Starting phenix.real_space_refine on Thu Mar 5 15:20:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u5i_26351/03_2026/7u5i_26351.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u5i_26351/03_2026/7u5i_26351.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7u5i_26351/03_2026/7u5i_26351.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u5i_26351/03_2026/7u5i_26351.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7u5i_26351/03_2026/7u5i_26351.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u5i_26351/03_2026/7u5i_26351.map" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.092 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 120 5.16 5 C 14688 2.51 5 N 4280 2.21 5 O 4451 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23539 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2927 Classifications: {'peptide': 363} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "C" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "E" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "F" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "G" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "H" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Restraints were copied for chains: B, C, D, E, F, G, H Time building chain proxies: 3.15, per 1000 atoms: 0.13 Number of scatterers: 23539 At special positions: 0 Unit cell: (133.75, 133.75, 103.79, 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 120 16.00 O 4451 8.00 N 4280 7.00 C 14688 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: 1.81 Conformation dependent library (CDL) restraints added in 711.6 milliseconds 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5376 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 8 sheets defined 43.3% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 48 through 53 Processing helix chain 'A' and resid 61 through 67 Processing helix chain 'A' and resid 68 through 77 removed outlier: 4.734A pdb=" N ASP A 77 " --> pdb=" O ALA A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 96 removed outlier: 5.008A pdb=" N THR A 92 " --> pdb=" O GLN A 88 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N GLY A 93 " --> pdb=" O CYS A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 118 Processing helix chain 'A' and resid 118 through 130 Proline residue: A 124 - end of helix Processing helix chain 'A' and resid 180 through 197 removed outlier: 3.868A pdb=" N GLY A 197 " --> pdb=" O ASP A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 223 Processing helix chain 'A' and resid 232 through 239 Processing helix chain 'A' and resid 278 through 301 removed outlier: 3.722A pdb=" N VAL A 282 " --> pdb=" O ASN A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 338 removed outlier: 3.511A pdb=" N ASP A 338 " --> pdb=" O LEU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 348 removed outlier: 3.567A pdb=" N LEU A 348 " --> pdb=" O ILE A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 403 Processing helix chain 'B' and resid 48 through 53 Processing helix chain 'B' and resid 61 through 67 Processing helix chain 'B' and resid 68 through 77 removed outlier: 4.734A pdb=" N ASP B 77 " --> pdb=" O ALA B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 96 removed outlier: 5.008A pdb=" N THR B 92 " --> pdb=" O GLN B 88 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N GLY B 93 " --> pdb=" O CYS B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 118 Processing helix chain 'B' and resid 118 through 130 Proline residue: B 124 - end of helix Processing helix chain 'B' and resid 180 through 197 removed outlier: 3.867A pdb=" N GLY B 197 " --> pdb=" O ASP B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 223 Processing helix chain 'B' and resid 232 through 239 Processing helix chain 'B' and resid 278 through 301 removed outlier: 3.721A pdb=" N VAL B 282 " --> pdb=" O ASN B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 338 removed outlier: 3.512A pdb=" N ASP B 338 " --> pdb=" O LEU B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 348 removed outlier: 3.567A pdb=" N LEU B 348 " --> pdb=" O ILE B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 403 Processing helix chain 'C' and resid 48 through 53 Processing helix chain 'C' and resid 61 through 67 Processing helix chain 'C' and resid 68 through 77 removed outlier: 4.734A pdb=" N ASP C 77 " --> pdb=" O ALA C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 96 removed outlier: 5.008A pdb=" N THR C 92 " --> pdb=" O GLN C 88 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N GLY C 93 " --> pdb=" O CYS C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 118 Processing helix chain 'C' and resid 118 through 130 Proline residue: C 124 - end of helix Processing helix chain 'C' and resid 180 through 197 removed outlier: 3.867A pdb=" N GLY C 197 " --> pdb=" O ASP C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 223 Processing helix chain 'C' and resid 232 through 239 Processing helix chain 'C' and resid 278 through 301 removed outlier: 3.722A pdb=" N VAL C 282 " --> pdb=" O ASN C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 338 removed outlier: 3.511A pdb=" N ASP C 338 " --> pdb=" O LEU C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 348 removed outlier: 3.568A pdb=" N LEU C 348 " --> pdb=" O ILE C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 403 Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 61 through 67 Processing helix chain 'D' and resid 68 through 77 removed outlier: 4.735A pdb=" N ASP D 77 " --> pdb=" O ALA D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 96 removed outlier: 5.008A pdb=" N THR D 92 " --> pdb=" O GLN D 88 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N GLY D 93 " --> pdb=" O CYS D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 118 Processing helix chain 'D' and resid 118 through 130 Proline residue: D 124 - end of helix Processing helix chain 'D' and resid 180 through 197 removed outlier: 3.868A pdb=" N GLY D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 223 Processing helix chain 'D' and resid 232 through 239 Processing helix chain 'D' and resid 278 through 301 removed outlier: 3.722A pdb=" N VAL D 282 " --> pdb=" O ASN D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 338 removed outlier: 3.510A pdb=" N ASP D 338 " --> pdb=" O LEU D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 348 removed outlier: 3.568A pdb=" N LEU D 348 " --> pdb=" O ILE D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 403 Processing helix chain 'E' and resid 48 through 53 Processing helix chain 'E' and resid 61 through 67 Processing helix chain 'E' and resid 68 through 77 removed outlier: 4.734A pdb=" N ASP E 77 " --> pdb=" O ALA E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 96 removed outlier: 5.009A pdb=" N THR E 92 " --> pdb=" O GLN E 88 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N GLY E 93 " --> pdb=" O CYS E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 118 Processing helix chain 'E' and resid 118 through 130 Proline residue: E 124 - end of helix Processing helix chain 'E' and resid 180 through 197 removed outlier: 3.867A pdb=" N GLY E 197 " --> pdb=" O ASP E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 223 Processing helix chain 'E' and resid 232 through 239 Processing helix chain 'E' and resid 278 through 301 removed outlier: 3.721A pdb=" N VAL E 282 " --> pdb=" O ASN E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 338 removed outlier: 3.511A pdb=" N ASP E 338 " --> pdb=" O LEU E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 348 removed outlier: 3.567A pdb=" N LEU E 348 " --> pdb=" O ILE E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 378 through 403 Processing helix chain 'F' and resid 48 through 53 Processing helix chain 'F' and resid 61 through 67 Processing helix chain 'F' and resid 68 through 77 removed outlier: 4.734A pdb=" N ASP F 77 " --> pdb=" O ALA F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 96 removed outlier: 5.009A pdb=" N THR F 92 " --> pdb=" O GLN F 88 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N GLY F 93 " --> pdb=" O CYS F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 118 Processing helix chain 'F' and resid 118 through 130 Proline residue: F 124 - end of helix Processing helix chain 'F' and resid 180 through 197 removed outlier: 3.867A pdb=" N GLY F 197 " --> pdb=" O ASP F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 223 Processing helix chain 'F' and resid 232 through 239 Processing helix chain 'F' and resid 278 through 301 removed outlier: 3.721A pdb=" N VAL F 282 " --> pdb=" O ASN F 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 338 removed outlier: 3.510A pdb=" N ASP F 338 " --> pdb=" O LEU F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 348 removed outlier: 3.567A pdb=" N LEU F 348 " --> pdb=" O ILE F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 378 through 403 Processing helix chain 'G' and resid 48 through 53 Processing helix chain 'G' and resid 61 through 67 Processing helix chain 'G' and resid 68 through 77 removed outlier: 4.734A pdb=" N ASP G 77 " --> pdb=" O ALA G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 96 removed outlier: 5.008A pdb=" N THR G 92 " --> pdb=" O GLN G 88 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N GLY G 93 " --> pdb=" O CYS G 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 118 Processing helix chain 'G' and resid 118 through 130 Proline residue: G 124 - end of helix Processing helix chain 'G' and resid 180 through 197 removed outlier: 3.868A pdb=" N GLY G 197 " --> pdb=" O ASP G 193 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 223 Processing helix chain 'G' and resid 232 through 239 Processing helix chain 'G' and resid 278 through 301 removed outlier: 3.722A pdb=" N VAL G 282 " --> pdb=" O ASN G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 332 through 338 removed outlier: 3.511A pdb=" N ASP G 338 " --> pdb=" O LEU G 334 " (cutoff:3.500A) Processing helix chain 'G' and resid 340 through 348 removed outlier: 3.567A pdb=" N LEU G 348 " --> pdb=" O ILE G 344 " (cutoff:3.500A) Processing helix chain 'G' and resid 378 through 403 Processing helix chain 'H' and resid 48 through 53 Processing helix chain 'H' and resid 61 through 67 Processing helix chain 'H' and resid 68 through 77 removed outlier: 4.734A pdb=" N ASP H 77 " --> pdb=" O ALA H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 96 removed outlier: 5.008A pdb=" N THR H 92 " --> pdb=" O GLN H 88 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N GLY H 93 " --> pdb=" O CYS H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 118 Processing helix chain 'H' and resid 118 through 130 Proline residue: H 124 - end of helix Processing helix chain 'H' and resid 180 through 197 removed outlier: 3.868A pdb=" N GLY H 197 " --> pdb=" O ASP H 193 " (cutoff:3.500A) Processing helix chain 'H' and resid 213 through 223 Processing helix chain 'H' and resid 232 through 239 Processing helix chain 'H' and resid 278 through 301 removed outlier: 3.722A pdb=" N VAL H 282 " --> pdb=" O ASN H 278 " (cutoff:3.500A) Processing helix chain 'H' and resid 332 through 338 removed outlier: 3.511A pdb=" N ASP H 338 " --> pdb=" O LEU H 334 " (cutoff:3.500A) Processing helix chain 'H' and resid 340 through 348 removed outlier: 3.567A pdb=" N LEU H 348 " --> pdb=" O ILE H 344 " (cutoff:3.500A) Processing helix chain 'H' and resid 378 through 403 Processing sheet with id=AA1, first strand: chain 'A' and resid 204 through 208 removed outlier: 3.720A pdb=" N GLY A 249 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N PHE A 258 " --> pdb=" O ASN A 253 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N HIS A 329 " --> pdb=" O LEU A 160 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N SER A 162 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N GLY A 327 " --> pdb=" O SER A 162 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 204 through 208 removed outlier: 3.720A pdb=" N GLY B 249 " --> pdb=" O VAL B 262 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N PHE B 258 " --> pdb=" O ASN B 253 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N HIS B 329 " --> pdb=" O LEU B 160 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N SER B 162 " --> pdb=" O GLY B 327 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N GLY