Starting phenix.real_space_refine on Tue Jan 14 17:57:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ilp_60672/01_2025/9ilp_60672.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ilp_60672/01_2025/9ilp_60672.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ilp_60672/01_2025/9ilp_60672.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ilp_60672/01_2025/9ilp_60672.map" model { file = "/net/cci-nas-00/data/ceres_data/9ilp_60672/01_2025/9ilp_60672.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ilp_60672/01_2025/9ilp_60672.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.007 sd= 2.338 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 252 5.16 5 C 32472 2.51 5 N 8580 2.21 5 O 9876 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 105 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 51180 Number of models: 1 Model: "" Number of chains: 24 Chain: "a" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1347 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 9, 'TRANS': 160} Chain: "b" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1347 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 9, 'TRANS': 160} Chain: "c" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1347 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 9, 'TRANS': 160} Chain: "d" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1347 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 9, 'TRANS': 160} Chain: "e" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1347 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 9, 'TRANS': 160} Chain: "f" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1347 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 9, 'TRANS': 160} Chain: "g" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1347 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 9, 'TRANS': 160} Chain: "h" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1347 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 9, 'TRANS': 160} Chain: "i" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1347 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 9, 'TRANS': 160} Chain: "j" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1347 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 9, 'TRANS': 160} Chain: "k" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1347 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 9, 'TRANS': 160} Chain: "l" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1347 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 9, 'TRANS': 160} Chain: "A" Number of atoms: 2918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2918 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 14, 'TRANS': 352} Chain: "B" Number of atoms: 2918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2918 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 14, 'TRANS': 352} Chain: "C" Number of atoms: 2918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2918 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 14, 'TRANS': 352} Chain: "D" Number of atoms: 2918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2918 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 14, 'TRANS': 352} Chain: "E" Number of atoms: 2918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2918 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 14, 'TRANS': 352} Chain: "F" Number of atoms: 2918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2918 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 14, 'TRANS': 352} Chain: "G" Number of atoms: 2918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2918 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 14, 'TRANS': 352} Chain: "H" Number of atoms: 2918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2918 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 14, 'TRANS': 352} Chain: "I" Number of atoms: 2918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2918 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 14, 'TRANS': 352} Chain: "J" Number of atoms: 2918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2918 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 14, 'TRANS': 352} Chain: "K" Number of atoms: 2918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2918 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 14, 'TRANS': 352} Chain: "L" Number of atoms: 2918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2918 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 14, 'TRANS': 352} Time building chain proxies: 21.76, per 1000 atoms: 0.43 Number of scatterers: 51180 At special positions: 0 Unit cell: (156.4, 156.4, 163.2, 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 252 16.00 O 9876 8.00 N 8580 7.00 C 32472 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: 9.49 Conformation dependent library (CDL) restraints added in 4.9 seconds 12792 Ramachandran restraints generated. 6396 Oldfield, 0 Emsley, 6396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12144 Finding SS restraints... Secondary structure from input PDB file: 222 helices and 85 sheets defined 47.6% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.58 Creating SS restraints... Processing helix chain 'a' and resid 4 through 13 removed outlier: 3.568A pdb=" N ASP a 8 " --> pdb=" O ILE a 4 " (cutoff:3.500A) Processing helix chain 'a' and resid 21 through 39 removed outlier: 3.804A pdb=" N GLU a 25 " --> pdb=" O GLU a 21 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL a 26 " --> pdb=" O SER a 22 " (cutoff:3.500A) Processing helix chain 'a' and resid 81 through 83 No H-bonds generated for 'chain 'a' and resid 81 through 83' Processing helix chain 'a' and resid 117 through 133 Processing helix chain 'a' and resid 158 through 168 Processing helix chain 'b' and resid 4 through 13 removed outlier: 3.622A pdb=" N ASP b 8 " --> pdb=" O ILE b 4 " (cutoff:3.500A) Processing helix chain 'b' and resid 21 through 39 removed outlier: 3.839A pdb=" N GLU b 25 " --> pdb=" O GLU b 21 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL b 26 " --> pdb=" O SER b 22 " (cutoff:3.500A) Processing helix chain 'b' and resid 81 through 83 No H-bonds generated for 'chain 'b' and resid 81 through 83' Processing helix chain 'b' and resid 117 through 133 removed outlier: 3.593A pdb=" N LYS b 121 " --> pdb=" O PRO b 117 " (cutoff:3.500A) Processing helix chain 'b' and resid 158 through 168 Processing helix chain 'c' and resid 4 through 13 removed outlier: 3.580A pdb=" N ASP c 8 " --> pdb=" O ILE c 4 " (cutoff:3.500A) Processing helix chain 'c' and resid 21 through 39 removed outlier: 3.639A pdb=" N GLU c 25 " --> pdb=" O GLU c 21 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL c 26 " --> pdb=" O SER c 22 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR c 36 " --> pdb=" O ASN c 32 " (cutoff:3.500A) Processing helix chain 'c' and resid 81 through 83 No H-bonds generated for 'chain 'c' and resid 81 through 83' Processing helix chain 'c' and resid 117 through 133 removed outlier: 3.575A pdb=" N LYS c 121 " --> pdb=" O PRO c 117 " (cutoff:3.500A) Processing helix chain 'c' and resid 158 through 168 Processing helix chain 'd' and resid 4 through 13 removed outlier: 3.565A pdb=" N ASP d 8 " --> pdb=" O ILE d 4 " (cutoff:3.500A) Processing helix chain 'd' and resid 21 through 39 removed outlier: 3.782A pdb=" N GLU d 25 " --> pdb=" O GLU d 21 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL d 26 " --> pdb=" O SER d 22 " (cutoff:3.500A) Processing helix chain 'd' and resid 81 through 83 No H-bonds generated for 'chain 'd' and resid 81 through 83' Processing helix chain 'd' and resid 117 through 133 Processing helix chain 'd' and resid 158 through 168 Processing helix chain 'e' and resid 4 through 14 removed outlier: 3.597A pdb=" N ASP e 8 " --> pdb=" O ILE e 4 " (cutoff:3.500A) Processing helix chain 'e' and resid 21 through 39 removed outlier: 3.816A pdb=" N GLU e 25 " --> pdb=" O GLU e 21 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL e 26 " --> pdb=" O SER e 22 " (cutoff:3.500A) Processing helix chain 'e' and resid 81 through 83 No H-bonds generated for 'chain 'e' and resid 81 through 83' Processing helix chain 'e' and resid 117 through 133 removed outlier: 3.617A pdb=" N LYS e 121 " --> pdb=" O PRO e 117 " (cutoff:3.500A) Processing helix chain 'e' and resid 158 through 168 Processing helix chain 'f' and resid 4 through 13 removed outlier: 3.668A pdb=" N ASP f 8 " --> pdb=" O ILE f 4 " (cutoff:3.500A) Processing helix chain 'f' and resid 21 through 39 removed outlier: 3.632A pdb=" N GLU f 25 " --> pdb=" O GLU f 21 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL f 26 " --> pdb=" O SER f 22 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR f 36 " --> pdb=" O ASN f 32 " (cutoff:3.500A) Processing helix chain 'f' and resid 81 through 83 No H-bonds generated for 'chain 'f' and resid 81 through 83' Processing helix chain 'f' and resid 117 through 133 removed outlier: 3.524A pdb=" N LYS f 121 " --> pdb=" O PRO f 117 " (cutoff:3.500A) Processing helix chain 'f' and resid 158 through 168 Processing helix chain 'g' and resid 4 through 14 removed outlier: 3.570A pdb=" N ASP g 8 " --> pdb=" O ILE g 4 " (cutoff:3.500A) Processing helix chain 'g' and resid 21 through 39 removed outlier: 3.778A pdb=" N GLU g 25 " --> pdb=" O GLU g 21 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL g 26 " --> pdb=" O SER g 22 " (cutoff:3.500A) Processing helix chain 'g' and resid 81 through 83 No H-bonds generated for 'chain 'g' and resid 81 through 83' Processing helix chain 'g' and resid 117 through 133 Processing helix chain 'g' and resid 158 through 168 Processing helix chain 'h' and resid 4 through 13 removed outlier: 3.567A pdb=" N ASP h 8 " --> pdb=" O ILE h 4 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY h 13 " --> pdb=" O TYR h 9 " (cutoff:3.500A) Processing helix chain 'h' and resid 21 through 39 removed outlier: 3.855A pdb=" N GLU h 25 " --> pdb=" O GLU h 21 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N VAL h 26 " --> pdb=" O SER h 22 " (cutoff:3.500A) Processing helix chain 'h' and resid 81 through 83 No H-bonds generated for 'chain 'h' and resid 81 through 83' Processing helix chain 'h' and resid 117 through 133 removed outlier: 3.671A pdb=" N LYS h 121 " --> pdb=" O PRO h 117 " (cutoff:3.500A) Processing helix chain 'h' and resid 158 through 168 Processing helix chain 'i' and resid 4 through 13 removed outlier: 3.635A pdb=" N ASP i 8 " --> pdb=" O ILE i 4 " (cutoff:3.500A) Processing helix chain 'i' and resid 21 through 39 removed outlier: 3.825A pdb=" N GLU i 25 " --> pdb=" O GLU i 21 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL i 26 " --> pdb=" O SER i 22 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR i 36 " --> pdb=" O ASN i 32 " (cutoff:3.500A) Processing helix chain 'i' and resid 81 through 83 No H-bonds generated for 'chain 'i' and resid 81 through 83' Processing helix chain 'i' and resid 117 through 133 removed outlier: 3.610A pdb=" N LYS i 121 " --> pdb=" O PRO i 117 " (cutoff:3.500A) Processing helix chain 'i' and resid 158 through 168 Processing helix chain 'j' and resid 4 through 13 removed outlier: 3.563A pdb=" N ASP j 8 " --> pdb=" O ILE j 4 " (cutoff:3.500A) Processing helix chain 'j' and resid 21 through 39 removed outlier: 3.826A pdb=" N GLU j 25 " --> pdb=" O GLU j 21 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL j 26 " --> pdb=" O SER j 22 " (cutoff:3.500A) Processing helix chain 'j' and resid 81 through 83 No H-bonds generated for 'chain 'j' and resid 81 through 83' Processing helix chain 'j' and resid 117 through 133 Processing helix chain 'j' and resid 158 through 168 Processing helix chain 'k' and resid 4 through 13 removed outlier: 3.620A pdb=" N ASP k 8 " --> pdb=" O ILE k 4 " (cutoff:3.500A) Processing helix chain 'k' and resid 21 through 39 removed outlier: 3.832A pdb=" N GLU k 25 " --> pdb=" O GLU k 21 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL k 26 " --> pdb=" O SER k 22 " (cutoff:3.500A) Processing helix chain 'k' and resid 81 through 83 No H-bonds generated for 'chain 'k' and resid 81 through 83' Processing helix chain 'k' and resid 117 through 133 removed outlier: 3.691A pdb=" N LYS k 121 " --> pdb=" O PRO k 117 " (cutoff:3.500A) Processing helix chain 'k' and resid 158 through 168 Processing helix chain 'l' and resid 4 through 13 removed outlier: 3.652A pdb=" N ASP l 8 " --> pdb=" O ILE l 4 " (cutoff:3.500A) Processing helix chain 'l' and resid 21 through 39 removed outlier: 3.634A pdb=" N GLU l 25 " --> pdb=" O GLU l 21 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL l 26 " --> pdb=" O SER l 22 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR l 36 " --> pdb=" O ASN l 32 " (cutoff:3.500A) Processing helix chain 'l' and resid 81 through 83 No H-bonds generated for 'chain 'l' and resid 81 through 83' Processing helix chain 'l' and resid 117 through 133 removed outlier: 3.523A pdb=" N LYS l 121 " --> pdb=" O PRO l 117 " (cutoff:3.500A) Processing helix chain 'l' and resid 158 through 168 Processing helix chain 'A' and resid 14 through 22 removed outlier: 3.587A pdb=" N ILE A 18 " --> pdb=" O GLY A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 42 Processing helix chain 'A' and resid 42 through 59 removed outlier: 3.839A pdb=" N CYS A 59 " --> pdb=" O SER A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 Processing helix chain 'A' and resid 94 through 109 Processing helix chain 'A' and resid 175 through 201 removed outlier: 4.156A pdb=" N THR A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL A 180 " --> pdb=" O ARG A 176 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE A 181 " --> pdb=" O VAL A 177 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ASP A 182 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N SER A 183 " --> pdb=" O THR A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 231 removed outlier: 3.715A pdb=" N ASN A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 278 Processing helix chain 'A' and resid 280 through 286 removed outlier: 3.732A pdb=" N LEU A 284 " --> pdb=" O PRO A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 320 Proline residue: A 294 - end of helix Proline residue: A 306 - end of helix removed outlier: 3.717A pdb=" N LEU A 311 " --> pdb=" O MET A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 334 Processing helix chain 'A' and resid 336 through 350 Processing helix chain 'A' and resid 354 through 362 Processing helix chain 'B' and resid 14 through 22 removed outlier: 3.536A pdb=" N ILE B 18 " --> pdb=" O GLY B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 42 Processing helix chain 'B' and resid 42 through 59 removed outlier: 3.704A pdb=" N THR B 48 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N CYS B 59 " --> pdb=" O SER B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 Processing helix chain 'B' and resid 94 through 109 Processing helix chain 'B' and resid 175 through 181 removed outlier: 3.914A pdb=" N THR B 179 " --> pdb=" O SER B 175 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL B 180 " --> pdb=" O ARG B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 201 Processing helix chain 'B' and resid 215 through 230 Processing helix chain 'B' and resid 262 through 278 Processing helix chain 'B' and resid 280 through 286 removed outlier: 3.719A pdb=" N LEU B 284 " --> pdb=" O PRO B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 320 Proline residue: B 294 - end of helix Proline residue: B 306 - end of helix removed outlier: 3.852A pdb=" N LEU B 311 " --> pdb=" O MET B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 334 Processing helix chain 'B' and resid 336 through 351 Processing helix chain 'B' and resid 354 through 362 Processing helix chain 'C' and resid 14 through 22 removed outlier: 3.585A pdb=" N ILE C 18 " --> pdb=" O GLY C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 42 Processing helix chain 'C' and resid 42 through 59 removed outlier: 3.880A pdb=" N CYS C 59 " --> pdb=" O SER C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 87 Processing helix chain 'C' and resid 94 through 109 Processing helix chain 'C' and resid 175 through 181 removed outlier: 3.931A pdb=" N THR C 179 " --> pdb=" O SER C 175 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL C 180 " --> pdb=" O ARG C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 201 Processing helix chain 'C' and resid 215 through 230 Processing helix chain 'C' and resid 262 through 278 Processing helix chain 'C' and resid 280 through 286 removed outlier: 3.964A pdb=" N LEU C 284 " --> pdb=" O PRO C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 320 removed outlier: 3.998A pdb=" N ARG C 293 " --> pdb=" O ASN C 289 " (cutoff:3.500A) Proline residue: C 294 - end of helix Proline residue: C 306 - end of helix removed outlier: 3.822A pdb=" N LEU C 311 " --> pdb=" O MET C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 334 Processing helix chain 'C' and resid 336 through 351 Processing helix chain 'C' and resid 354 through 362 Processing helix chain 'D' and resid 14 through 22 removed outlier: 3.594A pdb=" N ILE D 18 " --> pdb=" O GLY D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 42 Processing helix chain 'D' and resid 42 through 59 removed outlier: 3.860A pdb=" N CYS D 59 " --> pdb=" O SER D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 87 Processing helix chain 'D' and resid 94 through 109 Processing helix chain 'D' and resid 175 through 181 removed outlier: 4.132A pdb=" N THR D 179 " --> pdb=" O SER D 175 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL D 180 " --> pdb=" O ARG D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 201 Processing helix chain 'D' and resid 215 through 230 Processing helix chain 'D' and resid 262 through 278 Processing helix chain 'D' and resid 280 through 286 removed outlier: 3.731A pdb=" N LEU D 284 " --> pdb=" O PRO D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 320 Proline residue: D 294 - end of helix Proline residue: D 306 - end of helix removed outlier: 3.806A pdb=" N LEU D 311 " --> pdb=" O MET D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 334 Processing helix chain 'D' and resid 336 through 350 Processing helix chain 'D' and resid 354 through 362 Processing helix chain 'E' and resid 14 through 22 removed outlier: 3.535A pdb=" N ILE E 18 " --> pdb=" O GLY E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 42 Processing helix chain 'E' and resid 42 through 59 removed outlier: 3.832A pdb=" N CYS E 59 " --> pdb=" O SER E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 87 Processing helix chain 'E' and resid 94 through 109 Processing helix chain 'E' and resid 175 through 201 removed outlier: 3.969A pdb=" N THR E 179 " --> pdb=" O SER E 175 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL E 180 " --> pdb=" O ARG E 176 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE E 181 " --> pdb=" O VAL E 177 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ASP