (mtm110) REVERT: GX 459 MET cc_start: 0.8716 (mtp) cc_final: 0.8357 (mtp) REVERT: GY 1685 LYS cc_start: 0.6948 (mmtm) cc_final: 0.6629 (mmtt) REVERT: HT 49 GLU cc_start: 0.7441 (mp0) cc_final: 0.7161 (mp0) REVERT: HT 64 GLN cc_start: 0.8138 (tt0) cc_final: 0.7555 (mt0) REVERT: HT 194 LYS cc_start: 0.7795 (pttm) cc_final: 0.7327 (tptp) REVERT: HT 201 THR cc_start: 0.8375 (p) cc_final: 0.7989 (t) REVERT: HT 208 GLN cc_start: 0.7696 (tp40) cc_final: 0.7474 (tp40) REVERT: HT 216 ASN cc_start: 0.7699 (m110) cc_final: 0.7494 (m-40) REVERT: HT 292 GLU cc_start: 0.7860 (tp30) cc_final: 0.6887 (mt-10) REVERT: HT 296 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7236 (tm-30) REVERT: HT 300 ASN cc_start: 0.6790 (m-40) cc_final: 0.6441 (m-40) REVERT: HT 301 GLN cc_start: 0.7443 (tp40) cc_final: 0.7190 (tp-100) REVERT: HX 374 LYS cc_start: 0.8142 (ptmm) cc_final: 0.7615 (ptpp) REVERT: HX 386 GLN cc_start: 0.8387 (tm-30) cc_final: 0.8027 (tp40) REVERT: IT 64 GLN cc_start: 0.7993 (tt0) cc_final: 0.7384 (mt0) REVERT: IT 67 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9098 (mt) REVERT: IT 194 LYS cc_start: 0.7947 (pttm) cc_final: 0.7460 (tptp) REVERT: IT 209 GLU cc_start: 0.7228 (tm-30) cc_final: 0.6622 (tp30) REVERT: IT 210 TYR cc_start: 0.8222 (t80) cc_final: 0.7994 (t80) REVERT: IT 296 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7171 (tm-30) REVERT: IT 300 ASN cc_start: 0.6895 (m-40) cc_final: 0.6270 (m-40) REVERT: IX 371 GLU cc_start: 0.7706 (tm-30) cc_final: 0.7235 (tm-30) REVERT: IX 378 ASP cc_start: 0.8280 (m-30) cc_final: 0.7946 (m-30) REVERT: IX 384 GLU cc_start: 0.8290 (tt0) cc_final: 0.7901 (tt0) REVERT: IX 401 TYR cc_start: 0.9006 (m-80) cc_final: 0.8497 (m-80) REVERT: IX 410 ARG cc_start: 0.7730 (ptp-170) cc_final: 0.7098 (ptt-90) REVERT: IY 1873 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7868 (pm20) REVERT: IY 1907 GLN cc_start: 0.7470 (tt0) cc_final: 0.7095 (tt0) REVERT: JT 210 TYR cc_start: 0.8345 (t80) cc_final: 0.8063 (t80) REVERT: JT 216 ASN cc_start: 0.7748 (m110) cc_final: 0.7468 (m110) REVERT: JT 296 GLU cc_start: 0.7687 (tm-30) cc_final: 0.7204 (tm-30) REVERT: JT 300 ASN cc_start: 0.6321 (m-40) cc_final: 0.5979 (m110) REVERT: JX 378 ASP cc_start: 0.8160 (m-30) cc_final: 0.7738 (t0) REVERT: JX 386 GLN cc_start: 0.8528 (tm-30) cc_final: 0.8281 (tp40) REVERT: JX 484 LEU cc_start: 0.9098 (tp) cc_final: 0.8885 (tp) REVERT: JY 1739 TYR cc_start: 0.8953 (m-80) cc_final: 0.8653 (m-80) REVERT: KT 49 GLU cc_start: 0.7469 (mp0) cc_final: 0.7149 (mp0) REVERT: KT 194 LYS cc_start: 0.7814 (pttm) cc_final: 0.7397 (tptp) REVERT: KT 208 GLN cc_start: 0.7551 (tp40) cc_final: 0.7321 (tp-100) REVERT: KT 209 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7801 (tp30) REVERT: KT 216 ASN cc_start: 0.7763 (m110) cc_final: 0.7447 (m110) REVERT: KT 292 GLU cc_start: 0.7978 (tp30) cc_final: 0.6961 (mt-10) REVERT: KT 296 GLU cc_start: 0.7761 (tm-30) cc_final: 0.7261 (tm-30) REVERT: KT 300 ASN cc_start: 0.6901 (m-40) cc_final: 0.6510 (m110) REVERT: KX 371 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7444 (tm-30) REVERT: KX 378 ASP cc_start: 0.8297 (m-30) cc_final: 0.7833 (t0) REVERT: KX 386 GLN cc_start: 0.8532 (tm-30) cc_final: 0.8201 (tp40) REVERT: KX 409 LYS cc_start: 0.7412 (ttmt) cc_final: 0.7101 (ttpt) REVERT: KX 410 ARG cc_start: 0.7371 (mtm110) cc_final: 0.7096 (mtm110) REVERT: KY 1739 TYR cc_start: 0.9018 (m-80) cc_final: 0.8806 (m-80) REVERT: KY 1772 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.8071 (pp) REVERT: LT 105 TYR cc_start: 0.8606 (m-80) cc_final: 0.8275 (m-80) REVERT: LT 194 LYS cc_start: 0.7679 (pttm) cc_final: 0.7285 (tptp) REVERT: LT 210 TYR cc_start: 0.8218 (t80) cc_final: 0.7892 (t80) REVERT: LT 216 ASN cc_start: 0.7719 (m110) cc_final: 0.7392 (m110) REVERT: LT 292 GLU cc_start: 0.7800 (tp30) cc_final: 0.6910 (mt-10) REVERT: LT 296 GLU cc_start: 0.7631 (tm-30) cc_final: 0.6940 (tm-30) REVERT: LT 300 ASN cc_start: 0.6732 (m-40) cc_final: 0.6361 (m-40) REVERT: LX 378 ASP cc_start: 0.8192 (m-30) cc_final: 0.7707 (t0) REVERT: LY 1739 TYR cc_start: 0.8997 (m-80) cc_final: 0.8716 (m-80) REVERT: MT 194 LYS cc_start: 0.7682 (pttm) cc_final: 0.7265 (tptp) REVERT: MT 296 GLU cc_start: 0.7568 (tm-30) cc_final: 0.7140 (tm-30) REVERT: MT 300 ASN cc_start: 0.6966 (m-40) cc_final: 0.6618 (m110) REVERT: MX 378 ASP cc_start: 0.8219 (m-30) cc_final: 0.7591 (t0) REVERT: MX 386 GLN cc_start: 0.8414 (tm-30) cc_final: 0.8200 (tp40) REVERT: MX 405 GLN cc_start: 0.7791 (pt0) cc_final: 0.7436 (pt0) REVERT: MX 410 ARG cc_start: 0.7866 (ttp-110) cc_final: 0.7165 (ptt-90) REVERT: MX 415 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.7952 (mmm) REVERT: MY 1685 LYS cc_start: 0.7077 (mmtm) cc_final: 0.6750 (mmtm) REVERT: NT 216 ASN cc_start: 0.7669 (m110) cc_final: 0.7365 (m-40) REVERT: NT 296 GLU cc_start: 0.7684 (tm-30) cc_final: 0.7435 (tm-30) REVERT: NT 300 ASN cc_start: 0.6939 (m-40) cc_final: 0.6637 (m110) REVERT: NX 459 MET cc_start: 0.8705 (mtp) cc_final: 0.8336 (mtp) REVERT: NY 1685 LYS cc_start: 0.6948 (mmtm) cc_final: 0.6629 (mmtt) outliers start: 195 outliers final: 116 residues processed: 1759 average time/residue: 0.6004 time to fit residues: 1776.5882 Evaluate side-chains 1688 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 1562 time to evaluate : 5.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AT residue 35 VAL Chi-restraints excluded: chain AT residue 80 VAL Chi-restraints excluded: chain AT residue 136 SER Chi-restraints excluded: chain AT residue 173 VAL Chi-restraints excluded: chain AX residue 411 SER Chi-restraints excluded: chain AX residue 415 MET Chi-restraints excluded: chain AY residue 1711 THR Chi-restraints excluded: chain AY residue 1713 ILE Chi-restraints excluded: chain AY residue 1725 MET Chi-restraints excluded: chain AY residue 1752 MET Chi-restraints excluded: chain BT residue 29 VAL Chi-restraints excluded: chain BT residue 35 VAL Chi-restraints excluded: chain BT residue 67 LEU Chi-restraints excluded: chain BT residue 80 VAL Chi-restraints excluded: chain BT residue 136 SER Chi-restraints excluded: chain BT residue 173 VAL Chi-restraints excluded: chain BX residue 415 MET Chi-restraints excluded: chain BX residue 459 MET Chi-restraints excluded: chain BX residue 471 GLU Chi-restraints excluded: chain BY residue 1751 ILE Chi-restraints excluded: chain BY residue 1809 SER Chi-restraints excluded: chain BY residue 1873 GLU Chi-restraints excluded: chain BY residue 1879 ILE Chi-restraints excluded: chain CT residue 29 VAL Chi-restraints excluded: chain CT residue 80 VAL Chi-restraints excluded: chain CT residue 136 SER Chi-restraints excluded: chain CT residue 173 VAL Chi-restraints excluded: chain CX residue 415 MET Chi-restraints excluded: chain CX residue 508 GLU Chi-restraints excluded: chain CY residue 1711 THR Chi-restraints excluded: chain CY residue 1729 MET Chi-restraints excluded: chain CY residue 1873 GLU Chi-restraints excluded: chain DT residue 35 VAL Chi-restraints excluded: chain DT residue 52 LEU Chi-restraints excluded: chain DT residue 80 VAL Chi-restraints excluded: chain DT residue 136 SER Chi-restraints excluded: chain DT residue 173 VAL Chi-restraints excluded: chain DX residue 383 LEU Chi-restraints excluded: chain DX residue 415 MET Chi-restraints excluded: chain DY residue 1725 MET Chi-restraints excluded: chain DY residue 1772 LEU Chi-restraints excluded: chain DY residue 1809 SER Chi-restraints excluded: chain DY residue 1873 GLU Chi-restraints excluded: chain DY residue 1879 ILE Chi-restraints excluded: chain DY residue 1880 LEU Chi-restraints excluded: chain DY residue 1903 GLU Chi-restraints excluded: chain ET residue 80 VAL Chi-restraints excluded: chain ET residue 136 SER Chi-restraints excluded: chain ET residue 173 VAL Chi-restraints excluded: chain EX residue 508 GLU Chi-restraints excluded: chain EY residue 1694 GLN Chi-restraints excluded: chain EY residue 1711 THR Chi-restraints excluded: chain EY residue 1713 ILE Chi-restraints excluded: chain EY residue 1873 GLU Chi-restraints excluded: chain FT residue 80 VAL Chi-restraints excluded: chain FT residue 136 SER Chi-restraints excluded: chain FT residue 173 VAL Chi-restraints excluded: chain FX residue 383 LEU Chi-restraints excluded: chain FX residue 415 MET Chi-restraints excluded: chain FX residue 459 MET Chi-restraints excluded: chain FY residue 1711 THR Chi-restraints excluded: chain FY residue 1713 ILE Chi-restraints excluded: chain FY residue 1752 MET Chi-restraints excluded: chain FY residue 1809 SER Chi-restraints excluded: chain GT residue 67 LEU Chi-restraints excluded: chain GT residue 80 VAL Chi-restraints excluded: chain GT residue 136 SER Chi-restraints excluded: chain GT residue 173 VAL Chi-restraints excluded: chain GX residue 415 MET Chi-restraints excluded: chain HT residue 80 VAL Chi-restraints excluded: chain HT residue 136 SER Chi-restraints excluded: chain HT residue 173 VAL Chi-restraints excluded: chain HX residue 411 SER Chi-restraints excluded: chain HY residue 1711 THR Chi-restraints excluded: chain HY residue 1713 ILE Chi-restraints excluded: chain HY residue 1751 ILE Chi-restraints excluded: chain HY residue 1752 MET Chi-restraints excluded: chain IT residue 35 VAL Chi-restraints excluded: chain IT residue 67 LEU Chi-restraints excluded: chain IT residue 80 VAL Chi-restraints excluded: chain IT residue 136 SER Chi-restraints excluded: chain IT residue 173 VAL Chi-restraints excluded: chain IX residue 383 LEU Chi-restraints excluded: chain IX residue 415 MET Chi-restraints excluded: chain IY residue 1751 ILE Chi-restraints excluded: chain IY residue 1809 SER Chi-restraints excluded: chain IY residue 1873 GLU Chi-restraints excluded: chain JT residue 29 VAL Chi-restraints excluded: chain JT residue 80 VAL Chi-restraints excluded: chain JT residue 136 SER Chi-restraints excluded: chain JT residue 173 VAL Chi-restraints excluded: chain JX residue 508 GLU Chi-restraints excluded: chain JY residue 1873 GLU Chi-restraints excluded: chain KT residue 35 VAL Chi-restraints excluded: chain KT residue 80 VAL Chi-restraints excluded: chain KT residue 136 SER Chi-restraints excluded: chain KT residue 173 VAL Chi-restraints excluded: chain KX residue 415 MET Chi-restraints excluded: chain KX residue 418 GLU Chi-restraints excluded: chain KX residue 497 LEU Chi-restraints excluded: chain KX residue 508 GLU Chi-restraints excluded: chain KY residue 1772 LEU Chi-restraints excluded: chain KY residue 1873 GLU Chi-restraints excluded: chain KY residue 1879 ILE Chi-restraints excluded: chain KY residue 1880 LEU Chi-restraints excluded: chain LT residue 67 LEU Chi-restraints excluded: chain LT residue 80 VAL Chi-restraints excluded: chain LT residue 136 SER Chi-restraints excluded: chain LT residue 173 VAL Chi-restraints excluded: chain LX residue 385 THR Chi-restraints excluded: chain LX residue 508 GLU Chi-restraints excluded: chain LY residue 1711 THR Chi-restraints excluded: chain LY residue 1713 ILE Chi-restraints excluded: chain MT residue 80 VAL Chi-restraints excluded: chain MT residue 136 SER Chi-restraints excluded: chain MT residue 173 VAL Chi-restraints excluded: chain MX residue 415 MET Chi-restraints excluded: chain MX residue 459 MET Chi-restraints excluded: chain MY residue 1711 THR Chi-restraints excluded: chain MY residue 1713 ILE Chi-restraints excluded: chain MY residue 1752 MET Chi-restraints excluded: chain MY residue 1809 SER Chi-restraints excluded: chain NT residue 80 VAL Chi-restraints excluded: chain NT residue 136 SER Chi-restraints excluded: chain NT residue 173 VAL Chi-restraints excluded: chain NX residue 415 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 679 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 401 optimal weight: 2.9990 chunk 514 optimal weight: 1.9990 chunk 398 optimal weight: 0.9980 chunk 592 optimal weight: 7.9990 chunk 393 optimal weight: 2.9990 chunk 701 optimal weight: 0.7980 chunk 439 optimal weight: 0.6980 chunk 427 optimal weight: 9.9990 chunk 323 optimal weight: 10.