B 327 " --> pdb=" O SER B 162 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 204 through 208 removed outlier: 3.720A pdb=" N GLY C 249 " --> pdb=" O VAL C 262 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N PHE C 258 " --> pdb=" O ASN C 253 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N HIS C 329 " --> pdb=" O LEU C 160 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N SER C 162 " --> pdb=" O GLY C 327 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N GLY C 327 " --> pdb=" O SER C 162 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 204 through 208 removed outlier: 3.720A pdb=" N GLY D 249 " --> pdb=" O VAL D 262 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N PHE D 258 " --> pdb=" O ASN D 253 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N HIS D 329 " --> pdb=" O LEU D 160 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N SER D 162 " --> pdb=" O GLY D 327 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N GLY D 327 " --> pdb=" O SER D 162 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 204 through 208 removed outlier: 3.721A pdb=" N GLY E 249 " --> pdb=" O VAL E 262 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N PHE E 258 " --> pdb=" O ASN E 253 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N HIS E 329 " --> pdb=" O LEU E 160 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N SER E 162 " --> pdb=" O GLY E 327 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N GLY E 327 " --> pdb=" O SER E 162 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 204 through 208 removed outlier: 3.720A pdb=" N GLY F 249 " --> pdb=" O VAL F 262 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N PHE F 258 " --> pdb=" O ASN F 253 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N HIS F 329 " --> pdb=" O LEU F 160 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N SER F 162 " --> pdb=" O GLY F 327 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N GLY F 327 " --> pdb=" O SER F 162 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 204 through 208 removed outlier: 3.721A pdb=" N GLY G 249 " --> pdb=" O VAL G 262 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N PHE G 258 " --> pdb=" O ASN G 253 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N HIS G 329 " --> pdb=" O LEU G 160 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N SER G 162 " --> pdb=" O GLY G 327 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N GLY G 327 " --> pdb=" O SER G 162 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 204 through 208 removed outlier: 3.721A pdb=" N GLY H 249 " --> pdb=" O VAL H 262 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N PHE H 258 " --> pdb=" O ASN H 253 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N HIS H 329 " --> pdb=" O LEU H 160 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N SER H 162 " --> pdb=" O GLY H 327 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N GLY H 327 " --> pdb=" O SER H 162 " (cutoff:3.500A) 1000 hydrogen bonds defined for protein. 2904 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: 4.72 Time building geometry restraints manager: 2.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6184 1.33 - 1.45: 4173 1.45 - 1.57: 13371 1.57 - 1.69: 0 1.69 - 1.81: 184 Bond restraints: 23912 Sorted by residual: bond pdb=" CA THR H 80 " pdb=" C THR H 80 " ideal model delta sigma weight residual 1.527 1.497 0.030 1.32e-02 5.74e+03 5.26e+00 bond pdb=" CA THR E 80 " pdb=" C THR E 80 " ideal model delta sigma weight residual 1.527 1.497 0.030 1.32e-02 5.74e+03 5.23e+00 bond pdb=" CA THR F 80 " pdb=" C THR F 80 " ideal model delta sigma weight residual 1.527 1.497 0.030 1.32e-02 5.74e+03 5.02e+00 bond pdb=" CA THR G 80 " pdb=" C THR G 80 " ideal model delta sigma weight residual 1.527 1.497 0.030 1.32e-02 5.74e+03 5.02e+00 bond pdb=" CA THR C 80 " pdb=" C THR C 80 " ideal model delta sigma weight residual 1.527 1.497 0.029 1.32e-02 5.74e+03 4.99e+00 ... (remaining 23907 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 31796 1.72 - 3.44: 396 3.44 - 5.15: 80 5.15 - 6.87: 24 6.87 - 8.59: 8 Bond angle restraints: 32304 Sorted by residual: angle pdb=" C THR G 166 " pdb=" CA THR G 166 " pdb=" CB THR G 166 " ideal model delta sigma weight residual 111.95 103.36 8.59 2.38e+00 1.77e-01 1.30e+01 angle pdb=" C THR F 166 " pdb=" CA THR F 166 " pdb=" CB THR F 166 " ideal model delta sigma weight residual 111.95 103.36 8.59 2.38e+00 1.77e-01 1.30e+01 angle pdb=" C THR E 166 " pdb=" CA THR E 166 " pdb=" CB THR E 166 " ideal model delta sigma weight residual 111.95 103.37 8.58 2.38e+00 1.77e-01 1.30e+01 angle pdb=" C THR A 166 " pdb=" CA THR A 166 " pdb=" CB THR A 166 " ideal model delta sigma weight residual 111.95 103.37 8.58 2.38e+00 1.77e-01 1.30e+01 angle pdb=" C THR B 166 " pdb=" CA THR B 166 " pdb=" CB THR B 166 " ideal model delta sigma weight residual 111.95 103.37 8.58 2.38e+00 1.77e-01 1.30e+01 ... (remaining 32299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.15: 13440 16.15 - 32.30: 824 32.30 - 48.45: 240 48.45 - 64.61: 48 64.61 - 80.76: 16 Dihedral angle restraints: 14568 sinusoidal: 6224 harmonic: 8344 Sorted by residual: dihedral pdb=" N ARG B 205 " pdb=" CA ARG B 205 " pdb=" CB ARG B 205 " pdb=" CG ARG B 205 " ideal model delta sinusoidal sigma weight residual -60.00 -119.04 59.04 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N ARG H 205 " pdb=" CA ARG H 205 " pdb=" CB ARG H 205 " pdb=" CG ARG H 205 " ideal model delta sinusoidal sigma weight residual -60.00 -119.01 59.01 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N ARG C 205 " pdb=" CA ARG C 205 " pdb=" CB ARG C 205 " pdb=" CG ARG C 205 " ideal model delta sinusoidal sigma weight residual -60.00 -119.01 59.01 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 14565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2803 0.050 - 0.100: 560 0.100 - 0.150: 101 0.150 - 0.200: 0 0.200 - 0.250: 8 Chirality restraints: 3472 Sorted by residual: chirality pdb=" CA THR B 82 " pdb=" N THR B 82 " pdb=" C THR B 82 " pdb=" CB THR B 82 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA THR D 82 " pdb=" N THR D 82 " pdb=" C THR D 82 " pdb=" CB THR D 82 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA THR H 82 " pdb=" N THR H 82 " pdb=" C THR H 82 " pdb=" CB THR H 82 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 3469 not shown) Planarity restraints: 4248 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 80 " 0.048 5.00e-02 4.00e+02 7.30e-02 8.53e+00 pdb=" N PRO D 81 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO D 81 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 81 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 80 " -0.048 5.00e-02 4.00e+02 7.30e-02 8.53e+00 pdb=" N PRO E 81 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO E 81 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO E 81 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 80 " 0.048 5.00e-02 4.00e+02 7.30e-02 8.52e+00 pdb=" N PRO F 81 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO F 81 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO F 81 " 0.041 5.00e-02 4.00e+02 ... (remaining 4245 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3112 2.76 - 3.29: 23296 3.29 - 3.83: 41535 3.83 - 4.36: 48904 4.36 - 4.90: 83235 Nonbonded interactions: 200082 Sorted by model distance: nonbonded pdb=" OD2 ASP F 223 " pdb=" O HOH F 501 " model vdw 2.219 3.040 nonbonded pdb=" OD2 ASP B 223 " pdb=" O HOH B 501 " model vdw 2.221 3.040 nonbonded pdb=" OD2 ASP H 223 " pdb=" O HOH H 501 " model vdw 2.221 3.040 nonbonded pdb=" OD2 ASP E 223 " pdb=" O HOH E 501 " model vdw 2.222 3.040 nonbonded pdb=" OD2 ASP G 223 " pdb=" O HOH G 501 " model vdw 2.223 3.040 ... (remaining 200077 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 1.110 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: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 18.320 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 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 : 0.002 0.037 23912 Z= 0.145 Angle : 0.557 8.590 32304 Z= 0.306 Chirality : 0.042 0.250 3472 Planarity : 0.005 0.073 4248 Dihedral : 11.618 80.757 9192 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.82 % Allowed : 5.64 % Favored : 91.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.15), residues: 2872 helix: 2.02 (0.16), residues: 1096 sheet: 0.11 (0.24), residues: 432 loop : -0.46 (0.15), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 285 TYR 0.003 0.001 TYR H 207 PHE 0.010 0.001 PHE G 286 TRP 0.015 0.001 TRP H 84 HIS 0.002 0.000 HIS G 66 Details of bonding type rmsd covalent geometry : bond 0.00250 (23912) covalent geometry : angle 0.55741 (32304) hydrogen bonds : bond 0.10914 ( 1000) hydrogen bonds : angle 4.89125 ( 2904) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 807 residues out of total 2552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 735 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 ASP cc_start: 0.7500 (t0) cc_final: 0.7202 (t0) REVERT: A 148 LYS cc_start: 0.8094 (mtpt) cc_final: 0.7886 (mtpt) REVERT: A 227 PHE cc_start: 0.7875 (p90) cc_final: 0.7476 (p90) REVERT: A 279 MET cc_start: 0.8406 (mmm) cc_final: 0.8028 (mmm) REVERT: A 280 LYS cc_start: 0.7844 (ptpp) cc_final: 0.7638 (ptpp) REVERT: A 281 LYS cc_start: 0.7785 (ptmt) cc_final: 0.7487 (ptmm) REVERT: A 298 GLN cc_start: 0.7884 (mt0) cc_final: 0.7585 (mt0) REVERT: A 324 LEU cc_start: 0.8715 (tp) cc_final: 0.7913 (tp) REVERT: A 325 ARG cc_start: 0.7752 (ttt-90) cc_final: 0.7384 (ttt180) REVERT: A 346 GLU cc_start: 0.7646 (tm-30) cc_final: 0.7280 (tm-30) REVERT: A 352 LYS cc_start: 0.7511 (tmtt) cc_final: 0.7226 (tmtt) REVERT: A 381 GLU cc_start: 0.7505 (mt-10) cc_final: 0.7265 (mt-10) REVERT: B 134 ASP cc_start: 0.7486 (t0) cc_final: 0.7194 (t0) REVERT: B 148 LYS cc_start: 0.8104 (mtpt) cc_final: 0.7894 (mtpt) REVERT: B 227 PHE cc_start: 0.7829 (p90) cc_final: 0.7420 (p90) REVERT: B 279 MET cc_start: 0.8396 (mmm) cc_final: 0.8033 (mmm) REVERT: B 281 LYS cc_start: 0.7765 (ptmt) cc_final: 0.7465 (ptmm) REVERT: B 298 GLN cc_start: 0.7908 (mt0) cc_final: 0.7586 (mt0) REVERT: B 324 LEU cc_start: 0.8713 (tp) cc_final: 0.7896 (tp) REVERT: B 325 ARG cc_start: 0.7752 (ttt-90) cc_final: 0.7383 (ttt180) REVERT: B 344 ILE cc_start: 0.8526 (mt) cc_final: 0.8293 (mt) REVERT: B 346 GLU cc_start: 0.7626 (tm-30) cc_final: 0.7316 (tm-30) REVERT: B 352 LYS cc_start: 0.7497 (tmtt) cc_final: 0.7219 (tmtt) REVERT: B 381 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7263 (mt-10) REVERT: C 134 ASP cc_start: 0.7503 (t0) cc_final: 0.7210 (t0) REVERT: C 148 LYS cc_start: 0.8098 (mtpt) cc_final: 0.7871 (mtpt) REVERT: C 227 PHE cc_start: 0.7830 (p90) cc_final: 0.7432 (p90) REVERT: C 279 MET cc_start: 0.8398 (mmm) cc_final: 0.8032 (mmm) REVERT: C 281 LYS cc_start: 0.7769 (ptmt) cc_final: 0.7473 (ptmm) REVERT: C 298 GLN cc_start: 0.7907 (mt0) cc_final: 0.7574 (mt0) REVERT: C 324 LEU cc_start: 0.8714 (tp) cc_final: 0.7897 (tp) REVERT: C 325 ARG cc_start: 0.7749 (ttt-90) cc_final: 0.7379 (ttt180) REVERT: C 346 GLU cc_start: 0.7645 (tm-30) cc_final: 0.7289 (tm-30) REVERT: C 352 LYS cc_start: 0.7478 (tmtt) cc_final: 0.7210 (tmtt) REVERT: C 381 GLU cc_start: 0.7522 (mt-10) cc_final: 0.7277 (mt-10) REVERT: D 134 ASP cc_start: 0.7512 (t0) cc_final: 0.7199 (t0) REVERT: D 148 LYS cc_start: 0.8079 (mtpt) cc_final: 0.7800 (mtpt) REVERT: D 227 PHE cc_start: 0.7830 (p90) cc_final: 0.7422 (p90) REVERT: D 279 MET cc_start: 0.8397 (mmm) cc_final: 0.8030 (mmm) REVERT: D 281 LYS cc_start: 0.7768 (ptmt) cc_final: 0.7465 (ptmm) REVERT: D 298 GLN cc_start: 0.7923 (mt0) cc_final: 0.7612 (mt0) REVERT: D 324 LEU cc_start: 0.8714 (tp) cc_final: 0.7897 (tp) REVERT: D 325 ARG cc_start: 0.7746 (ttt-90) cc_final: 0.7389 (ttt180) REVERT: D 346 GLU cc_start: 0.7643 (tm-30) cc_final: 0.7316 (tm-30) REVERT: D 352 LYS cc_start: 0.7497 (tmtt) cc_final: 0.7222 (tmtt) REVERT: D 381 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7261 (mt-10) REVERT: E 134 ASP cc_start: 0.7555 (t0) cc_final: 0.7270 (t0) REVERT: E 227 PHE cc_start: 0.7814 (p90) cc_final: 0.7395 (p90) REVERT: E 279 MET cc_start: 0.8432 (mmm) cc_final: 0.8041 (mmm) REVERT: E 280 LYS cc_start: 0.7805 (ptpp) cc_final: 0.7575 (ptpp) REVERT: E 281 LYS cc_start: 0.7761 (ptmt) cc_final: 0.7466 (ptmm) REVERT: E 298 GLN cc_start: 0.7941 (mt0) cc_final: 0.7632 (mt0) REVERT: E 324 LEU cc_start: 0.8705 (tp) cc_final: 0.7869 (tp) REVERT: E 325 ARG cc_start: 0.7758 (ttt-90) cc_final: 0.7430 (ttt180) REVERT: E 346 GLU cc_start: 0.7661 (tm-30) cc_final: 0.7296 (tm-30) REVERT: E 352 LYS cc_start: 0.7526 (tmtt) cc_final: 0.7240 (tmtt) REVERT: E 381 GLU cc_start: 0.7514 (mt-10) cc_final: 0.7279 (mt-10) REVERT: F 134 ASP cc_start: 0.7533 (t0) cc_final: 0.7261 (t0) REVERT: F 227 PHE cc_start: 0.7817 (p90) cc_final: 0.7404 (p90) REVERT: F 279 MET cc_start: 0.8430 (mmm) cc_final: 0.8041 (mmm) REVERT: F 280 LYS cc_start: 0.7822 (ptpp) cc_final: 0.7596 (ptpp) REVERT: F 281 LYS cc_start: 0.7744 (ptmt) cc_final: 0.7447 (ptmm) REVERT: F 298 GLN cc_start: 0.7908 (mt0) cc_final: 0.7589 (mt0) REVERT: F 324 LEU cc_start: 0.8704 (tp) cc_final: 0.7861 (tp) REVERT: F 325 ARG cc_start: 0.7761 (ttt-90) cc_final: 0.7426 (ttt180) REVERT: F 346 GLU cc_start: 0.7648 (tm-30) cc_final: 0.7337 (tm-30) REVERT: F 352 LYS cc_start: 0.7534 (tmtt) cc_final: 0.7249 (tmtt) REVERT: F 381 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7268 (mt-10) REVERT: G 134 ASP cc_start: 0.7555 (t0) cc_final: 0.7249 (t0) REVERT: G 148 LYS cc_start: 0.8084 (mtpt) cc_final: 0.7818 (mtpt) REVERT: G 227 PHE cc_start: 0.7816 (p90) cc_final: 0.7398 (p90) REVERT: G 279 MET cc_start: 0.8430 (mmm) cc_final: 0.8040 (mmm) REVERT: G 280 LYS cc_start: 0.7810 (ptpp) cc_final: 0.7578 (ptpp) REVERT: G 281 LYS cc_start: 0.7747 (ptmt) cc_final: 0.7452 (ptmm) REVERT: G 298 GLN cc_start: 0.7923 (mt0) cc_final: 0.7618 (mt0) REVERT: G 324 LEU cc_start: 0.8704 (tp) cc_final: 0.7864 (tp) REVERT: G 325 ARG cc_start: 0.7756 (ttt-90) cc_final: 0.7431 (ttt180) REVERT: G 346 GLU cc_start: 0.7662 (tm-30) cc_final: 0.7338 (tm-30) REVERT: G 352 LYS cc_start: 0.7535 (tmtt) cc_final: 0.7250 (tmtt) REVERT: G 381 GLU cc_start: 0.7502 (mt-10) cc_final: 0.7271 (mt-10) REVERT: H 134 ASP cc_start: 0.7548 (t0) cc_final: 0.7260 (t0) REVERT: H 227 PHE cc_start: 0.7819 (p90) cc_final: 0.7408 (p90) REVERT: H 279 MET cc_start: 0.8431 (mmm) cc_final: 0.8043 (mmm) REVERT: H 280 LYS cc_start: 0.7820 (ptpp) cc_final: 0.7595 (ptpp) REVERT: H 281 LYS cc_start: 0.7747 (ptmt) cc_final: 0.7455 (ptmm) REVERT: H 298 GLN cc_start: 0.7906 (mt0) cc_final: 0.7577 (mt0) REVERT: H 324 LEU cc_start: 0.8706 (tp) cc_final: 0.7863 (tp) REVERT: H 325 ARG cc_start: 0.7776 (ttt-90) cc_final: 0.7422 (ttt180) REVERT: H 346 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7322 (tm-30) REVERT: H 352 LYS cc_start: 0.7518 (tmtt) cc_final: 0.7240 (tmtt) REVERT: H 381 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7284 (mt-10) outliers start: 72 outliers final: 24 residues processed: 776 average time/residue: 0.1988 time to fit residues: 221.0686 Evaluate side-chains 571 residues out of total 2552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 547 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 408 ILE Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 408 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 320 LEU Chi-restraints excluded: chain F residue 408 ILE Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 320 LEU Chi-restraints excluded: chain G residue 408 ILE Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain H residue 408 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN A 131 ASN A 263 ASN B 96 ASN B 131 ASN B 263 ASN C 96 ASN C 131 ASN C 263 ASN D 96 ASN D 263 ASN E 96 ASN E 131 ASN E 263 ASN F 96 ASN F 131 ASN F 263 ASN G 96 ASN G 131 ASN G 263 ASN H 96 ASN H 131 ASN H 263 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.182811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.130568 restraints weight = 29509.103| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.78 r_work: 0.3218 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 23912 Z= 0.286 Angle : 0.672 7.454 32304 Z= 0.358 Chirality : 0.047 0.153 3472 Planarity : 0.006 0.050 4248 Dihedral : 5.498 53.687 3296 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.76 % Allowed : 10.23 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.15), residues: 2872 helix: 1.48 (0.15), residues: 1112 sheet: -0.10 (0.24), residues: 448 loop : -0.88 (0.14), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 208 TYR 0.016 0.002 TYR D 207 PHE 0.020 0.002 PHE C 225 TRP 0.009 0.002 TRP A 84 HIS 0.008 0.002 HIS F 99 Details of bonding type rmsd covalent geometry : bond 0.00677 (23912) covalent geometry : angle 0.67197 (32304) hydrogen bonds : bond 0.03978 ( 1000) hydrogen bonds : angle 4.60274 ( 2904) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 2552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 610 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8469 (tp) REVERT: A 251 TRP cc_start: 0.8617 (t60) cc_final: 0.8410 (t60) REVERT: A 281 LYS cc_start: 0.7806 (ptmt) cc_final: 0.7577 (ptmm) REVERT: A 298 GLN cc_start: 0.8049 (mt0) cc_final: 0.7698 (mt0) REVERT: A 300 ARG cc_start: 0.8251 (tpp80) cc_final: 0.7966 (tpt90) REVERT: A 325 ARG cc_start: 0.8052 (ttt-90) cc_final: 0.7801 (ttt180) REVERT: A 346 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7408 (tm-30) REVERT: A 352 LYS cc_start: 0.7727 (tmtt) cc_final: 0.7366 (tmtt) REVERT: B 250 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8502 (tp) REVERT: B 265 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7602 (tt0) REVERT: B 281 LYS cc_start: 0.7844 (ptmt) cc_final: 0.7614 (ptmm) REVERT: B 291 LYS cc_start: 0.7908 (mmmm) cc_final: 0.7608 (pttp) REVERT: B 298 GLN cc_start: 0.8018 (mt0) cc_final: 0.7663 (mt0) REVERT: B 300 ARG cc_start: 0.8300 (tpp80) cc_final: 0.7976 (tpt90) REVERT: B 325 ARG cc_start: 0.8055 (ttt-90) cc_final: 0.7809 (ttt180) REVERT: B 346 GLU cc_start: 0.7809 (tm-30) cc_final: 0.7483 (tm-30) REVERT: B 352 LYS cc_start: 0.7740 (tmtt) cc_final: 0.7380 (tmtt) REVERT: C 250 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8484 (tp) REVERT: C 265 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7582 (tt0) REVERT: C 281 LYS cc_start: 0.7824 (ptmt) cc_final: 0.7606 (ptmm) REVERT: C 291 LYS cc_start: 0.7903 (mmmm) cc_final: 0.7614 (pttp) REVERT: C 298 GLN cc_start: 0.8017 (mt0) cc_final: 0.7642 (mt0) REVERT: C 300 ARG cc_start: 0.8281 (tpp80) cc_final: 0.7978 (tpt90) REVERT: C 325 ARG cc_start: 0.8048 (ttt-90) cc_final: 0.7803 (ttt180) REVERT: C 344 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8443 (mp) REVERT: C 346 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7418 (tm-30) REVERT: C 352 LYS cc_start: 0.7724 (tmtt) cc_final: 0.7371 (tmtt) REVERT: D 250 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8494 (tp) REVERT: D 265 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7591 (tt0) REVERT: D 281 LYS cc_start: 0.7843 (ptmt) cc_final: 0.7617 (ptmm) REVERT: D 298 GLN cc_start: 0.8028 (mt0) cc_final: 0.7695 (mt0) REVERT: D 325 ARG cc_start: 0.8061 (ttt-90) cc_final: 0.7813 (ttt180) REVERT: D 346 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7438 (tm-30) REVERT: D 352 LYS cc_start: 0.7742 (tmtt) cc_final: 0.7386 (tmtt) REVERT: E 211 GLU cc_start: 0.7553 (pm20) cc_final: 0.7242 (pm20) REVERT: E 250 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8490 (tp) REVERT: E 251 TRP cc_start: 0.8615 (t60) cc_final: 0.8405 (t60) REVERT: E 265 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7568 (tt0) REVERT: E 281 LYS cc_start: 0.7821 (ptmt) cc_final: 0.7598 (ptmm) REVERT: E 298 GLN cc_start: 0.8041 (mt0) cc_final: 0.7705 (mt0) REVERT: E 300 ARG cc_start: 0.8268 (tpp80) cc_final: 0.7969 (tpt90) REVERT: E 325 ARG cc_start: 0.8044 (ttt-90) cc_final: 0.7798 (ttt180) REVERT: E 346 GLU cc_start: 0.7810 (tm-30) cc_final: 0.7403 (tm-30) REVERT: E 352 LYS cc_start: 0.7734 (tmtt) cc_final: 0.7371 (tmtt) REVERT: F 250 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8502 (tp) REVERT: F 251 TRP cc_start: 0.8631 (t60) cc_final: 0.8419 (t60) REVERT: F 265 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7594 (tt0) REVERT: F 280 LYS cc_start: 0.7923 (ptpp) cc_final: 0.7722 (ptpp) REVERT: F 281 LYS cc_start: 0.7801 (ptmt) cc_final: 0.7575 (ptmm) REVERT: F 291 LYS cc_start: 0.7913 (mmmm) cc_final: 0.7615 (pttp) REVERT: F 298 GLN cc_start: 0.8015 (mt0) cc_final: 0.7666 (mt0) REVERT: F 300 ARG cc_start: 0.8300 (tpp80) cc_final: 0.7972 (tpt90) REVERT: F 325 ARG cc_start: 0.8043 (ttt-90) cc_final: 0.7795 (ttt180) REVERT: F 346 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7432 (tm-30) REVERT: F 352 LYS cc_start: 0.7749 (tmtt) cc_final: 0.7387 (tmtt) REVERT: G 250 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8502 (tp) REVERT: G 251 TRP cc_start: 0.8627 (t60) cc_final: 0.8416 (t60) REVERT: G 265 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7579 (tt0) REVERT: G 280 LYS cc_start: 0.7905 (ptpp) cc_final: 0.7705 (ptpp) REVERT: G 281 LYS cc_start: 0.7811 (ptmt) cc_final: 0.7585 (ptmm) REVERT: G 298 GLN cc_start: 0.8030 (mt0) cc_final: 0.7701 (mt0) REVERT: G 325 ARG cc_start: 0.8040 (ttt-90) cc_final: 0.7792 (ttt180) REVERT: G 346 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7437 (tm-30) REVERT: G 352 LYS cc_start: 0.7744 (tmtt) cc_final: 0.7385 (tmtt) REVERT: H 211 GLU cc_start: 0.7561 (pm20) cc_final: 0.7210 (pm20) REVERT: H 251 TRP cc_start: 0.8612 (t60) cc_final: 0.8400 (t60) REVERT: H 265 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7595 (tt0) REVERT: H 280 LYS cc_start: 0.7928 (ptpp) cc_final: 0.7724 (ptpp) REVERT: H 281 LYS cc_start: 0.7806 (ptmt) cc_final: 0.7580 (ptmm) REVERT: H 291 LYS cc_start: 0.7895 (mmmm) cc_final: 0.7617 (pttp) REVERT: H 298 GLN cc_start: 0.8016 (mt0) cc_final: 0.7647 (mt0) REVERT: H 300 ARG cc_start: 0.8280 (tpp80) cc_final: 0.7969 (tpt90) REVERT: H 325 ARG cc_start: 0.8021 (ttt-90) cc_final: 0.7767 (ttt180) REVERT: H 346 GLU cc_start: 0.7808 (tm-30) cc_final: 0.7417 (tm-30) REVERT: H 352 LYS cc_start: 0.7734 (tmtt) cc_final: 0.7381 (tmtt) outliers start: 96 outliers final: 45 residues processed: 668 average time/residue: 0.2023 time to fit residues: 193.8447 Evaluate side-chains 611 residues out of total 2552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 558 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 127 GLN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 127 GLN Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 127 GLN Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 320 LEU Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 272 SER Chi-restraints excluded: chain G residue 320 LEU Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 127 GLN Chi-restraints excluded: chain H residue 236 THR Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 272 SER Chi-restraints excluded: chain H residue 320 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 194 optimal weight: 0.8980 chunk 116 optimal weight: 0.2980 chunk 27 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 216 optimal weight: 0.0670 chunk 195 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 170 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 ASN A 384 GLN A 391 ASN B 263 ASN B 384 GLN B 391 ASN C 263 ASN C 384 GLN C 391 ASN D 263 ASN D 384 GLN D 391 ASN E 263 ASN ** E 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 384 GLN E 391 ASN F 263 ASN F 384 GLN F 391 ASN G 263 ASN ** G 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 384 GLN G 391 ASN H 263 ASN ** H 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 384 GLN H 391 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.184778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.131929 restraints weight = 29660.478| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.86 r_work: 0.3280 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 23912 Z= 0.138 Angle : 0.600 6.659 32304 Z= 0.316 Chirality : 0.043 0.155 3472 Planarity : 0.005 0.043 4248 Dihedral : 4.970 46.138 3282 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 4.15 % Allowed : 14.34 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.15), residues: 2872 helix: 1.62 (0.15), residues: 1112 sheet: -0.24 (0.23), residues: 448 loop : -0.86 (0.15), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 340 TYR 0.012 0.001 TYR H 207 PHE 0.018 0.002 PHE D 227 TRP 0.009 0.001 TRP D 251 HIS 0.004 0.001 HIS F 99 Details of bonding type rmsd covalent geometry : bond 0.00331 (23912) covalent geometry : angle 0.59988 (32304) hydrogen bonds : bond 0.03302 ( 1000) hydrogen bonds : angle 4.47836 ( 2904) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 