E 182 " --> pdb=" O ALA E 178 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N SER E 183 " --> pdb=" O THR E 179 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU E 184 " --> pdb=" O VAL E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 230 Processing helix chain 'E' and resid 262 through 278 Processing helix chain 'E' and resid 280 through 286 removed outlier: 3.731A pdb=" N LEU E 284 " --> pdb=" O PRO E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 320 Proline residue: E 294 - end of helix Proline residue: E 306 - end of helix removed outlier: 3.822A pdb=" N LEU E 311 " --> pdb=" O MET E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 334 Processing helix chain 'E' and resid 336 through 351 Processing helix chain 'E' and resid 354 through 362 Processing helix chain 'F' and resid 14 through 22 removed outlier: 3.537A pdb=" N ILE F 18 " --> pdb=" O GLY F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 42 Processing helix chain 'F' and resid 42 through 59 removed outlier: 3.854A pdb=" N CYS F 59 " --> pdb=" O SER F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 86 Processing helix chain 'F' and resid 94 through 109 Processing helix chain 'F' and resid 175 through 201 removed outlier: 3.956A pdb=" N THR F 179 " --> pdb=" O SER F 175 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL F 180 " --> pdb=" O ARG F 176 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE F 181 " --> pdb=" O VAL F 177 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ASP F 182 " --> pdb=" O ALA F 178 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N SER F 183 " --> pdb=" O THR F 179 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU F 185 " --> pdb=" O ILE F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 230 Processing helix chain 'F' and resid 262 through 278 Processing helix chain 'F' and resid 280 through 286 removed outlier: 3.960A pdb=" N LEU F 284 " --> pdb=" O PRO F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 320 removed outlier: 4.002A pdb=" N ARG F 293 " --> pdb=" O ASN F 289 " (cutoff:3.500A) Proline residue: F 294 - end of helix Proline residue: F 306 - end of helix removed outlier: 3.739A pdb=" N LEU F 311 " --> pdb=" O MET F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 334 Processing helix chain 'F' and resid 336 through 351 Processing helix chain 'F' and resid 354 through 362 Processing helix chain 'G' and resid 14 through 22 removed outlier: 3.587A pdb=" N ILE G 18 " --> pdb=" O GLY G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 31 through 42 Processing helix chain 'G' and resid 42 through 59 removed outlier: 3.848A pdb=" N CYS G 59 " --> pdb=" O SER G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 Processing helix chain 'G' and resid 94 through 109 Processing helix chain 'G' and resid 175 through 181 removed outlier: 4.159A pdb=" N THR G 179 " --> pdb=" O SER G 175 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL G 180 " --> pdb=" O ARG G 176 " (cutoff:3.500A) Processing helix chain 'G' and resid 182 through 201 removed outlier: 3.501A pdb=" N MET G 190 " --> pdb=" O LYS G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 231 removed outlier: 3.715A pdb=" N ASN G 231 " --> pdb=" O GLN G 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 262 through 278 Processing helix chain 'G' and resid 280 through 286 removed outlier: 3.727A pdb=" N LEU G 284 " --> pdb=" O PRO G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 288 through 320 Proline residue: G 294 - end of helix Proline residue: G 306 - end of helix removed outlier: 3.711A pdb=" N LEU G 311 " --> pdb=" O MET G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 330 through 334 Processing helix chain 'G' and resid 336 through 350 Processing helix chain 'G' and resid 354 through 362 Processing helix chain 'H' and resid 14 through 22 removed outlier: 3.539A pdb=" N ILE H 18 " --> pdb=" O GLY H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 42 Processing helix chain 'H' and resid 42 through 59 removed outlier: 3.806A pdb=" N CYS H 59 " --> pdb=" O SER H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 Processing helix chain 'H' and resid 94 through 109 Processing helix chain 'H' and resid 176 through 181 removed outlier: 3.976A pdb=" N VAL H 180 " --> pdb=" O ARG H 176 " (cutoff:3.500A) Processing helix chain 'H' and resid 182 through 201 Processing helix chain 'H' and resid 215 through 230 Processing helix chain 'H' and resid 262 through 278 Processing helix chain 'H' and resid 280 through 286 removed outlier: 3.710A pdb=" N LEU H 284 " --> pdb=" O PRO H 280 " (cutoff:3.500A) Processing helix chain 'H' and resid 288 through 320 Proline residue: H 294 - end of helix Proline residue: H 306 - end of helix removed outlier: 3.826A pdb=" N LEU H 311 " --> pdb=" O MET H 307 " (cutoff:3.500A) Processing helix chain 'H' and resid 330 through 334 Processing helix chain 'H' and resid 336 through 350 Processing helix chain 'H' and resid 354 through 362 Processing helix chain 'I' and resid 14 through 22 removed outlier: 3.517A pdb=" N ILE I 18 " --> pdb=" O GLY I 14 " (cutoff:3.500A) Processing helix chain 'I' and resid 31 through 42 Processing helix chain 'I' and resid 42 through 59 removed outlier: 3.830A pdb=" N CYS I 59 " --> pdb=" O SER I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 87 Processing helix chain 'I' and resid 94 through 109 Processing helix chain 'I' and resid 175 through 201 removed outlier: 3.942A pdb=" N THR I 179 " --> pdb=" O SER I 175 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL I 180 " --> pdb=" O ARG I 176 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE I 181 " --> pdb=" O VAL I 177 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ASP I 182 " --> pdb=" O ALA I 178 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N SER I 183 " --> pdb=" O THR I 179 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS I 189 " --> pdb=" O GLU I 185 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET I 190 " --> pdb=" O LYS I 186 " (cutoff:3.500A) Processing helix chain 'I' and resid 215 through 230 Processing helix chain 'I' and resid 262 through 278 Processing helix chain 'I' and resid 280 through 286 removed outlier: 3.921A pdb=" N LEU I 284 " --> pdb=" O PRO I 280 " (cutoff:3.500A) Processing helix chain 'I' and resid 288 through 320 Proline residue: I 294 - end of helix Proline residue: I 306 - end of helix removed outlier: 3.818A pdb=" N LEU I 311 " --> pdb=" O MET I 307 " (cutoff:3.500A) Processing helix chain 'I' and resid 330 through 334 Processing helix chain 'I' and resid 336 through 351 Processing helix chain 'I' and resid 354 through 362 Processing helix chain 'J' and resid 14 through 22 removed outlier: 3.574A pdb=" N ILE J 18 " --> pdb=" O GLY J 14 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 42 Processing helix chain 'J' and resid 42 through 59 removed outlier: 4.215A pdb=" N THR J 48 " --> pdb=" O ILE J 44 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N CYS J 59 " --> pdb=" O SER J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 87 Processing helix chain 'J' and resid 94 through 109 Processing helix chain 'J' and resid 176 through 201 removed outlier: 4.003A pdb=" N VAL J 180 " --> pdb=" O ARG J 176 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ASP J 182 " --> pdb=" O ALA J 178 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N SER J 183 " --> pdb=" O THR J 179 " (cutoff:3.500A) Processing helix chain 'J' and resid 215 through 231 removed outlier: 3.751A pdb=" N ASN J 231 " --> pdb=" O GLN J 227 " (cutoff:3.500A) Processing helix chain 'J' and resid 262 through 278 Processing helix chain 'J' and resid 280 through 286 removed outlier: 3.770A pdb=" N LEU J 284 " --> pdb=" O PRO J 280 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 320 Proline residue: J 294 - end of helix Proline residue: J 306 - end of helix removed outlier: 3.812A pdb=" N LEU J 311 " --> pdb=" O MET J 307 " (cutoff:3.500A) Processing helix chain 'J' and resid 330 through 334 Processing helix chain 'J' and resid 336 through 350 Processing helix chain 'J' and resid 354 through 362 Processing helix chain 'K' and resid 14 through 22 removed outlier: 3.538A pdb=" N ILE K 18 " --> pdb=" O GLY K 14 " (cutoff:3.500A) Processing helix chain 'K' and resid 31 through 42 Processing helix chain 'K' and resid 42 through 59 removed outlier: 3.840A pdb=" N CYS K 59 " --> pdb=" O SER K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 87 Processing helix chain 'K' and resid 94 through 109 Processing helix chain 'K' and resid 176 through 201 removed outlier: 3.829A pdb=" N SER K 183 " --> pdb=" O THR K 179 " (cutoff:3.500A) Processing helix chain 'K' and resid 215 through 230 Processing helix chain 'K' and resid 262 through 278 Processing helix chain 'K' and resid 280 through 286 removed outlier: 3.729A pdb=" N LEU K 284 " --> pdb=" O PRO K 280 " (cutoff:3.500A) Processing helix chain 'K' and resid 288 through 320 Proline residue: K 294 - end of helix Proline residue: K 306 - end of helix removed outlier: 3.819A pdb=" N LEU K 311 " --> pdb=" O MET K 307 " (cutoff:3.500A) Processing helix chain 'K' and resid 330 through 334 Processing helix chain 'K' and resid 336 through 351 Processing helix chain 'K' and resid 354 through 362 Processing helix chain 'L' and resid 14 through 22 removed outlier: 3.510A pdb=" N ILE L 18 " --> pdb=" O GLY L 14 " (cutoff:3.500A) Processing helix chain 'L' and resid 31 through 40 Processing helix chain 'L' and resid 42 through 59 removed outlier: 3.522A pdb=" N ARG L 47 " --> pdb=" O GLU L 43 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N CYS L 59 " --> pdb=" O SER L 55 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 87 Processing helix chain 'L' and resid 94 through 109 Processing helix chain 'L' and resid 175 through 181 removed outlier: 3.903A pdb=" N THR L 179 " --> pdb=" O SER L 175 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL L 180 " --> pdb=" O ARG L 176 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 201 Processing helix chain 'L' and resid 215 through 230 Processing helix chain 'L' and resid 262 through 278 Processing helix chain 'L' and resid 280 through 286 removed outlier: 3.918A pdb=" N LEU L 284 " --> pdb=" O PRO L 280 " (cutoff:3.500A) Processing helix chain 'L' and resid 288 through 320 removed outlier: 3.945A pdb=" N ARG L 293 " --> pdb=" O ASN L 289 " (cutoff:3.500A) Proline residue: L 294 - end of helix Proline residue: L 306 - end of helix removed outlier: 3.820A pdb=" N LEU L 311 " --> pdb=" O MET L 307 " (cutoff:3.500A) Processing helix chain 'L' and resid 330 through 334 Processing helix chain 'L' and resid 336 through 351 Processing helix chain 'L' and resid 354 through 362 Processing sheet with id=AA1, first strand: chain 'a' and resid 46 through 53 removed outlier: 3.759A pdb=" N TYR a 108 " --> pdb=" O VAL a 47 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR a 53 " --> pdb=" O GLY a 102 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY a 102 " --> pdb=" O THR a 53 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N THR a 109 " --> pdb=" O VAL a 70 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL a 70 " --> pdb=" O THR a 109 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 59 through 61 removed outlier: 4.227A pdb=" N LEU a 94 " --> pdb=" O LYS a 86 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS a 86 " --> pdb=" O LEU a 94 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 139 through 142 removed outlier: 3.531A pdb=" N ALA b 139 " --> pdb=" O THR a 148 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU c 145 " --> pdb=" O ILE c 142 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR c 148 " --> pdb=" O ALA d 139 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA d 139 " --> pdb=" O THR c 148 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA e 139 " --> pdb=" O THR d 148 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR f 148 " --> pdb=" O ALA g 139 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA g 139 " --> pdb=" O THR f 148 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR i 148 " --> pdb=" O ALA j 139 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA j 139 " --> pdb=" O THR i 148 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA k 139 " --> pdb=" O THR j 148 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU l 145 " --> pdb=" O ILE l 142 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR l 148 " --> pdb=" O ALA a 139 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA a 139 " --> pdb=" O THR l 148 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'a' and resid 152 through 153 removed outlier: 3.528A pdb=" N ILE a 156 " --> pdb=" O LYS a 153 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'b' and resid 46 through 53 removed outlier: 3.670A pdb=" N TYR b 108 " --> pdb=" O VAL b 47 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN b 49 " --> pdb=" O VAL b 106 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL b 106 " --> pdb=" O GLN b 49 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR b 53 " --> pdb=" O GLY b 102 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY b 102 " --> pdb=" O THR b 53 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS b 72 " --> pdb=" O GLU b 107 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N THR b 109 " --> pdb=" O VAL b 70 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL b 70 " --> pdb=" O THR b 109 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'b' and resid 59 through 61 removed outlier: 4.125A pdb=" N LEU b 94 " --> pdb=" O LYS b 86 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS b 86 " --> pdb=" O LEU b 94 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'b' and resid 152 through 153 removed outlier: 3.574A pdb=" N ILE b 156 " --> pdb=" O LYS b 153 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'c' and resid 46 through 50 removed outlier: 3.591A pdb=" N TYR c 108 " --> pdb=" O VAL c 47 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL c 106 " --> pdb=" O GLN c 49 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS c 72 " --> pdb=" O GLU c 107 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THR c 109 " --> pdb=" O VAL c 70 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL c 70 " --> pdb=" O THR c 109 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'c' and resid 59 through 61 Processing sheet with id=AB1, first strand: chain 'c' and resid 152 through 153 removed outlier: 3.564A pdb=" N ILE c 156 " --> pdb=" O LYS c 153 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'd' and resid 46 through 53 removed outlier: 3.506A pdb=" N VAL d 47 " --> pdb=" O TYR d 108 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR d 108 " --> pdb=" O VAL d 47 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR d 53 " --> pdb=" O GLY d 102 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY d 102 " --> pdb=" O THR d 53 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS d 72 " --> pdb=" O GLU d 107 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR d 109 " --> pdb=" O VAL d 70 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL d 70 " --> pdb=" O THR d 109 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'd' and resid 59 through 61 removed outlier: 3.931A pdb=" N LEU d 94 " --> pdb=" O LYS d 86 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS d 86 " --> pdb=" O LEU d 94 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'd' and resid 152 through 153 removed outlier: 3.563A pdb=" N ILE d 156 " --> pdb=" O LYS d 153 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'e' and resid 46 through 53 removed outlier: 3.670A pdb=" N TYR e 108 " --> pdb=" O VAL e 47 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL e 106 " --> pdb=" O GLN e 49 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR e 53 " --> pdb=" O GLY e 102 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY e 102 " --> pdb=" O THR e 53 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N THR e 109 " --> pdb=" O VAL e 70 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL e 70 " --> pdb=" O THR e 109 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'e' and resid 59 through 61 removed outlier: 3.997A pdb=" N LEU e 94 " --> pdb=" O LYS e 86 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS e 86 " --> pdb=" O LEU e 94 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'e' and resid 152 through 153 removed outlier: 3.578A pdb=" N ILE e 156 " --> pdb=" O LYS e 153 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'f' and resid 46 through 52 removed outlier: 3.589A pdb=" N TYR f 108 " --> pdb=" O VAL f 47 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL f 106 " --> pdb=" O GLN f 49 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS f 72 " --> pdb=" O GLU f 107 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N THR f 109 " --> pdb=" O VAL f 70 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL f 70 " --> pdb=" O THR f 109 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'f' and resid 59 through 61 Processing sheet with id=AC1, first strand: chain 'f' and resid 152 through 153 removed outlier: 3.600A pdb=" N ILE f 156 " --> pdb=" O LYS f 153 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'g' and resid 46 through 53 removed outlier: 3.503A pdb=" N VAL g 47 " --> pdb=" O TYR g 108 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR g 108 " --> pdb=" O VAL g 47 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR g 53 " --> pdb=" O GLY g 102 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY g 102 " --> pdb=" O THR g 53 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS g 72 " --> pdb=" O GLU g 107 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR g 109 " --> pdb=" O VAL g 70 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL g 70 " --> pdb=" O THR g 109 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'g' and resid 59 through 61 removed outlier: 3.926A pdb=" N LEU g 94 " --> pdb=" O LYS g 86 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS g 86 " --> pdb=" O LEU g 94 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'g' and resid 152 through 153 removed outlier: 3.521A pdb=" N ILE g 156 " --> pdb=" O LYS g 153 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'h' and resid 46 through 53 removed outlier: 3.666A pdb=" N TYR h 108 " --> pdb=" O VAL h 47 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN h 49 " --> pdb=" O VAL h 106 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL h 106 " --> pdb=" O GLN h 49 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR h 53 " --> pdb=" O GLY h 102 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY h 102 " --> pdb=" O THR h 53 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS h 72 " --> pdb=" O GLU h 107 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N THR h 109 " --> pdb=" O VAL h 70 