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AT 301 GLN BT 301 GLN BX 443 GLN ** BY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BY1907 GLN CT 196 ASN CY1856 ASN DX 432 ASN ** EX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** EX 432 ASN EX 443 GLN EY1694 GLN ** EY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** FX 443 GLN ** FY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** FY1856 ASN GX 432 ASN ** HY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** IT 301 GLN ** IX 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** IX 443 GLN ** IY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** JT 64 GLN JT 197 GLN JY1856 ASN KX 432 ASN ** KY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LX 443 GLN MT 33 ASN ** MX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** MY1856 ASN MY1907 GLN NX 432 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 61992 Z= 0.235 Angle : 0.617 14.669 83594 Z= 0.324 Chirality : 0.046 0.175 9520 Planarity : 0.004 0.043 10598 Dihedral : 4.945 26.281 8134 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.97 % Allowed : 17.19 % Favored : 79.84 % 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: -0.28 (0.10), residues: 7406 helix: 1.43 (0.11), residues: 2240 sheet: -1.07 (0.12), residues: 1624 loop : -0.74 (0.10), residues: 3542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPJX 466 HIS 0.002 0.000 HISCT 89 PHE 0.010 0.001 PHEAX 420 TYR 0.021 0.001 TYRET 210 ARG 0.007 0.000 ARGDX 394 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14812 Ramachandran restraints generated. 7406 Oldfield, 0 Emsley, 7406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14812 Ramachandran restraints generated. 7406 Oldfield, 0 Emsley, 7406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1811 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 1609 time to evaluate : 5.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: AT 49 GLU cc_start: 0.7419 (mp0) cc_final: 0.6996 (mp0) REVERT: AT 64 GLN cc_start: 0.8166 (tt0) cc_final: 0.7507 (mt0) REVERT: AT 194 LYS cc_start: 0.7596 (pttm) cc_final: 0.7165 (tptp) REVERT: AT 208 GLN cc_start: 0.7708 (tp-100) cc_final: 0.7456 (tp40) REVERT: AT 292 GLU cc_start: 0.8113 (tp30) cc_final: 0.7159 (mt-10) REVERT: AT 296 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7241 (tm-30) REVERT: AT 300 ASN cc_start: 0.6688 (m-40) cc_final: 0.6395 (m-40) REVERT: AT 301 GLN cc_start: 0.7408 (tp40) cc_final: 0.7181 (tp-100) REVERT: AX 386 GLN cc_start: 0.8401 (tm-30) cc_final: 0.8128 (tp40) REVERT: BT 49 GLU cc_start: 0.7388 (mp0) cc_final: 0.7062 (mp0) REVERT: BT 64 GLN cc_start: 0.8006 (tt0) cc_final: 0.7428 (mt0) REVERT: BT 67 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9081 (mt) REVERT: BT 194 LYS cc_start: 0.7855 (pttm) cc_final: 0.7396 (tptp) REVERT: BT 210 TYR cc_start: 0.8155 (t80) cc_final: 0.7877 (t80) REVERT: BT 216 ASN cc_start: 0.7910 (m110) cc_final: 0.7535 (m110) REVERT: BT 300 ASN cc_start: 0.6840 (m-40) cc_final: 0.6542 (m110) REVERT: BX 371 GLU cc_start: 0.7693 (tm-30) cc_final: 0.7247 (tm-30) REVERT: BX 384 GLU cc_start: 0.8271 (tt0) cc_final: 0.7876 (tt0) REVERT: BX 401 TYR cc_start: 0.9005 (m-80) cc_final: 0.8580 (m-80) REVERT: BX 410 ARG cc_start: 0.7711 (ptp-170) cc_final: 0.7089 (mtm110) REVERT: BY 1739 TYR cc_start: 0.9026 (m-80) cc_final: 0.8722 (m-80) REVERT: BY 1873 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7854 (pm20) REVERT: CT 49 GLU cc_start: 0.7404 (mp0) cc_final: 0.7123 (mp0) REVERT: CT 208 GLN cc_start: 0.7753 (tp40) cc_final: 0.7394 (tp40) REVERT: CT 209 GLU cc_start: 0.8304 (mm-30) cc_final: 0.8047 (tm-30) REVERT: CT 216 ASN cc_start: 0.7684 (m110) cc_final: 0.7309 (m110) REVERT: CT 292 GLU cc_start: 0.8044 (tp30) cc_final: 0.6991 (mt-10) REVERT: CT 296 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7511 (tm-30) REVERT: CT 300 ASN cc_start: 0.6642 (m-40) cc_final: 0.6209 (m110) REVERT: CX 371 GLU cc_start: 0.7628 (tm-30) cc_final: 0.7157 (tm-30) REVERT: CX 378 ASP cc_start: 0.8056 (m-30) cc_final: 0.7804 (m-30) REVERT: CX 386 GLN cc_start: 0.8491 (tm-30) cc_final: 0.8269 (tp40) REVERT: CY 1783 GLU cc_start: 0.8810 (pm20) cc_final: 0.8577 (pm20) REVERT: DT 49 GLU cc_start: 0.7484 (mp0) cc_final: 0.7111 (mp0) REVERT: DT 194 LYS cc_start: 0.7791 (pttm) cc_final: 0.7340 (tptp) REVERT: DT 208 GLN cc_start: 0.7653 (tp40) cc_final: 0.7390 (tp40) REVERT: DT 296 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7002 (tm-30) REVERT: DT 300 ASN cc_start: 0.7075 (m-40) cc_final: 0.6710 (m-40) REVERT: DT 301 GLN cc_start: 0.7522 (tp40) cc_final: 0.7263 (tp-100) REVERT: DX 378 ASP cc_start: 0.8296 (m-30) cc_final: 0.7748 (t0) REVERT: DX 410 ARG cc_start: 0.7251 (mtm110) cc_final: 0.7045 (mtm110) REVERT: DY 1772 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.8079 (pp) REVERT: DY 1903 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.8076 (tm-30) REVERT: DY 1904 ILE cc_start: 0.8232 (mt) cc_final: 0.7894 (mt) REVERT: ET 49 GLU cc_start: 0.7341 (mp0) cc_final: 0.7056 (mp0) REVERT: ET 64 GLN cc_start: 0.8000 (tt0) cc_final: 0.7463 (mt0) REVERT: ET 194 LYS cc_start: 0.7720 (pttm) cc_final: 0.7344 (tptp) REVERT: ET 209 GLU cc_start: 0.7210 (tm-30) cc_final: 0.6208 (tp30) REVERT: ET 210 TYR cc_start: 0.8018 (t80) cc_final: 0.7549 (t80) REVERT: ET 292 GLU cc_start: 0.7727 (tp30) cc_final: 0.6820 (mt-10) REVERT: ET 296 GLU cc_start: 0.7654 (tm-30) cc_final: 0.7302 (tm-30) REVERT: ET 300 ASN cc_start: 0.6847 (m-40) cc_final: 0.6391 (m110) REVERT: ET 301 GLN cc_start: 0.7390 (tp40) cc_final: 0.6617 (mm110) REVERT: EX 368 ILE cc_start: 0.6411 (OUTLIER) cc_final: 0.6157 (mm) REVERT: EX 378 ASP cc_start: 0.8221 (m-30) cc_final: 0.7732 (t0) REVERT: EY 1739 TYR cc_start: 0.9001 (m-80) cc_final: 0.8522 (m-80) REVERT: FT 194 LYS cc_start: 0.7763 (pttm) cc_final: 0.7328 (tptp) REVERT: FT 292 GLU cc_start: 0.7713 (tp30) cc_final: 0.6890 (mt-10) REVERT: FT 296 GLU cc_start: 0.7699 (tm-30) cc_final: 0.7311 (tm-30) REVERT: FT 300 ASN cc_start: 0.7113 (m-40) cc_final: 0.6692 (m110) REVERT: FT 301 GLN cc_start: 0.7498 (tp40) cc_final: 0.6940 (mm110) REVERT: FX 378 ASP cc_start: 0.8263 (m-30) cc_final: 0.7647 (t0) REVERT: FX 410 ARG cc_start: 0.7714 (ttp-110) cc_final: 0.7092 (ptt-90) REVERT: FY 1685 LYS cc_start: 0.7047 (mmtm) cc_final: 0.6727 (mmtm) REVERT: GT 201 THR cc_start: 0.8170 (p) cc_final: 0.7792 (t) REVERT: GT 216 ASN cc_start: 0.7778 (m110) cc_final: 0.7492 (m110) REVERT: GT 292 GLU cc_start: 0.7625 (tp30) cc_final: 0.6907 (mt-10) REVERT: GT 296 GLU cc_start: 0.7843 (tm-30) cc_final: 0.6992 (tm-30) REVERT: GT 300 ASN cc_start: 0.6703 (m-40) cc_final: 0.6193 (m110) REVERT: GX 409 LYS cc_start: 0.7356 (ttmt) cc_final: 0.6850 (ttpt) REVERT: GX 410 ARG cc_start: 0.7187 (mtm110) cc_final: 0.6878 (mtm110) REVERT: GX 459 MET cc_start: 0.8731 (mtp) cc_final: 0.8370 (mtp) REVERT: GY 1685 LYS cc_start: 0.6945 (mmtm) cc_final: 0.6617 (mmtt) REVERT: HT 49 GLU cc_start: 0.7505 (mp0) cc_final: 0.7205 (mp0) REVERT: HT 64 GLN cc_start: 0.8163 (tt0) cc_final: 0.7556 (mt0) REVERT: HT 194 LYS cc_start: 0.7798 (pttm) cc_final: 0.7270 (tptp) REVERT: HT 201 THR cc_start: 0.8242 (p) cc_final: 0.7858 (t) REVERT: HT 208 GLN cc_start: 0.7643 (tp40) cc_final: 0.7386 (tp40) REVERT: HT 216 ASN cc_start: 0.7669 (m110) cc_final: 0.7460 (m110) REVERT: HT 292 GLU cc_start: 0.7865 (tp30) cc_final: 0.6921 (mt-10) REVERT: HT 296 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7175 (tm-30) REVERT: HT 300 ASN cc_start: 0.6925 (m-40) cc_final: 0.6558 (m110) REVERT: HX 374 LYS cc_start: 0.8143 (ptmm) cc_final: 0.7610 (ptpp) REVERT: HX 386 GLN cc_start: 0.8400 (tm-30) cc_final: 0.8115 (tp40) REVERT: IT 49 GLU cc_start: 0.7403 (mp0) cc_final: 0.7076 (mp0) REVERT: IT 64 GLN cc_start: 0.8001 (tt0) cc_final: 0.7435 (mt0) REVERT: IT 67 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9127 (mt) REVERT: IT 194 LYS cc_start: 0.7824 (pttm) cc_final: 0.7370 (tptp) REVERT: IT 209 GLU cc_start: 0.7221 (tm-30) cc_final: 0.6624 (tp30) REVERT: IT 296 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7204 (tm-30) REVERT: IT 300 ASN cc_start: 0.6919 (m-40) cc_final: 0.6304 (m-40) REVERT: IX 371 GLU cc_start: 0.7701 (tm-30) cc_final: 0.7227 (tm-30) REVERT: IX 384 GLU cc_start: 0.8287 (tt0) cc_final: 0.7938 (tt0) REVERT: IX 401 TYR cc_start: 0.9024 (m-80) cc_final: 0.8544 (m-80) REVERT: IX 410 ARG cc_start: 0.7693 (ptp-170) cc_final: 0.7089 (ptt-90) REVERT: IY 1715 SER cc_start: 0.8635 (p) cc_final: 0.8406 (p) REVERT: IY 1873 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7918 (pm20) REVERT: IY 1907 GLN cc_start: 0.7508 (tt0) cc_final: 0.7166 (tt0) REVERT: JT 216 ASN cc_start: 0.7746 (m110) cc_final: 0.7468 (m110) REVERT: JT 296 GLU cc_start: 0.7714 (tm-30) cc_final: 0.7071 (tm-30) REVERT: JT 300 ASN cc_start: 0.6345 (m-40) cc_final: 0.5912 (m-40) REVERT: JX 378 ASP cc_start: 0.8145 (m-30) cc_final: 0.7655 (t0) REVERT: JX 386 GLN cc_start: 0.8569 (tm-30) cc_final: 0.8311 (tp40) REVERT: JX 410 ARG cc_start: 0.7719 (ptp-170) cc_final: 0.7261 (ptt-90) REVERT: JX 484 LEU cc_start: 0.9127 (tp) cc_final: 0.8911 (tp) REVERT: KT 49 GLU cc_start: 0.7474 (mp0) cc_final: 0.7151 (mp0) REVERT: KT 194 LYS cc_start: 0.7808 (pttm) cc_final: 0.7154 (tptp) REVERT: KT 208 GLN cc_start: 0.7591 (tp40) cc_final: 0.7372 (tp-100) REVERT: KT 209 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7799 (tp30) REVERT: KT 216 ASN cc_start: 0.7754 (m110) cc_final: 0.7441 (m110) REVERT: KT 292 GLU cc_start: 0.8017 (tp30) cc_final: 0.6900 (mt-10) REVERT: KT 296 GLU cc_start: 0.7759 (tm-30) cc_final: 0.6772 (tm-30) REVERT: KT 300 ASN cc_start: 0.7001 (m-40) cc_final: 0.6578 (m110) REVERT: KX 371 GLU cc_start: 0.7834 (tm-30) cc_final: 0.7371 (tm-30) REVERT: KX 378 ASP cc_start: 0.8295 (m-30) cc_final: 0.7824 (t0) REVERT: KX 386 GLN cc_start: 0.8492 (tm-30) cc_final: 0.8224 (tp40) REVERT: KX 409 LYS cc_start: 0.7275 (ttmt) cc_final: 0.6772 (ttpt) REVERT: KX 410 ARG cc_start: 0.7340 (mtm110) cc_final: 0.7055 (mtm110) REVERT: KX 509 LEU cc_start: 0.9054 (mt) cc_final: 0.8727 (mt) REVERT: KY 1739 TYR cc_start: 0.9056 (m-80) cc_final: 0.8719 (m-80) REVERT: KY 1772 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8058 (pp) REVERT: KY 1907 GLN cc_start: 0.7599 (tt0) cc_final: 0.7368 (tt0) REVERT: LT 49 GLU cc_start: 0.7482 (mp0) cc_final: 0.7219 (mp0) REVERT: LT 194 LYS cc_start: 0.7576 (pttm) cc_final: 0.7158 (tptp) REVERT: LT 210 TYR cc_start: 0.8203 (t80) cc_final: 0.7962 (t80) REVERT: LT 216 ASN cc_start: 0.7689 (m110) cc_final: 0.7395 (m110) REVERT: LT 292 GLU cc_start: 0.7742 (tp30) cc_final: 0.6891 (mt-10) REVERT: LT 296 GLU cc_start: 0.7618 (tm-30) cc_final: 0.7229 (tm-30) REVERT: LT 300 ASN cc_start: 0.6806 (m-40) cc_final: 0.6458 (m110) REVERT: LX 378 ASP cc_start: 0.8228 (m-30) cc_final: 0.7713 (t0) REVERT: LY 1739 TYR cc_start: 0.9004 (m-80) cc_final: 0.8520 (m-80) REVERT: LY 1907 GLN cc_start: 0.8252 (tm-30) cc_final: 0.7721 (tm-30) REVERT: MT 194 LYS cc_start: 0.7762 (pttm) cc_final: 0.7350 (tptp) REVERT: MT 296 GLU cc_start: 0.7573 (tm-30) cc_final: 0.6684 (tm-30) REVERT: MT 300 ASN cc_start: 0.7043 (m-40) cc_final: 0.6715 (m110) REVERT: MX 378 ASP cc_start: 0.8240 (m-30) cc_final: 0.7610 (t0) REVERT: MX 405 GLN cc_start: 0.7766 (pt0) cc_final: 0.7345 (pt0) REVERT: MX 410 ARG cc_start: 0.7690 (ttp-110) cc_final: 0.7045 (ptt-90) REVERT: MX 415 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.7913 (mmm) REVERT: MY 1685 LYS cc_start: 0.7048 (mmtm) cc_final: 0.6729 (mmtm) REVERT: NT 201 THR cc_start: 0.8162 (p) cc_final: 0.7779 (t) REVERT: NT 216 ASN cc_start: 0.7671 (m110) cc_final: 0.7371 (m-40) REVERT: NT 296 GLU cc_start: 0.7675 (tm-30) cc_final: 0.7350 (tm-30) REVERT: NT 300 ASN cc_start: 0.6966 (m-40) cc_final: 0.6571 (m110) REVERT: NX 409 LYS cc_start: 0.6966 (ttmt) cc_final: 0.6720 (ttpt) REVERT: NX 459 MET cc_start: 0.8725 (mtp) cc_final: 0.8360 (mtp) REVERT: NY 1685 LYS cc_start: 0.6946 (mmtm) cc_final: 0.6617 (mmtt) outliers start: 202 outliers final: 139 residues processed: 1726 average time/residue: 0.5930 time to fit residues: 1727.0618 Evaluate side-chains 1709 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 1561 time to evaluate : 5.