2552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 630 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.7516 (tt0) REVERT: A 225 PHE cc_start: 0.7949 (m-10) cc_final: 0.7722 (m-80) REVERT: A 250 ILE cc_start: 0.8604 (OUTLIER) cc_final: 0.8389 (tp) REVERT: A 265 GLU cc_start: 0.8299 (tt0) cc_final: 0.7972 (tt0) REVERT: A 281 LYS cc_start: 0.7774 (ptmt) cc_final: 0.7553 (ptmm) REVERT: A 298 GLN cc_start: 0.8095 (mt0) cc_final: 0.7711 (mt0) REVERT: A 300 ARG cc_start: 0.8107 (tpp80) cc_final: 0.7864 (tpt90) REVERT: A 346 GLU cc_start: 0.7828 (tm-30) cc_final: 0.7432 (tm-30) REVERT: A 352 LYS cc_start: 0.7596 (tmtt) cc_final: 0.7198 (tmtt) REVERT: B 127 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7518 (tt0) REVERT: B 148 LYS cc_start: 0.8437 (mtpt) cc_final: 0.8210 (mtpt) REVERT: B 225 PHE cc_start: 0.7932 (m-10) cc_final: 0.7720 (m-80) REVERT: B 250 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8407 (tp) REVERT: B 263 ASN cc_start: 0.8471 (OUTLIER) cc_final: 0.8269 (p0) REVERT: B 265 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7462 (tt0) REVERT: B 291 LYS cc_start: 0.7910 (mmmm) cc_final: 0.7584 (pttp) REVERT: B 298 GLN cc_start: 0.8067 (mt0) cc_final: 0.7639 (mt0) REVERT: B 300 ARG cc_start: 0.8121 (tpp80) cc_final: 0.7872 (tpt90) REVERT: B 331 LYS cc_start: 0.7007 (ptmt) cc_final: 0.6163 (tttm) REVERT: B 346 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7591 (tm-30) REVERT: B 352 LYS cc_start: 0.7647 (tmtt) cc_final: 0.7233 (tmtt) REVERT: C 127 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.7516 (tt0) REVERT: C 211 GLU cc_start: 0.7411 (pm20) cc_final: 0.7203 (pm20) REVERT: C 225 PHE cc_start: 0.7937 (m-10) cc_final: 0.7717 (m-80) REVERT: C 250 ILE cc_start: 0.8632 (OUTLIER) cc_final: 0.8418 (tp) REVERT: C 263 ASN cc_start: 0.8467 (OUTLIER) cc_final: 0.8267 (p0) REVERT: C 265 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7444 (tt0) REVERT: C 291 LYS cc_start: 0.7909 (mmmm) cc_final: 0.7599 (pttp) REVERT: C 298 GLN cc_start: 0.8070 (mt0) cc_final: 0.7616 (mt0) REVERT: C 300 ARG cc_start: 0.8129 (tpp80) cc_final: 0.7860 (tpt90) REVERT: C 344 ILE cc_start: 0.8732 (OUTLIER) cc_final: 0.8443 (mp) REVERT: C 346 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7467 (tm-30) REVERT: C 352 LYS cc_start: 0.7613 (tmtt) cc_final: 0.7209 (tmtt) REVERT: D 127 GLN cc_start: 0.7864 (OUTLIER) cc_final: 0.7492 (tt0) REVERT: D 148 LYS cc_start: 0.8444 (mtpt) cc_final: 0.8093 (mtmt) REVERT: D 211 GLU cc_start: 0.7420 (pm20) cc_final: 0.7187 (pm20) REVERT: D 225 PHE cc_start: 0.7935 (m-10) cc_final: 0.7709 (m-80) REVERT: D 250 ILE cc_start: 0.8637 (OUTLIER) cc_final: 0.8431 (tp) REVERT: D 265 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7446 (tt0) REVERT: D 281 LYS cc_start: 0.7783 (ptmt) cc_final: 0.7554 (ptmm) REVERT: D 298 GLN cc_start: 0.8081 (mt0) cc_final: 0.7675 (mt0) REVERT: D 325 ARG cc_start: 0.7873 (ttt-90) cc_final: 0.7608 (ttt180) REVERT: D 346 GLU cc_start: 0.7832 (tm-30) cc_final: 0.7466 (tm-30) REVERT: D 352 LYS cc_start: 0.7620 (tmtt) cc_final: 0.7226 (tmtt) REVERT: E 127 GLN cc_start: 0.7866 (OUTLIER) cc_final: 0.7518 (tt0) REVERT: E 211 GLU cc_start: 0.7462 (pm20) cc_final: 0.7131 (pm20) REVERT: E 225 PHE cc_start: 0.7946 (m-10) cc_final: 0.7734 (m-80) REVERT: E 250 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8412 (tp) REVERT: E 265 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7436 (tt0) REVERT: E 298 GLN cc_start: 0.8092 (mt0) cc_final: 0.7677 (mt0) REVERT: E 300 ARG cc_start: 0.8110 (tpp80) cc_final: 0.7875 (tpt90) REVERT: E 346 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7428 (tm-30) REVERT: E 352 LYS cc_start: 0.7614 (tmtt) cc_final: 0.7216 (tmtt) REVERT: F 127 GLN cc_start: 0.7843 (OUTLIER) cc_final: 0.7522 (tt0) REVERT: F 211 GLU cc_start: 0.7441 (pm20) cc_final: 0.7205 (pm20) REVERT: F 225 PHE cc_start: 0.7950 (m-10) cc_final: 0.7728 (m-80) REVERT: F 250 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8413 (tp) REVERT: F 265 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7464 (tt0) REVERT: F 291 LYS cc_start: 0.7910 (mmmm) cc_final: 0.7592 (pttp) REVERT: F 298 GLN cc_start: 0.8059 (mt0) cc_final: 0.7630 (mt0) REVERT: F 300 ARG cc_start: 0.8117 (tpp80) cc_final: 0.7857 (tpt90) REVERT: F 331 LYS cc_start: 0.7002 (ptmt) cc_final: 0.6163 (tttm) REVERT: F 346 GLU cc_start: 0.7832 (tm-30) cc_final: 0.7465 (tm-30) REVERT: F 352 LYS cc_start: 0.7620 (tmtt) cc_final: 0.7217 (tmtt) REVERT: G 127 GLN cc_start: 0.7866 (OUTLIER) cc_final: 0.7516 (tt0) REVERT: G 148 LYS cc_start: 0.8446 (mtpt) cc_final: 0.8159 (mtmt) REVERT: G 211 GLU cc_start: 0.7430 (pm20) cc_final: 0.7201 (pm20) REVERT: G 225 PHE cc_start: 0.7942 (m-10) cc_final: 0.7736 (m-80) REVERT: G 250 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8414 (tp) REVERT: G 265 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7438 (tt0) REVERT: G 298 GLN cc_start: 0.8057 (mt0) cc_final: 0.7648 (mt0) REVERT: G 325 ARG cc_start: 0.7869 (ttt-90) cc_final: 0.7595 (ttt180) REVERT: G 346 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7470 (tm-30) REVERT: G 352 LYS cc_start: 0.7635 (tmtt) cc_final: 0.7244 (tmtt) REVERT: H 127 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.7506 (tt0) REVERT: H 211 GLU cc_start: 0.7488 (pm20) cc_final: 0.7192 (pm20) REVERT: H 225 PHE cc_start: 0.7955 (m-10) cc_final: 0.7742 (m-80) REVERT: H 250 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8387 (tp) REVERT: H 263 ASN cc_start: 0.8460 (OUTLIER) cc_final: 0.8260 (p0) REVERT: H 265 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7440 (tt0) REVERT: H 291 LYS cc_start: 0.7905 (mmmm) cc_final: 0.7599 (pttp) REVERT: H 298 GLN cc_start: 0.8054 (mt0) cc_final: 0.7612 (mt0) REVERT: H 300 ARG cc_start: 0.8120 (tpp80) cc_final: 0.7862 (tpt90) REVERT: H 346 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7441 (tm-30) REVERT: H 352 LYS cc_start: 0.7608 (tmtt) cc_final: 0.7210 (tmtt) outliers start: 106 outliers final: 23 residues processed: 671 average time/residue: 0.1940 time to fit residues: 189.3312 Evaluate side-chains 605 residues out of total 2552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 562 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 127 GLN Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 95 ASP Chi-restraints excluded: chain C residue 127 GLN Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 263 ASN Chi-restraints excluded: chain C residue 280 LYS Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 127 GLN Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 199 LYS Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 280 LYS Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 127 GLN Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 127 GLN Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 166 THR Chi-restraints excluded: chain G residue 199 LYS Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 127 GLN Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 263 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 76 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 177 optimal weight: 5.9990 chunk 40 optimal weight: 0.0470 chunk 147 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 252 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 129 optimal weight: 5.9990 overall best weight: 1.8082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN A 263 ASN B 96 ASN ** B 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 ASN D 131 ASN D 263 ASN E 96 ASN E 263 ASN ** E 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 ASN F 263 ASN G 96 ASN G 263 ASN H 96 ASN ** H 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.181605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.127494 restraints weight = 29669.060| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.86 r_work: 0.3227 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 23912 Z= 0.208 Angle : 0.634 7.653 32304 Z= 0.332 Chirality : 0.044 0.164 3472 Planarity : 0.005 0.043 4248 Dihedral : 4.505 25.538 3266 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 4.51 % Allowed : 16.11 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.15), residues: 2872 helix: 1.46 (0.15), residues: 1112 sheet: -0.20 (0.23), residues: 448 loop : -0.95 (0.15), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 340 TYR 0.017 0.002 TYR A 207 PHE 0.018 0.002 PHE A 227 TRP 0.016 0.001 TRP A 251 HIS 0.004 0.001 HIS D 99 Details of bonding type rmsd covalent geometry : bond 0.00501 (23912) covalent geometry : angle 0.63351 (32304) hydrogen bonds : bond 0.03341 ( 1000) hydrogen bonds : angle 4.56626 ( 2904) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 2552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 579 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 VAL cc_start: 0.8699 (OUTLIER) cc_final: 0.8393 (t) REVERT: A 127 GLN cc_start: 0.7868 (OUTLIER) cc_final: 0.7502 (tt0) REVERT: A 225 PHE cc_start: 0.7991 (m-10) cc_final: 0.7775 (m-80) REVERT: A 250 ILE cc_start: 0.8626 (OUTLIER) cc_final: 0.8426 (tp) REVERT: A 263 ASN cc_start: 0.8746 (OUTLIER) cc_final: 0.8499 (p0) REVERT: A 265 GLU cc_start: 0.8355 (tt0) cc_final: 0.7916 (tt0) REVERT: A 298 GLN cc_start: 0.8172 (mt0) cc_final: 0.7843 (mt0) REVERT: A 300 ARG cc_start: 0.8162 (tpp80) cc_final: 0.7951 (tpt90) REVERT: A 331 LYS cc_start: 0.6929 (ptmt) cc_final: 0.6054 (tttm) REVERT: A 346 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7459 (tm-30) REVERT: A 352 LYS cc_start: 0.7649 (tmtt) cc_final: 0.7220 (tmtt) REVERT: B 105 VAL cc_start: 0.8698 (OUTLIER) cc_final: 0.8399 (t) REVERT: B 127 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.7514 (tt0) REVERT: B 165 ARG cc_start: 0.7264 (ttp80) cc_final: 0.6915 (ttp80) REVERT: B 225 PHE cc_start: 0.7984 (m-10) cc_final: 0.7757 (m-80) REVERT: B 250 ILE cc_start: 0.8649 (OUTLIER) cc_final: 0.8440 (tp) REVERT: B 262 VAL cc_start: 0.8977 (OUTLIER) cc_final: 0.8732 (t) REVERT: B 298 GLN cc_start: 0.8146 (mt0) cc_final: 0.7818 (mt0) REVERT: B 300 ARG cc_start: 0.8209 (tpp80) cc_final: 0.7983 (tpt90) REVERT: B 346 GLU cc_start: 0.7833 (tm-30) cc_final: 0.7478 (tm-30) REVERT: B 352 LYS cc_start: 0.7624 (tmtt) cc_final: 0.7215 (tmtt) REVERT: C 105 VAL cc_start: 0.8693 (OUTLIER) cc_final: 0.8396 (t) REVERT: C 127 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7492 (tt0) REVERT: C 225 PHE cc_start: 0.7957 (m-10) cc_final: 0.7754 (m-80) REVERT: C 250 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8446 (tp) REVERT: C 262 VAL cc_start: 0.8972 (OUTLIER) cc_final: 0.8734 (t) REVERT: C 298 GLN cc_start: 0.8085 (mt0) cc_final: 0.7734 (mt0) REVERT: C 300 ARG cc_start: 0.8175 (tpp80) cc_final: 0.7960 (tpt90) REVERT: C 331 LYS cc_start: 0.6887 (ptmt) cc_final: 0.6038 (tttp) REVERT: C 344 ILE cc_start: 0.8676 (OUTLIER) cc_final: 0.8361 (mp) REVERT: C 346 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7504 (tm-30) REVERT: C 352 LYS cc_start: 0.7633 (tmtt) cc_final: 0.7226 (tmtt) REVERT: D 105 VAL cc_start: 0.8702 (OUTLIER) cc_final: 0.8397 (t) REVERT: D 127 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.7479 (tt0) REVERT: D 225 PHE cc_start: 0.7980 (m-10) cc_final: 0.7769 (m-80) REVERT: D 250 ILE cc_start: 0.8664 (OUTLIER) cc_final: 0.8453 (tp) REVERT: D 263 ASN cc_start: 0.8633 (OUTLIER) cc_final: 0.8411 (p0) REVERT: D 265 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7531 (tt0) REVERT: D 281 LYS cc_start: 0.7764 (ptmt) cc_final: 0.7559 (ptmm) REVERT: D 298 GLN cc_start: 0.8068 (mt0) cc_final: 0.7774 (mt0) REVERT: D 331 LYS cc_start: 0.6895 (ptmt) cc_final: 0.6046 (tttm) REVERT: D 346 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7474 (tm-30) REVERT: D 352 LYS cc_start: 0.7655 (tmtt) cc_final: 0.7238 (tmtt) REVERT: E 105 VAL cc_start: 0.8698 (OUTLIER) cc_final: 0.8399 (t) REVERT: E 127 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.7526 (tt0) REVERT: E 211 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7367 (pm20) REVERT: E 225 PHE cc_start: 0.7992 (m-10) cc_final: 0.7772 (m-80) REVERT: E 250 ILE cc_start: 0.8600 (OUTLIER) cc_final: 0.8386 (tp) REVERT: E 263 ASN cc_start: 0.8595 (OUTLIER) cc_final: 0.8364 (p0) REVERT: E 298 GLN cc_start: 0.8096 (mt0) cc_final: 0.7791 (mt0) REVERT: E 331 LYS cc_start: 0.6917 (ptmt) cc_final: 0.6069 (tttm) REVERT: E 346 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7450 (tm-30) REVERT: E 352 LYS