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL h 70 " --> pdb=" O THR h 109 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'h' and resid 59 through 61 removed outlier: 3.975A pdb=" N LEU h 94 " --> pdb=" O LYS h 86 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS h 86 " --> pdb=" O LEU h 94 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'h' and resid 152 through 153 removed outlier: 3.593A pdb=" N ILE h 156 " --> pdb=" O LYS h 153 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'i' and resid 46 through 52 removed outlier: 3.605A pdb=" N TYR i 108 " --> pdb=" O VAL i 47 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL i 106 " --> pdb=" O GLN i 49 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS i 72 " --> pdb=" O GLU i 107 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR i 109 " --> pdb=" O VAL i 70 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL i 70 " --> pdb=" O THR i 109 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'i' and resid 59 through 61 Processing sheet with id=AD1, first strand: chain 'i' and resid 152 through 153 removed outlier: 3.604A pdb=" N ILE i 156 " --> pdb=" O LYS i 153 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'j' and resid 46 through 53 removed outlier: 3.708A pdb=" N TYR j 108 " --> pdb=" O VAL j 47 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR j 53 " --> pdb=" O GLY j 102 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY j 102 " --> pdb=" O THR j 53 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS j 72 " --> pdb=" O GLU j 107 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N THR j 109 " --> pdb=" O VAL j 70 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL j 70 " --> pdb=" O THR j 109 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'j' and resid 59 through 61 removed outlier: 4.097A pdb=" N LEU j 94 " --> pdb=" O LYS j 86 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS j 86 " --> pdb=" O LEU j 94 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'j' and resid 152 through 153 removed outlier: 3.525A pdb=" N ILE j 156 " --> pdb=" O LYS j 153 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'k' and resid 46 through 53 removed outlier: 3.653A pdb=" N TYR k 108 " --> pdb=" O VAL k 47 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL k 106 " --> pdb=" O GLN k 49 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR k 53 " --> pdb=" O GLY k 102 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY k 102 " --> pdb=" O THR k 53 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS k 72 " --> pdb=" O GLU k 107 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N THR k 109 " --> pdb=" O VAL k 70 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL k 70 " --> pdb=" O THR k 109 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'k' and resid 59 through 61 removed outlier: 4.130A pdb=" N LEU k 94 " --> pdb=" O LYS k 86 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS k 86 " --> pdb=" O LEU k 94 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'k' and resid 152 through 153 removed outlier: 3.582A pdb=" N ILE k 156 " --> pdb=" O LYS k 153 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'l' and resid 46 through 50 removed outlier: 3.604A pdb=" N TYR l 108 " --> pdb=" O VAL l 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL l 106 " --> pdb=" O GLN l 49 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS l 72 " --> pdb=" O GLU l 107 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR l 109 " --> pdb=" O VAL l 70 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL l 70 " --> pdb=" O THR l 109 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'l' and resid 59 through 61 Processing sheet with id=AE1, first strand: chain 'l' and resid 152 through 153 removed outlier: 3.589A pdb=" N ILE l 156 " --> pdb=" O LYS l 153 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 60 through 66 removed outlier: 4.674A pdb=" N TYR A 61 " --> pdb=" O ASN A 326 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASN A 326 " --> pdb=" O TYR A 61 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N VAL A 63 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N THR A 324 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ASP A 65 " --> pdb=" O LYS A 322 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 121 through 124 removed outlier: 3.878A pdb=" N VAL A 124 " --> pdb=" O TYR A 113 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N TYR A 113 " --> pdb=" O VAL A 124 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 129 through 133 removed outlier: 3.588A pdb=" N LYS A 141 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 247 through 248 removed outlier: 6.353A pdb=" N LEU A 206 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N LEU B 242 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU A 208 " --> pdb=" O LEU B 242 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 239 through 242 Processing sheet with id=AE7, first strand: chain 'B' and resid 60 through 66 removed outlier: 4.629A pdb=" N TYR B 61 " --> pdb=" O ASN B 326 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ASN B 326 " --> pdb=" O TYR B 61 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL B 63 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N THR B 324 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ASP B 65 " --> pdb=" O LYS B 322 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 121 through 124 removed outlier: 3.774A pdb=" N VAL B 124 " --> pdb=" O TYR B 113 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N TYR B 113 " --> pdb=" O VAL B 124 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 129 through 133 removed outlier: 3.545A pdb=" N LYS B 141 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 247 through 248 removed outlier: 6.359A pdb=" N LEU B 206 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N LEU C 242 " --> pdb=" O LEU B 206 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU B 208 " --> pdb=" O LEU C 242 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 60 through 66 removed outlier: 4.632A pdb=" N TYR C 61 " --> pdb=" O ASN C 326 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ASN C 326 " --> pdb=" O TYR C 61 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N VAL C 63 " --> pdb=" O THR C 324 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N THR C 324 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ASP C 65 " --> pdb=" O LYS C 322 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 121 through 124 removed outlier: 3.713A pdb=" N VAL C 124 " --> pdb=" O TYR C 113 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N TYR C 113 " --> pdb=" O VAL C 124 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 129 through 133 removed outlier: 3.566A pdb=" N LYS C 141 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 247 through 248 removed outlier: 6.364A pdb=" N LEU C 206 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N LEU D 242 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU C 208 " --> pdb=" O LEU D 242 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 60 through 66 removed outlier: 4.671A pdb=" N TYR D 61 " --> pdb=" O ASN D 326 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ASN D 326 " --> pdb=" O TYR D 61 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N VAL D 63 " --> pdb=" O THR D 324 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N THR D 324 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ASP D 65 " --> pdb=" O LYS D 322 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 121 through 124 removed outlier: 3.861A pdb=" N VAL D 124 " --> pdb=" O TYR D 113 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N TYR D 113 " --> pdb=" O VAL D 124 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 129 through 133 removed outlier: 3.580A pdb=" N LYS D 141 " --> pdb=" O GLU D 132 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 247 through 248 removed outlier: 6.357A pdb=" N LEU D 206 " --> pdb=" O LEU E 240 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N LEU E 242 " --> pdb=" O LEU D 206 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU D 208 " --> pdb=" O LEU E 242 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 60 through 66 removed outlier: 4.567A pdb=" N TYR E 61 " --> pdb=" O ASN E 326 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ASN E 326 " --> pdb=" O TYR E 61 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N VAL E 63 " --> pdb=" O THR E 324 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N THR E 324 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ASP E 65 " --> pdb=" O LYS E 322 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 121 through 124 removed outlier: 3.764A pdb=" N VAL E 124 " --> pdb=" O TYR E 113 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N TYR E 113 " --> pdb=" O VAL E 124 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 129 through 133 removed outlier: 3.543A pdb=" N LYS E 141 " --> pdb=" O GLU E 132 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 247 through 248 removed outlier: 6.374A pdb=" N LEU E 206 " --> pdb=" O LEU F 240 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N LEU F 242 " --> pdb=" O LEU E 206 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU E 208 " --> pdb=" O LEU F 242 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 60 through 66 removed outlier: 4.611A pdb=" N TYR F 61 " --> pdb=" O ASN F 326 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ASN F 326 " --> pdb=" O TYR F 61 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N VAL F 63 " --> pdb=" O THR F 324 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N THR F 324 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ASP F 65 " --> pdb=" O LYS F 322 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 121 through 124 removed outlier: 3.711A pdb=" N VAL F 124 " --> pdb=" O TYR F 113 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N TYR F 113 " --> pdb=" O VAL F 124 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 129 through 133 removed outlier: 3.572A pdb=" N LYS F 141 " --> pdb=" O GLU F 132 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 247 through 248 removed outlier: 6.407A pdb=" N LEU F 206 " --> pdb=" O LEU G 240 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N LEU G 242 " --> pdb=" O LEU F 206 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU F 208 " --> pdb=" O LEU G 242 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 60 through 66 removed outlier: 4.671A pdb=" N TYR G 61 " --> pdb=" O ASN G 326 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ASN G 326 " --> pdb=" O TYR G 61 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N VAL G 63 " --> pdb=" O THR G 324 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N THR G 324 " --> pdb=" O VAL G 63 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ASP G 65 " --> pdb=" O LYS G 322 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'G' and resid 121 through 124 removed outlier: 3.875A pdb=" N VAL G 124 " --> pdb=" O TYR G 113 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N TYR G 113 " --> pdb=" O VAL G 124 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'G' and resid 129 through 133 removed outlier: 3.586A pdb=" N LYS G 141 " --> pdb=" O GLU G 132 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'G' and resid 247 through 248 removed outlier: 6.361A pdb=" N LEU G 206 " --> pdb=" O LEU H 240 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N LEU H 242 " --> pdb=" O LEU G 206 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU G 208 " --> pdb=" O LEU H 242 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'H' and resid 60 through 66 removed outlier: 4.593A pdb=" N TYR H 61 " --> pdb=" O ASN H 326 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ASN H 326 " --> pdb=" O TYR H 61 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N VAL H 63 " --> pdb=" O THR H 324 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N THR H 324 " --> pdb=" O VAL H 63 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ASP H 65 " --> pdb=" O LYS H 322 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'H' and resid 121 through 124 removed outlier: 3.743A pdb=" N VAL H 124 " --> pdb=" O TYR H 113 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N TYR H 113 " --> pdb=" O VAL H 124 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'H' and resid 129 through 133 removed outlier: 3.506A pdb=" N LYS H 141 " --> pdb=" O GLU H 132 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'H' and resid 247 through 248 removed outlier: 6.376A pdb=" N LEU H 206 " --> pdb=" O LEU I 240 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N LEU I 242 " --> pdb=" O LEU H 206 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU H 208 " --> pdb=" O LEU I 242 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'I' and resid 60 through 66 removed outlier: 4.620A pdb=" N TYR I 61 " --> pdb=" O ASN I 326 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ASN I 326 " --> pdb=" O TYR I 61 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL I 63 " --> pdb=" O THR I 324 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N THR I 324 " --> pdb=" O VAL I 63 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ASP I 65 " --> pdb=" O LYS I 322 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'I' and resid 121 through 124 removed outlier: 3.710A pdb=" N VAL I 124 " --> pdb=" O TYR I 113 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N TYR I 113 " --> pdb=" O VAL I 124 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'I' and resid 129 through 133 removed outlier: 3.557A pdb=" N LYS I 141 " --> pdb=" O GLU I 132 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'I' and resid 247 through 248 removed outlier: 6.333A pdb=" N LEU I 206 " --> pdb=" O LEU J 240 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N LEU J 242 " --> pdb=" O LEU I 206 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU I 208 " --> pdb=" O LEU J 242 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'J' and resid 60 through 66 removed outlier: 4.673A pdb=" N TYR J 61 " --> pdb=" O ASN J 326 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ASN J 326 " --> pdb=" O TYR J 61 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N VAL J 63 " --> pdb=" O THR J 324 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N THR J 324 " --> pdb=" O VAL J 63 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ASP J 65 " --> pdb=" O LYS J 322 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'J' and resid 121 through 124 removed outlier: 3.803A pdb=" N VAL J 124 " --> pdb=" O TYR J 113 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N TYR J 113 " --> pdb=" O VAL J 124 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'J' and resid 129 through 133 removed outlier: 3.568A pdb=" N LYS J 141 " --> pdb=" O GLU J 132 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'J' and resid 247 through 248 removed outlier: 6.342A pdb=" N LEU J 206 " --> pdb=" O LEU K 240 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N LEU K 242 " --> pdb=" O LEU J 206 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU J 208 " --> pdb=" O LEU K 242 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'K' and resid 60 through 66 removed outlier: 4.608A pdb=" N TYR K 61 " --> pdb=" O ASN K 326 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ASN K 326 " --> pdb=" O TYR K 61 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N VAL K 63 " --> pdb=" O THR K 324 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N THR K 324 " --> pdb=" O VAL K 63 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ASP K 65 " --> pdb=" O LYS K 322 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'K' and resid 121 through 124 removed outlier: 3.742A pdb=" N VAL K 124 " --> pdb=" O TYR K 113 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N TYR K 113 " --> pdb=" O VAL K 124 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'K' and resid 129 through 133 removed outlier: 3.505A pdb=" N LYS K 141 " --> pdb=" O GLU K 132 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'K' and resid 247 through 248 removed outlier: 6.371A pdb=" N LEU K 206 " --> pdb=" O LEU L 240 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N LEU L 242 " --> pdb=" O LEU K 206 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU K 208 " --> pdb=" O LEU L 242 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'L' and resid 60 through 66 removed outlier: 4.619A pdb=" N TYR L 61 " --> pdb=" O ASN L 326 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ASN L 326 " --> pdb=" O TYR L 61 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL L 63 " --> pdb=" O THR L 324 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N THR L 324 " --> pdb=" O VAL L 63 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ASP L 65 " --> pdb=" O LYS L 322 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'L' and resid 121 through 124 removed outlier: 3.712A pdb=" N VAL L 124 " --> pdb=" O TYR L 113 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N TYR L 113 " --> pdb=" O VAL L 124 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'L' and resid 129 through 133 removed outlier: 3.555A pdb=" N LYS L 141 " --> pdb=" O GLU L 132 " (cutoff:3.500A) 2340 hydrogen bonds defined for protein. 6867 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: 18.00 Time building geometry restraints manager: 11.