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AT residue 35 VAL Chi-restraints excluded: chain AT residue 67 LEU Chi-restraints excluded: chain AT residue 80 VAL Chi-restraints excluded: chain AT residue 136 SER Chi-restraints excluded: chain AT residue 173 VAL Chi-restraints excluded: chain AY residue 1711 THR Chi-restraints excluded: chain AY residue 1725 MET Chi-restraints excluded: chain AY residue 1751 ILE Chi-restraints excluded: chain AY residue 1752 MET Chi-restraints excluded: chain BT residue 29 VAL Chi-restraints excluded: chain BT residue 35 VAL Chi-restraints excluded: chain BT residue 67 LEU Chi-restraints excluded: chain BT residue 80 VAL Chi-restraints excluded: chain BT residue 136 SER Chi-restraints excluded: chain BT residue 173 VAL Chi-restraints excluded: chain BX residue 415 MET Chi-restraints excluded: chain BX residue 459 MET Chi-restraints excluded: chain BY residue 1725 MET Chi-restraints excluded: chain BY residue 1751 ILE Chi-restraints excluded: chain BY residue 1809 SER Chi-restraints excluded: chain BY residue 1873 GLU Chi-restraints excluded: chain BY residue 1879 ILE Chi-restraints excluded: chain CT residue 29 VAL Chi-restraints excluded: chain CT residue 65 VAL Chi-restraints excluded: chain CT residue 80 VAL Chi-restraints excluded: chain CT residue 136 SER Chi-restraints excluded: chain CT residue 173 VAL Chi-restraints excluded: chain CT residue 196 ASN Chi-restraints excluded: chain CX residue 415 MET Chi-restraints excluded: chain CX residue 508 GLU Chi-restraints excluded: chain CY residue 1711 THR Chi-restraints excluded: chain CY residue 1746 LYS Chi-restraints excluded: chain CY residue 1873 GLU Chi-restraints excluded: chain CY residue 1904 ILE Chi-restraints excluded: chain DT residue 35 VAL Chi-restraints excluded: chain DT residue 52 LEU Chi-restraints excluded: chain DT residue 80 VAL Chi-restraints excluded: chain DT residue 136 SER Chi-restraints excluded: chain DT residue 173 VAL Chi-restraints excluded: chain DX residue 383 LEU Chi-restraints excluded: chain DX residue 415 MET Chi-restraints excluded: chain DX residue 418 GLU Chi-restraints excluded: chain DY residue 1711 THR Chi-restraints excluded: chain DY residue 1725 MET Chi-restraints excluded: chain DY residue 1772 LEU Chi-restraints excluded: chain DY residue 1809 SER Chi-restraints excluded: chain DY residue 1873 GLU Chi-restraints excluded: chain DY residue 1879 ILE Chi-restraints excluded: chain DY residue 1880 LEU Chi-restraints excluded: chain DY residue 1903 GLU Chi-restraints excluded: chain ET residue 80 VAL Chi-restraints excluded: chain ET residue 136 SER Chi-restraints excluded: chain ET residue 173 VAL Chi-restraints excluded: chain EX residue 368 ILE Chi-restraints excluded: chain EX residue 508 GLU Chi-restraints excluded: chain EY residue 1711 THR Chi-restraints excluded: chain EY residue 1713 ILE Chi-restraints excluded: chain FT residue 80 VAL Chi-restraints excluded: chain FT residue 136 SER Chi-restraints excluded: chain FT residue 173 VAL Chi-restraints excluded: chain FX residue 383 LEU Chi-restraints excluded: chain FX residue 415 MET Chi-restraints excluded: chain FX residue 508 GLU Chi-restraints excluded: chain FY residue 1711 THR Chi-restraints excluded: chain FY residue 1713 ILE Chi-restraints excluded: chain FY residue 1751 ILE Chi-restraints excluded: chain FY residue 1752 MET Chi-restraints excluded: chain FY residue 1809 SER Chi-restraints excluded: chain GT residue 67 LEU Chi-restraints excluded: chain GT residue 80 VAL Chi-restraints excluded: chain GT residue 136 SER Chi-restraints excluded: chain GT residue 173 VAL Chi-restraints excluded: chain GX residue 415 MET Chi-restraints excluded: chain GY residue 1751 ILE Chi-restraints excluded: chain HT residue 29 VAL Chi-restraints excluded: chain HT residue 67 LEU Chi-restraints excluded: chain HT residue 80 VAL Chi-restraints excluded: chain HT residue 136 SER Chi-restraints excluded: chain HT residue 173 VAL Chi-restraints excluded: chain HX residue 383 LEU Chi-restraints excluded: chain HX residue 411 SER Chi-restraints excluded: chain HY residue 1711 THR Chi-restraints excluded: chain HY residue 1724 ASN Chi-restraints excluded: chain HY residue 1751 ILE Chi-restraints excluded: chain HY residue 1752 MET Chi-restraints excluded: chain IT residue 67 LEU Chi-restraints excluded: chain IT residue 80 VAL Chi-restraints excluded: chain IT residue 136 SER Chi-restraints excluded: chain IT residue 173 VAL Chi-restraints excluded: chain IX residue 375 ILE Chi-restraints excluded: chain IX residue 383 LEU Chi-restraints excluded: chain IX residue 415 MET Chi-restraints excluded: chain IX residue 459 MET Chi-restraints excluded: chain IX residue 508 GLU Chi-restraints excluded: chain IY residue 1725 MET Chi-restraints excluded: chain IY residue 1751 ILE Chi-restraints excluded: chain IY residue 1809 SER Chi-restraints excluded: chain IY residue 1873 GLU Chi-restraints excluded: chain JT residue 29 VAL Chi-restraints excluded: chain JT residue 80 VAL Chi-restraints excluded: chain JT residue 82 LEU Chi-restraints excluded: chain JT residue 136 SER Chi-restraints excluded: chain JT residue 173 VAL Chi-restraints excluded: chain JX residue 508 GLU Chi-restraints excluded: chain JY residue 1711 THR Chi-restraints excluded: chain JY residue 1746 LYS Chi-restraints excluded: chain JY residue 1873 GLU Chi-restraints excluded: chain KT residue 35 VAL Chi-restraints excluded: chain KT residue 80 VAL Chi-restraints excluded: chain KT residue 136 SER Chi-restraints excluded: chain KT residue 173 VAL Chi-restraints excluded: chain KX residue 415 MET Chi-restraints excluded: chain KX residue 418 GLU Chi-restraints excluded: chain KX residue 497 LEU Chi-restraints excluded: chain KX residue 508 GLU Chi-restraints excluded: chain KY residue 1711 THR Chi-restraints excluded: chain KY residue 1772 LEU Chi-restraints excluded: chain KY residue 1873 GLU Chi-restraints excluded: chain KY residue 1879 ILE Chi-restraints excluded: chain KY residue 1880 LEU Chi-restraints excluded: chain LT residue 67 LEU Chi-restraints excluded: chain LT residue 80 VAL Chi-restraints excluded: chain LT residue 136 SER Chi-restraints excluded: chain LT residue 173 VAL Chi-restraints excluded: chain LX residue 383 LEU Chi-restraints excluded: chain LX residue 385 THR Chi-restraints excluded: chain LX residue 412 LYS Chi-restraints excluded: chain LX residue 508 GLU Chi-restraints excluded: chain LY residue 1711 THR Chi-restraints excluded: chain LY residue 1713 ILE Chi-restraints excluded: chain MT residue 80 VAL Chi-restraints excluded: chain MT residue 136 SER Chi-restraints excluded: chain MT residue 173 VAL Chi-restraints excluded: chain MX residue 383 LEU Chi-restraints excluded: chain MX residue 415 MET Chi-restraints excluded: chain MX residue 508 GLU Chi-restraints excluded: chain MY residue 1711 THR Chi-restraints excluded: chain MY residue 1713 ILE Chi-restraints excluded: chain MY residue 1724 ASN Chi-restraints excluded: chain MY residue 1752 MET Chi-restraints excluded: chain MY residue 1809 SER Chi-restraints excluded: chain NT residue 67 LEU Chi-restraints excluded: chain NT residue 80 VAL Chi-restraints excluded: chain NT residue 136 SER Chi-restraints excluded: chain NT residue 173 VAL Chi-restraints excluded: chain NX residue 415 MET Chi-restraints excluded: chain NY residue 1711 THR Chi-restraints excluded: chain NY residue 1751 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 434 optimal weight: 8.9990 chunk 280 optimal weight: 6.9990 chunk 419 optimal weight: 4.9990 chunk 211 optimal weight: 8.9990 chunk 137 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 446 optimal weight: 4.9990 chunk 478 optimal weight: 9.9990 chunk 346 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 551 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AT 197 GLN BT 301 GLN BX 443 GLN ** BY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CT 196 ASN CY1856 ASN DX 432 ASN ** EX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** EX 432 ASN EX 443 GLN ** EY1856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** FY1856 ASN FY1907 GLN GT 41 ASN GX 432 ASN ** GY1856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** HX 432 ASN ** IX 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** IY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** JT 64 GLN JT 196 ASN JY1856 ASN ** KY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LX 443 GLN LY1907 GLN ** MX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** MY1856 ASN ** NT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NT 41 ASN NX 432 ASN ** NY1856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 61992 Z= 0.374 Angle : 0.681 16.217 83594 Z= 0.356 Chirality : 0.048 0.190 9520 Planarity : 0.004 0.049 10598 Dihedral : 5.110 26.482 8134 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.95 % Allowed : 17.48 % Favored : 79.57 % 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: -0.37 (0.10), residues: 7406 helix: 1.34 (0.11), residues: 2240 sheet: -1.06 (0.12), residues: 1610 loop : -0.82 (0.10), residues: 3556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRPNY1723 HIS 0.003 0.001 HISHX 413 PHE 0.029 0.002 PHEJT 109 TYR 0.019 0.002 TYRNT 36 ARG 0.008 0.000 ARGLX 394 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14812 Ramachandran restraints generated. 7406 Oldfield, 0 Emsley, 7406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14812 Ramachandran restraints generated. 7406 Oldfield, 0 Emsley, 7406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1767 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 1567 time to evaluate : 5.