cc_start: 0.7650 (tmtt) cc_final: 0.7224 (tmtt) REVERT: F 105 VAL cc_start: 0.8711 (OUTLIER) cc_final: 0.8405 (t) REVERT: F 127 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.7519 (tt0) REVERT: F 211 GLU cc_start: 0.7573 (pm20) cc_final: 0.7188 (pm20) REVERT: F 225 PHE cc_start: 0.7978 (m-10) cc_final: 0.7767 (m-80) REVERT: F 250 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8441 (tp) REVERT: F 263 ASN cc_start: 0.8593 (OUTLIER) cc_final: 0.8354 (p0) REVERT: F 281 LYS cc_start: 0.7726 (ptmt) cc_final: 0.7523 (ptmm) REVERT: F 298 GLN cc_start: 0.8069 (mt0) cc_final: 0.7753 (mt0) REVERT: F 300 ARG cc_start: 0.8208 (tpp80) cc_final: 0.7974 (tpt90) REVERT: F 331 LYS cc_start: 0.7023 (ptmt) cc_final: 0.6222 (tttm) REVERT: F 346 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7463 (tm-30) REVERT: F 352 LYS cc_start: 0.7659 (tmtt) cc_final: 0.7224 (tmtt) REVERT: G 105 VAL cc_start: 0.8704 (OUTLIER) cc_final: 0.8400 (t) REVERT: G 127 GLN cc_start: 0.7836 (OUTLIER) cc_final: 0.7464 (tt0) REVERT: G 225 PHE cc_start: 0.7993 (m-10) cc_final: 0.7782 (m-80) REVERT: G 263 ASN cc_start: 0.8602 (OUTLIER) cc_final: 0.8368 (p0) REVERT: G 281 LYS cc_start: 0.7782 (ptmt) cc_final: 0.7563 (ptmm) REVERT: G 298 GLN cc_start: 0.8086 (mt0) cc_final: 0.7789 (mt0) REVERT: G 331 LYS cc_start: 0.6893 (ptmt) cc_final: 0.6047 (tttm) REVERT: G 346 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7480 (tm-30) REVERT: G 352 LYS cc_start: 0.7646 (tmtt) cc_final: 0.7226 (tmtt) REVERT: H 105 VAL cc_start: 0.8704 (OUTLIER) cc_final: 0.8404 (t) REVERT: H 127 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.7484 (tt0) REVERT: H 211 GLU cc_start: 0.7572 (pm20) cc_final: 0.7201 (pm20) REVERT: H 251 TRP cc_start: 0.8589 (t60) cc_final: 0.8354 (t60) REVERT: H 262 VAL cc_start: 0.8984 (OUTLIER) cc_final: 0.8743 (t) REVERT: H 281 LYS cc_start: 0.7729 (ptmt) cc_final: 0.7526 (ptmm) REVERT: H 298 GLN cc_start: 0.8068 (mt0) cc_final: 0.7741 (mt0) REVERT: H 300 ARG cc_start: 0.8198 (tpp80) cc_final: 0.7967 (tpt90) REVERT: H 331 LYS cc_start: 0.6881 (ptmt) cc_final: 0.6044 (tttm) REVERT: H 346 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7448 (tm-30) REVERT: H 352 LYS cc_start: 0.7623 (tmtt) cc_final: 0.7217 (tmtt) outliers start: 115 outliers final: 63 residues processed: 643 average time/residue: 0.1951 time to fit residues: 181.3640 Evaluate side-chains 640 residues out of total 2552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 545 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 127 GLN Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 273 MET Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain C residue 95 ASP Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 127 GLN Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 263 ASN Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 280 LYS Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 127 GLN Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain D residue 280 LYS Chi-restraints excluded: chain E residue 95 ASP Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 127 GLN Chi-restraints excluded: chain E residue 161 SER Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 263 ASN Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 273 MET Chi-restraints excluded: chain E residue 280 LYS Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 127 GLN Chi-restraints excluded: chain F residue 139 LYS Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 263 ASN Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 273 MET Chi-restraints excluded: chain G residue 95 ASP Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 161 SER Chi-restraints excluded: chain G residue 199 LYS Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 263 ASN Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 272 SER Chi-restraints excluded: chain G residue 273 MET Chi-restraints excluded: chain H residue 95 ASP Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 127 GLN Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain H residue 236 THR Chi-restraints excluded: chain H residue 262 VAL Chi-restraints excluded: chain H residue 263 ASN Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 272 SER Chi-restraints excluded: chain H residue 273 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 246 optimal weight: 3.9990 chunk 177 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 190 optimal weight: 20.0000 chunk 35 optimal weight: 7.9990 chunk 76 optimal weight: 0.7980 chunk 136 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 262 optimal weight: 20.0000 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 ASN B 263 ASN ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 263 ASN ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.185158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.133612 restraints weight = 29453.805| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.79 r_work: 0.3252 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23912 Z= 0.172 Angle : 0.610 7.324 32304 Z= 0.321 Chirality : 0.044 0.213 3472 Planarity : 0.005 0.050 4248 Dihedral : 4.313 19.036 3258 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.37 % Allowed : 18.57 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.15), residues: 2872 helix: 1.46 (0.15), residues: 1112 sheet: -0.19 (0.23), residues: 448 loop : -1.02 (0.15), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 205 TYR 0.017 0.001 TYR H 207 PHE 0.026 0.002 PHE H 225 TRP 0.011 0.001 TRP A 251 HIS 0.003 0.001 HIS B 99 Details of bonding type rmsd covalent geometry : bond 0.00412 (23912) covalent geometry : angle 0.61019 (32304) hydrogen bonds : bond 0.03195 ( 1000) hydrogen bonds : angle 4.53728 ( 2904) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 2552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 571 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.7507 (tt0) REVERT: A 225 PHE cc_start: 0.7984 (m-10) cc_final: 0.7765 (m-10) REVERT: A 265 GLU cc_start: 0.8412 (tt0) cc_final: 0.7862 (tt0) REVERT: A 298 GLN cc_start: 0.8135 (mt0) cc_final: 0.7815 (mt0) REVERT: A 331 LYS cc_start: 0.6965 (ptmt) cc_final: 0.6157 (tttm) REVERT: A 346 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7485 (tm-30) REVERT: A 352 LYS cc_start: 0.7642 (tmtt) cc_final: 0.7206 (tmtt) REVERT: B 127 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7549 (tt0) REVERT: B 165 ARG cc_start: 0.7295 (ttp80) cc_final: 0.6925 (ttp80) REVERT: B 225 PHE cc_start: 0.7972 (m-10) cc_final: 0.7762 (m-10) REVERT: B 265 GLU cc_start: 0.8467 (tt0) cc_final: 0.8103 (tt0) REVERT: B 298 GLN cc_start: 0.8113 (mt0) cc_final: 0.7782 (mt0) REVERT: B 346 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7503 (tm-30) REVERT: B 352 LYS cc_start: 0.7620 (tmtt) cc_final: 0.7201 (tmtt) REVERT: C 105 VAL cc_start: 0.8672 (OUTLIER) cc_final: 0.8363 (t) REVERT: C 127 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.7485 (tt0) REVERT: C 225 PHE cc_start: 0.7975 (m-10) cc_final: 0.7768 (m-10) REVERT: C 265 GLU cc_start: 0.8329 (tt0) cc_final: 0.7886 (tt0) REVERT: C 275 LYS cc_start: 0.8927 (mmtm) cc_final: 0.8636 (mmmt) REVERT: C 298 GLN cc_start: 0.8106 (mt0) cc_final: 0.7766 (mt0) REVERT: C 331 LYS cc_start: 0.6949 (ptmt) cc_final: 0.6161 (tttm) REVERT: C 340 ARG cc_start: 0.6031 (ttp-110) cc_final: 0.5605 (ttp-110) REVERT: C 344 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8359 (mp) REVERT: C 346 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7511 (tm-30) REVERT: C 352 LYS cc_start: 0.7636 (tmtt) cc_final: 0.7206 (tmtt) REVERT: D 127 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.7480 (tt0) REVERT: D 165 ARG cc_start: 0.7292 (ttp80) cc_final: 0.6938 (ttp80) REVERT: D 225 PHE cc_start: 0.7971 (m-10) cc_final: 0.7759 (m-10) REVERT: D 298 GLN cc_start: 0.8097 (mt0) cc_final: 0.7786 (mt0) REVERT: D 331 LYS cc_start: 0.6941 (ptmt) cc_final: 0.6162 (tttm) REVERT: D 346 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7461 (tm-30) REVERT: D 352 LYS cc_start: 0.7664 (tmtt) cc_final: 0.7229 (tmtt) REVERT: E 127 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7543 (tt0) REVERT: E 225 PHE cc_start: 0.7978 (m-10) cc_final: 0.7759 (m-10) REVERT: E 265 GLU cc_start: 0.8484 (tt0) cc_final: 0.8092 (tt0) REVERT: E 298 GLN cc_start: 0.8077 (mt0) cc_final: 0.7765 (mt0) REVERT: E 331 LYS cc_start: 0.6962 (ptmt) cc_final: 0.6192 (tttm) REVERT: E 346 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7464 (tm-30) REVERT: F 127 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.7517 (tt0) REVERT: F 165 ARG cc_start: 0.7295 (ttp80) cc_final: 0.6945 (ttp80) REVERT: F 265 GLU cc_start: 0.8466 (tt0) cc_final: 0.8102 (tt0) REVERT: F 298 GLN cc_start: 0.8054 (mt0) cc_final: 0.7726 (mt0) REVERT: F 331 LYS cc_start: 0.6967 (ptmt) cc_final: 0.5966 (tttm) REVERT: F 346 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7464 (tm-30) REVERT: F 352 LYS cc_start: 0.7660 (tmtt) cc_final: 0.7231 (tmtt) REVERT: G 127 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.7468 (tt0) REVERT: G 148 LYS cc_start: 0.8326 (mtpt) cc_final: 0.8124 (mtmt) REVERT: G 165 ARG cc_start: 0.7295 (ttp80) cc_final: 0.6945 (ttp80) REVERT: G 225 PHE cc_start: 0.8001 (m-10) cc_final: 0.7791 (m-80) REVERT: G 265 GLU cc_start: 0.8526 (tt0) cc_final: 0.8127 (tt0) REVERT: G 298 GLN cc_start: 0.8053 (mt0) cc_final: 0.7743 (mt0) REVERT: G 331 LYS cc_start: 0.6986 (ptmt) cc_final: 0.6213 (tttm) REVERT: G 346 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7481 (tm-30) REVERT: G 352 LYS cc_start: 0.7691 (tmtt) cc_final: 0.7263 (tmtt) REVERT: H 127 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.7477 (tt0) REVERT: H 211 GLU cc_start: 0.7514 (pm20) cc_final: 0.7266 (pm20) REVERT: H 265 GLU cc_start: 0.8323 (tt0) cc_final: 0.7902 (tt0) REVERT: H 275 LYS cc_start: 0.8892 (mmtm) cc_final: 0.8596 (mmmt) REVERT: H 298 GLN cc_start: 0.8041 (mt0) cc_final: 0.7705 (mt0) REVERT: H 331 LYS cc_start: 0.6945 (ptmt) cc_final: 0.6165 (tttm) REVERT: H 346 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7488 (tm-30) REVERT: H 352 LYS cc_start: 0.7659 (tmtt) cc_final: 0.7240 (tmtt) outliers start: 86 outliers final: 51 residues processed: 616 average time/residue: 0.1924 time to fit residues: 171.5075 Evaluate side-chains 585 residues out of total 2552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 524 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 127 GLN Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 273 MET Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain C residue 95 ASP Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 127 GLN Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 280 LYS Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 127 GLN Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain D residue 280 LYS Chi-restraints excluded: chain D residue 408 ILE Chi-restraints excluded: chain E residue 95 ASP Chi-restraints excluded: chain E residue 127 GLN Chi-restraints excluded: chain E residue 263 ASN Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 280 LYS Chi-restraints excluded: chain E residue 408 ILE Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain F residue 127 GLN Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 273 MET Chi-restraints excluded: chain F residue 280 LYS Chi-restraints excluded: chain G residue 95 ASP Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 139 LYS Chi-restraints excluded: chain G residue 199 LYS Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 272 SER Chi-restraints excluded: chain G residue 273 MET Chi-restraints excluded: chain G residue 280 LYS Chi-restraints excluded: chain G residue 408 ILE Chi-restraints excluded: chain H residue 95 ASP Chi-restraints excluded: chain H residue 127 GLN Chi-restraints excluded: chain H residue 161 SER Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 272 SER Chi-restraints excluded: chain H residue 273 MET Chi-restraints excluded: chain H residue 280 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 187 optimal weight: 0.8980 chunk 209 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 chunk 236 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 232 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 38 optimal weight: 4.9990 chunk 178 optimal weight: 10.0000 chunk 244 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 ASN ** B 