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 8748 1.28 - 1.41: 12057 1.41 - 1.55: 30803 1.55 - 1.68: 40 1.68 - 1.81: 444 Bond restraints: 52092 Sorted by residual: bond pdb=" C GLU J 43 " pdb=" O GLU J 43 " ideal model delta sigma weight residual 1.236 1.150 0.086 1.15e-02 7.56e+03 5.65e+01 bond pdb=" C LEU e 15 " pdb=" O LEU e 15 " ideal model delta sigma weight residual 1.234 1.150 0.084 1.24e-02 6.50e+03 4.60e+01 bond pdb=" CA SER D 175 " pdb=" C SER D 175 " ideal model delta sigma weight residual 1.523 1.446 0.077 1.24e-02 6.50e+03 3.86e+01 bond pdb=" CA SER A 175 " pdb=" C SER A 175 " ideal model delta sigma weight residual 1.523 1.447 0.077 1.24e-02 6.50e+03 3.83e+01 bond pdb=" CA SER G 175 " pdb=" C SER G 175 " ideal model delta sigma weight residual 1.523 1.449 0.074 1.24e-02 6.50e+03 3.61e+01 ... (remaining 52087 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 69142 2.53 - 5.07: 1117 5.07 - 7.60: 151 7.60 - 10.14: 43 10.14 - 12.67: 11 Bond angle restraints: 70464 Sorted by residual: angle pdb=" N GLU B 43 " pdb=" CA GLU B 43 " pdb=" C GLU B 43 " ideal model delta sigma weight residual 111.28 122.94 -11.66 1.09e+00 8.42e-01 1.14e+02 angle pdb=" N LEU I 214 " pdb=" CA LEU I 214 " pdb=" C LEU I 214 " ideal model delta sigma weight residual 110.65 123.32 -12.67 1.26e+00 6.30e-01 1.01e+02 angle pdb=" N ILE L 292 " pdb=" CA ILE L 292 " pdb=" C ILE L 292 " ideal model delta sigma weight residual 111.05 122.12 -11.07 1.25e+00 6.40e-01 7.85e+01 angle pdb=" N ILE I 292 " pdb=" CA ILE I 292 " pdb=" C ILE I 292 " ideal model delta sigma weight residual 111.09 122.07 -10.98 1.25e+00 6.40e-01 7.72e+01 angle pdb=" N VAL A 180 " pdb=" CA VAL A 180 " pdb=" C VAL A 180 " ideal model delta sigma weight residual 110.53 118.30 -7.77 9.40e-01 1.13e+00 6.83e+01 ... (remaining 70459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 28831 18.00 - 35.99: 2513 35.99 - 53.99: 437 53.99 - 71.99: 82 71.99 - 89.99: 33 Dihedral angle restraints: 31896 sinusoidal: 13056 harmonic: 18840 Sorted by residual: dihedral pdb=" C ILE C 292 " pdb=" N ILE C 292 " pdb=" CA ILE C 292 " pdb=" CB ILE C 292 " ideal model delta harmonic sigma weight residual -122.00 -136.71 14.71 0 2.50e+00 1.60e-01 3.46e+01 dihedral pdb=" C ILE F 292 " pdb=" N ILE F 292 " pdb=" CA ILE F 292 " pdb=" CB ILE F 292 " ideal model delta harmonic sigma weight residual -122.00 -136.33 14.33 0 2.50e+00 1.60e-01 3.29e+01 dihedral pdb=" C ILE L 292 " pdb=" N ILE L 292 " pdb=" CA ILE L 292 " pdb=" CB ILE L 292 " ideal model delta harmonic sigma weight residual -122.00 -135.91 13.91 0 2.50e+00 1.60e-01 3.10e+01 ... (remaining 31893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 7824 0.120 - 0.241: 164 0.241 - 0.361: 34 0.361 - 0.481: 12 0.481 - 0.602: 6 Chirality restraints: 8040 Sorted by residual: chirality pdb=" CA ILE C 292 " pdb=" N ILE C 292 " pdb=" C ILE C 292 " pdb=" CB ILE C 292 " both_signs ideal model delta sigma weight residual False 2.43 1.83 0.60 2.00e-01 2.50e+01 9.05e+00 chirality pdb=" CA ILE F 292 " pdb=" N ILE F 292 " pdb=" C ILE F 292 " pdb=" CB ILE F 292 " both_signs ideal model delta sigma weight residual False 2.43 1.85 0.59 2.00e-01 2.50e+01 8.63e+00 chirality pdb=" CA ILE L 292 " pdb=" N ILE L 292 " pdb=" C ILE L 292 " pdb=" CB ILE L 292 " both_signs ideal model delta sigma weight residual False 2.43 1.86 0.57 2.00e-01 2.50e+01 8.20e+00 ... (remaining 8037 not shown) Planarity restraints: 9096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN D 174 " 0.021 2.00e-02 2.50e+03 4.39e-02 1.92e+01 pdb=" C GLN D 174 " -0.076 2.00e-02 2.50e+03 pdb=" O GLN D 174 " 0.029 2.00e-02 2.50e+03 pdb=" N SER D 175 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 174 " -0.021 2.00e-02 2.50e+03 4.26e-02 1.82e+01 pdb=" C GLN A 174 " 0.074 2.00e-02 2.50e+03 pdb=" O GLN A 174 " -0.028 2.00e-02 2.50e+03 pdb=" N SER A 175 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU e 11 " 0.020 2.00e-02 2.50e+03 3.94e-02 1.55e+01 pdb=" C LEU e 11 " -0.068 2.00e-02 2.50e+03 pdb=" O LEU e 11 " 0.025 2.00e-02 2.50e+03 pdb=" N TYR e 12 " 0.023 2.00e-02 2.50e+03 ... (remaining 9093 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 4026 2.74 - 3.28: 49077 3.28 - 3.82: 80685 3.82 - 4.36: 95859 4.36 - 4.90: 170744 Nonbonded interactions: 400391 Sorted by model distance: nonbonded pdb=" OG1 THR i 146 " pdb=" OG1 THR j 141 " model vdw 2.197 3.040 nonbonded pdb=" O ARG K 176 " pdb=" OG1 THR K 179 " model vdw 2.201 3.040 nonbonded pdb=" O ASN K 291 " pdb=" ND2 ASN K 295 " model vdw 2.202 3.120 nonbonded pdb=" O ASN H 291 " pdb=" ND2 ASN H 295 " model vdw 2.209 3.120 nonbonded pdb=" O ASN E 291 " pdb=" ND2 ASN E 295 " model vdw 2.212 3.120 ... (remaining 400386 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' } 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: 1.780 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: 0.030 Extract box with map and model: 1.540 Check model and map are aligned: 0.300 Set scattering table: 0.360 Process input model: 85.840 Find NCS groups from input model: 1.490 Set up NCS constraints: 0.370 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 52092 Z= 0.334 Angle : 0.810 12.673 70464 Z= 0.506 Chirality : 0.053 0.602 8040 Planarity : 0.005 0.061 9096 Dihedral : 13.887 89.986 19752 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 1.17 % Allowed : 7.07 % Favored : 91.76 % Rotamer: Outliers : 0.49 % Allowed : 0.94 % Favored : 98.57 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.10), residues: 6396 helix: 1.23 (0.10), residues: 2772 sheet: -0.27 (0.24), residues: 624 loop : -1.65 (0.10), residues: 3000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 131 HIS 0.007 0.002 HIS H 343 PHE 0.024 0.001 PHE I 92 TYR 0.020 0.001 TYR g 12 ARG 0.006 0.000 ARG F 176 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12792 Ramachandran restraints generated. 6396 Oldfield, 0 Emsley, 6396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12792 Ramachandran restraints generated. 6396 Oldfield, 0 Emsley, 6396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1893 residues out of total 5724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 1865 time to evaluate : 4.583 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: a 3 ILE cc_start: 0.8317 (mt) cc_final: 0.8074 (mt) REVERT: a 8 ASP cc_start: 0.8123 (m-30) cc_final: 0.7923 (m-30) REVERT: a 60 TYR cc_start: 0.8864 (m-80) cc_final: 0.8609 (m-80) REVERT: a 96 LYS cc_start: 0.8161 (mttm) cc_final: 0.7921 (mmtt) REVERT: b 2 GLN cc_start: 0.7465 (tt0) cc_final: 0.7225 (tt0) REVERT: b 41 MET cc_start: 0.8213 (mtm) cc_final: 0.7944 (mpp) REVERT: b 58 LYS cc_start: 0.8710 (mtpt) cc_final: 0.8402 (mtmm) REVERT: b 96 LYS cc_start: 0.8118 (mttp) cc_final: 0.7716 (mmtm) REVERT: c 167 TYR cc_start: 0.7790 (m-80) cc_final: 0.7580 (m-80) REVERT: d 8 ASP cc_start: 0.8088 (m-30) cc_final: 0.7831 (m-30) REVERT: d 49 GLN cc_start: 0.8463 (tt0) cc_final: 0.8214 (tt0) REVERT: d 60 TYR cc_start: 0.8850 (m-80) cc_final: 0.8607 (m-80) REVERT: d 96 LYS cc_start: 0.8399 (mttm) cc_final: 0.7957 (mmtt) REVERT: e 58 LYS cc_start: 0.8719 (mtpt) cc_final: 0.8391 (mtmm) REVERT: e 68 THR cc_start: 0.7963 (p) cc_final: 0.7594 (p) REVERT: e 96 LYS cc_start: 0.8044 (mttp) cc_final: 0.7576 (mmtm) REVERT: f 8 ASP cc_start: 0.7611 (m-30) cc_final: 0.7337 (m-30) REVERT: f 16 LYS cc_start: 0.6011 (OUTLIER) cc_final: 0.4874 (pttp) REVERT: f 49 GLN cc_start: 0.8130 (tt0) cc_final: 0.7678 (tt0) REVERT: g 3 ILE cc_start: 0.8247 (mt) cc_final: 0.7934 (mt) REVERT: g 49 GLN cc_start: 0.8408 (tt0) cc_final: 0.8200 (tt0) REVERT: g 60 TYR cc_start: 0.8836 (m-80) cc_final: 0.8633 (m-80) REVERT: g 96 LYS cc_start: 0.8372 (mttm) cc_final: 0.8027 (mmtt) REVERT: g 142 ILE cc_start: 0.7153 (mt) cc_final: 0.6939 (pt) REVERT: h 2 GLN cc_start: 0.7580 (tt0) cc_final: 0.7133 (tt0) REVERT: h 58 LYS cc_start: 0.8710 (mtpt) cc_final: 0.8333 (mtmm) REVERT: h 96 LYS cc_start: 0.7877 (mttp) cc_final: 0.7458 (mmtm) REVERT: h 146 THR cc_start: 0.9128 (m) cc_final: 0.8896 (m) REVERT: i 16 LYS cc_start: 0.6151 (OUTLIER) cc_final: 0.5066 (pttp) REVERT: j 60 TYR cc_start: 0.8806 (m-80) cc_final: 0.8604 (m-80) REVERT: j 96 LYS cc_start: 0.8037 (mttm) cc_final: 0.7489 (mmtt) REVERT: k 49 GLN cc_start: 0.8026 (tt0) cc_final: 0.7808 (tt0) REVERT: k 58 LYS cc_start: 0.8685 (mtpt) cc_final: 0.8353 (mtmm) REVERT: k 96 LYS cc_start: 0.7913 (mttp) cc_final: 0.7549 (mmtm) REVERT: l 2 GLN cc_start: 0.6815 (tt0) cc_final: 0.6614 (tt0) REVERT: l 49 GLN cc_start: 0.8270 (tt0) cc_final: 0.7878 (tt0) REVERT: l 167 TYR cc_start: 0.7877 (m-80) cc_final: 0.7605 (m-80) REVERT: A 21 MET cc_start: 0.6711 (mmp) cc_final: 0.6270 (tpp) REVERT: A 22 GLU cc_start: 0.7371 (tp30) cc_final: 0.6895 (tp30) REVERT: A 188 SER cc_start: 0.8269 (p) cc_final: 0.8066 (t) REVERT: B 79 LYS cc_start: 0.7114 (mtpt) cc_final: 0.6752 (mmmt) REVERT: C 31 LYS cc_start: 0.8242 (mttt) cc_final: 0.8012 (mtmt) REVERT: C 50 ASN cc_start: 0.8910 (m-40) cc_final: 0.8580 (m-40) REVERT: C 130 GLN cc_start: 0.7930 (tt0) cc_final: 0.7534 (tt0) REVERT: C 188 SER cc_start: 0.8312 (p) cc_final: 0.8059 (t) REVERT: C 291 ASN cc_start: 0.7866 (OUTLIER) cc_final: 0.7102 (m-40) REVERT: C 297 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7740 (mt-10) REVERT: D 22 GLU cc_start: 0.7346 (tp30) cc_final: 0.6852 (tp30) REVERT: D 188 SER cc_start: 0.8317 (p) cc_final: 0.8097 (t) REVERT: E 31 LYS cc_start: 0.8409 (mttt) cc_final: 0.8160 (mttt) REVERT: E 79 LYS cc_start: 0.7020 (mtpt) cc_final: 0.6686 (mmmt) REVERT: F 20 ASP cc_start: 0.6919 (m-30) cc_final: 0.6553 (m-30) REVERT: F 50 ASN cc_start: 0.8906 (m-40) cc_final: 0.8279 (m-40) REVERT: F 188 SER cc_start: 0.8287 (p) cc_final: 0.7920 (t) REVERT: F 203 VAL cc_start: 0.8690 (m) cc_final: 0.8219 (t) REVERT: F 291 ASN cc_start: 0.7851 (OUTLIER) cc_final: 0.7055 (m-40) REVERT: G 21 MET cc_start: 0.6699 (mmp) cc_final: 0.6246 (tpp) REVERT: G 22 GLU cc_start: 0.7066 (tp30) cc_final: 0.6663 (tp30) REVERT: G 50 ASN cc_start: 0.8844 (m-40) cc_final: 0.8635 (m110) REVERT: G 188 SER cc_start: 0.8312 (p) cc_final: 0.7978 (t) REVERT: H 26 HIS cc_start: 0.6869 (m90) cc_final: 0.6633 (m-70) REVERT: H 41 LYS cc_start: 0.7743 (mttt) cc_final: 0.7361 (mttt) REVERT: H 79 LYS cc_start: 0.7127 (mtpt) cc_final: 0.6786 (mmmt) REVERT: H 297 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7317 (mt-10) REVERT: I 20 ASP cc_start: 0.7244 (m-30) cc_final: 0.7008 (m-30) REVERT: I 31 LYS cc_start: 0.8377 (mttt) cc_final: 0.8150 (mtmt) REVERT: I 61 TYR cc_start: 0.8022 (m-80) cc_final: 0.7794 (m-80) REVERT: I 136 ASN cc_start: 0.7964 (m-40) cc_final: 0.7401 (m-40) REVERT: I 227 GLN cc_start: 0.8620 (tm-30) cc_final: 0.8400 (tm-30) REVERT: I 297 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7677 (mt-10) REVERT: J 21 MET cc_start: 0.6668 (mmp) cc_final: 0.6189 (tpp) REVERT: J 31 LYS cc_start: 0.8581 (mttt) cc_final: 0.8276 (mtmt) REVERT: J 50 ASN cc_start: 0.8992 (m-40) cc_final: 0.8786 (m110) REVERT: J 188 SER cc_start: 0.8318 (p) cc_final: 0.8104 (t) REVERT: K 26 HIS cc_start: 0.6853 (m90) cc_final: 0.6571 (m-70) REVERT: K 31 LYS cc_start: 0.8321 (mttt) cc_final: 0.7951 (mttt) REVERT: K 79 LYS cc_start: 0.7185 (mtpt) cc_final: 0.6805 (mmmt) REVERT: L 31 LYS cc_start: 0.8246 (mttt) cc_final: 0.8008 (mtmt) REVERT: L 188 SER cc_start: 0.8307 (p) cc_final: 0.7956 (t) REVERT: L 227 GLN cc_start: 0.8673 (tm-30) cc_final: 0.8439 (tm-30) REVERT: L 297 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7741 (mt-10) outliers start: 28 outliers final: 14 residues processed: 1879 average time/residue: 0.5099 time to fit residues: 1570.7596 Evaluate side-chains 1202 residues out of total 5724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 1184 time to evaluate : 4.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 15 LEU Chi-restraints excluded: chain f residue 16 LYS Chi-restraints excluded: chain i residue 16 LYS Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain C residue 291 ASN Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 291 ASN Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 291 ASN Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain L residue 214 LEU Chi-restraints excluded: chain L residue 291 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 537 optimal weight: 0.7980 chunk 482 optimal weight: 2.9990 chunk 267 optimal weight: 0.9990 chunk 164 optimal weight: 0.0870 chunk 325 optimal weight: 4.9990 chunk 257 optimal weight: 1.9990 chunk 498 optimal weight: 0.3980 chunk 192 optimal weight: 10.0000 chunk 303 optimal weight: 5.9990 chunk 371 optimal weight: 9.9990 chunk 577 optimal weight: 10.0000 overall best weight: 0.8562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 151 ASN b 138 GLN c 151 ASN ** c 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 151 ASN ** f 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 138 GLN i 151 ASN ** i 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 151 ASN k 138 GLN l 151 ASN ** l 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 37 GLN A 223 GLN A 326 ASN ** A 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 373 ASN B 90 ASN B 146 ASN B 174 GLN B 295 ASN B 326 ASN ** B 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 373 ASN C 37 GLN C 90 ASN C 174 GLN C 326 ASN ** C 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 373 ASN D 37 GLN ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 223 GLN D 326 ASN ** D 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 373 ASN ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 ASN E 174 GLN E 223 GLN E 326 ASN E 343 HIS E 373 ASN F 90 ASN F 174 GLN F 281 GLN F 326 ASN ** F 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 373 ASN G 37 GLN ** G 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 223 GLN G 231 ASN G 326 ASN ** G 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 373 ASN ** H 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 146 ASN H 326 ASN ** H 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 373 ASN I 37 GLN I 90 ASN I 174 GLN I 281 GLN I 326 ASN ** I 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN J 223 GLN J 231 ASN J 326 ASN ** J 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 373 ASN K 90 ASN K 146 ASN K 295 ASN K 326 ASN K 343 HIS K 373 ASN L 37 GLN L 90 ASN L 130 GLN L 174 GLN L 223 GLN L 326 ASN L 373 ASN Total number of N/Q/H flips: 70 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.128865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.115177 restraints weight = 67541.860| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.40 r_work: 0.3013 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 52092 Z= 0.180 Angle : 0.597 8.394 70464 Z= 0.318 Chirality : 0.043 0.317 8040 Planarity : 0.005 0.051 9096 Dihedral : 5.251 55.200 7029 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.84 % Allowed : 6.74 % Favored : 92.42 % Rotamer: Outliers : 2.25 % Allowed : 9.49 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.11), residues: 6396 helix: 1.63 (0.10), residues: 2772 sheet: 0.93 (0.21), residues: 792 loop : -1.75 (0.11), residues: 2832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP a 131 HIS 0.006 0.001 HIS H 343 PHE 0.014 0.001 PHE K 92 TYR 0.013 0.001 TYR I 300 ARG 0.003 0.000 ARG c 140 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12792 Ramachandran restraints generated. 6396 Oldfield, 0 Emsley, 6396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12792 Ramachandran restraints generated. 6396 Oldfield, 0 Emsley, 6396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1387 residues out of total 5724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 1258 time to evaluate : 4.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 8 ASP cc_start: 0.8459 (m-30) cc_final: 0.8247 (m-30) REVERT: a 49 GLN cc_start: 0.8451 (tt0) cc_final: 0.8113 (tt0) REVERT: a 60 TYR cc_start: 0.9095 (m-80) cc_final: 0.8670 (m-80) REVERT: a 96 LYS cc_start: 0.8395 (mttm) cc_final: 0.8026 (mmtt) REVERT: b 2 GLN cc_start: 0.7895 (tt0) cc_final: 0.7604 (tt0) REVERT: b 21 GLU cc_start: 0.7041 (mt-10) cc_final: 0.6530 (tt0) REVERT: b 41 MET cc_start: 0.8687 (mtm) cc_final: 0.8376 (mpp) REVERT: b 96 LYS cc_start: 0.8390 (mttp) cc_final: 0.7854 (mmtm) REVERT: d 8 ASP cc_start: 0.8395 (m-30) cc_final: 0.8125 (m-30) REVERT: d 60 TYR cc_start: 0.9125 (m-80) cc_final: 0.8597 (m-80) REVERT: d 96 LYS cc_start: 0.8520 (mttm) cc_final: 0.8065 (mmtt) REVERT: e 2 GLN cc_start: 0.7660 (tt0) cc_final: 0.7363 (tt0) REVERT: e 96 LYS cc_start: 0.8189 (mttp) cc_final: 0.7680 (mmtm) REVERT: f 5 THR cc_start: 0.8031 (p) cc_final: 0.7677 (t) REVERT: f 16 LYS cc_start: 0.6102 (OUTLIER) cc_final: 0.4897 (pttp) REVERT: f 116 MET cc_start: 0.8458 (tpt) cc_final: 0.8178 (tpt) REVERT: g 49 GLN cc_start: 0.8707 (tt0) cc_final: 0.8041 (tt0) REVERT: g 60 TYR cc_start: 0.9058 (m-80) cc_final: 0.8693 (m-80) REVERT: g 96 LYS cc_start: 0.8560 (mttm) cc_final: 0.8084 (mmtt) REVERT: h 2 GLN cc_start: 0.7877 (tt0) cc_final: 0.7623 (tt0) REVERT: h 96 LYS cc_start: 0.8202 (mttp) cc_final: 0.7625 (mmtm) REVERT: i 5 THR cc_start: 0.7869 (p) cc_final: 0.7461 (t) REVERT: i 8 ASP cc_start: 0.8317 (m-30) cc_final: 0.7728 (m-30) REVERT: i 16 LYS cc_start: 0.6210 (OUTLIER) cc_final: 0.5007 (pttp) REVERT: j 9 TYR cc_start: 0.8801 (t80) cc_final: 0.8582 (t80) REVERT: j 49 GLN cc_start: 0.8489 (tt0) cc_final: 0.8103 (tt0) REVERT: j 60 TYR cc_start: 0.9100 (m-80) cc_final: 0.8839 (m-80) REVERT: j 96 LYS cc_start: 0.8213 (mttm) cc_final: 0.7588 (mmtt) REVERT: k 2 GLN cc_start: 0.7752 (tt0) cc_final: 0.7400 (tt0) REVERT: k 21 GLU cc_start: 0.6845 (mt-10) cc_final: 0.6463 (tm-30) REVERT: k 73 MET cc_start: 0.8759 (ttm) cc_final: 0.8524 (ttm) REVERT: k 96 LYS cc_start: 0.8140 (mttp) cc_final: 0.7664 (mmtm) REVERT: l 5 THR cc_start: 0.8096 (p) cc_final: 0.7608 (t) REVERT: l 8 ASP cc_start: 0.8255 (m-30) cc_final: 0.7615 (m-30) REVERT: l 16 LYS cc_start: 0.6909 (OUTLIER) cc_final: 0.5192 (pttm) REVERT: l 167 TYR cc_start: 0.8322 (m-80) cc_final: 0.8104 (m-80) REVERT: A 21 MET cc_start: 0.7711 (mmp) cc_final: 0.7022 (tpp) REVERT: A 31 LYS cc_start: 0.8747 (mtmt) cc_final: 0.8272 (mtpt) REVERT: B 41 LYS cc_start: 0.8192 (mttt) cc_final: 0.7900 (mttt) REVERT: B 79 LYS cc_start: 0.7454 (mtpt) cc_final: 0.6874 (mmmt) REVERT: B 271 LYS cc_start: 0.8402 (mmmt) cc_final: 0.8135 (mmmt) REVERT: B 326 ASN cc_start: 0.6440 (OUTLIER) cc_final: 0.6222 (t0) REVERT: C 37 GLN cc_start: 0.8506 (mm-40) cc_final: 0.8228 (mp10) REVERT: C 61 TYR cc_start: 0.8347 (m-80) cc_final: 0.8058 (m-80) REVERT: C 271 LYS cc_start: 0.8634 (mmtp) cc_final: 0.8396 (mmmt) REVERT: C 297 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8112 (mt-10) REVERT: D 21 MET cc_start: 0.7823 (mmm) cc_final: 0.6622 (tpp) REVERT: D 31 LYS cc_start: 0.8694 (mtmt) cc_final: 0.8474 (mtmt) REVERT: D 79 LYS cc_start: 0.8421 (mmmt) cc_final: 0.7776 (tptp) REVERT: D 225 GLU cc_start: 0.8216 (tt0) cc_final: 0.7847 (tt0) REVERT: E 50 ASN cc_start: 0.8821 (m110) cc_final: 0.8596 (m110) REVERT: E 79 LYS cc_start: 0.7456 (mtpt) cc_final: 0.6875 (mmmt) REVERT: E 188 SER cc_start: 0.8611 (m) cc_final: 0.8309 (p) REVERT: E 192 ASN cc_start: 0.8687 (m-40) cc_final: 0.8413 (m110) REVERT: E 271 LYS cc_start: 0.8412 (mmmt) cc_final: 0.8119 (mmmt) REVERT: E 326 ASN cc_start: 0.6642 (OUTLIER) cc_final: 0.6360 (t0) REVERT: F 61 TYR cc_start: 0.8277 (m-80) cc_final: 0.7992 (m-80) REVERT: F 92 PHE cc_start: 0.7330 (m-10) cc_final: 0.7008 (m-10) REVERT: F 130 GLN cc_start: 0.8220 (tt0) cc_final: 0.7967 (tt0) REVERT: F 291 ASN cc_start: 0.8248 (OUTLIER) cc_final: 0.7933 (m-40) REVERT: G 17 ILE cc_start: 0.8662 (mp) cc_final: 0.8329 (mm) REVERT: G 21 MET cc_start: 0.7621 (mmp) cc_final: 0.6857 (tpp) REVERT: G 50 ASN cc_start: 0.9035 (m-40) cc_final: 0.8605 (m110) REVERT: H 26 HIS cc_start: 0.7468 (m90) cc_final: 0.7154 (m-70) REVERT: H 41 LYS cc_start: 0.8013 (mttt) cc_final: 0.7803 (mttt) REVERT: H 51 MET cc_start: 0.8923 (ttm) cc_final: 0.8592 (mtp) REVERT: H 79 LYS cc_start: 0.7487 (mtpt) cc_final: 0.6867 (mmmt) REVERT: H 180 VAL cc_start: 0.8410 (OUTLIER) cc_final: 0.8191 (t) REVERT: H 297 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8060 (mt-10) REVERT: H 326 ASN cc_start: 0.6522 (OUTLIER) cc_final: 0.6264 (t0) REVERT: I 61 TYR cc_start: 0.8286 (m-80) cc_final: 0.7990 (m-80) REVERT: I 267 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7734 (mt-10) REVERT: I 297 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8095 (mt-10) REVERT: J 21 MET cc_start: 0.7492 (mmp) cc_final: 0.6855 (tpp) REVERT: J 31 LYS cc_start: 0.8701 (mttt) cc_final: 0.8079 (mtpt) REVERT: J 50 ASN cc_start: 0.9089 (m-40) cc_final: 0.8737 (m110) REVERT: J 119 THR cc_start: 0.8126 (p) cc_final: 0.7755 (p) REVERT: K 26 HIS cc_start: 0.7238 (m90) cc_final: 0.6987 (m-70) REVERT: K 31 LYS cc_start: 0.8602 (mttt) cc_final: 0.8280 (mttt) REVERT: K 79 LYS cc_start: 0.7535 (mtpt) cc_final: 0.6903 (mmmt) REVERT: K 271 LYS cc_start: 0.8512 (mttm) cc_final: 0.8298 (mmmt) REVERT: K 300 TYR cc_start: 0.8467 (OUTLIER) cc_final: 0.7619 (t80) REVERT: K 326 ASN cc_start: 0.6294 (OUTLIER) cc_final: 0.6074 (t0) REVERT: L 61 TYR cc_start: 0.8378 (m-80) cc_final: 0.8001 (m-80) REVERT: L 79 LYS cc_start: 0.8289 (mmmt) cc_final: 0.7981 (mmmt) REVERT: L 267 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7803 (mt-10) REVERT: L 297 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8059 (mt-10) REVERT: L 326 ASN cc_start: 0.6526 (OUTLIER) cc_final: 0.6318 (t0) outliers start: 129 outliers final: 72 residues processed: 1343 average time/residue: 0.5001 time to fit residues: 1125.0822 Evaluate side-chains 1206 residues out of total 5724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 1123 time to evaluate : 4.