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: AT 49 GLU cc_start: 0.7461 (mp0) cc_final: 0.7047 (mp0) REVERT: AT 64 GLN cc_start: 0.8153 (tt0) cc_final: 0.7547 (mt0) REVERT: AT 194 LYS cc_start: 0.7709 (pttm) cc_final: 0.7143 (tptp) REVERT: AT 208 GLN cc_start: 0.7533 (tp-100) cc_final: 0.7270 (tp40) REVERT: AT 292 GLU cc_start: 0.8086 (tp30) cc_final: 0.7087 (mt-10) REVERT: AT 296 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7193 (tm-30) REVERT: AT 300 ASN cc_start: 0.6642 (m-40) cc_final: 0.6274 (m-40) REVERT: AX 386 GLN cc_start: 0.8411 (tm-30) cc_final: 0.8120 (tp40) REVERT: AY 1795 MET cc_start: 0.7716 (tpp) cc_final: 0.7446 (tpp) REVERT: BT 64 GLN cc_start: 0.8032 (tt0) cc_final: 0.7513 (mt0) REVERT: BT 67 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.9103 (mt) REVERT: BT 194 LYS cc_start: 0.7839 (pttm) cc_final: 0.7433 (tptp) REVERT: BT 201 THR cc_start: 0.8327 (p) cc_final: 0.7923 (t) REVERT: BT 210 TYR cc_start: 0.8167 (t80) cc_final: 0.7965 (t80) REVERT: BT 214 LYS cc_start: 0.7777 (pptt) cc_final: 0.7551 (pptt) REVERT: BT 216 ASN cc_start: 0.7695 (m110) cc_final: 0.7261 (m110) REVERT: BX 371 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7264 (tm-30) REVERT: BX 384 GLU cc_start: 0.8297 (tt0) cc_final: 0.7917 (tt0) REVERT: BX 386 GLN cc_start: 0.8497 (tp40) cc_final: 0.8277 (tp40) REVERT: BX 401 TYR cc_start: 0.9070 (m-80) cc_final: 0.8557 (m-80) REVERT: BX 410 ARG cc_start: 0.7743 (ptp-170) cc_final: 0.7445 (mtm110) REVERT: BY 1739 TYR cc_start: 0.9075 (m-80) cc_final: 0.8764 (m-80) REVERT: BY 1873 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8063 (pm20) REVERT: CT 49 GLU cc_start: 0.7426 (mp0) cc_final: 0.7162 (mp0) REVERT: CT 208 GLN cc_start: 0.7754 (tp40) cc_final: 0.7387 (tp40) REVERT: CT 209 GLU cc_start: 0.8290 (mm-30) cc_final: 0.8064 (tm-30) REVERT: CT 214 LYS cc_start: 0.7357 (pptt) cc_final: 0.6844 (pptt) REVERT: CT 216 ASN cc_start: 0.7748 (m110) cc_final: 0.7436 (m110) REVERT: CT 296 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7331 (tm-30) REVERT: CT 300 ASN cc_start: 0.6694 (m-40) cc_final: 0.6186 (m-40) REVERT: CX 371 GLU cc_start: 0.7705 (tm-30) cc_final: 0.7314 (tm-30) REVERT: CX 374 LYS cc_start: 0.7741 (ptmm) cc_final: 0.7393 (ptpp) REVERT: CX 386 GLN cc_start: 0.8438 (tm-30) cc_final: 0.8196 (tp40) REVERT: CY 1783 GLU cc_start: 0.8813 (pm20) cc_final: 0.8589 (pm20) REVERT: DT 49 GLU cc_start: 0.7576 (mp0) cc_final: 0.7324 (mp0) REVERT: DT 194 LYS cc_start: 0.7761 (pttm) cc_final: 0.7337 (tptp) REVERT: DT 296 GLU cc_start: 0.7783 (tm-30) cc_final: 0.6889 (tm-30) REVERT: DT 300 ASN cc_start: 0.7037 (m-40) cc_final: 0.6561 (m-40) REVERT: DX 378 ASP cc_start: 0.8311 (m-30) cc_final: 0.7716 (t0) REVERT: DX 410 ARG cc_start: 0.7272 (mtm110) cc_final: 0.7048 (mtm110) REVERT: DX 509 LEU cc_start: 0.9173 (mt) cc_final: 0.8749 (mt) REVERT: DY 1772 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8153 (pp) REVERT: DY 1903 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8093 (tm-30) REVERT: DY 1904 ILE cc_start: 0.8445 (mt) cc_final: 0.8096 (mt) REVERT: ET 49 GLU cc_start: 0.7406 (mp0) cc_final: 0.7093 (mp0) REVERT: ET 194 LYS cc_start: 0.7828 (pttm) cc_final: 0.7461 (tptp) REVERT: ET 209 GLU cc_start: 0.7365 (tm-30) cc_final: 0.6338 (tp30) REVERT: ET 210 TYR cc_start: 0.8049 (t80) cc_final: 0.7630 (t80) REVERT: ET 292 GLU cc_start: 0.7740 (tp30) cc_final: 0.6852 (mt-10) REVERT: ET 296 GLU cc_start: 0.7545 (tm-30) cc_final: 0.7173 (tm-30) REVERT: ET 300 ASN cc_start: 0.6877 (m-40) cc_final: 0.6390 (m110) REVERT: EX 368 ILE cc_start: 0.6443 (OUTLIER) cc_final: 0.6228 (mm) REVERT: EX 378 ASP cc_start: 0.8266 (m-30) cc_final: 0.7712 (t0) REVERT: EY 1739 TYR cc_start: 0.9036 (m-80) cc_final: 0.8537 (m-80) REVERT: FT 194 LYS cc_start: 0.7887 (pttm) cc_final: 0.7499 (tptp) REVERT: FT 292 GLU cc_start: 0.7632 (tp30) cc_final: 0.6850 (mt-10) REVERT: FT 296 GLU cc_start: 0.7579 (tm-30) cc_final: 0.7024 (tm-30) REVERT: FT 300 ASN cc_start: 0.7009 (m-40) cc_final: 0.6564 (m110) REVERT: FX 386 GLN cc_start: 0.8636 (tp40) cc_final: 0.8304 (tp40) REVERT: FY 1685 LYS cc_start: 0.7071 (mmtm) cc_final: 0.6706 (mmtm) REVERT: GT 201 THR cc_start: 0.8240 (p) cc_final: 0.7861 (t) REVERT: GT 216 ASN cc_start: 0.7803 (m110) cc_final: 0.7462 (m110) REVERT: GT 292 GLU cc_start: 0.7672 (tp30) cc_final: 0.6907 (mt-10) REVERT: GT 296 GLU cc_start: 0.7848 (tm-30) cc_final: 0.7362 (tm-30) REVERT: GT 300 ASN cc_start: 0.6718 (m-40) cc_final: 0.6213 (m110) REVERT: GX 374 LYS cc_start: 0.7817 (ptmm) cc_final: 0.7455 (ptpp) REVERT: GX 410 ARG cc_start: 0.7232 (mtm110) cc_final: 0.6838 (mtm110) REVERT: GX 459 MET cc_start: 0.8763 (mtp) cc_final: 0.8381 (mtp) REVERT: GY 1685 LYS cc_start: 0.7017 (mmtm) cc_final: 0.6677 (mmtt) REVERT: HT 49 GLU cc_start: 0.7487 (mp0) cc_final: 0.7185 (mp0) REVERT: HT 64 GLN cc_start: 0.8148 (tt0) cc_final: 0.7550 (mt0) REVERT: HT 194 LYS cc_start: 0.7843 (pttm) cc_final: 0.7346 (tptp) REVERT: HT 208 GLN cc_start: 0.7711 (tp40) cc_final: 0.7441 (tp40) REVERT: HT 216 ASN cc_start: 0.7615 (m110) cc_final: 0.7347 (m-40) REVERT: HT 292 GLU cc_start: 0.7868 (tp30) cc_final: 0.6907 (mt-10) REVERT: HT 296 GLU cc_start: 0.7844 (tm-30) cc_final: 0.6991 (tm-30) REVERT: HT 300 ASN cc_start: 0.6874 (m-40) cc_final: 0.6463 (m-40) REVERT: HT 301 GLN cc_start: 0.7449 (tp40) cc_final: 0.6918 (mm110) REVERT: HX 386 GLN cc_start: 0.8410 (tm-30) cc_final: 0.8112 (tp40) REVERT: HY 1795 MET cc_start: 0.7718 (tpp) cc_final: 0.7452 (tpp) REVERT: HY 1854 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.7711 (mpp) REVERT: HY 1907 GLN cc_start: 0.7769 (tt0) cc_final: 0.7307 (tt0) REVERT: IT 49 GLU cc_start: 0.7406 (mp0) cc_final: 0.7085 (mp0) REVERT: IT 64 GLN cc_start: 0.8036 (tt0) cc_final: 0.7483 (mt0) REVERT: IT 67 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9145 (mt) REVERT: IT 194 LYS cc_start: 0.7978 (pttm) cc_final: 0.7507 (tptp) REVERT: IT 209 GLU cc_start: 0.7202 (tm-30) cc_final: 0.6590 (tp30) REVERT: IT 210 TYR cc_start: 0.8228 (t80) cc_final: 0.7957 (t80) REVERT: IT 296 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7674 (tm-30) REVERT: IX 371 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7270 (tm-30) REVERT: IX 410 ARG cc_start: 0.7727 (ptp-170) cc_final: 0.7237 (mtm110) REVERT: IY 1873 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8016 (pm20) REVERT: IY 1907 GLN cc_start: 0.7584 (tt0) cc_final: 0.7225 (tt0) REVERT: JT 210 TYR cc_start: 0.8302 (t80) cc_final: 0.8058 (t80) REVERT: JT 216 ASN cc_start: 0.7685 (m110) cc_final: 0.7358 (m110) REVERT: JT 296 GLU cc_start: 0.7820 (tm-30) cc_final: 0.7129 (tm-30) REVERT: JT 300 ASN cc_start: 0.6457 (m-40) cc_final: 0.5973 (m-40) REVERT: JX 410 ARG cc_start: 0.7751 (ptp-170) cc_final: 0.7376 (ptt-90) REVERT: JX 474 GLU cc_start: 0.8049 (tp30) cc_final: 0.7842 (tp30) REVERT: JX 484 LEU cc_start: 0.9170 (tp) cc_final: 0.8935 (tp) REVERT: KT 49 GLU cc_start: 0.7479 (mp0) cc_final: 0.7176 (mp0) REVERT: KT 59 THR cc_start: 0.8835 (m) cc_final: 0.8584 (m) REVERT: KT 194 LYS cc_start: 0.7864 (pttm) cc_final: 0.7339 (tptp) REVERT: KT 208 GLN cc_start: 0.7595 (tp40) cc_final: 0.7344 (tp-100) REVERT: KT 209 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7801 (tp30) REVERT: KT 292 GLU cc_start: 0.8025 (tp30) cc_final: 0.6904 (mt-10) REVERT: KT 296 GLU cc_start: 0.7802 (tm-30) cc_final: 0.6919 (tm-30) REVERT: KT 297 TYR cc_start: 0.7711 (t80) cc_final: 0.7492 (t80) REVERT: KT 300 ASN cc_start: 0.6966 (m-40) cc_final: 0.6536 (m-40) REVERT: KX 371 GLU cc_start: 0.7854 (tm-30) cc_final: 0.7380 (tm-30) REVERT: KX 378 ASP cc_start: 0.8335 (m-30) cc_final: 0.7832 (t0) REVERT: KX 386 GLN cc_start: 0.8474 (tm-30) cc_final: 0.8220 (tp40) REVERT: KX 409 LYS cc_start: 0.7513 (ttmt) cc_final: 0.7278 (ttpt) REVERT: KX 509 LEU cc_start: 0.9132 (mt) cc_final: 0.8774 (mt) REVERT: KY 1739 TYR cc_start: 0.9088 (m-80) cc_final: 0.8766 (m-80) REVERT: KY 1772 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8187 (pp) REVERT: LT 49 GLU cc_start: 0.7529 (mp0) cc_final: 0.7210 (mp0) REVERT: LT 194 LYS cc_start: 0.7687 (pttm) cc_final: 0.7301 (tptp) REVERT: LT 201 THR cc_start: 0.8153 (p) cc_final: 0.7793 (t) REVERT: LT 210 TYR cc_start: 0.8222 (t80) cc_final: 0.8018 (t80) REVERT: LT 216 ASN cc_start: 0.7768 (m110) cc_final: 0.7424 (m110) REVERT: LT 292 GLU cc_start: 0.7712 (tp30) cc_final: 0.6852 (mt-10) REVERT: LT 296 GLU cc_start: 0.7575 (tm-30) cc_final: 0.7192 (tm-30) REVERT: LT 300 ASN cc_start: 0.6913 (m-40) cc_final: 0.6476 (m110) REVERT: LX 378 ASP cc_start: 0.8310 (m-30) cc_final: 0.7722 (t0) REVERT: LY 1739 TYR cc_start: 0.9027 (m-80) cc_final: 0.8743 (m-80) REVERT: MT 49 GLU cc_start: 0.7414 (mp0) cc_final: 0.7190 (mp0) REVERT: MT 194 LYS cc_start: 0.7831 (pttm) cc_final: 0.7443 (tptp) REVERT: MT 296 GLU cc_start: 0.7575 (tm-30) cc_final: 0.7092 (tm-30) REVERT: MT 300 ASN cc_start: 0.7075 (m-40) cc_final: 0.6676 (m110) REVERT: MX 378 ASP cc_start: 0.8190 (m-30) cc_final: 0.7549 (t0) REVERT: MX 386 GLN cc_start: 0.8613 (tp40) cc_final: 0.8252 (tp40) REVERT: MX 405 GLN cc_start: 0.7933 (pt0) cc_final: 0.7388 (pt0) REVERT: MX 415 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.8002 (mmm) REVERT: MY 1685 LYS cc_start: 0.7057 (mmtm) cc_final: 0.6698 (mmtm) REVERT: NT 216 ASN cc_start: 0.7722 (m110) cc_final: 0.7381 (m-40) REVERT: NT 296 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7296 (tm-30) REVERT: NT 300 ASN cc_start: 0.6950 (m-40) cc_final: 0.6509 (m110) REVERT: NX 374 LYS cc_start: 0.7827 (ptmm) cc_final: 0.7470 (ptpp) REVERT: NX 409 LYS cc_start: 0.7389 (ttmt) cc_final: 0.7169 (ttpt) REVERT: NX 459 MET cc_start: 0.8763 (mtp) cc_final: 0.8370 (mtp) REVERT: NY 1685 LYS cc_start: 0.7020 (mmtm) cc_final: 0.6678 (mmtt) outliers start: 200 outliers final: 149 residues processed: 1686 average time/residue: 0.5939 time to fit residues: 1677.9424 Evaluate side-chains 1666 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 1507 time to evaluate : 5.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AT residue 35 VAL Chi-restraints excluded: chain AT residue 80 VAL Chi-restraints excluded: chain AT residue 136 SER Chi-restraints excluded: chain AT residue 173 VAL Chi-restraints excluded: chain AX residue 411 SER Chi-restraints excluded: chain AY residue 1711 THR Chi-restraints excluded: chain AY residue 1725 MET Chi-restraints excluded: chain AY residue 1751 ILE Chi-restraints excluded: chain AY residue 1752 MET Chi-restraints excluded: chain BT residue 29 VAL Chi-restraints excluded: chain BT residue 35 VAL Chi-restraints excluded: chain BT residue 67 LEU Chi-restraints excluded: chain BT residue 80 VAL Chi-restraints excluded: chain BT residue 136 SER Chi-restraints excluded: chain BT residue 173 VAL Chi-restraints excluded: chain BX residue 415 MET Chi-restraints excluded: chain BX residue 459 MET Chi-restraints excluded: chain BX residue 508 GLU Chi-restraints excluded: chain BY residue 1711 THR Chi-restraints excluded: chain BY residue 1725 MET Chi-restraints excluded: chain BY residue 1751 ILE Chi-restraints excluded: chain BY residue 1809 SER Chi-restraints excluded: chain BY residue 1873 GLU Chi-restraints excluded: chain BY residue 1879 ILE Chi-restraints excluded: chain CT residue 29 VAL Chi-restraints excluded: chain CT residue 52 LEU Chi-restraints excluded: chain CT residue 65 VAL Chi-restraints excluded: chain CT residue 80 VAL Chi-restraints excluded: chain CT residue 136 SER Chi-restraints excluded: chain CT residue 173 VAL Chi-restraints excluded: chain CT residue 196 ASN Chi-restraints excluded: chain CX residue 383 LEU Chi-restraints excluded: chain CX residue 415 MET Chi-restraints excluded: chain CX residue 508 GLU Chi-restraints excluded: chain CY residue 1711 THR Chi-restraints excluded: chain CY residue 1746 LYS Chi-restraints excluded: chain CY residue 1873 GLU Chi-restraints excluded: chain CY residue 1904 ILE Chi-restraints excluded: chain DT residue 52 LEU Chi-restraints excluded: chain DT residue 80 VAL Chi-restraints excluded: chain DT residue 93 ILE Chi-restraints excluded: chain DT residue 136 SER Chi-restraints excluded: chain DT residue 173 VAL Chi-restraints excluded: chain DX residue 383 LEU Chi-restraints excluded: chain DX residue 415 MET Chi-restraints excluded: chain DX residue 418 GLU Chi-restraints excluded: chain DY residue 1711 THR Chi-restraints excluded: chain DY residue 1725 MET Chi-restraints excluded: chain DY residue 1772 LEU Chi-restraints excluded: chain DY residue 1809 SER Chi-restraints excluded: chain DY residue 1873 GLU Chi-restraints excluded: chain DY residue 1879 ILE Chi-restraints excluded: chain DY residue 1880 LEU Chi-restraints excluded: chain DY residue 1903 GLU Chi-restraints excluded: chain ET residue 80 VAL Chi-restraints excluded: chain ET residue 136 SER Chi-restraints excluded: chain ET residue 173 VAL Chi-restraints excluded: chain EX residue 368 ILE Chi-restraints excluded: chain EX residue 385 THR Chi-restraints excluded: chain EX residue 508 GLU Chi-restraints excluded: chain EY residue 1711 THR Chi-restraints excluded: chain EY residue 1713 ILE Chi-restraints excluded: chain FT residue 80 VAL Chi-restraints excluded: chain FT residue 136 SER Chi-restraints excluded: chain FT residue 