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 263 ASN ** G 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 263 ASN ** H 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.185960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.133735 restraints weight = 29462.921| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.87 r_work: 0.3262 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 23912 Z= 0.137 Angle : 0.594 7.416 32304 Z= 0.312 Chirality : 0.043 0.194 3472 Planarity : 0.005 0.051 4248 Dihedral : 4.169 16.523 3256 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.13 % Allowed : 19.55 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.15), residues: 2872 helix: 1.54 (0.15), residues: 1112 sheet: -0.24 (0.23), residues: 448 loop : -1.01 (0.15), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 43 TYR 0.012 0.001 TYR H 207 PHE 0.022 0.002 PHE H 225 TRP 0.020 0.001 TRP H 251 HIS 0.003 0.001 HIS B 99 Details of bonding type rmsd covalent geometry : bond 0.00329 (23912) covalent geometry : angle 0.59449 (32304) hydrogen bonds : bond 0.02922 ( 1000) hydrogen bonds : angle 4.48900 ( 2904) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 2552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 557 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 VAL cc_start: 0.8649 (OUTLIER) cc_final: 0.8332 (t) REVERT: A 111 ASP cc_start: 0.8413 (m-30) cc_final: 0.8207 (m-30) REVERT: A 127 GLN cc_start: 0.7814 (mm-40) cc_final: 0.7498 (tt0) REVERT: A 265 GLU cc_start: 0.8348 (tt0) cc_final: 0.8003 (tt0) REVERT: A 298 GLN cc_start: 0.8165 (mt0) cc_final: 0.7835 (mt0) REVERT: A 331 LYS cc_start: 0.7143 (ptmt) cc_final: 0.6319 (tttm) REVERT: A 346 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7466 (tm-30) REVERT: B 53 TYR cc_start: 0.8589 (t80) cc_final: 0.8278 (t80) REVERT: B 105 VAL cc_start: 0.8624 (OUTLIER) cc_final: 0.8308 (t) REVERT: B 127 GLN cc_start: 0.7851 (OUTLIER) cc_final: 0.7507 (tt0) REVERT: B 265 GLU cc_start: 0.8397 (tt0) cc_final: 0.8101 (tt0) REVERT: B 298 GLN cc_start: 0.8126 (mt0) cc_final: 0.7800 (mt0) REVERT: B 331 LYS cc_start: 0.6240 (ptpp) cc_final: 0.5649 (tttm) REVERT: B 346 GLU cc_start: 0.7819 (tm-30) cc_final: 0.7458 (tm-30) REVERT: B 352 LYS cc_start: 0.7510 (tmtt) cc_final: 0.7076 (tmtt) REVERT: C 53 TYR cc_start: 0.8594 (t80) cc_final: 0.8276 (t80) REVERT: C 127 GLN cc_start: 0.7821 (OUTLIER) cc_final: 0.7492 (tt0) REVERT: C 265 GLU cc_start: 0.8361 (tt0) cc_final: 0.8036 (tt0) REVERT: C 298 GLN cc_start: 0.8127 (mt0) cc_final: 0.7779 (mt0) REVERT: C 331 LYS cc_start: 0.7079 (ptmt) cc_final: 0.6266 (tttm) REVERT: C 344 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8343 (mp) REVERT: C 346 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7524 (tm-30) REVERT: C 352 LYS cc_start: 0.7571 (tmtt) cc_final: 0.7135 (tmtt) REVERT: D 105 VAL cc_start: 0.8620 (OUTLIER) cc_final: 0.8309 (t) REVERT: D 127 GLN cc_start: 0.7826 (OUTLIER) cc_final: 0.7489 (tt0) REVERT: D 225 PHE cc_start: 0.7975 (m-10) cc_final: 0.7775 (m-10) REVERT: D 298 GLN cc_start: 0.8137 (mt0) cc_final: 0.7827 (mt0) REVERT: D 331 LYS cc_start: 0.7117 (ptmt) cc_final: 0.6318 (tttm) REVERT: D 346 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7477 (tm-30) REVERT: D 352 LYS cc_start: 0.7620 (tmtt) cc_final: 0.7170 (tmtt) REVERT: E 105 VAL cc_start: 0.8652 (OUTLIER) cc_final: 0.8341 (t) REVERT: E 127 GLN cc_start: 0.7864 (OUTLIER) cc_final: 0.7511 (tt0) REVERT: E 265 GLU cc_start: 0.8556 (tt0) cc_final: 0.8285 (tt0) REVERT: E 298 GLN cc_start: 0.8180 (mt0) cc_final: 0.7856 (mt0) REVERT: E 331 LYS cc_start: 0.7143 (ptmt) cc_final: 0.6355 (tttm) REVERT: E 346 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7439 (tm-30) REVERT: F 105 VAL cc_start: 0.8650 (OUTLIER) cc_final: 0.8331 (t) REVERT: F 127 GLN cc_start: 0.7837 (OUTLIER) cc_final: 0.7499 (tt0) REVERT: F 225 PHE cc_start: 0.7873 (m-10) cc_final: 0.7634 (m-80) REVERT: F 265 GLU cc_start: 0.8503 (tt0) cc_final: 0.8205 (tt0) REVERT: F 298 GLN cc_start: 0.8140 (mt0) cc_final: 0.7811 (mt0) REVERT: F 331 LYS cc_start: 0.7100 (ptmt) cc_final: 0.6065 (tttm) REVERT: F 346 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7485 (tm-30) REVERT: F 352 LYS cc_start: 0.7675 (tmtt) cc_final: 0.7234 (tmtt) REVERT: G 105 VAL cc_start: 0.8650 (OUTLIER) cc_final: 0.8325 (t) REVERT: G 127 GLN cc_start: 0.7795 (OUTLIER) cc_final: 0.7485 (tt0) REVERT: G 265 GLU cc_start: 0.8498 (tt0) cc_final: 0.8199 (tt0) REVERT: G 275 LYS cc_start: 0.8962 (mmtm) cc_final: 0.8591 (mmmt) REVERT: G 298 GLN cc_start: 0.8139 (mt0) cc_final: 0.7817 (mt0) REVERT: G 331 LYS cc_start: 0.7149 (ptmt) cc_final: 0.6247 (tttm) REVERT: G 346 GLU cc_start: 0.7857 (tm-30) cc_final: 0.7478 (tm-30) REVERT: G 352 LYS cc_start: 0.7700 (tmtt) cc_final: 0.7244 (tmtt) REVERT: H 43 ARG cc_start: 0.7816 (mmm160) cc_final: 0.7607 (mmm160) REVERT: H 105 VAL cc_start: 0.8629 (OUTLIER) cc_final: 0.8317 (t) REVERT: H 127 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.7467 (tt0) REVERT: H 256 LYS cc_start: 0.6924 (mptt) cc_final: 0.6675 (mppt) REVERT: H 265 GLU cc_start: 0.8362 (tt0) cc_final: 0.8027 (tt0) REVERT: H 275 LYS cc_start: 0.8904 (mmtm) cc_final: 0.8529 (mmmt) REVERT: H 298 GLN cc_start: 0.8119 (mt0) cc_final: 0.7777 (mt0) REVERT: H 331 LYS cc_start: 0.7128 (ptmt) cc_final: 0.6320 (tttm) REVERT: H 346 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7479 (tm-30) REVERT: H 352 LYS cc_start: 0.7687 (tmtt) cc_final: 0.7241 (tmtt) outliers start: 80 outliers final: 30 residues processed: 593 average time/residue: 0.1836 time to fit residues: 161.4803 Evaluate side-chains 559 residues out of total 2552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 514 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain C residue 95 ASP Chi-restraints excluded: chain C residue 127 GLN Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 280 LYS Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 127 GLN Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 280 LYS Chi-restraints excluded: chain E residue 95 ASP Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 127 GLN Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 280 LYS Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 127 GLN Chi-restraints excluded: chain F residue 139 LYS Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 263 ASN Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 280 LYS Chi-restraints excluded: chain G residue 95 ASP Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 139 LYS Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain G residue 263 ASN Chi-restraints excluded: chain H residue 95 ASP Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 127 GLN Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 280 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 52 optimal weight: 4.9990 chunk 272 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 chunk 153 optimal weight: 5.9990 chunk 198 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 214 optimal weight: 0.9980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 218 GLN ** H 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.182176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.129984 restraints weight = 29517.510| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.89 r_work: 0.3190 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 23912 Z= 0.275 Angle : 0.696 10.299 32304 Z= 0.363 Chirality : 0.048 0.217 3472 Planarity : 0.006 0.054 4248 Dihedral : 4.527 16.817 3256 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.80 % Allowed : 19.20 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.15), residues: 2872 helix: 1.18 (0.15), residues: 1112 sheet: -0.34 (0.24), residues: 448 loop : -1.11 (0.15), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 43 TYR 0.019 0.002 TYR E 207 PHE 0.025 0.002 PHE H 225 TRP 0.013 0.002 TRP H 251 HIS 0.003 0.001 HIS F 99 Details of bonding type rmsd covalent geometry : bond 0.00657 (23912) covalent geometry : angle 0.69646 (32304) hydrogen bonds : bond 0.03674 ( 1000) hydrogen bonds : angle 4.70252 ( 2904) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 2552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 505 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ASN cc_start: 0.8348 (m-40) cc_final: 0.8107 (m-40) REVERT: A 105 VAL cc_start: 0.8737 (OUTLIER) cc_final: 0.8478 (t) REVERT: A 127 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.7509 (tt0) REVERT: A 265 GLU cc_start: 0.8466 (tt0) cc_final: 0.8177 (tt0) REVERT: A 298 GLN cc_start: 0.8126 (mt0) cc_final: 0.7812 (mt0) REVERT: A 331 LYS cc_start: 0.7112 (ptmt) cc_final: 0.6299 (tttm) REVERT: A 346 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7489 (tm-30) REVERT: B 96 ASN cc_start: 0.8330 (m-40) cc_final: 0.8082 (m-40) REVERT: B 105 VAL cc_start: 0.8722 (OUTLIER) cc_final: 0.8464 (t) REVERT: B 127 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7510 (tt0) REVERT: B 211 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.7150 (pm20) REVERT: B 265 GLU cc_start: 0.8547 (tt0) cc_final: 0.8282 (tt0) REVERT: B 298 GLN cc_start: 0.8100 (mt0) cc_final: 0.7777 (mt0) REVERT: B 346 GLU cc_start: 0.7844 (tm-30) cc_final: 0.7489 (tm-30) REVERT: B 352 LYS cc_start: 0.7652 (tmtt) cc_final: 0.7219 (tmtt) REVERT: C 96 ASN cc_start: 0.8349 (m-40) cc_final: 0.8103 (m-40) REVERT: C 105 VAL cc_start: 0.8731 (OUTLIER) cc_final: 0.8451 (t) REVERT: C 127 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7492 (tt0) REVERT: C 211 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7182 (mm-30) REVERT: C 225 PHE cc_start: 0.7793 (m-10) cc_final: 0.7588 (m-80) REVERT: C 265 GLU cc_start: 0.8490 (tt0) cc_final: 0.8181 (tt0) REVERT: C 298 GLN cc_start: 0.8105 (mt0) cc_final: 0.7770 (mt0) REVERT: C 331 LYS cc_start: 0.7104 (ptmt) cc_final: 0.6280 (tttm) REVERT: C 346 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7511 (tm-30) REVERT: C 352 LYS cc_start: 0.7639 (tmtt) cc_final: 0.7212 (tmtt) REVERT: D 96 ASN cc_start: 0.8344 (m-40) cc_final: 0.8098 (m-40) REVERT: D 105 VAL cc_start: 0.8717 (OUTLIER) cc_final: 0.8440 (t) REVERT: D 127 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.7492 (tt0) REVERT: D 211 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7333 (pm20) REVERT: D 225 PHE cc_start: 0.8023 (m-10) cc_final: 0.7768 (m-10) REVERT: D 251 TRP cc_start: 0.8565 (t60) cc_final: 0.8228 (t60) REVERT: D 298 GLN cc_start: 0.8133 (mt0) cc_final: 0.7817 (mt0) REVERT: D 331 LYS cc_start: 0.7088 (ptmt) cc_final: 0.6284 (tttm) REVERT: D 346 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7495 (tm-30) REVERT: E 96 ASN cc_start: 0.8339 (m-40) cc_final: 0.8096 (m-40) REVERT: E 105 VAL cc_start: 0.8733 (OUTLIER) cc_final: 0.8452 (t) REVERT: E 127 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7568 (tt0) REVERT: E 265 GLU cc_start: 0.8601 (tt0) cc_final: 0.8316 (tt0) REVERT: E 298 GLN cc_start: 0.8146 (mt0) cc_final: 0.7827 (mt0) REVERT: E 331 LYS cc_start: 0.7120 (ptmt) cc_final: 0.6306 (tttm) REVERT: E 346 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7465 (tm-30) REVERT: F 96 ASN cc_start: 0.8328 (m-40) cc_final: 0.8070 (m-40) REVERT: F 105 VAL cc_start: 0.8735 (OUTLIER) cc_final: 0.8477 (t) REVERT: F 127 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7509 (tt0) REVERT: F 225 PHE cc_start: 0.7967 (m-10) cc_final: 0.7682 (m-80) REVERT: F 265 GLU cc_start: 0.8553 (tt0) cc_final: 0.8341 (tt0) REVERT: F 298 GLN cc_start: 0.8129 (mt0) cc_final: 0.7804 (mt0) REVERT: F 331 LYS cc_start: 0.6964 (ptmt) cc_final: 0.5966 (tttm) REVERT: F 346 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7512 (tm-30) REVERT: F 352 LYS cc_start: 0.7695 (tmtt) cc_final: 0.7265 (tmtt) REVERT: G 96 ASN cc_start: 0.8345 (m-40) cc_final: 0.8106 (m-40) REVERT: G 105 VAL cc_start: 0.8728 (OUTLIER) cc_final: 0.8473 (t) REVERT: G 127 GLN cc_start: 0.7959 (OUTLIER) cc_final: 0.7465 (tt0) REVERT: G 211 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7358 (pm20) REVERT: G 225 PHE cc_start: 0.7891 (m-10) cc_final: 0.7691 (m-80) REVERT: G 265 GLU cc_start: 0.8575 (tt0) cc_final: 0.8360 (tt0) REVERT: G 298 GLN cc_start: 0.8130 (mt0) cc_final: 0.7817 (mt0) REVERT: G 331 LYS cc_start: 0.7124 (ptmt) cc_final: 0.6238 (tttm) REVERT: G 346 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7487 (tm-30) REVERT: H 96 ASN cc_start: 0.8343 (m-40) cc_final: 0.8102 (m-40) REVERT: H 105 VAL