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 142 ILE Chi-restraints excluded: chain a residue 156 ILE Chi-restraints excluded: chain b residue 63 SER Chi-restraints excluded: chain b residue 156 ILE Chi-restraints excluded: chain c residue 69 SER Chi-restraints excluded: chain c residue 98 ASN Chi-restraints excluded: chain c residue 141 THR Chi-restraints excluded: chain c residue 156 ILE Chi-restraints excluded: chain d residue 109 THR Chi-restraints excluded: chain d residue 156 ILE Chi-restraints excluded: chain e residue 15 LEU Chi-restraints excluded: chain e residue 63 SER Chi-restraints excluded: chain e residue 69 SER Chi-restraints excluded: chain e residue 156 ILE Chi-restraints excluded: chain e residue 166 VAL Chi-restraints excluded: chain f residue 16 LYS Chi-restraints excluded: chain f residue 69 SER Chi-restraints excluded: chain f residue 98 ASN Chi-restraints excluded: chain f residue 141 THR Chi-restraints excluded: chain f residue 156 ILE Chi-restraints excluded: chain g residue 109 THR Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 156 ILE Chi-restraints excluded: chain h residue 63 SER Chi-restraints excluded: chain h residue 156 ILE Chi-restraints excluded: chain h residue 166 VAL Chi-restraints excluded: chain i residue 16 LYS Chi-restraints excluded: chain i residue 63 SER Chi-restraints excluded: chain i residue 69 SER Chi-restraints excluded: chain i residue 98 ASN Chi-restraints excluded: chain i residue 141 THR Chi-restraints excluded: chain i residue 156 ILE Chi-restraints excluded: chain j residue 35 ILE Chi-restraints excluded: chain j residue 53 THR Chi-restraints excluded: chain j residue 69 SER Chi-restraints excluded: chain j residue 156 ILE Chi-restraints excluded: chain k residue 63 SER Chi-restraints excluded: chain k residue 156 ILE Chi-restraints excluded: chain l residue 16 LYS Chi-restraints excluded: chain l residue 69 SER Chi-restraints excluded: chain l residue 98 ASN Chi-restraints excluded: chain l residue 141 THR Chi-restraints excluded: chain l residue 156 ILE Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 326 ASN Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 326 ASN Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 291 ASN Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 154 GLU Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 296 ILE Chi-restraints excluded: chain H residue 326 ASN Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 217 LYS Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain K residue 43 GLU Chi-restraints excluded: chain K residue 119 THR Chi-restraints excluded: chain K residue 154 GLU Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 296 ILE Chi-restraints excluded: chain K residue 300 TYR Chi-restraints excluded: chain K residue 326 ASN Chi-restraints excluded: chain L residue 43 GLU Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain L residue 214 LEU Chi-restraints excluded: chain L residue 217 LYS Chi-restraints excluded: chain L residue 300 TYR Chi-restraints excluded: chain L residue 326 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 256 optimal weight: 9.9990 chunk 311 optimal weight: 7.9990 chunk 262 optimal weight: 8.9990 chunk 454 optimal weight: 1.9990 chunk 373 optimal weight: 4.9990 chunk 482 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 218 optimal weight: 6.9990 chunk 595 optimal weight: 10.0000 chunk 205 optimal weight: 9.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 110 GLN a 151 ASN c 151 ASN f 2 GLN f 151 ASN i 151 ASN j 151 ASN l 2 GLN l 151 ASN A 326 ASN A 343 HIS ** B 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 HIS C 130 GLN C 161 ASN C 326 ASN C 371 GLN D 326 ASN D 343 HIS ** E 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 326 ASN F 37 GLN ** F 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 326 ASN ** G 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 326 ASN G 343 HIS ** H 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 161 ASN H 291 ASN ** H 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 343 HIS I 37 GLN I 326 ASN I 371 GLN ** J 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 326 ASN J 343 HIS K 90 ASN ** K 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 174 GLN K 291 ASN ** K 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 223 GLN L 326 ASN L 371 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.115865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.101573 restraints weight = 68811.692| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 1.45 r_work: 0.2833 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 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 : 0.006 0.115 52092 Z= 0.366 Angle : 0.725 10.728 70464 Z= 0.383 Chirality : 0.048 0.293 8040 Planarity : 0.005 0.052 9096 Dihedral : 5.694 51.250 7009 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.98 % Allowed : 7.07 % Favored : 91.95 % Rotamer: Outliers : 3.48 % Allowed : 12.28 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.11), residues: 6396 helix: 1.26 (0.10), residues: 2796 sheet: 0.71 (0.20), residues: 888 loop : -1.98 (0.11), residues: 2712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP L 116 HIS 0.010 0.002 HIS A 26 PHE 0.020 0.002 PHE F 277 TYR 0.028 0.002 TYR I 300 ARG 0.007 0.001 ARG B 187 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12792 Ramachandran restraints generated. 6396 Oldfield, 0 Emsley, 6396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12792 Ramachandran restraints generated. 6396 Oldfield, 0 Emsley, 6396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1355 residues out of total 5724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 1156 time to evaluate : 4.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 8 ASP cc_start: 0.8477 (m-30) cc_final: 0.8227 (m-30) REVERT: a 49 GLN cc_start: 0.8746 (tt0) cc_final: 0.8296 (tt0) REVERT: a 96 LYS cc_start: 0.8717 (mttm) cc_final: 0.8179 (mmtt) REVERT: b 2 GLN cc_start: 0.7927 (tt0) cc_final: 0.7711 (tt0) REVERT: b 96 LYS cc_start: 0.8495 (mttp) cc_final: 0.8062 (mmtm) REVERT: c 110 GLN cc_start: 0.7701 (tt0) cc_final: 0.7397 (tt0) REVERT: c 167 TYR cc_start: 0.8431 (m-80) cc_final: 0.8220 (m-80) REVERT: d 8 ASP cc_start: 0.8455 (m-30) cc_final: 0.8159 (m-30) REVERT: d 96 LYS cc_start: 0.8762 (mttm) cc_final: 0.8177 (mmtt) REVERT: e 2 GLN cc_start: 0.8072 (tt0) cc_final: 0.7700 (tt0) REVERT: e 12 TYR cc_start: 0.8724 (t80) cc_final: 0.8398 (t80) REVERT: e 83 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7324 (mp0) REVERT: e 96 LYS cc_start: 0.8408 (mttp) cc_final: 0.7980 (mmtm) REVERT: f 5 THR cc_start: 0.8339 (p) cc_final: 0.7980 (t) REVERT: f 16 LYS cc_start: 0.6004 (OUTLIER) cc_final: 0.4766 (pttp) REVERT: f 110 GLN cc_start: 0.7750 (tt0) cc_final: 0.7468 (tt0) REVERT: g 49 GLN cc_start: 0.8769 (tt0) cc_final: 0.8097 (tt0) REVERT: g 96 LYS cc_start: 0.8703 (mttm) cc_final: 0.8134 (mmtt) REVERT: h 2 GLN cc_start: 0.8033 (tt0) cc_final: 0.7779 (tt0) REVERT: h 96 LYS cc_start: 0.8517 (mttp) cc_final: 0.8063 (mmtm) REVERT: i 5 THR cc_start: 0.8311 (p) cc_final: 0.7941 (t) REVERT: i 16 LYS cc_start: 0.6367 (OUTLIER) cc_final: 0.4966 (pttp) REVERT: i 110 GLN cc_start: 0.7764 (tt0) cc_final: 0.7494 (tt0) REVERT: j 8 ASP cc_start: 0.8338 (m-30) cc_final: 0.8100 (m-30) REVERT: j 49 GLN cc_start: 0.8794 (tt0) cc_final: 0.8381 (tt0) REVERT: j 96 LYS cc_start: 0.8623 (mttm) cc_final: 0.7809 (mmtt) REVERT: k 96 LYS cc_start: 0.8552 (mttp) cc_final: 0.8110 (mmtm) REVERT: l 5 THR cc_start: 0.8370 (p) cc_final: 0.8001 (t) REVERT: l 7 GLU cc_start: 0.8489 (mt-10) cc_final: 0.7954 (mp0) REVERT: l 16 LYS cc_start: 0.6983 (OUTLIER) cc_final: 0.5125 (pttm) REVERT: l 83 GLU cc_start: 0.6691 (mp0) cc_final: 0.6225 (mp0) REVERT: l 110 GLN cc_start: 0.7734 (tt0) cc_final: 0.7474 (tt0) REVERT: l 167 TYR cc_start: 0.8470 (m-80) cc_final: 0.8255 (m-80) REVERT: A 21 MET cc_start: 0.8054 (mmp) cc_final: 0.7205 (tpp) REVERT: A 105 ASP cc_start: 0.8573 (OUTLIER) cc_final: 0.8369 (m-30) REVERT: A 185 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7476 (mt-10) REVERT: A 326 ASN cc_start: 0.7091 (OUTLIER) cc_final: 0.6847 (t0) REVERT: B 41 LYS cc_start: 0.8677 (mttt) cc_final: 0.8456 (mttt) REVERT: B 79 LYS cc_start: 0.7494 (mtpt) cc_final: 0.6836 (mmmt) REVERT: B 130 GLN cc_start: 0.8417 (tt0) cc_final: 0.8143 (tt0) REVERT: B 146 ASN cc_start: 0.6602 (m-40) cc_final: 0.6100 (m110) REVERT: C 61 TYR cc_start: 0.8626 (m-80) cc_final: 0.8415 (m-80) REVERT: C 203 VAL cc_start: 0.8997 (m) cc_final: 0.8433 (t) REVERT: C 231 ASN cc_start: 0.8926 (t0) cc_final: 0.8704 (t0) REVERT: C 271 LYS cc_start: 0.8648 (mmtp) cc_final: 0.8416 (mmmt) REVERT: D 26 HIS cc_start: 0.7764 (m90) cc_final: 0.7522 (m90) REVERT: D 79 LYS cc_start: 0.8515 (mmmt) cc_final: 0.7971 (tptp) REVERT: D 185 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7495 (mt-10) REVERT: D 224 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7910 (mt-10) REVERT: D 275 LEU cc_start: 0.8799 (tt) cc_final: 0.8513 (tt) REVERT: D 326 ASN cc_start: 0.6975 (OUTLIER) cc_final: 0.6689 (t0) REVERT: E 42 ILE cc_start: 0.8594 (mm) cc_final: 0.8328 (mm) REVERT: E 79 LYS cc_start: 0.7475 (mtpt) cc_final: 0.6836 (mmmt) REVERT: E 130 GLN cc_start: 0.8479 (tt0) cc_final: 0.8168 (tt0) REVERT: E 132 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8140 (tt0) REVERT: E 146 ASN cc_start: 0.6712 (m-40) cc_final: 0.6283 (m110) REVERT: E 326 ASN cc_start: 0.7764 (OUTLIER) cc_final: 0.6640 (t0) REVERT: F 203 VAL cc_start: 0.8955 (m) cc_final: 0.8342 (t) REVERT: F 271 LYS cc_start: 0.8702 (mmtt) cc_final: 0.8334 (tptt) REVERT: G 21 MET cc_start: 0.7710 (mmp) cc_final: 0.7160 (tpp) REVERT: G 26 HIS cc_start: 0.7807 (m90) cc_final: 0.7519 (m170) REVERT: G 326 ASN cc_start: 0.7188 (OUTLIER) cc_final: 0.6935 (t0) REVERT: H 41 LYS cc_start: 0.8425 (mttt) cc_final: 0.8190 (mttt) REVERT: H 43 GLU cc_start: 0.7996 (mp0) cc_final: 0.7721 (mp0) REVERT: H 79 LYS cc_start: 0.7544 (mtpt) cc_final: 0.6838 (mmmt) REVERT: H 180 VAL cc_start: 0.8956 (OUTLIER) cc_final: 0.8574 (t) REVERT: I 31 LYS cc_start: 0.8779 (mttt) cc_final: 0.8471 (mtmt) REVERT: I 203 VAL cc_start: 0.8950 (m) cc_final: 0.8366 (t) REVERT: I 231 ASN cc_start: 0.8926 (t0) cc_final: 0.8689 (t0) REVERT: J 21 MET cc_start: 0.7696 (mmp) cc_final: 0.7099 (tpp) REVERT: J 31 LYS cc_start: 0.8911 (mttt) cc_final: 0.8466 (mtpt) REVERT: J 119 THR cc_start: 0.8780 (OUTLIER) cc_final: 0.8532 (p) REVERT: J 326 ASN cc_start: 0.6957 (OUTLIER) cc_final: 0.6683 (t0) REVERT: K 31 LYS cc_start: 0.8832 (mttt) cc_final: 0.8442 (mttt) REVERT: K 79 LYS cc_start: 0.7552 (mtpt) cc_final: 0.6818 (mmmt) REVERT: K 130 GLN cc_start: 0.8093 (tt0) cc_final: 0.7855 (tt0) REVERT: K 188 SER cc_start: 0.8836 (p) cc_final: 0.8581 (t) REVERT: K 265 ASP cc_start: 0.8797 (m-30) cc_final: 0.8538 (m-30) REVERT: K 300 TYR cc_start: 0.8639 (OUTLIER) cc_final: 0.7889 (t80) REVERT: L 44 ILE cc_start: 0.8998 (OUTLIER) cc_final: 0.8744 (tp) REVERT: L 79 LYS cc_start: 0.8385 (mmmt) cc_final: 0.8100 (mmmt) REVERT: L 203 VAL cc_start: 0.8968 (m) cc_final: 0.8341 (t) REVERT: L 231 ASN cc_start: 0.8936 (t0) cc_final: 0.8687 (t0) outliers start: 199 outliers final: 145 residues processed: 1255 average time/residue: 0.4980 time to fit residues: 1040.2708 Evaluate side-chains 1223 residues out of total 5724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 1064 time to evaluate : 4.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 69 SER Chi-restraints excluded: chain a residue 109 THR Chi-restraints excluded: chain a residue 156 ILE Chi-restraints excluded: chain a residue 166 VAL Chi-restraints excluded: chain b residue 63 SER Chi-restraints excluded: chain b residue 69 SER Chi-restraints excluded: chain b residue 87 LEU Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain b residue 147 VAL Chi-restraints excluded: chain b residue 156 ILE Chi-restraints excluded: chain b residue 166 VAL Chi-restraints excluded: chain c residue 69 SER Chi-restraints excluded: chain c residue 70 VAL Chi-restraints excluded: chain c residue 93 ILE Chi-restraints excluded: chain c residue 98 ASN Chi-restraints excluded: chain c residue 105 ASP Chi-restraints excluded: chain c residue 109 THR Chi-restraints excluded: chain c residue 141 THR Chi-restraints excluded: chain c residue 156 ILE Chi-restraints excluded: chain c residue 166 VAL Chi-restraints excluded: chain d residue 69 SER Chi-restraints excluded: chain d residue 109 THR Chi-restraints excluded: chain d residue 110 GLN Chi-restraints excluded: chain d residue 156 ILE Chi-restraints excluded: chain d residue 166 VAL Chi-restraints excluded: chain e residue 69 SER Chi-restraints excluded: chain e residue 70 VAL Chi-restraints excluded: chain e residue 109 THR Chi-restraints excluded: chain e residue 147 VAL Chi-restraints excluded: chain e residue 156 ILE Chi-restraints excluded: chain e residue 166 VAL Chi-restraints excluded: chain f residue 16 LYS Chi-restraints excluded: chain f residue 69 SER Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 98 ASN Chi-restraints excluded: chain f residue 105 ASP Chi-restraints excluded: chain f residue 109 THR Chi-restraints excluded: chain f residue 141 THR Chi-restraints excluded: chain f residue 156 ILE Chi-restraints excluded: chain f residue 166 VAL Chi-restraints excluded: chain g residue 63 SER Chi-restraints excluded: chain g residue 69 SER Chi-restraints excluded: chain g residue 109 THR Chi-restraints excluded: chain g residue 110 GLN Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 156 ILE Chi-restraints excluded: chain g residue 164 ILE Chi-restraints excluded: chain g residue 166 VAL Chi-restraints excluded: chain h residue 63 SER Chi-restraints excluded: chain h residue 69 SER Chi-restraints excluded: chain h residue 109 THR Chi-restraints excluded: chain h residue 147 VAL Chi-restraints excluded: chain h residue 156 ILE Chi-restraints excluded: chain h residue 166 VAL Chi-restraints excluded: chain i residue 16 LYS Chi-restraints excluded: chain i residue 63 SER Chi-restraints excluded: chain i residue 69 SER Chi-restraints excluded: chain i residue 70 VAL Chi-restraints excluded: chain i residue 98 ASN Chi-restraints excluded: chain i residue 105 ASP Chi-restraints excluded: chain i residue 109 THR Chi-restraints excluded: chain i residue 141 THR Chi-restraints excluded: chain i residue 156 ILE Chi-restraints excluded: chain i residue 166 VAL Chi-restraints excluded: chain j residue 63 SER Chi-restraints excluded: chain j residue 69 SER Chi-restraints excluded: chain j residue 109 THR Chi-restraints excluded: chain j residue 147 VAL Chi-restraints excluded: chain j residue 156 ILE Chi-restraints excluded: chain j residue 166 VAL Chi-restraints excluded: chain k residue 63 SER Chi-restraints excluded: chain k residue 69 SER Chi-restraints excluded: chain k residue 109 THR Chi-restraints excluded: chain k residue 147 VAL Chi-restraints excluded: chain k residue 156 ILE Chi-restraints excluded: chain k residue 166 VAL Chi-restraints excluded: chain l residue 16 LYS Chi-restraints excluded: chain l residue 69 SER Chi-restraints excluded: chain l residue 98 ASN Chi-restraints excluded: chain l residue 105 ASP Chi-restraints excluded: chain l residue 109 THR Chi-restraints excluded: chain l residue 141 THR Chi-restraints excluded: chain l residue 156 ILE Chi-restraints excluded: chain l residue 166 VAL Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 326 ASN Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 300 TYR Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 326 ASN Chi-restraints excluded: chain E residue 132 GLU Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 326 ASN Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 204 ILE Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 298 LEU Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 326 ASN Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 154 GLU Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 326 ASN Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain I residue 105 ASP Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 182 ASP Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 259 ASP Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain J residue 105 ASP Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain J residue 298 LEU Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain J residue 326 ASN Chi-restraints excluded: chain K residue 119 THR Chi-restraints excluded: chain K residue 154 GLU Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 300 TYR Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain K residue 326 ASN Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain L residue 105 ASP Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain L residue 214 LEU Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 300 TYR Chi-restraints excluded: chain L residue 326 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 443 optimal weight: 0.0170 chunk 257 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 502 optimal weight: 5.9990 chunk 331 optimal weight: 6.9990 chunk 583 optimal weight: 6.9990 chunk 615 optimal weight: 5.9990 chunk 518 optimal weight: 4.9990 chunk 564 optimal weight: 5.9990 chunk 301 optimal weight: 6.9990 chunk 193 optimal weight: 6.9990 overall best weight: 2.5622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 151 ASN d 151 ASN f 2 GLN j 151 ASN ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 ASN A 326 ASN B 15 GLN B 50 ASN B 161 ASN B 326 ASN C 37 GLN C 326 ASN C 371 GLN ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 326 ASN E 15 GLN ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 326 ASN ** F 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 281 GLN F 326 ASN G 161 ASN G 326 ASN H 50 ASN H 161 ASN H 326 ASN I 37 GLN ** I 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 326 ASN I 371 GLN J 161 ASN J 326 ASN ** K 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 326 ASN L 371 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.116344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.102056 restraints weight = 68479.989| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 1.46 r_work: 0.2832 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 52092 Z= 0.273 Angle : 0.650 12.636 70464 Z= 0.337 Chirality : 0.045 0.364 8040 Planarity : 0.004 0.049 9096 Dihedral : 5.503 50.656 7002 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.91 % Allowed : 6.71 % Favored : 92.39 % Rotamer: Outliers : 3.72 % Allowed : 13.98 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.10), residues: 6396 helix: 1.36 (0.10), residues: 2784 sheet: 0.80 (0.20), residues: 864 loop : -1.98 (0.11), residues: 2748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP L 116 HIS 0.007 0.002 HIS D 343 PHE 0.015 0.002 PHE K 277 TYR 0.020 0.002 TYR a 88 ARG 0.003 0.000 ARG H 176 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12792 Ramachandran restraints generated. 