173 VAL Chi-restraints excluded: chain FX residue 383 LEU Chi-restraints excluded: chain FX residue 415 MET Chi-restraints excluded: chain FX residue 508 GLU Chi-restraints excluded: chain FY residue 1711 THR Chi-restraints excluded: chain FY residue 1713 ILE Chi-restraints excluded: chain FY residue 1724 ASN Chi-restraints excluded: chain FY residue 1751 ILE Chi-restraints excluded: chain FY residue 1752 MET Chi-restraints excluded: chain FY residue 1809 SER Chi-restraints excluded: chain GT residue 80 VAL Chi-restraints excluded: chain GT residue 136 SER Chi-restraints excluded: chain GT residue 173 VAL Chi-restraints excluded: chain GX residue 415 MET Chi-restraints excluded: chain GY residue 1711 THR Chi-restraints excluded: chain GY residue 1725 MET Chi-restraints excluded: chain HT residue 29 VAL Chi-restraints excluded: chain HT residue 80 VAL Chi-restraints excluded: chain HT residue 136 SER Chi-restraints excluded: chain HT residue 173 VAL Chi-restraints excluded: chain HX residue 383 LEU Chi-restraints excluded: chain HX residue 411 SER Chi-restraints excluded: chain HY residue 1711 THR Chi-restraints excluded: chain HY residue 1724 ASN Chi-restraints excluded: chain HY residue 1751 ILE Chi-restraints excluded: chain HY residue 1752 MET Chi-restraints excluded: chain HY residue 1809 SER Chi-restraints excluded: chain HY residue 1854 MET Chi-restraints excluded: chain IT residue 35 VAL Chi-restraints excluded: chain IT residue 67 LEU Chi-restraints excluded: chain IT residue 80 VAL Chi-restraints excluded: chain IT residue 136 SER Chi-restraints excluded: chain IT residue 173 VAL Chi-restraints excluded: chain IX residue 375 ILE Chi-restraints excluded: chain IX residue 383 LEU Chi-restraints excluded: chain IX residue 415 MET Chi-restraints excluded: chain IX residue 508 GLU Chi-restraints excluded: chain IY residue 1711 THR Chi-restraints excluded: chain IY residue 1725 MET Chi-restraints excluded: chain IY residue 1751 ILE Chi-restraints excluded: chain IY residue 1809 SER Chi-restraints excluded: chain IY residue 1873 GLU Chi-restraints excluded: chain JT residue 29 VAL Chi-restraints excluded: chain JT residue 52 LEU Chi-restraints excluded: chain JT residue 80 VAL Chi-restraints excluded: chain JT residue 82 LEU Chi-restraints excluded: chain JT residue 136 SER Chi-restraints excluded: chain JT residue 173 VAL Chi-restraints excluded: chain JX residue 488 ILE Chi-restraints excluded: chain JX residue 508 GLU Chi-restraints excluded: chain JY residue 1711 THR Chi-restraints excluded: chain JY residue 1746 LYS Chi-restraints excluded: chain JY residue 1873 GLU Chi-restraints excluded: chain KT residue 52 LEU Chi-restraints excluded: chain KT residue 80 VAL Chi-restraints excluded: chain KT residue 136 SER Chi-restraints excluded: chain KT residue 173 VAL Chi-restraints excluded: chain KX residue 415 MET Chi-restraints excluded: chain KX residue 417 SER Chi-restraints excluded: chain KX residue 418 GLU Chi-restraints excluded: chain KX residue 449 SER Chi-restraints excluded: chain KX residue 497 LEU Chi-restraints excluded: chain KX residue 508 GLU Chi-restraints excluded: chain KY residue 1711 THR Chi-restraints excluded: chain KY residue 1772 LEU Chi-restraints excluded: chain KY residue 1873 GLU Chi-restraints excluded: chain KY residue 1879 ILE Chi-restraints excluded: chain KY residue 1880 LEU Chi-restraints excluded: chain LT residue 67 LEU Chi-restraints excluded: chain LT residue 80 VAL Chi-restraints excluded: chain LT residue 136 SER Chi-restraints excluded: chain LT residue 173 VAL Chi-restraints excluded: chain LX residue 383 LEU Chi-restraints excluded: chain LX residue 385 THR Chi-restraints excluded: chain LX residue 508 GLU Chi-restraints excluded: chain LY residue 1711 THR Chi-restraints excluded: chain LY residue 1713 ILE Chi-restraints excluded: chain LY residue 1752 MET Chi-restraints excluded: chain MT residue 80 VAL Chi-restraints excluded: chain MT residue 136 SER Chi-restraints excluded: chain MT residue 173 VAL Chi-restraints excluded: chain MX residue 383 LEU Chi-restraints excluded: chain MX residue 415 MET Chi-restraints excluded: chain MX residue 508 GLU Chi-restraints excluded: chain MY residue 1711 THR Chi-restraints excluded: chain MY residue 1713 ILE Chi-restraints excluded: chain MY residue 1724 ASN Chi-restraints excluded: chain MY residue 1751 ILE Chi-restraints excluded: chain MY residue 1752 MET Chi-restraints excluded: chain MY residue 1809 SER Chi-restraints excluded: chain NT residue 80 VAL Chi-restraints excluded: chain NT residue 136 SER Chi-restraints excluded: chain NT residue 173 VAL Chi-restraints excluded: chain NX residue 415 MET Chi-restraints excluded: chain NY residue 1711 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 638 optimal weight: 5.9990 chunk 672 optimal weight: 2.9990 chunk 613 optimal weight: 0.6980 chunk 653 optimal weight: 3.9990 chunk 393 optimal weight: 0.9990 chunk 284 optimal weight: 2.9990 chunk 513 optimal weight: 0.8980 chunk 200 optimal weight: 0.8980 chunk 590 optimal weight: 6.9990 chunk 618 optimal weight: 1.9990 chunk 651 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AT 301 GLN BT 300 ASN BX 443 GLN ** BY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CT 196 ASN CY1856 ASN DT 301 GLN ** EX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** EX 443 GLN FT 33 ASN FT 208 GLN ** FY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** FY1856 ASN GT 64 GLN GT 208 GLN GX 432 ASN ** IX 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** IX 443 GLN ** IY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** JX 373 GLN JY1856 ASN ** KY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LX 432 ASN LX 443 GLN ** LY1856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** MX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** MY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** MY1856 ASN ** NT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NX 432 ASN NY1856 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 61992 Z= 0.243 Angle : 0.646 14.912 83594 Z= 0.338 Chirality : 0.046 0.193 9520 Planarity : 0.004 0.043 10598 Dihedral : 4.999 24.769 8134 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.64 % Allowed : 18.41 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.10), residues: 7406 helix: 1.41 (0.11), residues: 2240 sheet: -1.26 (0.12), residues: 1666 loop : -0.69 (0.11), residues: 3500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRPCX 466 HIS 0.003 0.000 HISCT 89 PHE 0.028 0.001 PHECT 109 TYR 0.021 0.001 TYRFT 73 ARG 0.007 0.000 ARGDX 394 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14812 Ramachandran restraints generated. 7406 Oldfield, 0 Emsley, 7406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14812 Ramachandran restraints generated. 7406 Oldfield, 0 Emsley, 7406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1781 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 1602 time to evaluate : 5.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AT 49 GLU cc_start: 0.7449 (mp0) cc_final: 0.7026 (mp0) REVERT: AT 64 GLN cc_start: 0.8151 (tt0) cc_final: 0.7556 (mt0) REVERT: AT 194 LYS cc_start: 0.7590 (pttm) cc_final: 0.7108 (tptp) REVERT: AT 208 GLN cc_start: 0.7511 (tp-100) cc_final: 0.7217 (tp40) REVERT: AT 292 GLU cc_start: 0.8071 (tp30) cc_final: 0.7099 (mt-10) REVERT: AT 296 GLU cc_start: 0.7775 (tm-30) cc_final: 0.7179 (tm-30) REVERT: AT 300 ASN cc_start: 0.6637 (m-40) cc_final: 0.6290 (m-40) REVERT: AX 386 GLN cc_start: 0.8408 (tm-30) cc_final: 0.8116 (tp40) REVERT: AX 405 GLN cc_start: 0.7854 (pt0) cc_final: 0.7362 (pt0) REVERT: AX 415 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7937 (mmm) REVERT: AY 1795 MET cc_start: 0.7698 (tpp) cc_final: 0.7491 (tpp) REVERT: BT 64 GLN cc_start: 0.7993 (tt0) cc_final: 0.7402 (mt0) REVERT: BT 67 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9061 (mt) REVERT: BT 193 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7436 (mt-10) REVERT: BT 194 LYS cc_start: 0.7796 (pttm) cc_final: 0.7479 (tptp) REVERT: BT 201 THR cc_start: 0.8346 (p) cc_final: 0.8079 (t) REVERT: BT 216 ASN cc_start: 0.7883 (m110) cc_final: 0.7495 (m110) REVERT: BT 300 ASN cc_start: 0.6629 (m-40) cc_final: 0.6348 (m110) REVERT: BX 369 ARG cc_start: 0.7733 (mmm160) cc_final: 0.7402 (mtt-85) REVERT: BX 371 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7271 (tm-30) REVERT: BX 384 GLU cc_start: 0.8230 (tt0) cc_final: 0.7826 (tt0) REVERT: BX 401 TYR cc_start: 0.8956 (m-80) cc_final: 0.8567 (m-80) REVERT: BX 410 ARG cc_start: 0.7700 (ptp-170) cc_final: 0.7372 (mtm110) REVERT: BY 1739 TYR cc_start: 0.9011 (m-80) cc_final: 0.8693 (m-80) REVERT: BY 1873 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7774 (pm20) REVERT: CT 49 GLU cc_start: 0.7387 (mp0) cc_final: 0.7119 (mp0) REVERT: CT 208 GLN cc_start: 0.7762 (tp40) cc_final: 0.7412 (tp40) REVERT: CT 209 GLU cc_start: 0.8278 (mm-30) cc_final: 0.8034 (tm-30) REVERT: CT 216 ASN cc_start: 0.7724 (m110) cc_final: 0.7325 (m110) REVERT: CT 292 GLU cc_start: 0.8012 (tp30) cc_final: 0.7014 (mt-10) REVERT: CT 296 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7547 (tm-30) REVERT: CT 300 ASN cc_start: 0.6616 (m-40) cc_final: 0.6173 (m110) REVERT: CX 371 GLU cc_start: 0.7684 (tm-30) cc_final: 0.7305 (tm-30) REVERT: CX 374 LYS cc_start: 0.7695 (ptmm) cc_final: 0.7361 (ptpp) REVERT: CX 386 GLN cc_start: 0.8461 (tm-30) cc_final: 0.8244 (tp40) REVERT: CX 410 ARG cc_start: 0.7186 (mtm110) cc_final: 0.6850 (mtm110) REVERT: CY 1739 TYR cc_start: 0.8929 (m-80) cc_final: 0.8660 (m-80) REVERT: CY 1783 GLU cc_start: 0.8777 (pm20) cc_final: 0.8550 (pm20) REVERT: DT 49 GLU cc_start: 0.7483 (mp0) cc_final: 0.7246 (mp0) REVERT: DT 194 LYS cc_start: 0.7804 (pttm) cc_final: 0.7356 (tptp) REVERT: DT 296 GLU cc_start: 0.7776 (tm-30) cc_final: 0.6979 (tm-30) REVERT: DT 300 ASN cc_start: 0.7052 (m-40) cc_final: 0.6595 (m-40) REVERT: DX 410 ARG cc_start: 0.7250 (mtm110) cc_final: 0.7049 (mtm110) REVERT: DX 509 LEU cc_start: 0.9117 (mt) cc_final: 0.8700 (mt) REVERT: DY 1772 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8056 (pp) REVERT: DY 1795 MET cc_start: 0.7769 (tpp) cc_final: 0.7566 (tpp) REVERT: DY 1903 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.8084 (tm-30) REVERT: DY 1904 ILE cc_start: 0.8362 (mt) cc_final: 0.7987 (mt) REVERT: ET 49 GLU cc_start: 0.7328 (mp0) cc_final: 0.7034 (mp0) REVERT: ET 64 GLN cc_start: 0.7990 (tt0) cc_final: 0.7434 (mt0) REVERT: ET 194 LYS cc_start: 0.7800 (pttm) cc_final: 0.7422 (tptp) REVERT: ET 209 GLU cc_start: 0.7384 (tm-30) cc_final: 0.6357 (tp30) REVERT: ET 210 TYR cc_start: 0.8031 (t80) cc_final: 0.7631 (t80) REVERT: ET 292 GLU cc_start: 0.7652 (tp30) cc_final: 0.6846 (mt-10) REVERT: ET 296 GLU cc_start: 0.7505 (tm-30) cc_final: 0.7130 (tm-30) REVERT: ET 300 ASN cc_start: 0.6852 (m-40) cc_final: 0.6330 (m110) REVERT: ET 301 GLN cc_start: 0.7461 (tp40) cc_final: 0.6761 (mm110) REVERT: EX 378 ASP cc_start: 0.8251 (m-30) cc_final: 0.7704 (t0) REVERT: EX 387 TYR cc_start: 0.8373 (t80) cc_final: 0.7967 (t80) REVERT: EY 1739 TYR cc_start: 0.9001 (m-80) cc_final: 0.8730 (m-80) REVERT: FT 194 LYS cc_start: 0.7809 (pttm) cc_final: 0.7432 (tptp) REVERT: FT 292 GLU cc_start: 0.7697 (tp30) cc_final: 0.6881 (mt-10) REVERT: FT 296 GLU cc_start: 0.7561 (tm-30) cc_final: 0.6970 (tm-30) REVERT: FT 300 ASN cc_start: 0.7153 (m-40) cc_final: 0.6697 (m110) REVERT: FX 386 GLN cc_start: 0.8635 (tp40) cc_final: 0.8296 (tp40) REVERT: FX 410 ARG cc_start: 0.8141 (ttp-110) cc_final: 0.7449 (ptt-90) REVERT: FY 1685 LYS cc_start: 0.7060 (mmtm) cc_final: 0.6641 (mmtm) REVERT: GT 201 THR cc_start: 0.8208 (p) cc_final: 0.7834 (t) REVERT: GT 216 ASN cc_start: 0.7754 (m110) cc_final: 0.7474 (m-40) REVERT: GT 292 GLU cc_start: 