cc_start: 0.8723 (OUTLIER) cc_final: 0.8443 (t) REVERT: H 127 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7487 (tt0) REVERT: H 211 GLU cc_start: 0.7631 (pm20) cc_final: 0.7399 (pm20) REVERT: H 265 GLU cc_start: 0.8525 (tt0) cc_final: 0.8200 (tt0) REVERT: H 298 GLN cc_start: 0.8125 (mt0) cc_final: 0.7790 (mt0) REVERT: H 331 LYS cc_start: 0.7108 (ptmt) cc_final: 0.6260 (tttp) REVERT: H 346 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7516 (tm-30) REVERT: H 352 LYS cc_start: 0.7665 (tmtt) cc_final: 0.7241 (tmtt) outliers start: 97 outliers final: 64 residues processed: 542 average time/residue: 0.1836 time to fit residues: 147.3247 Evaluate side-chains 575 residues out of total 2552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 491 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 127 GLN Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 273 MET Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 127 GLN Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 280 LYS Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 99 HIS Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 127 GLN Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 280 LYS Chi-restraints excluded: chain E residue 95 ASP Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 127 GLN Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 280 LYS Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 408 ILE Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 127 GLN Chi-restraints excluded: chain F residue 139 LYS Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 280 LYS Chi-restraints excluded: chain G residue 95 ASP Chi-restraints excluded: chain G residue 99 HIS Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 139 LYS Chi-restraints excluded: chain G residue 211 GLU Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 272 SER Chi-restraints excluded: chain G residue 280 LYS Chi-restraints excluded: chain G residue 408 ILE Chi-restraints excluded: chain H residue 95 ASP Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 127 GLN Chi-restraints excluded: chain H residue 236 THR Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 272 SER Chi-restraints excluded: chain H residue 280 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 264 optimal weight: 6.9990 chunk 238 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 174 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 282 optimal weight: 0.7980 chunk 271 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 chunk 246 optimal weight: 0.0870 chunk 139 optimal weight: 6.9990 overall best weight: 0.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.186220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.133616 restraints weight = 29344.567| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.94 r_work: 0.3240 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23912 Z= 0.146 Angle : 0.628 8.907 32304 Z= 0.326 Chirality : 0.044 0.206 3472 Planarity : 0.005 0.057 4248 Dihedral : 4.274 16.158 3256 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.55 % Allowed : 20.85 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.15), residues: 2872 helix: 1.39 (0.15), residues: 1112 sheet: -0.37 (0.23), residues: 448 loop : -1.07 (0.15), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 340 TYR 0.014 0.001 TYR C 47 PHE 0.026 0.002 PHE E 225 TRP 0.015 0.001 TRP H 251 HIS 0.003 0.001 HIS B 99 Details of bonding type rmsd covalent geometry : bond 0.00348 (23912) covalent geometry : angle 0.62756 (32304) hydrogen bonds : bond 0.02950 ( 1000) hydrogen bonds : angle 4.59234 ( 2904) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 2552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 523 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ASN cc_start: 0.8160 (m-40) cc_final: 0.7889 (m-40) REVERT: A 105 VAL cc_start: 0.8644 (OUTLIER) cc_final: 0.8371 (t) REVERT: A 127 GLN cc_start: 0.7905 (OUTLIER) cc_final: 0.7506 (tt0) REVERT: A 265 GLU cc_start: 0.8354 (tt0) cc_final: 0.8070 (tt0) REVERT: A 298 GLN cc_start: 0.8187 (mt0) cc_final: 0.7856 (mt0) REVERT: A 331 LYS cc_start: 0.7224 (ptmt) cc_final: 0.6420 (tttm) REVERT: A 346 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7488 (tm-30) REVERT: B 53 TYR cc_start: 0.8606 (t80) cc_final: 0.8246 (t80) REVERT: B 105 VAL cc_start: 0.8646 (OUTLIER) cc_final: 0.8377 (t) REVERT: B 127 GLN cc_start: 0.7952 (OUTLIER) cc_final: 0.7507 (tt0) REVERT: B 211 GLU cc_start: 0.7335 (pm20) cc_final: 0.7094 (pm20) REVERT: B 265 GLU cc_start: 0.8418 (tt0) cc_final: 0.8137 (tt0) REVERT: B 298 GLN cc_start: 0.8158 (mt0) cc_final: 0.7832 (mt0) REVERT: B 346 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7464 (tm-30) REVERT: B 352 LYS cc_start: 0.7617 (tmtt) cc_final: 0.7185 (tmtt) REVERT: C 53 TYR cc_start: 0.8603 (t80) cc_final: 0.8186 (t80) REVERT: C 96 ASN cc_start: 0.8168 (m-40) cc_final: 0.7892 (m-40) REVERT: C 105 VAL cc_start: 0.8652 (OUTLIER) cc_final: 0.8382 (t) REVERT: C 127 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7491 (tt0) REVERT: C 211 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7445 (pm20) REVERT: C 251 TRP cc_start: 0.8471 (t60) cc_final: 0.8167 (t60) REVERT: C 265 GLU cc_start: 0.8376 (tt0) cc_final: 0.8018 (tt0) REVERT: C 298 GLN cc_start: 0.8158 (mt0) cc_final: 0.7808 (mt0) REVERT: C 331 LYS cc_start: 0.7184 (ptmt) cc_final: 0.6374 (tttm) REVERT: C 346 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7596 (tm-30) REVERT: C 352 LYS cc_start: 0.7561 (tmtt) cc_final: 0.7125 (tmtt) REVERT: D 105 VAL cc_start: 0.8621 (OUTLIER) cc_final: 0.8330 (t) REVERT: D 127 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.7445 (tt0) REVERT: D 251 TRP cc_start: 0.8477 (t60) cc_final: 0.8128 (t60) REVERT: D 298 GLN cc_start: 0.8166 (mt0) cc_final: 0.7873 (mt0) REVERT: D 331 LYS cc_start: 0.7191 (ptmt) cc_final: 0.6380 (tttm) REVERT: D 346 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7492 (tm-30) REVERT: E 105 VAL cc_start: 0.8648 (OUTLIER) cc_final: 0.8356 (t) REVERT: E 127 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7571 (tt0) REVERT: E 265 GLU cc_start: 0.8442 (tt0) cc_final: 0.8118 (tt0) REVERT: E 298 GLN cc_start: 0.8187 (mt0) cc_final: 0.7851 (mt0) REVERT: E 331 LYS cc_start: 0.7275 (ptmt) cc_final: 0.6363 (tttm) REVERT: E 346 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7531 (tm-30) REVERT: F 105 VAL cc_start: 0.8642 (OUTLIER) cc_final: 0.8371 (t) REVERT: F 127 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.7478 (tt0) REVERT: F 225 PHE cc_start: 0.7904 (m-10) cc_final: 0.7630 (m-80) REVERT: F 265 GLU cc_start: 0.8433 (tt0) cc_final: 0.8097 (tt0) REVERT: F 298 GLN cc_start: 0.8162 (mt0) cc_final: 0.7820 (mt0) REVERT: F 331 LYS cc_start: 0.7113 (ptmt) cc_final: 0.6107 (tttm) REVERT: F 346 GLU cc_start: 0.7833 (tm-30) cc_final: 0.7478 (tm-30) REVERT: G 105 VAL cc_start: 0.8641 (OUTLIER) cc_final: 0.8370 (t) REVERT: G 127 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7433 (tt0) REVERT: G 251 TRP cc_start: 0.8473 (t60) cc_final: 0.8159 (t60) REVERT: G 265 GLU cc_start: 0.8402 (tt0) cc_final: 0.8085 (tt0) REVERT: G 298 GLN cc_start: 0.8167 (mt0) cc_final: 0.7866 (mt0) REVERT: G 331 LYS cc_start: 0.7252 (ptmt) cc_final: 0.6347 (tttm) REVERT: G 346 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7493 (tm-30) REVERT: H 105 VAL cc_start: 0.8637 (OUTLIER) cc_final: 0.8319 (t) REVERT: H 127 GLN cc_start: 0.7864 (OUTLIER) cc_final: 0.7453 (tt0) REVERT: H 265 GLU cc_start: 0.8359 (tt0) cc_final: 0.8022 (tt0) REVERT: H 298 GLN cc_start: 0.8155 (mt0) cc_final: 0.7799 (mt0) REVERT: H 331 LYS cc_start: 0.7247 (ptmt) cc_final: 0.6361 (tttm) REVERT: H 346 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7492 (tm-30) outliers start: 65 outliers final: 33 residues processed: 553 average time/residue: 0.1808 time to fit residues: 149.5910 Evaluate side-chains 544 residues out of total 2552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 494 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 127 GLN Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 127 GLN Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 280 LYS Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 127 GLN Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 280 LYS Chi-restraints excluded: chain E residue 95 ASP Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 127 GLN Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 280 LYS Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 127 GLN Chi-restraints excluded: chain F residue 139 LYS Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 280 LYS Chi-restraints excluded: chain G residue 95 ASP Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 139 LYS Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain G residue 280 LYS Chi-restraints excluded: chain H residue 95 ASP Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 127 GLN Chi-restraints excluded: chain H residue 272 SER Chi-restraints excluded: chain H residue 280 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 227 optimal weight: 9.9990 chunk 130 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 72 optimal weight: 0.4980 chunk 119 optimal weight: 9.9990 chunk 51 optimal weight: 0.1980 chunk 253 optimal weight: 3.9990 chunk 57 optimal weight: 0.0770 chunk 234 optimal weight: 0.0000 chunk 92 optimal weight: 0.7980 chunk 287 optimal weight: 9.9990 overall best weight: 0.3142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.189174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.136968 restraints weight = 29388.648| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.97 r_work: 0.3285 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23912 Z= 0.125 Angle : 0.634 8.257 32304 Z= 0.326 Chirality : 0.043 0.178 3472 Planarity : 0.005 0.050 4248 Dihedral : 4.115 17.996 3256 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.08 % Allowed : 21.98 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.15), residues: 2872 helix: 1.33 (0.15), residues: 1160 sheet: -0.42 (0.23), residues: 448 loop : -1.26 (0.15), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 340 TYR 0.010 0.001 TYR G 47 PHE 0.028 0.002 PHE E 225 TRP 0.020 0.001 TRP H 251 HIS 0.003 0.001 HIS G 99 Details of bonding type rmsd covalent geometry : bond 0.00287 (23912) covalent geometry : angle 0.63359 (32304) hydrogen bonds : bond 0.02804 ( 1000) hydrogen bonds : angle 4.58247 ( 2904) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 2552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 531 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 TYR cc_start: 0.8555 (t80) cc_final: 0.8165 (t80) REVERT: A 105 VAL cc_start: 0.8578 (OUTLIER) cc_final: 0.8281 (t) REVERT: A 127 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7489 (tt0) REVERT: A 251 TRP cc_start: 0.8386 (t60) cc_final: 0.8045 (t60) REVERT: A 265 GLU cc_start: 0.8341 (tt0) cc_final: 0.8061 (tt0) REVERT: A 298 GLN cc_start: 0.8150 (mt0) cc_final: 0.7832 (mt0) REVERT: A 331 LYS cc_start: 0.7224 (ptmt) cc_final: 0.6290 (tttm) REVERT: A 346 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7547 (tm-30) REVERT: A 352 LYS cc_start: 0.7701 (tmtt) cc_final: 0.6867 (tptp) REVERT: B 53 TYR cc_start: 0.8543 (t80) cc_final: 0.8133 (t80) REVERT: B 105 VAL cc_start: 0.8584 (OUTLIER) cc_final: 0.8289 (t) REVERT: B 127 GLN cc_start: 0.7877 (OUTLIER) cc_final: 0.7450 (tt0) REVERT: B 251 TRP cc_start: 0.8566 (t60) cc_final: 0.8288 (t60) REVERT: B 265 GLU cc_start: 0.8415 (tt0) cc_final: 0.8162 (tt0) REVERT: B 298 GLN cc_start: 0.8132 (mt0) cc_final: 0.7807 (mt0) REVERT: B 346 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7486 (tm-30) REVERT: C 53 TYR cc_start: 0.8526 (t80) cc_final: 0.8116 (t80) REVERT: C 105 VAL cc_start: 0.8577 (OUTLIER) cc_final: 0.8284 (t) REVERT: C 127 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.7415 (tt0) REVERT: C 205 ARG cc_start: 0.7148 (ttm110) cc_final: 0.6943 (ttm110) REVERT: C 251 TRP cc_start: 0.8449 (t60) cc_final: 0.8125 (t60) REVERT: C 265 GLU cc_start: 0.8295 (tt0) cc_final: 0.7947 (tt0) REVERT: C 298 GLN cc_start: 0.8114 (mt0) cc_final: 0.7775 (mt0) REVERT: C 331 LYS cc_start: 0.7214 (ptmt) cc_final: 0.6257 (tttp) REVERT: C 346 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7605 (tm-30) REVERT: D 53 TYR cc_start: 0.8536 (t80) cc_final: 0.8137 (t80) REVERT: D 105 VAL cc_start: 0.8579 (OUTLIER) cc_final: 0.8288 (t) REVERT: D 127 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.7422 (tt0) REVERT: D 251 TRP cc_start: 0.8480 (t60) cc_final: 0.8133 (t60) REVERT: D 275 LYS cc_start: 0.8991 (mmtm) cc_final: 0.8618 (mmmt) REVERT: D 298 GLN cc_start: 0.8130 (mt0) cc_final: 0.7818 (mt0) REVERT: D 331 LYS cc_start: 0.7197 (ptmt) cc_final: 0.6259 (tttm) REVERT: D 346 GLU cc_start: 0.7857 (tm-30) cc_final: 0.7554 (tm-30) REVERT: D 352 LYS cc_start: 0.7833 (tmtt) cc_final: 0.7043 (tptp) REVERT: E 53 TYR cc_start: 0.8541 (t80) cc_final: 0.8149 (t80) REVERT: E 105 VAL cc_start: 0.8589 (OUTLIER) cc_final: 0.8297 (t) REVERT: E 127 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7510 (tt0) REVERT: E 251 TRP cc_start: 0.8551 (t60) cc_final: 0.8283 (t60) REVERT: E 265 GLU cc_start: 0.8396 (tt0) cc_final: 0.8082 (tt0) REVERT: E 266 ASP cc_start: 0.8244 (t0) cc_final: 0.8042 (t0) REVERT: E 298 GLN cc_start: 0.8151 (mt0) cc_final: 0.7831 (mt0) REVERT: E 331 LYS cc_start: 0.7220 (ptmt) cc_final: 0.6288 (tttm) REVERT: E 346 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7547 (tm-30) REVERT: F 53 TYR cc_start: 0.8534 (t80) cc_final: 0.8143 (t80) REVERT: F 105 VAL cc_start: 0.8582 (OUTLIER) cc_final: 0.8280 (t) REVERT: F 127 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.7408 (tt0) REVERT: F 225 PHE cc_start: 0.7830 (m-10) cc_final: 0.7583 (m-80) REVERT: F 265 GLU cc_start: 0.8348 (tt0) cc_final: 0.8027 (tt0) REVERT: F 266 ASP cc_start: 0.8252 (t0) cc_final: 0.8042 (t0) REVERT: F 298 GLN cc_start: 0.8147 (mt0) cc_final: 0.7815 (mt0) REVERT: F 346 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7508 (tm-30) REVERT: F 352 LYS cc_start: 0.7965 (tmtt) cc_final: 0.7172 (tptp) REVERT: G 53 TYR cc_start: 0.8557 (t80) cc_final: 0.8170 (t80) REVERT: G 105 VAL cc_start: 0.8574 (OUTLIER) cc_final: 0.8276 (t) REVERT: G 127 GLN cc_start: 0.7713 (OUTLIER) cc_final: 0.7393 (tt0) REVERT: G 251 TRP cc_start: 0.8441 (t60) cc_final: 0.8176 (t60) REVERT: G 265 GLU cc_start: 0.8347 (tt0) cc_final: 0.8087 (tt0) REVERT: G 266 ASP cc_start: 0.8237 (t0) cc_final: 0.8033 (t0) REVERT: G 298 GLN cc_start: 0.8144 (mt0) cc_final: 0.7840 (mt0) REVERT: G 331 LYS cc_start: 0.7235 (ptmt) cc_final: 0.6339 (tttp) REVERT: G 346 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7575 (tm-30) REVERT: G 352 LYS cc_start: 0.7867 (tmtt) cc_final: 0.7099 (tptp) REVERT: H 53 TYR cc_start: 0.8559 (t80) cc_final: 0.8177 (t80) REVERT: H 105 VAL cc_start: 0.8583 (OUTLIER) cc_final: 0.8250 (t) REVERT: H 127 GLN cc_start: 0.7733 (OUTLIER) cc_final: 0.7407 (tt0) REVERT: H 265 GLU cc_start: 0.8321 (tt0) cc_final: 0.8026 (tt0) REVERT: H 298 GLN cc_start: 0.8119 (mt0) cc_final: 0.7776 (mt0) REVERT: H 331 LYS cc_start: 0.7211 (ptmt) cc_final: 0.6252 (tttp) REVERT: H 346 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7565 (tm-30) REVERT: H 352 LYS cc_start: 0.7992 (tmtt) cc_final: 0.7180 (tptp) outliers start: 53 outliers final: 16 residues processed: 552 average time/residue: 0.1771 time to fit residues: 145.7530 Evaluate side-chains 548 residues out of total 2552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 516 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 127 GLN Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 127 GLN Chi-restraints excluded: chain C residue 280 LYS Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 127 GLN Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain D residue 280 LYS Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 127 GLN Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 280 LYS Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 127 GLN Chi-restraints excluded: chain F residue 139 LYS Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 280 LYS Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 139 LYS Chi-restraints excluded: chain G residue 272 SER Chi-restraints excluded: chain G residue 280 LYS Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 127 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 72 optimal weight: 0.5980 chunk 194 optimal weight: 0.9980 chunk 233 optimal weight: 3.9990 chunk 261 optimal weight: 0.1980 chunk 157 optimal weight: 0.7980 chunk 15 optimal weight: 0.0670 chunk 204 optimal weight: 3.9990 chunk 215 optimal weight: 0.0970 chunk 286 optimal weight: 4.9990 chunk 270 optimal weight: 4.9990 chunk 100 optimal weight: 9.9990 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.190536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.136791 restraints weight = 29486.062| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 3.02 r_work: 0.3368 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23912 Z= 0.127 Angle : 0.637 8.176 32304 Z= 0.329 Chirality : 0.044 0.182 3472 Planarity : 0.005 0.048 4248 Dihedral : 4.042 17.220 3256 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.49 % Allowed : 22.73 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.15), residues: 2872 helix: 1.38 (0.15), residues: 1160 sheet: -0.30 (0.24), residues: 448 loop : -1.25 (0.15), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 340 TYR 0.011 0.001 TYR H 47 PHE 0.021 0.002 PHE H 227 TRP 0.020 0.001 TRP H 251 HIS 0.003 0.001 HIS G 224 Details of bonding type rmsd covalent geometry : bond 0.00294 (23912) covalent geometry : angle 0.63722 (32304) hydrogen bonds : bond 0.02764 ( 1000) hydrogen bonds : angle 4.60712 ( 2904) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 2552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 528 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 TYR cc_start: 0.8532 (t80) cc_final: 0.8199 (t80) REVERT: A 105 VAL cc_start: 0.8614 (OUTLIER) cc_final: 0.8314 (t) REVERT: A 127 GLN cc_start: 0.7793 (OUTLIER) cc_final: 0.7525 (tt0) REVERT: A 251 TRP cc_start: 0.8362 (t60) cc_final: 0.8108 (t60) REVERT: A 298 GLN cc_start: 0.8077 (mt0) cc_final: 0.7776 (mt0) REVERT: A 331 LYS cc_start: 0.7110 (ptmt) cc_final: 0.6194 (tttp) REVERT: A 346 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7562 (tm-30) REVERT: A 352 LYS cc_start: 0.7859 (tmtt) cc_final: 0.6991 (tptp) REVERT: B 53 TYR cc_start: 0.8556 (t80) cc_final: 0.8161 (t80) REVERT: B 105 VAL cc_start: 0.8607 (OUTLIER) cc_final: 0.8284 (t) REVERT: B 127 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.7501 (tt0) REVERT: B 265 GLU cc_start: 0.8431 (tt0) cc_final: 0.8188 (tt0) REVERT: B 298 GLN cc_start: 0.8012 (mt0) cc_final: 0.7695 (mt0) REVERT: B 346 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7548 (tm-30) REVERT: B 352 LYS cc_start: 0.7964 (tmtt) cc_final: 0.7202 (tptp) REVERT: C 53 TYR cc_start: 0.8538 (t80) cc_final: 0.8147 (t80) REVERT: C 105 VAL cc_start: 0.8586 (OUTLIER) cc_final: 0.8285 (t) REVERT: C 251 TRP cc_start: 0.8470 (t60) cc_final: 0.8180 (t60) REVERT: C 265 GLU cc_start: 0.8269 (tt0) cc_final: 0.8015 (tt0) REVERT: C 298 GLN cc_start: 0.8028 (mt0) cc_final: 0.7718 (mt0) REVERT: C 331 LYS cc_start: 0.7098 (ptmt) cc_final: 0.6178 (tttp) REVERT: C 346 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7591 (tm-30) REVERT: C 352 LYS cc_start: 0.8006 (tmtt) cc_final: 0.7230 (tptp) REVERT: D 53 TYR cc_start: 0.8542 (t80) cc_final: 0.8155 (t80) REVERT: D 105 VAL cc_start: 0.8593 (OUTLIER) cc_final: 0.8273 (t) REVERT: D 127 GLN cc_start: 0.7755 (OUTLIER) cc_final: 0.7464 (tt0) REVERT: D 251 TRP cc_start: 0.8454 (t60) cc_final: 0.8149 (t60) REVERT: D 275 LYS cc_start: 0.8955 (mmtm) cc_final: 0.8582 (mmmt) REVERT: D 298 GLN cc_start: 0.8049 (mt0) cc_final: 0.7764 (mt0) REVERT: D 331 LYS cc_start: 0.7082 (ptmt) cc_final: 0.6193 (tttm) REVERT: D 346 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7594 (tm-30) REVERT: D 352 LYS cc_start: 0.7816 (tmtt) cc_final: 0.6923 (tptp) REVERT: E 53 TYR cc_start: 0.8527 (t80) cc_final: 0.8192 (t80) REVERT: E 105 VAL cc_start: 0.8604 (OUTLIER) cc_final: 0.8281 (t) REVERT: E 127 GLN cc_start: 0.7795 (OUTLIER) cc_final: 0.7496 (tt0) REVERT: E 251 TRP cc_start: 0.8507 (t60) cc_final: 0.8278 (t60) REVERT: E 265 GLU cc_start: 0.8376 (tt0) cc_final: 0.8073 (tt0) REVERT: E 298 GLN cc_start: 0.8099 (mt0) cc_final: 0.7796 (mt0) REVERT: E 331 LYS cc_start: 0.7104 (ptmt) cc_final: 0.6182 (tttm) REVERT: E 346 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7537 (tm-30) REVERT: F 53 TYR cc_start: 0.8508 (t80) cc_final: 0.8176 (t80) REVERT: F 105 VAL cc_start: 0.8610 (OUTLIER) cc_final: 0.8313 (t) REVERT: F 127 GLN cc_start: 0.7823 (OUTLIER) cc_final: 0.7492 (tt0) REVERT: F 225 PHE cc_start: 0.7783 (m-10) cc_final: 0.7511 (m-80) REVERT: F 251 TRP cc_start: 0.8487 (t60) cc_final: 0.8154 (t60) REVERT: F 265 GLU cc_start: 0.8393 (tt0) cc_final: 0.8144 (tt0) REVERT: F 298 GLN cc_start: 0.8020 (mt0) cc_final: 0.7699 (mt0) REVERT: F 346 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7553 (tm-30) REVERT: F 352 LYS cc_start: 0.7916 (tmtt) cc_final: 0.7608 (tmtt) REVERT: G 53 TYR cc_start: 0.8539 (t80) cc_final: 0.8148 (t80) REVERT: G 105 VAL cc_start: 0.8606 (OUTLIER) cc_final: 0.8309 (t) REVERT: G 127 GLN cc_start: 0.7732 (OUTLIER) cc_final: 0.7441 (tt0) REVERT: G 251 TRP cc_start: 0.8467 (t60) cc_final: 0.8179 (t60) REVERT: G 265 GLU cc_start: 0.8384 (tt0) cc_final: 0.8128 (tt0) REVERT: G 298 GLN cc_start: 0.8040 (mt0) cc_final: 0.7746 (mt0) REVERT: G 331 LYS cc_start: 0.7148 (ptmt) cc_final: 0.6233 (tttp) REVERT: G 352 LYS cc_start: 0.7842 (tmtt) cc_final: 0.7029 (tptp) REVERT: H 53 TYR cc_start: 0.8532 (t80) cc_final: 0.8199 (t80) REVERT: H 105 VAL cc_start: 0.8608 (OUTLIER) cc_final: 0.8287 (t) REVERT: H 127 GLN cc_start: 0.7634 (OUTLIER) cc_final: 0.7433 (tt0) REVERT: H 298 GLN cc_start: 0.8021 (mt0) cc_final: 0.7721 (mt0) REVERT: H 331 LYS cc_start: 0.7093 (ptmt) cc_final: 0.6617 (ptmm) REVERT: H 346 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7593 (tm-30) REVERT: H 352 LYS cc_start: 0.7912 (tmtt) cc_final: 0.7688 (tmtt) outliers start: 38 outliers final: 13 residues processed: 546 average time/residue: 0.1846 time to fit residues: 149.8150 Evaluate side-chains 540 residues out of total 2552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 512 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 127 GLN Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 280 LYS Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 127 GLN Chi-restraints excluded: chain D residue 280 LYS Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 127 GLN Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 280 LYS Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 127 GLN Chi-restraints excluded: chain F residue 139 LYS Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 280 LYS Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 272 SER Chi-restraints excluded: chain G residue 280 LYS Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 127 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 48 optimal weight: 4.9990 chunk 197 optimal weight: 0.8980 chunk 169 optimal weight: 0.8980 chunk 146 optimal weight: 0.9980 chunk 148 optimal weight: 2.9990 chunk 260 optimal weight: 3.9990 chunk 240 optimal weight: 3.9990 chunk 280 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 chunk 206 optimal weight: 5.9990 chunk 277 optimal weight: 0.8980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN ** B 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 ASN ** D 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.190840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.136222 restraints weight = 29635.108| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 3.02 r_work: 0.3309 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23912 Z= 0.171 Angle : 0.667 8.235 32304 Z= 0.341 Chirality : 0.045 0.198 3472 Planarity : 0.005 0.044 4248 Dihedral : 4.185 15.619 3256 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.92 % Allowed : 22.06 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.15), residues: 2872 helix: 1.36 (0.15), residues: 1160 sheet: -0.29 (0.24), residues: 448 loop : -1.29 (0.15), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 340 TYR 0.017 0.001 TYR B 47 PHE 0.023 0.002 PHE D 227 TRP 0.034 0.001 TRP B 251 HIS 0.003 0.001 HIS B 252 Details of bonding type rmsd covalent geometry : bond 0.00411 (23912) covalent geometry : angle 0.66722 (32304) hydrogen bonds : bond 0.03048 ( 1000) hydrogen bonds : angle 4.62251 ( 2904) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5494.69 seconds wall clock time: 94 minutes 47.13 seconds (5687.13 seconds total)