6396 Oldfield, 0 Emsley, 6396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12792 Ramachandran restraints generated. 6396 Oldfield, 0 Emsley, 6396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1318 residues out of total 5724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 213 poor density : 1105 time to evaluate : 4.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 49 GLN cc_start: 0.8738 (tt0) cc_final: 0.8392 (tt0) REVERT: a 96 LYS cc_start: 0.8712 (mttm) cc_final: 0.8196 (mmtt) REVERT: b 2 GLN cc_start: 0.8015 (tt0) cc_final: 0.7767 (tt0) REVERT: b 96 LYS cc_start: 0.8409 (mttp) cc_final: 0.7807 (mptt) REVERT: b 110 GLN cc_start: 0.7905 (mt0) cc_final: 0.7294 (mt0) REVERT: c 110 GLN cc_start: 0.7808 (tt0) cc_final: 0.7581 (tt0) REVERT: c 165 GLU cc_start: 0.8782 (tp30) cc_final: 0.8211 (mm-30) REVERT: d 8 ASP cc_start: 0.8514 (m-30) cc_final: 0.8270 (m-30) REVERT: d 49 GLN cc_start: 0.8492 (tt0) cc_final: 0.8144 (tt0) REVERT: d 96 LYS cc_start: 0.8725 (mttm) cc_final: 0.8267 (mmtt) REVERT: e 2 GLN cc_start: 0.8138 (tt0) cc_final: 0.7862 (tt0) REVERT: e 12 TYR cc_start: 0.8778 (t80) cc_final: 0.8254 (t80) REVERT: e 83 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7297 (mp0) REVERT: e 96 LYS cc_start: 0.8538 (mttp) cc_final: 0.8159 (mmtm) REVERT: f 5 THR cc_start: 0.8221 (p) cc_final: 0.7866 (t) REVERT: f 16 LYS cc_start: 0.6121 (OUTLIER) cc_final: 0.4747 (pttp) REVERT: f 110 GLN cc_start: 0.7717 (tt0) cc_final: 0.7419 (tt0) REVERT: f 167 TYR cc_start: 0.8235 (m-80) cc_final: 0.8004 (m-10) REVERT: g 49 GLN cc_start: 0.8737 (tt0) cc_final: 0.8225 (tt0) REVERT: g 96 LYS cc_start: 0.8686 (mttm) cc_final: 0.8250 (mmtt) REVERT: h 2 GLN cc_start: 0.8017 (tt0) cc_final: 0.7761 (tt0) REVERT: h 96 LYS cc_start: 0.8510 (mttp) cc_final: 0.8129 (mmtm) REVERT: h 110 GLN cc_start: 0.7618 (mt0) cc_final: 0.7150 (mt0) REVERT: i 5 THR cc_start: 0.8268 (p) cc_final: 0.7908 (t) REVERT: i 16 LYS cc_start: 0.6319 (OUTLIER) cc_final: 0.4979 (pttp) REVERT: i 42 ASP cc_start: 0.6755 (t0) cc_final: 0.6422 (t70) REVERT: i 110 GLN cc_start: 0.7714 (tt0) cc_final: 0.7419 (tt0) REVERT: i 167 TYR cc_start: 0.8235 (m-80) cc_final: 0.7971 (m-10) REVERT: j 49 GLN cc_start: 0.8755 (tt0) cc_final: 0.8353 (tt0) REVERT: j 96 LYS cc_start: 0.8676 (mttm) cc_final: 0.7866 (mmtt) REVERT: k 25 GLU cc_start: 0.8257 (mm-30) cc_final: 0.8001 (mm-30) REVERT: k 96 LYS cc_start: 0.8555 (mttp) cc_final: 0.8217 (mmtm) REVERT: k 110 GLN cc_start: 0.7588 (mt0) cc_final: 0.7143 (mt0) REVERT: l 5 THR cc_start: 0.8324 (p) cc_final: 0.7984 (t) REVERT: l 16 LYS cc_start: 0.6936 (OUTLIER) cc_final: 0.5090 (pttm) REVERT: l 42 ASP cc_start: 0.6891 (t0) cc_final: 0.6590 (t70) REVERT: A 21 MET cc_start: 0.8052 (mmp) cc_final: 0.7270 (tpp) REVERT: A 79 LYS cc_start: 0.8473 (mmmt) cc_final: 0.7890 (tptp) REVERT: A 105 ASP cc_start: 0.8580 (OUTLIER) cc_final: 0.8370 (m-30) REVERT: A 195 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8167 (tt0) REVERT: B 41 LYS cc_start: 0.8684 (mttt) cc_final: 0.8441 (mttt) REVERT: B 79 LYS cc_start: 0.7545 (mtpt) cc_final: 0.6830 (mmmt) REVERT: B 132 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.8122 (tt0) REVERT: B 326 ASN cc_start: 0.7404 (OUTLIER) cc_final: 0.7015 (t0) REVERT: C 152 VAL cc_start: 0.7454 (OUTLIER) cc_final: 0.7149 (t) REVERT: C 203 VAL cc_start: 0.9008 (m) cc_final: 0.8390 (t) REVERT: C 271 LYS cc_start: 0.8617 (mmtp) cc_final: 0.8354 (mmmt) REVERT: C 326 ASN cc_start: 0.6673 (OUTLIER) cc_final: 0.6443 (t0) REVERT: D 21 MET cc_start: 0.8154 (mmm) cc_final: 0.7183 (tpt) REVERT: D 26 HIS cc_start: 0.7771 (m90) cc_final: 0.7506 (m90) REVERT: D 79 LYS cc_start: 0.8529 (mmmt) cc_final: 0.7989 (tptp) REVERT: D 185 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7523 (mt-10) REVERT: D 275 LEU cc_start: 0.8676 (tt) cc_final: 0.8421 (tt) REVERT: E 79 LYS cc_start: 0.7527 (mtpt) cc_final: 0.6826 (mmmt) REVERT: E 302 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.8125 (mtt) REVERT: F 152 VAL cc_start: 0.7453 (OUTLIER) cc_final: 0.7141 (t) REVERT: F 203 VAL cc_start: 0.8949 (m) cc_final: 0.8275 (t) REVERT: F 271 LYS cc_start: 0.7938 (mmtt) cc_final: 0.7698 (tptt) REVERT: G 21 MET cc_start: 0.7915 (mmp) cc_final: 0.7138 (tpp) REVERT: G 26 HIS cc_start: 0.7832 (m90) cc_final: 0.7530 (m170) REVERT: G 141 LYS cc_start: 0.8455 (pttt) cc_final: 0.8234 (pttm) REVERT: G 149 ASN cc_start: 0.7300 (t0) cc_final: 0.7002 (t0) REVERT: H 41 LYS cc_start: 0.8334 (mttt) cc_final: 0.8015 (mttt) REVERT: H 43 GLU cc_start: 0.8081 (mp0) cc_final: 0.7704 (mp0) REVERT: H 79 LYS cc_start: 0.7547 (mtpt) cc_final: 0.6816 (mmmt) REVERT: H 146 ASN cc_start: 0.6394 (m-40) cc_final: 0.5795 (m110) REVERT: H 180 VAL cc_start: 0.8865 (OUTLIER) cc_final: 0.8532 (t) REVERT: H 300 TYR cc_start: 0.8493 (OUTLIER) cc_final: 0.7910 (t80) REVERT: H 326 ASN cc_start: 0.7529 (OUTLIER) cc_final: 0.7140 (t0) REVERT: I 79 LYS cc_start: 0.8095 (mmmt) cc_final: 0.7134 (pttt) REVERT: I 146 ASN cc_start: 0.6235 (m-40) cc_final: 0.6033 (m110) REVERT: I 152 VAL cc_start: 0.7476 (OUTLIER) cc_final: 0.7217 (t) REVERT: I 203 VAL cc_start: 0.8945 (m) cc_final: 0.8332 (t) REVERT: J 21 MET cc_start: 0.7964 (mmp) cc_final: 0.7166 (tpp) REVERT: J 31 LYS cc_start: 0.8897 (mttt) cc_final: 0.8447 (mtpt) REVERT: J 119 THR cc_start: 0.8718 (p) cc_final: 0.8481 (p) REVERT: K 15 GLN cc_start: 0.8479 (tp-100) cc_final: 0.8243 (tp40) REVERT: K 26 HIS cc_start: 0.7536 (m90) cc_final: 0.7228 (m90) REVERT: K 31 LYS cc_start: 0.8924 (mttt) cc_final: 0.8440 (mttt) REVERT: K 50 ASN cc_start: 0.9160 (m-40) cc_final: 0.8814 (m110) REVERT: K 79 LYS cc_start: 0.7552 (mtpt) cc_final: 0.6813 (mmmt) REVERT: K 130 GLN cc_start: 0.8143 (tt0) cc_final: 0.7926 (tt0) REVERT: K 146 ASN cc_start: 0.6347 (m-40) cc_final: 0.5747 (m110) REVERT: K 188 SER cc_start: 0.8867 (p) cc_final: 0.8603 (t) REVERT: K 300 TYR cc_start: 0.8574 (OUTLIER) cc_final: 0.7846 (t80) REVERT: L 79 LYS cc_start: 0.8373 (mmmt) cc_final: 0.7342 (pttt) REVERT: L 152 VAL cc_start: 0.7494 (OUTLIER) cc_final: 0.7224 (t) REVERT: L 203 VAL cc_start: 0.8987 (m) cc_final: 0.8309 (t) REVERT: L 231 ASN cc_start: 0.8908 (t0) cc_final: 0.8668 (t0) outliers start: 213 outliers final: 147 residues processed: 1215 average time/residue: 0.4899 time to fit residues: 994.8120 Evaluate side-chains 1246 residues out of total 5724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 1082 time to evaluate : 4.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 35 ILE Chi-restraints excluded: chain a residue 69 SER Chi-restraints excluded: chain a residue 109 THR Chi-restraints excluded: chain a residue 110 GLN Chi-restraints excluded: chain a residue 156 ILE Chi-restraints excluded: chain a residue 159 HIS Chi-restraints excluded: chain a residue 166 VAL Chi-restraints excluded: chain b residue 20 LEU Chi-restraints excluded: chain b residue 63 SER Chi-restraints excluded: chain b residue 98 ASN Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain b residue 156 ILE Chi-restraints excluded: chain c residue 69 SER Chi-restraints excluded: chain c residue 70 VAL Chi-restraints excluded: chain c residue 98 ASN Chi-restraints excluded: chain c residue 109 THR Chi-restraints excluded: chain c residue 141 THR Chi-restraints excluded: chain c residue 156 ILE Chi-restraints excluded: chain c residue 166 VAL Chi-restraints excluded: chain d residue 69 SER Chi-restraints excluded: chain d residue 77 ASP Chi-restraints excluded: chain d residue 109 THR Chi-restraints excluded: chain d residue 156 ILE Chi-restraints excluded: chain d residue 159 HIS Chi-restraints excluded: chain e residue 63 SER Chi-restraints excluded: chain e residue 69 SER Chi-restraints excluded: chain e residue 70 VAL Chi-restraints excluded: chain e residue 98 ASN Chi-restraints excluded: chain e residue 156 ILE Chi-restraints excluded: chain f residue 16 LYS Chi-restraints excluded: chain f residue 69 SER Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 98 ASN Chi-restraints excluded: chain f residue 105 ASP Chi-restraints excluded: chain f residue 109 THR Chi-restraints excluded: chain f residue 141 THR Chi-restraints excluded: chain f residue 156 ILE Chi-restraints excluded: chain g residue 63 SER Chi-restraints excluded: chain g residue 69 SER Chi-restraints excluded: chain g residue 109 THR Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 156 ILE Chi-restraints excluded: chain g residue 159 HIS Chi-restraints excluded: chain g residue 166 VAL Chi-restraints excluded: chain h residue 63 SER Chi-restraints excluded: chain h residue 69 SER Chi-restraints excluded: chain h residue 98 ASN Chi-restraints excluded: chain h residue 109 THR Chi-restraints excluded: chain h residue 156 ILE Chi-restraints excluded: chain i residue 16 LYS Chi-restraints excluded: chain i residue 63 SER Chi-restraints excluded: chain i residue 66 SER Chi-restraints excluded: chain i residue 69 SER Chi-restraints excluded: chain i residue 70 VAL Chi-restraints excluded: chain i residue 98 ASN Chi-restraints excluded: chain i residue 105 ASP Chi-restraints excluded: chain i residue 109 THR Chi-restraints excluded: chain i residue 141 THR Chi-restraints excluded: chain i residue 156 ILE Chi-restraints excluded: chain i residue 166 VAL Chi-restraints excluded: chain j residue 69 SER Chi-restraints excluded: chain j residue 77 ASP Chi-restraints excluded: chain j residue 109 THR Chi-restraints excluded: chain j residue 156 ILE Chi-restraints excluded: chain j residue 159 HIS Chi-restraints excluded: chain j residue 166 VAL Chi-restraints excluded: chain k residue 63 SER Chi-restraints excluded: chain k residue 69 SER Chi-restraints excluded: chain k residue 98 ASN Chi-restraints excluded: chain k residue 109 THR Chi-restraints excluded: chain k residue 156 ILE Chi-restraints excluded: chain l residue 16 LYS Chi-restraints excluded: chain l residue 98 ASN Chi-restraints excluded: chain l residue 105 ASP Chi-restraints excluded: chain l residue 109 THR Chi-restraints excluded: chain l residue 141 THR Chi-restraints excluded: chain l residue 156 ILE Chi-restraints excluded: chain l residue 166 VAL Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 326 ASN Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 300 TYR Chi-restraints excluded: chain C residue 326 ASN Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 326 ASN Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 302 MET Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 326 ASN Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 154 GLU Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 300 TYR Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 326 ASN Chi-restraints excluded: chain H residue 154 GLU Chi-restraints excluded: chain H residue 161 ASN Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 300 TYR Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 326 ASN Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 154 GLU Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 259 ASP Chi-restraints excluded: chain I residue 300 TYR Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain J residue 105 ASP Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain J residue 326 ASN Chi-restraints excluded: chain K residue 154 GLU Chi-restraints excluded: chain K residue 179 THR Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 300 TYR Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain K residue 326 ASN Chi-restraints excluded: chain L residue 93 MET Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 154 GLU Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain L residue 214 LEU Chi-restraints excluded: chain L residue 224 GLU Chi-restraints excluded: chain L residue 259 ASP Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 300 TYR Chi-restraints excluded: chain L residue 326 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 561 optimal weight: 5.9990 chunk 341 optimal weight: 3.9990 chunk 236 optimal weight: 7.9990 chunk 228 optimal weight: 7.9990 chunk 581 optimal weight: 3.9990 chunk 396 optimal weight: 6.9990 chunk 196 optimal weight: 9.9990 chunk 337 optimal weight: 3.9990 chunk 184 optimal weight: 5.9990 chunk 343 optimal weight: 8.9990 chunk 411 optimal weight: 0.9980 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 151 ASN d 151 ASN e 110 GLN i 2 GLN j 110 GLN j 151 ASN k 132 HIS ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 ASN B 161 ASN C 288 ASN C 326 ASN ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 161 ASN F 130 GLN F 326 ASN G 161 ASN H 161 ASN I 37 GLN I 130 GLN I 223 GLN I 326 ASN I 371 GLN J 161 ASN K 161 ASN K 326 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.113844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.099691 restraints weight = 68733.270| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 1.45 r_work: 0.2797 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.113 52092 Z= 0.363 Angle : 0.696 14.540 70464 Z= 0.360 Chirality : 0.046 0.320 8040 Planarity : 0.005 0.048 9096 Dihedral : 5.635 54.953 7000 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.86 % Allowed : 7.15 % Favored : 91.99 % Rotamer: Outliers : 4.51 % Allowed : 14.36 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.10), residues: 6396 helix: 1.20 (0.09), residues: 2796 sheet: 1.00 (0.20), residues: 792 loop : -2.10 (0.10), residues: 2808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 116 HIS 0.009 0.002 HIS A 343 PHE 0.016 0.002 PHE C 277 TYR 0.026 0.002 TYR a 88 ARG 0.004 0.001 ARG I 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12792 Ramachandran restraints generated. 6396 Oldfield, 0 Emsley, 6396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12792 Ramachandran restraints generated. 6396 Oldfield, 0 Emsley, 6396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1349 residues out of total 5724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 258 poor density : 1091 time to evaluate : 4.681 Fit side-chains revert: symmetry clash REVERT: a 10 ARG cc_start: 0.8425 (ttm170) cc_final: 0.8176 (ttm-80) REVERT: a 49 GLN cc_start: 0.8799 (tt0) cc_final: 0.8430 (tt0) REVERT: a 96 LYS cc_start: 0.8750 (mttm) cc_final: 0.8347 (mmtt) REVERT: b 2 GLN cc_start: 0.7930 (tt0) cc_final: 0.7676 (tt0) REVERT: b 21 GLU cc_start: 0.7248 (mt-10) cc_final: 0.6716 (tt0) REVERT: b 96 LYS cc_start: 0.8479 (mttp) cc_final: 0.8127 (mmtm) REVERT: c 110 GLN cc_start: 0.7814 (tt0) cc_final: 0.7549 (tt0) REVERT: d 8 ASP cc_start: 0.8459 (m-30) cc_final: 0.8180 (m-30) REVERT: d 49 GLN cc_start: 0.8515 (tt0) cc_final: 0.8155 (tt0) REVERT: d 96 LYS cc_start: 0.8732 (mttm) cc_final: 0.8203 (mmtt) REVERT: e 2 GLN cc_start: 0.8087 (tt0) cc_final: 0.7836 (tt0) REVERT: e 12 TYR cc_start: 0.8691 (t80) cc_final: 0.8115 (t80) REVERT: e 83 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7066 (mp0) REVERT: e 96 LYS cc_start: 0.8518 (mttp) cc_final: 0.8173 (mmtm) REVERT: f 5 THR cc_start: 0.8269 (p) cc_final: 0.7894 (t) REVERT: f 16 LYS cc_start: 0.6140 (OUTLIER) cc_final: 0.4760 (pttp) REVERT: f 42 ASP cc_start: 0.6798 (t0) cc_final: 0.6506 (t70) REVERT: f 110 GLN cc_start: 0.7832 (tt0) cc_final: 0.7512 (tt0) REVERT: f 165 GLU cc_start: 0.8789 (tp30) cc_final: 0.8188 (mm-30) REVERT: f 167 TYR cc_start: 0.8401 (m-80) cc_final: 0.8166 (m-80) REVERT: g 49 GLN cc_start: 0.8789 (tt0) cc_final: 0.8251 (tt0) REVERT: g 96 LYS cc_start: 0.8705 (mttm) cc_final: 0.8188 (mmtt) REVERT: h 2 GLN cc_start: 0.8079 (tt0) cc_final: 0.7822 (tt0) REVERT: h 96 LYS cc_start: 0.8527 (mttp) cc_final: 0.8189 (mmtm) REVERT: h 110 GLN cc_start: 0.7641 (mt0) cc_final: 0.7258 (mt0) REVERT: i 5 THR cc_start: 0.8250 (p) cc_final: 0.7876 (t) REVERT: i 16 LYS cc_start: 0.6095 (OUTLIER) cc_final: 0.4943 (pttp) REVERT: i 42 ASP cc_start: 0.6779 (t0) cc_final: 0.6471 (t70) REVERT: i 110 GLN cc_start: 0.7849 (tt0) cc_final: 0.7596 (tt0) REVERT: i 167 TYR cc_start: 0.8394 (m-80) cc_final: 0.8150 (m-80) REVERT: j 49 GLN cc_start: 0.8810 (tt0) cc_final: 0.8371 (tt0) REVERT: j 96 LYS cc_start: 0.8731 (mttm) cc_final: 0.7936 (mmtt) REVERT: j 145 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7859 (mt-10) REVERT: k 25 GLU cc_start: 0.8260 (mm-30) cc_final: 0.8017 (mm-30) REVERT: k 96 LYS cc_start: 0.8524 (mttp) cc_final: 0.8204 (mmtm) REVERT: k 110 GLN cc_start: 0.7811 (mt0) cc_final: 0.7215 (mt0) REVERT: l 5 THR cc_start: 0.8306 (p) cc_final: 0.7931 (t) REVERT: A 21 MET cc_start: 0.7873 (mmp) cc_final: 0.7332 (tpp) REVERT: B 41 LYS cc_start: 0.8682 (mttt) cc_final: 0.8474 (mttt) REVERT: B 79 LYS cc_start: 0.7541 (mtpt) cc_final: 0.6831 (mmmt) REVERT: B 132 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.8093 (tt0) REVERT: C 152 VAL cc_start: 0.7582 (OUTLIER) cc_final: 0.7322 (t) REVERT: C 171 ILE cc_start: 0.8273 (OUTLIER) cc_final: 0.7493 (pt) REVERT: C 203 VAL cc_start: 0.9033 (m) cc_final: 0.8434 (t) REVERT: C 263 LYS cc_start: 0.8791 (ttpt) cc_final: 0.8550 (tttm) REVERT: C 343 HIS cc_start: 0.8611 (OUTLIER) cc_final: 0.8135 (p90) REVERT: D 26 HIS cc_start: 0.7833 (m90) cc_final: 0.7571 (m90) REVERT: D 79 LYS cc_start: 0.8545 (mmmt) cc_final: 0.8041 (tptp) REVERT: D 185 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7629 (mt-10) REVERT: D 275 LEU cc_start: 0.8749 (tt) cc_final: 0.8535 (tt) REVERT: E 79 LYS cc_start: 0.7534 (mtpt) cc_final: 0.6843 (mmmt) REVERT: E 302 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.8223 (mtt) REVERT: F 79 LYS cc_start: 0.7896 (mmmt) cc_final: 0.7001 (pttt) REVERT: F 92 PHE cc_start: 0.8787 (m-10) cc_final: 0.8525 (m-80) REVERT: F 152 VAL cc_start: 0.7548 (OUTLIER) cc_final: 0.7271 (t) REVERT: F 203 VAL cc_start: 0.8995 (m) cc_final: 0.8363 (t) REVERT: F 343 HIS cc_start: 0.8603 (OUTLIER) cc_final: 0.8128 (p90) REVERT: G 21 MET cc_start: 0.8053 (mmp) cc_final: 0.7268 (tpp) REVERT: G 26 HIS cc_start: 0.7835 (m90) cc_final: 0.7527 (m170) REVERT: H 15 GLN cc_start: 0.8431 (tp-100) cc_final: 0.8167 (tp-100) REVERT: H 41 LYS cc_start: 0.8331 (mttt) cc_final: 0.7969 (mttt) REVERT: H 43 GLU cc_start: 0.7958 (mp0) cc_final: 0.7686 (mp0) REVERT: H 79 LYS cc_start: 0.7547 (mtpt) cc_final: 0.6826 (mmmt) REVERT: H 130 GLN cc_start: 0.8095 (tt0) cc_final: 0.7883 (tt0) REVERT: H 180 VAL cc_start: 0.8894 (OUTLIER) cc_final: 0.8576 (t) REVERT: H 300 TYR cc_start: 0.8525 (OUTLIER) cc_final: 0.7903 (t80) REVERT: I 79 LYS cc_start: 0.8143 (mmmt) cc_final: 0.7119 (pttt) REVERT: I 152 VAL cc_start: 0.7480 (OUTLIER) cc_final: 0.7231 (t) REVERT: I 171 ILE cc_start: 0.8369 (OUTLIER) cc_final: 0.7595 (pt) REVERT: I 203 VAL cc_start: 0.8998 (m) cc_final: 0.8405 (t) REVERT: I 231 ASN cc_start: 0.8927 (t0) cc_final: 0.8724 (t0) REVERT: I 263 LYS cc_start: 0.8798 (ttpt) cc_final: 0.8598 (tttm) REVERT: I 343 HIS cc_start: 0.8633 (OUTLIER) cc_final: 0.8143 (p90) REVERT: J 21 MET cc_start: 0.7821 (mmp) cc_final: 0.7278 (tpp) REVERT: J 31 LYS cc_start: 0.8911 (mttt) cc_final: 0.8476 (mtpt) REVERT: J 105 ASP cc_start: 0.8536 (OUTLIER) cc_final: 0.8140 (m-30) REVERT: J 119 THR cc_start: 0.8821 (p) cc_final: 0.8557 (p) REVERT: J 255 SER cc_start: 0.8680 (m) cc_final: 0.8292 (p) REVERT: K 15 GLN cc_start: 0.8480 (tp-100) cc_final: 0.8251 (tp40) REVERT: K 26 HIS cc_start: 0.7483 (m90) cc_final: 0.7171 (m90) REVERT: K 31 LYS cc_start: 0.8925 (mttt) cc_final: 0.8449 (mttt) REVERT: K 50 ASN cc_start: 0.9248 (m-40) cc_final: 0.8884 (m110) REVERT: K 74 ASN cc_start: 0.6948 (OUTLIER) cc_final: 0.6603 (m-40) REVERT: K 79 LYS cc_start: 0.7552 (mtpt) cc_final: 0.6811 (mmmt) REVERT: K 130 GLN cc_start: 0.8160 (tt0) cc_final: 0.7918 (tt0) REVERT: K 265 ASP cc_start: 0.8744 (m-30) cc_final: 0.8423 (m-30) REVERT: K 300 TYR cc_start: 0.8579 (OUTLIER) cc_final: 0.7856 (t80) REVERT: K 326 ASN cc_start: 0.7447 (OUTLIER) cc_final: 0.7084 (t0) REVERT: L 44 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8700 (tp) REVERT: L 79 LYS cc_start: 0.8282 (mmmt) cc_final: 0.7174 (pttt) REVERT: L 152 VAL cc_start: 0.7621 (OUTLIER) cc_final: 0.7357 (t) REVERT: L 171 ILE cc_start: 0.8268 (OUTLIER) cc_final: 0.7481 (pt) REVERT: L 203 VAL cc_start: 0.9014 (m) cc_final: 0.8383 (t) REVERT: L 343 HIS cc_start: 0.8604 (OUTLIER) cc_final: 0.8125 (p90) outliers start: 258 outliers final: 191 residues processed: 1234 average time/residue: 0.5204 time to fit residues: 1073.5606 Evaluate side-chains 1277 residues out of total 5724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 213 poor density : 1064 time to evaluate : 4.