0.7703 (tp30) cc_final: 0.6926 (mt-10) REVERT: GT 296 GLU cc_start: 0.7818 (tm-30) cc_final: 0.6930 (tm-30) REVERT: GT 300 ASN cc_start: 0.6842 (m-40) cc_final: 0.6330 (m110) REVERT: GX 374 LYS cc_start: 0.7832 (ptmm) cc_final: 0.7470 (ptpp) REVERT: GX 409 LYS cc_start: 0.7442 (ttmt) cc_final: 0.6917 (ttpt) REVERT: GX 410 ARG cc_start: 0.7128 (mtm110) cc_final: 0.6832 (mtm110) REVERT: GX 459 MET cc_start: 0.8705 (mtp) cc_final: 0.8356 (mtp) REVERT: GY 1685 LYS cc_start: 0.6968 (mmtm) cc_final: 0.6628 (mmtt) REVERT: HT 64 GLN cc_start: 0.8148 (tt0) cc_final: 0.7564 (mt0) REVERT: HT 194 LYS cc_start: 0.7813 (pttm) cc_final: 0.7310 (tptp) REVERT: HT 201 THR cc_start: 0.8381 (p) cc_final: 0.7996 (t) REVERT: HT 208 GLN cc_start: 0.7695 (tp40) cc_final: 0.7414 (tp40) REVERT: HT 216 ASN cc_start: 0.7591 (m110) cc_final: 0.7320 (m110) REVERT: HT 296 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7115 (tm-30) REVERT: HT 300 ASN cc_start: 0.6851 (m-40) cc_final: 0.6503 (m-40) REVERT: HT 301 GLN cc_start: 0.7391 (tp40) cc_final: 0.6867 (mm110) REVERT: HX 386 GLN cc_start: 0.8404 (tm-30) cc_final: 0.8120 (tp40) REVERT: HY 1795 MET cc_start: 0.7697 (tpp) cc_final: 0.7475 (tpp) REVERT: HY 1854 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.7824 (mpp) REVERT: IT 64 GLN cc_start: 0.8006 (tt0) cc_final: 0.7399 (mt0) REVERT: IT 67 LEU cc_start: 0.9405 (OUTLIER) cc_final: 0.9099 (mt) REVERT: IT 194 LYS cc_start: 0.7798 (pttm) cc_final: 0.7471 (tptp) REVERT: IT 209 GLU cc_start: 0.7090 (tm-30) cc_final: 0.6539 (tp30) REVERT: IT 210 TYR cc_start: 0.8175 (t80) cc_final: 0.7914 (t80) REVERT: IT 216 ASN cc_start: 0.7780 (m110) cc_final: 0.7455 (m110) REVERT: IT 296 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7164 (tm-30) REVERT: IT 300 ASN cc_start: 0.6910 (m-40) cc_final: 0.6297 (m-40) REVERT: IX 371 GLU cc_start: 0.7717 (tm-30) cc_final: 0.7264 (tm-30) REVERT: IX 384 GLU cc_start: 0.8324 (tt0) cc_final: 0.7950 (tt0) REVERT: IX 410 ARG cc_start: 0.7674 (ptp-170) cc_final: 0.7104 (ptt-90) REVERT: IY 1873 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7805 (pm20) REVERT: IY 1907 GLN cc_start: 0.7544 (tt0) cc_final: 0.7228 (tt0) REVERT: JT 216 ASN cc_start: 0.7647 (m110) cc_final: 0.7328 (m110) REVERT: JT 292 GLU cc_start: 0.8021 (tp30) cc_final: 0.7007 (mt-10) REVERT: JT 296 GLU cc_start: 0.7809 (tm-30) cc_final: 0.7101 (tm-30) REVERT: JT 300 ASN cc_start: 0.6346 (m-40) cc_final: 0.5898 (m-40) REVERT: JX 410 ARG cc_start: 0.7704 (ptp-170) cc_final: 0.7301 (ptt-90) REVERT: JX 484 LEU cc_start: 0.9158 (tp) cc_final: 0.8925 (tp) REVERT: JY 1739 TYR cc_start: 0.8933 (m-80) cc_final: 0.8647 (m-80) REVERT: KT 49 GLU cc_start: 0.7438 (mp0) cc_final: 0.7130 (mp0) REVERT: KT 59 THR cc_start: 0.8781 (m) cc_final: 0.8530 (m) REVERT: KT 194 LYS cc_start: 0.7732 (pttm) cc_final: 0.7228 (tptp) REVERT: KT 208 GLN cc_start: 0.7629 (tp40) cc_final: 0.7413 (tp-100) REVERT: KT 209 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7791 (tp30) REVERT: KT 292 GLU cc_start: 0.7936 (tp30) cc_final: 0.6839 (mt-10) REVERT: KT 296 GLU cc_start: 0.7826 (tm-30) cc_final: 0.6700 (tm-30) REVERT: KT 300 ASN cc_start: 0.6878 (m-40) cc_final: 0.6383 (m110) REVERT: KX 371 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7378 (tm-30) REVERT: KX 378 ASP cc_start: 0.8280 (m-30) cc_final: 0.7709 (t0) REVERT: KX 386 GLN cc_start: 0.8483 (tm-30) cc_final: 0.8185 (tp40) REVERT: KX 409 LYS cc_start: 0.7109 (ttmt) cc_final: 0.6896 (ttpt) REVERT: KX 509 LEU cc_start: 0.9065 (mt) cc_final: 0.8727 (mt) REVERT: KY 1695 TYR cc_start: 0.9161 (m-80) cc_final: 0.8932 (m-80) REVERT: KY 1739 TYR cc_start: 0.9017 (m-80) cc_final: 0.8672 (m-80) REVERT: KY 1772 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8069 (pp) REVERT: KY 1795 MET cc_start: 0.7771 (tpp) cc_final: 0.7568 (tpp) REVERT: LT 49 GLU cc_start: 0.7455 (mp0) cc_final: 0.7149 (mp0) REVERT: LT 194 LYS cc_start: 0.7622 (pttm) cc_final: 0.7238 (tptp) REVERT: LT 216 ASN cc_start: 0.7717 (m110) cc_final: 0.7393 (m110) REVERT: LT 292 GLU cc_start: 0.7663 (tp30) cc_final: 0.6839 (mt-10) REVERT: LT 296 GLU cc_start: 0.7562 (tm-30) cc_final: 0.7185 (tm-30) REVERT: LT 300 ASN cc_start: 0.6876 (m-40) cc_final: 0.6448 (m110) REVERT: LX 378 ASP cc_start: 0.8279 (m-30) cc_final: 0.7723 (t0) REVERT: LX 387 TYR cc_start: 0.8340 (t80) cc_final: 0.7931 (t80) REVERT: LY 1739 TYR cc_start: 0.9007 (m-80) cc_final: 0.8731 (m-80) REVERT: MT 49 GLU cc_start: 0.7391 (mp0) cc_final: 0.7161 (mp0) REVERT: MT 194 LYS cc_start: 0.7765 (pttm) cc_final: 0.7403 (tptp) REVERT: MT 209 GLU cc_start: 0.7492 (tm-30) cc_final: 0.6418 (tp30) REVERT: MT 296 GLU cc_start: 0.7585 (tm-30) cc_final: 0.6865 (tm-30) REVERT: MT 300 ASN cc_start: 0.7066 (m-40) cc_final: 0.6687 (m-40) REVERT: MX 378 ASP cc_start: 0.8216 (m-30) cc_final: 0.7552 (t0) REVERT: MX 386 GLN cc_start: 0.8635 (tp40) cc_final: 0.8277 (tp40) REVERT: MX 415 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.8140 (mmm) REVERT: MY 1685 LYS cc_start: 0.7058 (mmtm) cc_final: 0.6702 (mmtm) REVERT: NT 216 ASN cc_start: 0.7698 (m110) cc_final: 0.7395 (m-40) REVERT: NT 296 GLU cc_start: 0.7638 (tm-30) cc_final: 0.7406 (tm-30) REVERT: NT 300 ASN cc_start: 0.6916 (m-40) cc_final: 0.6549 (m110) REVERT: NX 374 LYS cc_start: 0.7815 (ptmm) cc_final: 0.7467 (ptpp) REVERT: NX 409 LYS cc_start: 0.7101 (ttmt) cc_final: 0.6863 (ttpt) REVERT: NX 459 MET cc_start: 0.8705 (mtp) cc_final: 0.8361 (mtp) REVERT: NY 1685 LYS cc_start: 0.6969 (mmtm) cc_final: 0.6626 (mmtt) REVERT: NY 1873 GLU cc_start: 0.7192 (mt-10) cc_final: 0.6717 (mt-10) outliers start: 179 outliers final: 143 residues processed: 1703 average time/residue: 0.5851 time to fit residues: 1674.3812 Evaluate side-chains 1696 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 1543 time to evaluate : 5.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AT residue 35 VAL Chi-restraints excluded: chain AT residue 80 VAL Chi-restraints excluded: chain AT residue 136 SER Chi-restraints excluded: chain AT residue 173 VAL Chi-restraints excluded: chain AX residue 411 SER Chi-restraints excluded: chain AX residue 415 MET Chi-restraints excluded: chain AY residue 1711 THR Chi-restraints excluded: chain AY residue 1725 MET Chi-restraints excluded: chain AY residue 1751 ILE Chi-restraints excluded: chain AY residue 1752 MET Chi-restraints excluded: chain BT residue 29 VAL Chi-restraints excluded: chain BT residue 35 VAL Chi-restraints excluded: chain BT residue 67 LEU Chi-restraints excluded: chain BT residue 80 VAL Chi-restraints excluded: chain BT residue 136 SER Chi-restraints excluded: chain BT residue 173 VAL Chi-restraints excluded: chain BX residue 383 LEU Chi-restraints excluded: chain BX residue 415 MET Chi-restraints excluded: chain BX residue 459 MET Chi-restraints excluded: chain BX residue 508 GLU Chi-restraints excluded: chain BY residue 1711 THR Chi-restraints excluded: chain BY residue 1725 MET Chi-restraints excluded: chain BY residue 1751 ILE Chi-restraints excluded: chain BY residue 1809 SER Chi-restraints excluded: chain BY residue 1873 GLU Chi-restraints excluded: chain BY residue 1879 ILE Chi-restraints excluded: chain CT residue 29 VAL Chi-restraints excluded: chain CT residue 65 VAL Chi-restraints excluded: chain CT residue 80 VAL Chi-restraints excluded: chain CT residue 82 LEU Chi-restraints excluded: chain CT residue 136 SER Chi-restraints excluded: chain CT residue 173 VAL Chi-restraints excluded: chain CX residue 415 MET Chi-restraints excluded: chain CX residue 508 GLU Chi-restraints excluded: chain CY residue 1711 THR Chi-restraints excluded: chain CY residue 1746 LYS Chi-restraints excluded: chain CY residue 1873 GLU Chi-restraints excluded: chain CY residue 1904 ILE Chi-restraints excluded: chain DT residue 29 VAL Chi-restraints excluded: chain DT residue 52 LEU Chi-restraints excluded: chain DT residue 80 VAL Chi-restraints excluded: chain DT residue 136 SER Chi-restraints excluded: chain DT residue 173 VAL Chi-restraints excluded: chain DX residue 383 LEU Chi-restraints excluded: chain DX residue 415 MET Chi-restraints excluded: chain DX residue 418 GLU Chi-restraints excluded: chain DY residue 1711 THR Chi-restraints excluded: chain DY residue 1725 MET Chi-restraints excluded: chain DY residue 1772 LEU Chi-restraints excluded: chain DY residue 1809 SER Chi-restraints excluded: chain DY residue 1873 GLU Chi-restraints excluded: chain DY residue 1879 ILE Chi-restraints excluded: chain DY residue 1903 GLU Chi-restraints excluded: chain ET residue 80 VAL Chi-restraints excluded: chain ET residue 136 SER Chi-restraints excluded: chain ET residue 173 VAL Chi-restraints excluded: chain EX residue 383 LEU Chi-restraints excluded: chain EX residue 385 THR Chi-restraints excluded: chain EX residue 388 VAL Chi-restraints excluded: chain EX residue 508 GLU Chi-restraints excluded: chain EY residue 1711 THR Chi-restraints excluded: chain EY residue 1713 ILE Chi-restraints excluded: chain EY residue 1724 ASN Chi-restraints excluded: chain FT residue 33 ASN Chi-restraints excluded: chain FT residue 80 VAL Chi-restraints excluded: chain FT residue 136 SER Chi-restraints excluded: chain FT residue 173 VAL Chi-restraints excluded: chain FX residue 383 LEU Chi-restraints excluded: chain FX residue 415 MET Chi-restraints excluded: chain FX residue 508 GLU Chi-restraints excluded: chain FY residue 1711 THR Chi-restraints excluded: chain FY residue 1713 ILE Chi-restraints excluded: chain FY residue 1724 ASN Chi-restraints excluded: chain FY residue 1751 ILE Chi-restraints excluded: chain FY residue 1752 MET Chi-restraints excluded: chain FY residue 1809 SER Chi-restraints excluded: chain GT residue 80 VAL Chi-restraints excluded: chain GT residue 136 SER Chi-restraints excluded: chain GT residue 173 VAL Chi-restraints excluded: chain GX residue 415 MET Chi-restraints excluded: chain GY residue 1711 THR Chi-restraints excluded: chain GY residue 1725 MET Chi-restraints excluded: chain HT residue 29 VAL Chi-restraints excluded: chain HT residue 80 VAL Chi-restraints excluded: chain HT residue 136 SER Chi-restraints excluded: chain HT residue 173 VAL Chi-restraints excluded: chain HX residue 383 LEU Chi-restraints excluded: chain HY residue 1711 THR Chi-restraints excluded: chain HY residue 1751 ILE Chi-restraints excluded: chain HY residue 1752 MET Chi-restraints excluded: chain HY residue 1854 MET Chi-restraints excluded: chain IT residue 35 VAL Chi-restraints excluded: chain IT residue 67 LEU Chi-restraints excluded: chain IT residue 80 VAL Chi-restraints excluded: chain IT residue 136 SER Chi-restraints excluded: chain IT residue 173 VAL Chi-restraints excluded: chain IX residue 375 ILE Chi-restraints excluded: chain IX residue 383 LEU Chi-restraints excluded: chain IX residue 415 MET Chi-restraints excluded: chain IX residue 508 GLU Chi-restraints excluded: chain IY residue 1711 THR Chi-restraints excluded: chain IY residue 1725 MET Chi-restraints excluded: chain IY residue 1751 ILE Chi-restraints excluded: chain IY residue 1809 SER Chi-restraints excluded: chain IY residue 1873 GLU Chi-restraints excluded: chain JT residue 29 VAL Chi-restraints excluded: chain JT residue 80 VAL Chi-restraints excluded: chain JT residue 82 LEU Chi-restraints excluded: chain JT residue 136 SER Chi-restraints excluded: chain JT residue 173 VAL Chi-restraints excluded: chain JX residue 488 ILE Chi-restraints excluded: chain JX residue 508 GLU Chi-restraints excluded: chain JY residue 1711 THR Chi-restraints excluded: chain JY residue 1746 LYS Chi-restraints excluded: chain JY residue 1873 GLU Chi-restraints excluded: chain KT residue 52 LEU Chi-restraints excluded: chain KT residue 80 VAL Chi-restraints excluded: chain KT residue 136 SER Chi-restraints excluded: chain KT residue 