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 69 SER Chi-restraints excluded: chain a residue 109 THR Chi-restraints excluded: chain a residue 110 GLN Chi-restraints excluded: chain a residue 156 ILE Chi-restraints excluded: chain a residue 159 HIS Chi-restraints excluded: chain a residue 166 VAL Chi-restraints excluded: chain b residue 20 LEU Chi-restraints excluded: chain b residue 63 SER Chi-restraints excluded: chain b residue 69 SER Chi-restraints excluded: chain b residue 87 LEU Chi-restraints excluded: chain b residue 98 ASN Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain b residue 147 VAL Chi-restraints excluded: chain b residue 156 ILE Chi-restraints excluded: chain b residue 166 VAL Chi-restraints excluded: chain c residue 69 SER Chi-restraints excluded: chain c residue 70 VAL Chi-restraints excluded: chain c residue 93 ILE Chi-restraints excluded: chain c residue 98 ASN Chi-restraints excluded: chain c residue 105 ASP Chi-restraints excluded: chain c residue 109 THR Chi-restraints excluded: chain c residue 141 THR Chi-restraints excluded: chain c residue 156 ILE Chi-restraints excluded: chain c residue 166 VAL Chi-restraints excluded: chain d residue 69 SER Chi-restraints excluded: chain d residue 77 ASP Chi-restraints excluded: chain d residue 109 THR Chi-restraints excluded: chain d residue 110 GLN Chi-restraints excluded: chain d residue 156 ILE Chi-restraints excluded: chain d residue 159 HIS Chi-restraints excluded: chain d residue 166 VAL Chi-restraints excluded: chain e residue 63 SER Chi-restraints excluded: chain e residue 69 SER Chi-restraints excluded: chain e residue 70 VAL Chi-restraints excluded: chain e residue 98 ASN Chi-restraints excluded: chain e residue 109 THR Chi-restraints excluded: chain e residue 156 ILE Chi-restraints excluded: chain e residue 166 VAL Chi-restraints excluded: chain f residue 16 LYS Chi-restraints excluded: chain f residue 66 SER Chi-restraints excluded: chain f residue 69 SER Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 98 ASN Chi-restraints excluded: chain f residue 105 ASP Chi-restraints excluded: chain f residue 109 THR Chi-restraints excluded: chain f residue 141 THR Chi-restraints excluded: chain f residue 156 ILE Chi-restraints excluded: chain f residue 166 VAL Chi-restraints excluded: chain g residue 63 SER Chi-restraints excluded: chain g residue 69 SER Chi-restraints excluded: chain g residue 109 THR Chi-restraints excluded: chain g residue 110 GLN Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 156 ILE Chi-restraints excluded: chain g residue 159 HIS Chi-restraints excluded: chain g residue 166 VAL Chi-restraints excluded: chain h residue 63 SER Chi-restraints excluded: chain h residue 69 SER Chi-restraints excluded: chain h residue 98 ASN Chi-restraints excluded: chain h residue 109 THR Chi-restraints excluded: chain h residue 156 ILE Chi-restraints excluded: chain h residue 166 VAL Chi-restraints excluded: chain i residue 16 LYS Chi-restraints excluded: chain i residue 63 SER Chi-restraints excluded: chain i residue 66 SER Chi-restraints excluded: chain i residue 69 SER Chi-restraints excluded: chain i residue 70 VAL Chi-restraints excluded: chain i residue 93 ILE Chi-restraints excluded: chain i residue 98 ASN Chi-restraints excluded: chain i residue 105 ASP Chi-restraints excluded: chain i residue 109 THR Chi-restraints excluded: chain i residue 141 THR Chi-restraints excluded: chain i residue 156 ILE Chi-restraints excluded: chain i residue 166 VAL Chi-restraints excluded: chain j residue 35 ILE Chi-restraints excluded: chain j residue 69 SER Chi-restraints excluded: chain j residue 109 THR Chi-restraints excluded: chain j residue 147 VAL Chi-restraints excluded: chain j residue 156 ILE Chi-restraints excluded: chain j residue 159 HIS Chi-restraints excluded: chain j residue 166 VAL Chi-restraints excluded: chain k residue 63 SER Chi-restraints excluded: chain k residue 69 SER Chi-restraints excluded: chain k residue 109 THR Chi-restraints excluded: chain k residue 156 ILE Chi-restraints excluded: chain l residue 66 SER Chi-restraints excluded: chain l residue 70 VAL Chi-restraints excluded: chain l residue 93 ILE Chi-restraints excluded: chain l residue 98 ASN Chi-restraints excluded: chain l residue 105 ASP Chi-restraints excluded: chain l residue 109 THR Chi-restraints excluded: chain l residue 141 THR Chi-restraints excluded: chain l residue 156 ILE Chi-restraints excluded: chain l residue 166 VAL Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 161 ASN Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 326 ASN Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 182 ASP Chi-restraints excluded: chain C residue 249 LYS Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 288 ASN Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 300 TYR Chi-restraints excluded: chain C residue 326 ASN Chi-restraints excluded: chain C residue 343 HIS Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 326 ASN Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 302 MET Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 326 ASN Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 130 GLN Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 154 GLU Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 288 ASN Chi-restraints excluded: chain F residue 300 TYR Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 343 HIS Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain G residue 161 ASN Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 272 SER Chi-restraints excluded: chain G residue 298 LEU Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 326 ASN Chi-restraints excluded: chain H residue 154 GLU Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 275 LEU Chi-restraints excluded: chain H residue 300 TYR Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 326 ASN Chi-restraints excluded: chain I residue 16 ARG Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 105 ASP Chi-restraints excluded: chain I residue 130 GLN Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 171 ILE Chi-restraints excluded: chain I residue 259 ASP Chi-restraints excluded: chain I residue 300 TYR Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain I residue 343 HIS Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 105 ASP Chi-restraints excluded: chain J residue 161 ASN Chi-restraints excluded: chain J residue 182 ASP Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 298 LEU Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain J residue 326 ASN Chi-restraints excluded: chain K residue 74 ASN Chi-restraints excluded: chain K residue 154 GLU Chi-restraints excluded: chain K residue 179 THR Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 300 TYR Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain K residue 326 ASN Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain L residue 93 MET Chi-restraints excluded: chain L residue 105 ASP Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain L residue 171 ILE Chi-restraints excluded: chain L residue 181 ILE Chi-restraints excluded: chain L residue 182 ASP Chi-restraints excluded: chain L residue 210 THR Chi-restraints excluded: chain L residue 214 LEU Chi-restraints excluded: chain L residue 224 GLU Chi-restraints excluded: chain L residue 259 ASP Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 300 TYR Chi-restraints excluded: chain L residue 326 ASN Chi-restraints excluded: chain L residue 343 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 264 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 429 optimal weight: 3.9990 chunk 394 optimal weight: 0.8980 chunk 297 optimal weight: 5.9990 chunk 336 optimal weight: 4.9990 chunk 498 optimal weight: 0.9980 chunk 556 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 237 optimal weight: 10.0000 chunk 350 optimal weight: 2.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 151 ASN d 151 ASN e 110 GLN i 2 GLN j 151 ASN ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 ASN A 326 ASN B 161 ASN C 288 ASN C 326 ASN ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 326 ASN ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 161 ASN F 326 ASN G 161 ASN G 326 ASN H 161 ASN I 326 ASN J 161 ASN J 326 ASN K 161 ASN K 291 ASN K 326 ASN L 326 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.116866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.103079 restraints weight = 68652.933| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.43 r_work: 0.2857 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 52092 Z= 0.217 Angle : 0.615 10.945 70464 Z= 0.319 Chirality : 0.044 0.378 8040 Planarity : 0.004 0.044 9096 Dihedral : 5.305 35.737 6994 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.80 % Allowed : 7.00 % Favored : 92.20 % Rotamer: Outliers : 4.26 % Allowed : 15.04 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.10), residues: 6396 helix: 1.45 (0.10), residues: 2784 sheet: 0.99 (0.20), residues: 792 loop : -2.01 (0.11), residues: 2820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 116 HIS 0.006 0.002 HIS D 343 PHE 0.012 0.001 PHE K 277 TYR 0.022 0.001 TYR a 88 ARG 0.003 0.000 ARG d 161 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12792 Ramachandran restraints generated. 6396 Oldfield, 0 Emsley, 6396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12792 Ramachandran restraints generated. 6396 Oldfield, 0 Emsley, 6396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1364 residues out of total 5724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 244 poor density : 1120 time to evaluate : 4.811 Fit side-chains revert: symmetry clash REVERT: a 10 ARG cc_start: 0.8316 (ttm170) cc_final: 0.8091 (ttm-80) REVERT: a 49 GLN cc_start: 0.8802 (tt0) cc_final: 0.8414 (tt0) REVERT: a 96 LYS cc_start: 0.8792 (mttm) cc_final: 0.8389 (mmtt) REVERT: b 2 GLN cc_start: 0.7914 (tt0) cc_final: 0.7685 (tt0) REVERT: b 96 LYS cc_start: 0.8512 (mttp) cc_final: 0.8185 (mmtm) REVERT: d 8 ASP cc_start: 0.8524 (m-30) cc_final: 0.8297 (m-30) REVERT: d 49 GLN cc_start: 0.8542 (tt0) cc_final: 0.8212 (tt0) REVERT: d 96 LYS cc_start: 0.8732 (mttm) cc_final: 0.8232 (mmtt) REVERT: e 2 GLN cc_start: 0.8109 (tt0) cc_final: 0.7841 (tt0) REVERT: e 12 TYR cc_start: 0.8657 (t80) cc_final: 0.8096 (t80) REVERT: e 83 GLU cc_start: 0.7286 (mt-10) cc_final: 0.6745 (mp0) REVERT: e 96 LYS cc_start: 0.8566 (mttp) cc_final: 0.8276 (mmtm) REVERT: f 5 THR cc_start: 0.8192 (p) cc_final: 0.7837 (t) REVERT: f 16 LYS cc_start: 0.6157 (OUTLIER) cc_final: 0.5087 (pttp) REVERT: f 27 MET cc_start: 0.8690 (mtt) cc_final: 0.8464 (mtt) REVERT: f 42 ASP cc_start: 0.6706 (t0) cc_final: 0.6406 (t70) REVERT: f 110 GLN cc_start: 0.7753 (tt0) cc_final: 0.7532 (tt0) REVERT: f 167 TYR cc_start: 0.8142 (m-80) cc_final: 0.7892 (m-10) REVERT: g 49 GLN cc_start: 0.8830 (tt0) cc_final: 0.8414 (tt0) REVERT: g 96 LYS cc_start: 0.8703 (mttm) cc_final: 0.8200 (mmtt) REVERT: h 2 GLN cc_start: 0.8036 (tt0) cc_final: 0.7779 (tt0) REVERT: h 96 LYS cc_start: 0.8539 (mttp) cc_final: 0.8241 (mmtm) REVERT: h 110 GLN cc_start: 0.7483 (mt0) cc_final: 0.6974 (mt0) REVERT: i 5 THR cc_start: 0.8196 (p) cc_final: 0.7852 (t) REVERT: i 16 LYS cc_start: 0.6188 (OUTLIER) cc_final: 0.5233 (pttp) REVERT: i 42 ASP cc_start: 0.6794 (t0) cc_final: 0.6493 (t70) REVERT: i 110 GLN cc_start: 0.7749 (tt0) cc_final: 0.7456 (tt0) REVERT: i 167 TYR cc_start: 0.8147 (m-80) cc_final: 0.7871 (m-10) REVERT: j 49 GLN cc_start: 0.8768 (tt0) cc_final: 0.8362 (tt0) REVERT: j 96 LYS cc_start: 0.8712 (mttm) cc_final: 0.7972 (mmtt) REVERT: k 25 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7832 (mm-30) REVERT: k 96 LYS cc_start: 0.8548 (mttp) cc_final: 0.8232 (mmtm) REVERT: k 110 GLN cc_start: 0.7856 (mt0) cc_final: 0.7326 (mt0) REVERT: l 5 THR cc_start: 0.8251 (p) cc_final: 0.7871 (t) REVERT: A 21 MET cc_start: 0.8031 (mmp) cc_final: 0.7498 (tpt) REVERT: A 79 LYS cc_start: 0.8471 (mmmt) cc_final: 0.7942 (tptp) REVERT: A 295 ASN cc_start: 0.9061 (m-40) cc_final: 0.8794 (m110) REVERT: A 368 ASP cc_start: 0.7380 (t0) cc_final: 0.6290 (p0) REVERT: B 41 LYS cc_start: 0.8721 (mttt) cc_final: 0.8456 (mttt) REVERT: B 79 LYS cc_start: 0.7547 (mtpt) cc_final: 0.6840 (mmmt) REVERT: B 300 TYR cc_start: 0.8397 (OUTLIER) cc_final: 0.7906 (t80) REVERT: C 146 ASN cc_start: 0.6206 (m-40) cc_final: 0.5796 (m110) REVERT: C 152 VAL cc_start: 0.7482 (OUTLIER) cc_final: 0.7213 (t) REVERT: C 171 ILE cc_start: 0.8173 (OUTLIER) cc_final: 0.7471 (pt) REVERT: C 203 VAL cc_start: 0.9006 (m) cc_final: 0.8333 (t) REVERT: C 343 HIS cc_start: 0.8472 (OUTLIER) cc_final: 0.7778 (p90) REVERT: D 21 MET cc_start: 0.8120 (mmm) cc_final: 0.7287 (tpt) REVERT: D 26 HIS cc_start: 0.7746 (m90) cc_final: 0.7496 (m90) REVERT: D 79 LYS cc_start: 0.8496 (mmmt) cc_final: 0.7976 (tptp) REVERT: D 275 LEU cc_start: 0.8620 (tt) cc_final: 0.8397 (tt) REVERT: D 295 ASN cc_start: 0.9059 (m-40) cc_final: 0.8766 (m110) REVERT: E 79 LYS cc_start: 0.7553 (mtpt) cc_final: 0.6859 (mmmt) REVERT: E 152 VAL cc_start: 0.7211 (p) cc_final: 0.6973 (t) REVERT: E 300 TYR cc_start: 0.8435 (OUTLIER) cc_final: 0.7902 (t80) REVERT: E 302 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8349 (mtt) REVERT: F 79 LYS cc_start: 0.7930 (mmmt) cc_final: 0.7033 (pttt) REVERT: F 146 ASN cc_start: 0.6338 (m-40) cc_final: 0.5898 (m110) REVERT: F 152 VAL cc_start: 0.7479 (OUTLIER) cc_final: 0.7212 (t) REVERT: F 203 VAL cc_start: 0.8980 (m) cc_final: 0.8287 (t) REVERT: F 271 LYS cc_start: 0.7884 (mmtt) cc_final: 0.7573 (tptt) REVERT: F 343 HIS cc_start: 0.8450 (OUTLIER) cc_final: 0.7752 (p90) REVERT: G 21 MET cc_start: 0.7920 (mmp) cc_final: 0.7160 (tpp) REVERT: G 26 HIS cc_start: 0.7779 (m90) cc_final: 0.7451 (m170) REVERT: G 105 ASP cc_start: 0.8520 (OUTLIER) cc_final: 0.8210 (m-30) REVERT: G 149 ASN cc_start: 0.7380 (t0) cc_final: 0.6995 (t0) REVERT: G 189 LYS cc_start: 0.8757 (mtpt) cc_final: 0.8459 (mtpp) REVERT: G 300 TYR cc_start: 0.8195 (m-80) cc_final: 0.7664 (m-80) REVERT: H 41 LYS cc_start: 0.8247 (mttt) cc_final: 0.8036 (mttt) REVERT: H 43 GLU cc_start: 0.7932 (mp0) cc_final: 0.7667 (mp0) REVERT: H 50 ASN cc_start: 0.9033 (m-40) cc_final: 0.8810 (m110) REVERT: H 79 LYS cc_start: 0.7550 (mtpt) cc_final: 0.6830 (mmmt) REVERT: H 106 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8428 (tt) REVERT: H 152 VAL cc_start: 0.7213 (p) cc_final: 0.6952 (t) REVERT: H 180 VAL cc_start: 0.8878 (OUTLIER) cc_final: 0.8527 (t) REVERT: H 300 TYR cc_start: 0.8489 (OUTLIER) cc_final: 0.7851 (t80) REVERT: I 79 LYS cc_start: 0.8107 (mmmt) cc_final: 0.7102 (pttt) REVERT: I 152 VAL cc_start: 0.7530 (OUTLIER) cc_final: 0.7243 (t) REVERT: I 171 ILE cc_start: 0.8350 (OUTLIER) cc_final: 0.7591 (pt) REVERT: I 203 VAL cc_start: 0.8943 (m) cc_final: 0.8288 (t) REVERT: I 212 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7099 (mt-10) REVERT: I 326 ASN cc_start: 0.6595 (OUTLIER) cc_final: 0.6321 (t0) REVERT: I 343 HIS cc_start: 0.8461 (OUTLIER) cc_final: 0.7749 (p90) REVERT: J 21 MET cc_start: 0.7992 (mmp) cc_final: 0.7249 (tpt) REVERT: J 31 LYS cc_start: 0.8888 (mttt) cc_final: 0.8391 (mtpt) REVERT: J 119 THR cc_start: 0.8812 (p) cc_final: 0.8553 (p) REVERT: J 295 ASN cc_start: 0.9029 (m-40) cc_final: 0.8790 (m110) REVERT: K 26 HIS cc_start: 0.7456 (m90) cc_final: 0.7143 (m90) REVERT: K 31 LYS cc_start: 0.8892 (mttt) cc_final: 0.8402 (mttt) REVERT: K 50 ASN cc_start: 0.9069 (m-40) cc_final: 0.8667 (m110) REVERT: K 79 LYS cc_start: 0.7553 (mtpt) cc_final: 0.6824 (mmmt) REVERT: K 106 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8381 (tt) REVERT: K 152 VAL cc_start: 0.7149 (p) cc_final: 0.6918 (t) REVERT: K 188 SER cc_start: 0.8920 (p) cc_final: 0.8611 (t) REVERT: K 300 TYR cc_start: 0.8506 (OUTLIER) cc_final: 0.7831 (t80) REVERT: L 79 LYS cc_start: 0.8267 (mmmt) cc_final: 0.7175 (pttt) REVERT: L 152 VAL cc_start: 0.7545 (OUTLIER) cc_final: 0.7252 (t) REVERT: L 171 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.7585 (pt) REVERT: L 203 VAL cc_start: 0.8989 (m) cc_final: 0.8298 (t) REVERT: L 212 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7197 (mt-10) REVERT: L 275 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8512 (tp) REVERT: L 343 HIS cc_start: 0.8451 (OUTLIER) cc_final: 0.7837 (p90) outliers start: 244 outliers final: 168 residues processed: 1259 average time/residue: 0.4879 time to fit residues: 1027.5739 Evaluate side-chains 1284 residues out of total 5724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 1090 time to evaluate : 4.