173 VAL Chi-restraints excluded: chain KX residue 415 MET Chi-restraints excluded: chain KX residue 418 GLU Chi-restraints excluded: chain KX residue 449 SER Chi-restraints excluded: chain KY residue 1711 THR Chi-restraints excluded: chain KY residue 1772 LEU Chi-restraints excluded: chain KY residue 1873 GLU Chi-restraints excluded: chain KY residue 1879 ILE Chi-restraints excluded: chain KY residue 1880 LEU Chi-restraints excluded: chain LT residue 67 LEU Chi-restraints excluded: chain LT residue 80 VAL Chi-restraints excluded: chain LT residue 136 SER Chi-restraints excluded: chain LT residue 173 VAL Chi-restraints excluded: chain LX residue 388 VAL Chi-restraints excluded: chain LX residue 508 GLU Chi-restraints excluded: chain LY residue 1711 THR Chi-restraints excluded: chain LY residue 1713 ILE Chi-restraints excluded: chain LY residue 1724 ASN Chi-restraints excluded: chain MT residue 80 VAL Chi-restraints excluded: chain MT residue 136 SER Chi-restraints excluded: chain MT residue 173 VAL Chi-restraints excluded: chain MX residue 383 LEU Chi-restraints excluded: chain MX residue 415 MET Chi-restraints excluded: chain MX residue 508 GLU Chi-restraints excluded: chain MY residue 1713 ILE Chi-restraints excluded: chain MY residue 1724 ASN Chi-restraints excluded: chain MY residue 1751 ILE Chi-restraints excluded: chain MY residue 1752 MET Chi-restraints excluded: chain MY residue 1809 SER Chi-restraints excluded: chain NT residue 80 VAL Chi-restraints excluded: chain NT residue 136 SER Chi-restraints excluded: chain NT residue 173 VAL Chi-restraints excluded: chain NT residue 221 LEU Chi-restraints excluded: chain NX residue 415 MET Chi-restraints excluded: chain NY residue 1711 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 429 optimal weight: 8.9990 chunk 691 optimal weight: 6.9990 chunk 422 optimal weight: 2.9990 chunk 328 optimal weight: 5.9990 chunk 480 optimal weight: 9.9990 chunk 725 optimal weight: 4.9990 chunk 667 optimal weight: 3.9990 chunk 577 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 446 optimal weight: 0.7980 chunk 354 optimal weight: 8.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AX 432 ASN ** BY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CY1856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CY1907 GLN ** EX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** EX 443 GLN ** EY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** FY1907 GLN GT 64 GLN GX 432 ASN GY1808 ASN ** IY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** JT 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** JY1856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** KT 301 GLN ** KY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** KY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LX 443 GLN ** LY1856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** MX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** MX 432 ASN ** NT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NT 197 GLN NT 208 GLN NX 432 ASN NY1808 ASN ** NY1856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 61992 Z= 0.382 Angle : 0.710 15.540 83594 Z= 0.371 Chirality : 0.049 0.197 9520 Planarity : 0.005 0.051 10598 Dihedral : 5.156 25.555 8134 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.58 % Allowed : 18.97 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.10), residues: 7406 helix: 1.30 (0.11), residues: 2240 sheet: -1.23 (0.12), residues: 1652 loop : -0.75 (0.10), residues: 3514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRPCX 466 HIS 0.003 0.001 HISGT 169 PHE 0.020 0.002 PHEKT 109 TYR 0.022 0.002 TYREY1695 ARG 0.015 0.001 ARGIX 394 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14812 Ramachandran restraints generated. 7406 Oldfield, 0 Emsley, 7406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14812 Ramachandran restraints generated. 7406 Oldfield, 0 Emsley, 7406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1681 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 1506 time to evaluate : 5.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: AT 49 GLU cc_start: 0.7412 (mp0) cc_final: 0.7002 (mp0) REVERT: AT 194 LYS cc_start: 0.7598 (pttm) cc_final: 0.7068 (tptp) REVERT: AT 292 GLU cc_start: 0.8042 (tp30) cc_final: 0.7056 (mt-10) REVERT: AT 296 GLU cc_start: 0.7687 (tm-30) cc_final: 0.7031 (tm-30) REVERT: AT 300 ASN cc_start: 0.6591 (m-40) cc_final: 0.6226 (m-40) REVERT: AX 386 GLN cc_start: 0.8438 (tm-30) cc_final: 0.8073 (tp40) REVERT: AY 1795 MET cc_start: 0.7723 (tpp) cc_final: 0.7470 (tpp) REVERT: BT 67 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9080 (mt) REVERT: BT 194 LYS cc_start: 0.7881 (pttm) cc_final: 0.7318 (tptp) REVERT: BT 201 THR cc_start: 0.8365 (p) cc_final: 0.7886 (t) REVERT: BT 213 ARG cc_start: 0.6093 (ptt180) cc_final: 0.5716 (ptt180) REVERT: BT 216 ASN cc_start: 0.7691 (m110) cc_final: 0.7260 (m110) REVERT: BX 369 ARG cc_start: 0.7800 (mmm160) cc_final: 0.7446 (mtt-85) REVERT: BX 371 GLU cc_start: 0.7654 (tm-30) cc_final: 0.7190 (tm-30) REVERT: BX 410 ARG cc_start: 0.7788 (ptp-170) cc_final: 0.7498 (mtm110) REVERT: BY 1739 TYR cc_start: 0.9081 (m-80) cc_final: 0.8756 (m-80) REVERT: BY 1873 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8023 (pm20) REVERT: CT 49 GLU cc_start: 0.7425 (mp0) cc_final: 0.7159 (mp0) REVERT: CT 208 GLN cc_start: 0.7781 (tp40) cc_final: 0.7433 (tp40) REVERT: CT 209 GLU cc_start: 0.8310 (mm-30) cc_final: 0.8015 (tm-30) REVERT: CT 216 ASN cc_start: 0.7734 (m110) cc_final: 0.7416 (m110) REVERT: CT 292 GLU cc_start: 0.7946 (tp30) cc_final: 0.6956 (mt-10) REVERT: CT 296 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7662 (tm-30) REVERT: CT 300 ASN cc_start: 0.6677 (m-40) cc_final: 0.6361 (m-40) REVERT: CX 371 GLU cc_start: 0.7707 (tm-30) cc_final: 0.7316 (tm-30) REVERT: CX 374 LYS cc_start: 0.7715 (ptmm) cc_final: 0.7377 (ptpp) REVERT: CX 386 GLN cc_start: 0.8488 (tm-30) cc_final: 0.8217 (tp40) REVERT: DT 49 GLU cc_start: 0.7545 (mp0) cc_final: 0.7280 (mp0) REVERT: DT 194 LYS cc_start: 0.7812 (pttm) cc_final: 0.7369 (tptp) REVERT: DT 296 GLU cc_start: 0.7777 (tm-30) cc_final: 0.6893 (tm-30) REVERT: DT 300 ASN cc_start: 0.7076 (m-40) cc_final: 0.6548 (m-40) REVERT: DY 1772 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8193 (pp) REVERT: DY 1903 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8056 (tm-30) REVERT: DY 1904 ILE cc_start: 0.8507 (mt) cc_final: 0.8140 (mt) REVERT: ET 49 GLU cc_start: 0.7400 (mp0) cc_final: 0.7109 (mp0) REVERT: ET 64 GLN cc_start: 0.7993 (tt0) cc_final: 0.7486 (mt0) REVERT: ET 194 LYS cc_start: 0.7817 (pttm) cc_final: 0.7453 (tptp) REVERT: ET 209 GLU cc_start: 0.7383 (tm-30) cc_final: 0.6288 (tp30) REVERT: ET 210 TYR cc_start: 0.8053 (t80) cc_final: 0.7671 (t80) REVERT: ET 292 GLU cc_start: 0.7663 (tp30) cc_final: 0.6840 (mt-10) REVERT: ET 296 GLU cc_start: 0.7523 (tm-30) cc_final: 0.7145 (tm-30) REVERT: ET 300 ASN cc_start: 0.6863 (m-40) cc_final: 0.6365 (m110) REVERT: EX 368 ILE cc_start: 0.6456 (OUTLIER) cc_final: 0.6240 (mm) REVERT: EX 378 ASP cc_start: 0.8277 (m-30) cc_final: 0.8048 (m-30) REVERT: EY 1739 TYR cc_start: 0.9047 (m-80) cc_final: 0.8779 (m-80) REVERT: EY 1854 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.7999 (mpp) REVERT: FT 194 LYS cc_start: 0.7864 (pttm) cc_final: 0.7517 (tptp) REVERT: FT 292 GLU cc_start: 0.7750 (tp30) cc_final: 0.6988 (mt-10) REVERT: FT 296 GLU cc_start: 0.7531 (tm-30) cc_final: 0.7083 (tm-30) REVERT: FT 300 ASN cc_start: 0.6943 (m-40) cc_final: 0.6557 (m110) REVERT: FX 386 GLN cc_start: 0.8648 (tp40) cc_final: 0.8376 (tp40) REVERT: FY 1685 LYS cc_start: 0.7175 (mmtm) cc_final: 0.6696 (mmtm) REVERT: GT 201 THR cc_start: 0.8244 (p) cc_final: 0.7878 (t) REVERT: GT 216 ASN cc_start: 0.7726 (m110) cc_final: 0.7347 (m110) REVERT: GT 292 GLU cc_start: 0.7658 (tp30) cc_final: 0.6903 (mt-10) REVERT: GT 296 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7313 (tm-30) REVERT: GT 300 ASN cc_start: 0.6698 (m-40) cc_final: 0.6163 (m-40) REVERT: GX 374 LYS cc_start: 0.7858 (ptmm) cc_final: 0.7498 (ptpp) REVERT: GX 409 LYS cc_start: 0.7691 (ttmt) cc_final: 0.7343 (ttpt) REVERT: GX 459 MET cc_start: 0.8779 (mtp) cc_final: 0.8435 (mtp) REVERT: GY 1685 LYS cc_start: 0.7009 (mmtm) cc_final: 0.6662 (mmtt) REVERT: GY 1873 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7003 (mt-10) REVERT: HT 49 GLU cc_start: 0.7493 (mp0) cc_final: 0.7193 (mp0) REVERT: HT 194 LYS cc_start: 0.7864 (pttm) cc_final: 0.7378 (tptp) REVERT: HT 208 GLN cc_start: 0.7691 (tp40) cc_final: 0.7417 (tp40) REVERT: HT 216 ASN cc_start: 0.7554 (m110) cc_final: 0.7293 (m-40) REVERT: HT 296 GLU cc_start: 0.7771 (tm-30) cc_final: 0.6921 (tm-30) REVERT: HT 300 ASN cc_start: 0.6912 (m-40) cc_final: 0.6409 (m-40) REVERT: HT 301 GLN cc_start: 0.7493 (tp40) cc_final: 0.6954 (mm-40) REVERT: HX 386 GLN cc_start: 0.8428 (tm-30) cc_final: 0.8172 (tm-30) REVERT: HY 1795 MET cc_start: 0.7726 (tpp) cc_final: 0.7451 (tpp) REVERT: HY 1854 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.7849 (mpp) REVERT: IT 67 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9112 (mt) REVERT: IT 194 LYS cc_start: 0.7963 (pttm) cc_final: 0.7537 (tptp) REVERT: IT 209 GLU cc_start: 0.7052 (tm-30) cc_final: 0.6489 (tp30) REVERT: IT 210 TYR cc_start: 0.8167 (t80) cc_final: 0.7896 (t80) REVERT: IT 216 ASN cc_start: 0.7711 (m110) cc_final: 0.7307 (m110) REVERT: IT 296 GLU cc_start: 0.7832 (tm-30) cc_final: 0.7602 (tm-30) REVERT: IX 371 GLU cc_start: 0.7775 (tm-30) cc_final: 0.7270 (tm-30) REVERT: IX 410 ARG cc_start: 0.7735 (ptp-170) cc_final: 0.7189 (mtm110) REVERT: IY 1873 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8036 (pm20) REVERT: IY 1907 GLN cc_start: 0.7566 (tt0) cc_final: 0.7226 (tt0) REVERT: JT 216 ASN cc_start: 0.7653 (m110) cc_final: 0.7211 (m110) REVERT: JT 296 GLU cc_start: 0.7765 (tm-30) cc_final: 0.6842 (tm-30) REVERT: JT 300 ASN cc_start: 0.6375 (m-40) cc_final: 0.5874 (m110) REVERT: JX 410 ARG cc_start: 0.7742 (ptp-170) cc_final: 0.7407 (ptt-90) REVERT: JX 484 LEU cc_start: 0.9192 (tp) cc_final: 0.8961 (tp) REVERT: JY 1724 ASN cc_start: 0.9165 (OUTLIER) cc_final: 0.8965 (p0) REVERT: KT 49 GLU cc_start: 0.7503 (mp0) cc_final: 0.7198 (mp0) REVERT: KT 59 THR cc_start: 0.8818 (m) cc_final: 0.8525 (m) REVERT: KT 194 LYS cc_start: 0.7851 (pttm) cc_final: 0.7375 (tptp) REVERT: KT 208 GLN cc_start: 0.7588 (tp40) cc_final: 0.7354 (tp-100) REVERT: KT 209 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7744 (tp30) REVERT: KT 296 GLU cc_start: 0.7833 (tm-30) cc_final: 0.6991 (tm-30) REVERT: KT 297 TYR cc_start: 0.7707 (t80) cc_final: 0.7488 (t80) REVERT: KT 300 ASN cc_start: 0.6955 (m-40) cc_final: 0.6473 (m-40) REVERT: KX 371 GLU cc_start: 0.7830 (tm-30) cc_final: 0.7368 (tm-30) REVERT: KX 378 ASP cc_start: 0.8304 (m-30) cc_final: 0.7696 (t0) REVERT: KX 386 GLN cc_start: 0.8463 (tm-30) cc_final: 0.8200 (tp40) REVERT: KX 509 LEU cc_start: 0.9130 (mt) cc_final: 0.8776 (mt) REVERT: KY 1739 TYR cc_start: 0.9075 (m-80) cc_final: 0.8739 (m-80) REVERT: KY 1772 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8194 (pp) REVERT: KY 1907 GLN cc_start: 0.8196 (tm-30) cc_final: 0.7879 (tt0) REVERT: LT 49 GLU cc_start: 0.7501 (mp0) cc_final: 0.7163 (mp0) REVERT: LT 194 LYS cc_start: 0.7668 (pttm) cc_final: 0.7286 (tptp) REVERT: LT 216 ASN cc_start: 0.7769 (m110) cc_final: 0.7420 (m110) REVERT: LT 296 GLU cc_start: 0.7564 (tm-30) cc_final: 0.6859 (tm-30) REVERT: LT 300 ASN cc_start: 0.6877 (m-40) cc_final: 0.6350 (m-40) REVERT: LX 378 ASP cc_start: 0.8285 (m-30) cc_final: 0.7701 (t0) REVERT: LY 1739 TYR cc_start: 0.9034 (m-80) cc_final: 0.8762 (m-80) REVERT: MT 49 GLU cc_start: 0.7419 (mp0) cc_final: 0.7178 (mp0) REVERT: MT 194 LYS cc_start: 0.7808 (pttm) cc_final: 0.7457 (tptp) REVERT: MT 209 GLU cc_start: 0.7431 (tm-30) cc_final: 0.6349 (tp30) REVERT: MT 296 GLU cc_start: 0.7555 (tm-30) cc_final: 0.6742 (tm-30) REVERT: MT 300 ASN cc_start: 0.6909 (m-40) cc_final: 0.6469 (m-40) REVERT: MX 386 GLN cc_start: 0.8650 (tp40) cc_final: 0.8407 (tp40) REVERT: MY 1685 LYS cc_start: 0.7157 (mmtm) cc_final: 0.6686 (mmtm) REVERT: NT 216 ASN cc_start: 0.7643 (m110) cc_final: 0.7288 (m-40) REVERT: NT 296 GLU cc_start: 0.7587 (tm-30) cc_final: 0.7193 (tm-30) REVERT: NT 300 ASN cc_start: 0.6909 (m-40) cc_final: 0.6459 (m110) REVERT: NX 374 LYS cc_start: 0.7848 (ptmm) cc_final: 0.7507 (ptpp) REVERT: NX 459 MET cc_start: 0.8775 (mtp) cc_final: 0.8391 (mtp) REVERT: NY 1685 LYS cc_start: 0.7011 (mmtm) cc_final: 0.6662 (mmtt) REVERT: NY 1856 ASN cc_start: 0.8260 (t0) cc_final: 0.8016 (t0) REVERT: NY 1873 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7129 (mt-10) outliers start: 175 outliers final: 149 residues processed: 1610 average time/residue: 0.6146 time to fit residues: 1669.4159 Evaluate side-chains 1646 residues out of total 6790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 1486 time to evaluate : 5.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AT residue 35 VAL Chi-restraints excluded: chain AT residue 80 VAL Chi-restraints excluded: chain AT residue 136 SER Chi-restraints excluded: chain AT residue 173 VAL Chi-restraints excluded: chain AX residue 411 SER Chi-restraints excluded: chain AY residue 1711 THR Chi-restraints excluded: chain AY residue 1725 MET Chi-restraints excluded: chain AY residue 1751 ILE Chi-restraints excluded: chain AY residue 1752 MET Chi-restraints excluded: chain BT residue 29 VAL Chi-restraints excluded: chain BT residue 35 VAL Chi-restraints excluded: chain BT residue 67 LEU Chi-restraints excluded: chain BT residue 80 VAL Chi-restraints excluded: chain BT residue 136 SER Chi-restraints excluded: chain BT residue 173 VAL Chi-restraints excluded: chain BX residue 383 LEU Chi-restraints excluded: chain BX residue 415 MET Chi-restraints excluded: chain BX residue 459 MET Chi-restraints excluded: chain BX residue 508 GLU Chi-restraints excluded: chain BY residue 1711 THR Chi-restraints excluded: chain BY residue 1724 ASN Chi-restraints excluded: chain BY residue 1725 MET Chi-restraints excluded: chain BY residue 1751 ILE Chi-restraints excluded: chain BY residue 1809 SER Chi-restraints excluded: chain BY residue 1873 GLU Chi-restraints excluded: chain BY residue 1879 ILE Chi-restraints excluded: chain CT residue 29 VAL Chi-restraints excluded: chain CT residue 65 VAL Chi-restraints excluded: chain CT residue 80 VAL Chi-restraints excluded: chain CT residue 82 LEU Chi-restraints excluded: chain CT residue 136 SER Chi-restraints excluded: chain CT residue 173 VAL Chi-restraints excluded: chain CX residue 415 MET Chi-restraints excluded: chain CX residue 508 GLU Chi-restraints excluded: chain CY residue 1711 THR Chi-restraints excluded: chain CY residue 1746 LYS Chi-restraints excluded: chain CY residue 1873 GLU Chi-restraints excluded: chain CY residue 1904 ILE Chi-restraints excluded: chain DT residue 29 VAL Chi-restraints excluded: chain DT residue 52 LEU Chi-restraints excluded: chain DT residue 80 VAL Chi-restraints excluded: chain DT residue 136 SER Chi-restraints excluded: chain DT residue 173 VAL Chi-restraints excluded: chain DX residue 383 LEU Chi-restraints excluded: chain DX residue 415 MET Chi-restraints excluded: chain DX residue 418 GLU Chi-restraints excluded: chain DY residue 1711 THR Chi-restraints excluded: chain DY residue 1725 MET Chi-restraints excluded: chain DY residue 1772 LEU Chi-restraints excluded: chain DY residue 1809 SER Chi-restraints excluded: chain DY residue 1873 GLU Chi-restraints excluded: chain DY residue 1879 ILE Chi-restraints excluded: chain DY residue 1880 LEU Chi-restraints excluded: chain DY residue 1903 GLU Chi-restraints excluded: chain ET residue 80 VAL Chi-restraints excluded: chain ET residue 136 SER Chi-restraints excluded: chain ET residue 173 VAL Chi-restraints excluded: chain EX residue 368 ILE Chi-restraints excluded: chain EX residue 383 LEU Chi-restraints excluded: chain EX residue 385 THR Chi-restraints excluded: chain EX residue 508 GLU Chi-restraints excluded: chain EY residue 1711 THR Chi-restraints excluded: chain EY residue 1713 ILE Chi-restraints excluded: chain EY residue 1724 ASN Chi-restraints excluded: chain EY residue 1752 MET Chi-restraints excluded: chain EY residue 1854 MET Chi-restraints excluded: chain FT residue 80 VAL Chi-restraints excluded: chain FT residue 136 SER Chi-restraints excluded: chain FT residue 173 VAL Chi-restraints excluded: chain FX residue 383 LEU Chi-restraints excluded: chain FX residue 415 MET Chi-restraints excluded: chain FX residue 508 GLU Chi-restraints excluded: chain FY residue 1711 THR Chi-restraints excluded: chain FY residue 1713 ILE Chi-restraints excluded: chain FY residue 1724 ASN Chi-restraints excluded: chain FY residue 1751 ILE Chi-restraints excluded: chain FY residue 1752 MET Chi-restraints excluded: chain FY residue 1809 SER Chi-restraints excluded: chain GT residue 80 VAL Chi-restraints excluded: chain GT residue 136 SER Chi-restraints excluded: chain GT residue 173 VAL Chi-restraints excluded: chain GX residue 415 MET Chi-restraints excluded: chain GY residue 1711 THR Chi-restraints excluded: chain GY residue 1725 MET Chi-restraints excluded: chain HT residue 29 VAL Chi-restraints excluded: chain HT residue 80 VAL Chi-restraints excluded: chain HT residue 136 SER Chi-restraints excluded: chain HT residue 173 VAL Chi-restraints excluded: chain HX residue 383 LEU Chi-restraints excluded: chain HX residue 508 GLU Chi-restraints excluded: chain HY residue 1711 THR Chi-restraints excluded: chain HY residue 1751 ILE Chi-restraints excluded: chain HY residue 1752 MET Chi-restraints excluded: chain HY residue 1854 MET Chi-restraints excluded: chain IT residue 35 VAL Chi-restraints excluded: chain IT residue 67 LEU Chi-restraints excluded: chain IT residue 80 VAL Chi-restraints excluded: chain IT residue 136 SER Chi-restraints excluded: chain IT residue 173 VAL Chi-restraints excluded: chain IX residue 375 ILE Chi-restraints excluded: chain IX residue 383 LEU Chi-restraints excluded: chain IX residue 415 MET Chi-restraints excluded: chain IX residue 508 GLU Chi-restraints excluded: chain IY residue 1711 THR Chi-restraints excluded: chain IY residue 1724 ASN Chi-restraints excluded: chain IY residue 1725 MET Chi-restraints excluded: chain IY residue 1751 ILE Chi-restraints excluded: chain IY residue 1809 SER Chi-restraints excluded: chain IY residue 1873 GLU Chi-restraints excluded: chain JT residue 29 VAL Chi-restraints excluded: chain JT residue 80 VAL Chi-restraints excluded: chain JT residue 82 LEU Chi-restraints excluded: chain JT residue 136 SER Chi-restraints excluded: chain JT residue 173 VAL Chi-restraints excluded: chain JX residue 488 ILE Chi-restraints excluded: chain JX residue 508 GLU Chi-restraints excluded: chain JY residue 1711 THR Chi-restraints excluded: chain JY residue 1724 ASN Chi-restraints excluded: chain JY residue 1746 LYS Chi-restraints excluded: chain JY residue 1873 GLU Chi-restraints excluded: chain KT residue 52 LEU Chi-restraints excluded: chain KT residue 80 VAL Chi-restraints excluded: chain KT residue 136 SER Chi-restraints excluded: chain KT residue 173 VAL Chi-restraints excluded: chain KX residue 415 MET Chi-restraints excluded: chain KX residue 418 GLU Chi-restraints excluded: chain KX residue 449 SER Chi-restraints excluded: chain KX residue 508 GLU Chi-restraints excluded: chain KY residue 1711 THR Chi-restraints excluded: chain KY residue 1772 LEU Chi-restraints excluded: chain KY residue 1873 GLU Chi-restraints excluded: chain KY residue 1879 ILE Chi-restraints excluded: chain KY residue 1880 LEU Chi-restraints excluded: chain LT residue 67 LEU Chi-restraints excluded: chain LT residue 80 VAL Chi-restraints excluded: chain LT residue 136 SER Chi-restraints excluded: chain LT residue 173 VAL Chi-restraints excluded: chain LX residue 424 THR Chi-restraints excluded: chain LX residue 508 GLU Chi-restraints excluded: chain LY residue 1711 THR Chi-restraints excluded: chain LY residue 1713 ILE Chi-restraints excluded: chain LY residue 1724 ASN Chi-restraints excluded: chain MT residue 80 VAL Chi-restraints excluded: chain MT residue 136 SER Chi-restraints excluded: chain MT residue 173 VAL Chi-restraints excluded: chain MX residue 383 LEU Chi-restraints excluded: chain MX residue 415 MET Chi-restraints excluded: chain MX residue 508 GLU Chi-restraints excluded: chain MY residue 1713 ILE Chi-restraints excluded: chain MY residue 1724 ASN Chi-restraints excluded: chain MY residue 1751 ILE Chi-restraints excluded: chain MY residue 1752 MET Chi-restraints excluded: chain MY residue 1809 SER Chi-restraints excluded: chain NT residue 80 VAL Chi-restraints excluded: chain NT residue 136 SER Chi-restraints excluded: chain NT residue 173 VAL Chi-restraints excluded: chain NT residue 197 GLN Chi-restraints excluded: chain NT residue 221 LEU Chi-restraints excluded: chain NX residue 415 MET Chi-restraints excluded: chain NY residue 1711 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 458 optimal weight: 7.9990 chunk 615 optimal weight: 0.9990 chunk 176 optimal weight: 0.0050 chunk 532 optimal weight: 9.9990 chunk 85 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 578 optimal weight: 4.9990 chunk 242 optimal weight: 0.7980 chunk 593 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 chunk 106 optimal weight: 0.0970 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AT 64 GLN ** AY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BT 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CT 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CY1856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** EX 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** GT 64 GLN HT 64 GLN IX 443 GLN ** IY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** JT 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** JX 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** JY1856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** KY1726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** KY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LT 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LY1856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** MX 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** MX 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** MY1907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NT 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NT 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NT 197 GLN ** NY1856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.117389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.092722 restraints weight = 107930.376| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.97 r_work: 0.3076 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.206 61992 Z= 0.346 Angle : 0.757 59.199 83594 Z= 0.404 Chirality : 0.047 0.591 9520 Planarity : 0.005 0.052 10598 Dihedral : 5.155 25.515 8134 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.62 % Allowed : 19.37 % Favored : 78.01 % Cbeta Deviations : 0.01 % 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: -0.41 (0.10), residues: 7406 helix: 1.32 (0.11), residues: 2240 sheet: -1.24 (0.12), residues: 1652 loop : -0.76 (0.10), residues: 3514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRPCX 466 HIS 0.002 0.001 HISGT 169 PHE 0.030 0.002 PHECT 109 TYR 0.020 0.002 TYRJT 36 ARG 0.012 0.001 ARGIX 394 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24216.52 seconds wall clock time: 416 minutes 46.61 seconds (25006.61 seconds total)