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 35 ILE Chi-restraints excluded: chain a residue 69 SER Chi-restraints excluded: chain a residue 110 GLN Chi-restraints excluded: chain a residue 147 VAL Chi-restraints excluded: chain a residue 156 ILE Chi-restraints excluded: chain a residue 159 HIS Chi-restraints excluded: chain a residue 166 VAL Chi-restraints excluded: chain b residue 20 LEU Chi-restraints excluded: chain b residue 63 SER Chi-restraints excluded: chain b residue 69 SER Chi-restraints excluded: chain b residue 98 ASN Chi-restraints excluded: chain b residue 156 ILE Chi-restraints excluded: chain c residue 66 SER Chi-restraints excluded: chain c residue 70 VAL Chi-restraints excluded: chain c residue 98 ASN Chi-restraints excluded: chain c residue 109 THR Chi-restraints excluded: chain c residue 141 THR Chi-restraints excluded: chain c residue 156 ILE Chi-restraints excluded: chain c residue 166 VAL Chi-restraints excluded: chain d residue 77 ASP Chi-restraints excluded: chain d residue 110 GLN Chi-restraints excluded: chain d residue 145 GLU Chi-restraints excluded: chain d residue 147 VAL Chi-restraints excluded: chain d residue 156 ILE Chi-restraints excluded: chain d residue 159 HIS Chi-restraints excluded: chain d residue 166 VAL Chi-restraints excluded: chain e residue 70 VAL Chi-restraints excluded: chain e residue 98 ASN Chi-restraints excluded: chain e residue 156 ILE Chi-restraints excluded: chain f residue 16 LYS Chi-restraints excluded: chain f residue 66 SER Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 98 ASN Chi-restraints excluded: chain f residue 105 ASP Chi-restraints excluded: chain f residue 109 THR Chi-restraints excluded: chain f residue 141 THR Chi-restraints excluded: chain f residue 156 ILE Chi-restraints excluded: chain f residue 166 VAL Chi-restraints excluded: chain g residue 63 SER Chi-restraints excluded: chain g residue 69 SER Chi-restraints excluded: chain g residue 110 GLN Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 145 GLU Chi-restraints excluded: chain g residue 156 ILE Chi-restraints excluded: chain g residue 159 HIS Chi-restraints excluded: chain g residue 166 VAL Chi-restraints excluded: chain h residue 63 SER Chi-restraints excluded: chain h residue 69 SER Chi-restraints excluded: chain h residue 98 ASN Chi-restraints excluded: chain h residue 109 THR Chi-restraints excluded: chain h residue 156 ILE Chi-restraints excluded: chain i residue 16 LYS Chi-restraints excluded: chain i residue 63 SER Chi-restraints excluded: chain i residue 66 SER Chi-restraints excluded: chain i residue 70 VAL Chi-restraints excluded: chain i residue 98 ASN Chi-restraints excluded: chain i residue 105 ASP Chi-restraints excluded: chain i residue 109 THR Chi-restraints excluded: chain i residue 141 THR Chi-restraints excluded: chain i residue 156 ILE Chi-restraints excluded: chain i residue 166 VAL Chi-restraints excluded: chain j residue 35 ILE Chi-restraints excluded: chain j residue 109 THR Chi-restraints excluded: chain j residue 156 ILE Chi-restraints excluded: chain j residue 159 HIS Chi-restraints excluded: chain j residue 166 VAL Chi-restraints excluded: chain k residue 63 SER Chi-restraints excluded: chain k residue 69 SER Chi-restraints excluded: chain k residue 156 ILE Chi-restraints excluded: chain k residue 166 VAL Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 42 ASP Chi-restraints excluded: chain l residue 98 ASN Chi-restraints excluded: chain l residue 109 THR Chi-restraints excluded: chain l residue 141 THR Chi-restraints excluded: chain l residue 156 ILE Chi-restraints excluded: chain l residue 166 VAL Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 326 ASN Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 182 ASP Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 300 TYR Chi-restraints excluded: chain C residue 326 ASN Chi-restraints excluded: chain C residue 343 HIS Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 326 ASN Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 161 ASN Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 300 TYR Chi-restraints excluded: chain E residue 302 MET Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 326 ASN Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 154 GLU Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 288 ASN Chi-restraints excluded: chain F residue 300 TYR Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 343 HIS Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 105 ASP Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 272 SER Chi-restraints excluded: chain G residue 298 LEU Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 326 ASN Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 154 GLU Chi-restraints excluded: chain H residue 161 ASN Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 275 LEU Chi-restraints excluded: chain H residue 298 LEU Chi-restraints excluded: chain H residue 300 TYR Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 326 ASN Chi-restraints excluded: chain I residue 16 ARG Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 105 ASP Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 154 GLU Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 171 ILE Chi-restraints excluded: chain I residue 212 GLU Chi-restraints excluded: chain I residue 259 ASP Chi-restraints excluded: chain I residue 300 TYR Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain I residue 326 ASN Chi-restraints excluded: chain I residue 343 HIS Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 105 ASP Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 224 GLU Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain J residue 326 ASN Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain K residue 154 GLU Chi-restraints excluded: chain K residue 161 ASN Chi-restraints excluded: chain K residue 179 THR Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 298 LEU Chi-restraints excluded: chain K residue 300 TYR Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain L residue 93 MET Chi-restraints excluded: chain L residue 105 ASP Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 154 GLU Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain L residue 171 ILE Chi-restraints excluded: chain L residue 182 ASP Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain L residue 214 LEU Chi-restraints excluded: chain L residue 224 GLU Chi-restraints excluded: chain L residue 259 ASP Chi-restraints excluded: chain L residue 275 LEU Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 300 TYR Chi-restraints excluded: chain L residue 324 THR Chi-restraints excluded: chain L residue 326 ASN Chi-restraints excluded: chain L residue 343 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 244 optimal weight: 0.9990 chunk 356 optimal weight: 0.5980 chunk 141 optimal weight: 2.9990 chunk 351 optimal weight: 0.9980 chunk 431 optimal weight: 7.9990 chunk 366 optimal weight: 2.9990 chunk 575 optimal weight: 0.6980 chunk 68 optimal weight: 10.0000 chunk 448 optimal weight: 0.6980 chunk 120 optimal weight: 10.0000 chunk 632 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 151 ASN b 132 HIS d 151 ASN e 110 GLN f 2 GLN h 132 HIS j 151 ASN l 2 GLN ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 ASN A 326 ASN B 161 ASN B 326 ASN C 326 ASN C 343 HIS ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 326 ASN ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 161 ASN E 326 ASN ** F 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 288 ASN F 326 ASN F 343 HIS G 161 ASN G 326 ASN H 161 ASN H 291 ASN H 326 ASN I 37 GLN ** I 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 326 ASN I 343 HIS I 371 GLN J 161 ASN J 326 ASN K 161 ASN K 326 ASN L 161 ASN L 326 ASN L 343 HIS Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.119967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.106220 restraints weight = 68219.274| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 1.43 r_work: 0.2873 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 52092 Z= 0.160 Angle : 0.575 10.139 70464 Z= 0.298 Chirality : 0.042 0.351 8040 Planarity : 0.004 0.042 9096 Dihedral : 5.052 35.863 6994 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.73 % Allowed : 7.16 % Favored : 92.10 % Rotamer: Outliers : 3.51 % Allowed : 16.19 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.11), residues: 6396 helix: 1.66 (0.10), residues: 2784 sheet: 0.96 (0.20), residues: 792 loop : -1.94 (0.11), residues: 2820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 116 HIS 0.005 0.001 HIS G 343 PHE 0.011 0.001 PHE K 277 TYR 0.025 0.001 TYR b 88 ARG 0.003 0.000 ARG B 151 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12792 Ramachandran restraints generated. 6396 Oldfield, 0 Emsley, 6396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12792 Ramachandran restraints generated. 6396 Oldfield, 0 Emsley, 6396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1343 residues out of total 5724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 201 poor density : 1142 time to evaluate : 5.383 Fit side-chains revert: symmetry clash REVERT: a 41 MET cc_start: 0.8116 (mtt) cc_final: 0.7807 (mtt) REVERT: a 49 GLN cc_start: 0.8756 (tt0) cc_final: 0.8412 (tt0) REVERT: a 96 LYS cc_start: 0.8814 (mttm) cc_final: 0.8400 (mmtt) REVERT: b 2 GLN cc_start: 0.8025 (tt0) cc_final: 0.7776 (tt0) REVERT: b 21 GLU cc_start: 0.7027 (mt-10) cc_final: 0.6762 (tt0) REVERT: b 96 LYS cc_start: 0.8516 (mttp) cc_final: 0.8205 (mmtm) REVERT: c 165 GLU cc_start: 0.8672 (tp30) cc_final: 0.8399 (mm-30) REVERT: d 8 ASP cc_start: 0.8452 (m-30) cc_final: 0.8148 (m-30) REVERT: d 49 GLN cc_start: 0.8572 (tt0) cc_final: 0.8350 (tt0) REVERT: d 96 LYS cc_start: 0.8744 (mttm) cc_final: 0.8245 (mmtt) REVERT: e 2 GLN cc_start: 0.8104 (tt0) cc_final: 0.7846 (tt0) REVERT: e 12 TYR cc_start: 0.8668 (t80) cc_final: 0.8120 (t80) REVERT: e 83 GLU cc_start: 0.7314 (mt-10) cc_final: 0.6796 (mp0) REVERT: e 96 LYS cc_start: 0.8535 (mttp) cc_final: 0.8237 (mmtm) REVERT: f 5 THR cc_start: 0.8139 (p) cc_final: 0.7740 (t) REVERT: f 16 LYS cc_start: 0.6445 (OUTLIER) cc_final: 0.5040 (pttp) REVERT: f 27 MET cc_start: 0.8681 (mtt) cc_final: 0.8456 (mtt) REVERT: f 42 ASP cc_start: 0.6529 (t0) cc_final: 0.6303 (t70) REVERT: f 110 GLN cc_start: 0.7733 (tt0) cc_final: 0.7497 (tt0) REVERT: f 167 TYR cc_start: 0.8020 (m-80) cc_final: 0.7791 (m-10) REVERT: g 49 GLN cc_start: 0.8817 (tt0) cc_final: 0.8495 (tt0) REVERT: g 96 LYS cc_start: 0.8706 (mttm) cc_final: 0.8207 (mmtt) REVERT: g 118 GLU cc_start: 0.7569 (mp0) cc_final: 0.7150 (mp0) REVERT: h 2 GLN cc_start: 0.7970 (tt0) cc_final: 0.7728 (tt0) REVERT: h 96 LYS cc_start: 0.8500 (mttp) cc_final: 0.8216 (mmtm) REVERT: i 5 THR cc_start: 0.8099 (p) cc_final: 0.7752 (t) REVERT: i 16 LYS cc_start: 0.6509 (OUTLIER) cc_final: 0.5261 (pttp) REVERT: i 42 ASP cc_start: 0.6863 (t0) cc_final: 0.6661 (t70) REVERT: i 116 MET cc_start: 0.8526 (tpp) cc_final: 0.8202 (tpp) REVERT: i 167 TYR cc_start: 0.8030 (m-80) cc_final: 0.7777 (m-10) REVERT: j 49 GLN cc_start: 0.8737 (tt0) cc_final: 0.8393 (tt0) REVERT: j 96 LYS cc_start: 0.8705 (mttm) cc_final: 0.7962 (mmtt) REVERT: j 118 GLU cc_start: 0.7410 (mp0) cc_final: 0.7166 (mp0) REVERT: k 25 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7788 (mm-30) REVERT: k 96 LYS cc_start: 0.8495 (mttp) cc_final: 0.8218 (mmtm) REVERT: k 110 GLN cc_start: 0.7662 (mt0) cc_final: 0.7181 (mt0) REVERT: l 5 THR cc_start: 0.8175 (p) cc_final: 0.7757 (t) REVERT: A 21 MET cc_start: 0.8081 (mmp) cc_final: 0.7537 (tpt) REVERT: A 368 ASP cc_start: 0.7130 (t0) cc_final: 0.6079 (p0) REVERT: B 21 MET cc_start: 0.7537 (tpt) cc_final: 0.7230 (ttp) REVERT: B 41 LYS cc_start: 0.8611 (mttt) cc_final: 0.8361 (mttt) REVERT: B 79 LYS cc_start: 0.7565 (mtpt) cc_final: 0.6853 (mmmt) REVERT: B 152 VAL cc_start: 0.7193 (p) cc_final: 0.6959 (t) REVERT: B 300 TYR cc_start: 0.8382 (OUTLIER) cc_final: 0.7830 (t80) REVERT: B 326 ASN cc_start: 0.7544 (OUTLIER) cc_final: 0.7220 (t0) REVERT: C 79 LYS cc_start: 0.8011 (mmmt) cc_final: 0.7105 (pttt) REVERT: C 146 ASN cc_start: 0.6125 (m-40) cc_final: 0.5690 (m110) REVERT: C 152 VAL cc_start: 0.7421 (OUTLIER) cc_final: 0.7179 (t) REVERT: C 171 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7442 (pt) REVERT: C 203 VAL cc_start: 0.8974 (m) cc_final: 0.8245 (t) REVERT: C 288 ASN cc_start: 0.8127 (p0) cc_final: 0.7792 (p0) REVERT: D 21 MET cc_start: 0.8023 (mmm) cc_final: 0.7312 (tpt) REVERT: D 26 HIS cc_start: 0.7753 (m90) cc_final: 0.7493 (m170) REVERT: D 79 LYS cc_start: 0.8529 (mmmt) cc_final: 0.8016 (tptp) REVERT: D 275 LEU cc_start: 0.8547 (tt) cc_final: 0.8318 (tt) REVERT: D 368 ASP cc_start: 0.7345 (t0) cc_final: 0.6127 (p0) REVERT: E 43 GLU cc_start: 0.7994 (pm20) cc_final: 0.7767 (pm20) REVERT: E 50 ASN cc_start: 0.8995 (m110) cc_final: 0.8771 (m110) REVERT: E 79 LYS cc_start: 0.7604 (mtpt) cc_final: 0.6906 (mmmt) REVERT: E 146 ASN cc_start: 0.6414 (m-40) cc_final: 0.5840 (m110) REVERT: E 300 TYR cc_start: 0.8374 (OUTLIER) cc_final: 0.7812 (t80) REVERT: F 79 LYS cc_start: 0.7958 (mmmt) cc_final: 0.7061 (pttt) REVERT: F 146 ASN cc_start: 0.6364 (m-40) cc_final: 0.5925 (m110) REVERT: F 152 VAL cc_start: 0.7416 (OUTLIER) cc_final: 0.7189 (t) REVERT: F 171 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7529 (pt) REVERT: G 17 ILE cc_start: 0.8707 (mp) cc_final: 0.8411 (mm) REVERT: G 21 MET cc_start: 0.7941 (mmp) cc_final: 0.7159 (tpp) REVERT: G 105 ASP cc_start: 0.8563 (OUTLIER) cc_final: 0.8214 (m-30) REVERT: G 149 ASN cc_start: 0.7176 (t0) cc_final: 0.6945 (t0) REVERT: G 300 TYR cc_start: 0.8143 (m-80) cc_final: 0.7803 (m-80) REVERT: G 326 ASN cc_start: 0.8320 (OUTLIER) cc_final: 0.8110 (t0) REVERT: H 43 GLU cc_start: 0.7893 (mp0) cc_final: 0.7690 (mp0) REVERT: H 50 ASN cc_start: 0.8984 (m-40) cc_final: 0.8736 (m110) REVERT: H 79 LYS cc_start: 0.7569 (mtpt) cc_final: 0.6854 (mmmt) REVERT: H 106 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8527 (tt) REVERT: H 171 ILE cc_start: 0.7929 (OUTLIER) cc_final: 0.7465 (pt) REVERT: H 300 TYR cc_start: 0.8435 (OUTLIER) cc_final: 0.7742 (t80) REVERT: H 326 ASN cc_start: 0.7602 (OUTLIER) cc_final: 0.7244 (t0) REVERT: I 79 LYS cc_start: 0.8122 (mmmt) cc_final: 0.7139 (pttt) REVERT: I 146 ASN cc_start: 0.5878 (m-40) cc_final: 0.5443 (m110) REVERT: I 152 VAL cc_start: 0.7460 (OUTLIER) cc_final: 0.7203 (t) REVERT: I 171 ILE cc_start: 0.8224 (OUTLIER) cc_final: 0.7531 (pt) REVERT: I 212 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7111 (mt-10) REVERT: I 326 ASN cc_start: 0.6856 (OUTLIER) cc_final: 0.6492 (t0) REVERT: J 21 MET cc_start: 0.7962 (mmp) cc_final: 0.7250 (tpt) REVERT: J 31 LYS cc_start: 0.8870 (mttt) cc_final: 0.8438 (mtpt) REVERT: J 119 THR cc_start: 0.8684 (p) cc_final: 0.8452 (p) REVERT: J 271 LYS cc_start: 0.8611 (mmmt) cc_final: 0.8403 (tptt) REVERT: K 26 HIS cc_start: 0.7437 (m90) cc_final: 0.7182 (m90) REVERT: K 31 LYS cc_start: 0.8797 (mttt) cc_final: 0.8390 (mttt) REVERT: K 50 ASN cc_start: 0.9042 (m-40) cc_final: 0.8669 (m110) REVERT: K 79 LYS cc_start: 0.7586 (mtpt) cc_final: 0.6856 (mmmt) REVERT: K 188 SER cc_start: 0.8874 (p) cc_final: 0.8560 (t) REVERT: K 300 TYR cc_start: 0.8444 (OUTLIER) cc_final: 0.7753 (t80) REVERT: K 326 ASN cc_start: 0.7664 (OUTLIER) cc_final: 0.7411 (t0) REVERT: L 79 LYS cc_start: 0.8276 (mmmt) cc_final: 0.7155 (pttt) REVERT: L 146 ASN cc_start: 0.5990 (m-40) cc_final: 0.5543 (m110) REVERT: L 152 VAL cc_start: 0.7469 (OUTLIER) cc_final: 0.7217 (t) REVERT: L 171 ILE cc_start: 0.8168 (OUTLIER) cc_final: 0.7484 (pt) REVERT: L 212 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7192 (mt-10) outliers start: 201 outliers final: 120 residues processed: 1265 average time/residue: 0.5109 time to fit residues: 1084.9841 Evaluate side-chains 1223 residues out of total 5724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 1079 time to evaluate : 4.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 35 ILE Chi-restraints excluded: chain a residue 147 VAL Chi-restraints excluded: chain a residue 156 ILE Chi-restraints excluded: chain a residue 159 HIS Chi-restraints excluded: chain a residue 166 VAL Chi-restraints excluded: chain b residue 63 SER Chi-restraints excluded: chain b residue 141 THR Chi-restraints excluded: chain b residue 156 ILE Chi-restraints excluded: chain b residue 166 VAL Chi-restraints excluded: chain c residue 66 SER Chi-restraints excluded: chain c residue 69 SER Chi-restraints excluded: chain c residue 98 ASN Chi-restraints excluded: chain c residue 141 THR Chi-restraints excluded: chain c residue 156 ILE Chi-restraints excluded: chain d residue 147 VAL Chi-restraints excluded: chain d residue 156 ILE Chi-restraints excluded: chain d residue 159 HIS Chi-restraints excluded: chain d residue 166 VAL Chi-restraints excluded: chain e residue 70 VAL Chi-restraints excluded: chain e residue 141 THR Chi-restraints excluded: chain e residue 156 ILE Chi-restraints excluded: chain f residue 7 GLU Chi-restraints excluded: chain f residue 16 LYS Chi-restraints excluded: chain f residue 69 SER Chi-restraints excluded: chain f residue 98 ASN Chi-restraints excluded: chain f residue 141 THR Chi-restraints excluded: chain f residue 156 ILE Chi-restraints excluded: chain g residue 69 SER Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 156 ILE Chi-restraints excluded: chain g residue 159 HIS Chi-restraints excluded: chain h residue 63 SER Chi-restraints excluded: chain h residue 98 ASN Chi-restraints excluded: chain h residue 109 THR Chi-restraints excluded: chain h residue 156 ILE Chi-restraints excluded: chain i residue 1 MET Chi-restraints excluded: chain i residue 16 LYS Chi-restraints excluded: chain i residue 63 SER Chi-restraints excluded: chain i residue 66 SER Chi-restraints excluded: chain i residue 70 VAL Chi-restraints excluded: chain i residue 98 ASN Chi-restraints excluded: chain i residue 141 THR Chi-restraints excluded: chain i residue 156 ILE Chi-restraints excluded: chain j residue 35 ILE Chi-restraints excluded: chain j residue 69 SER Chi-restraints excluded: chain j residue 156 ILE Chi-restraints excluded: chain j residue 159 HIS Chi-restraints excluded: chain k residue 63 SER Chi-restraints excluded: chain k residue 156 ILE Chi-restraints excluded: chain k residue 166 VAL Chi-restraints excluded: chain l residue 98 ASN Chi-restraints excluded: chain l residue 141 THR Chi-restraints excluded: chain l residue 156 ILE Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 326 ASN Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 300 TYR Chi-restraints excluded: chain C residue 326 ASN Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 326 ASN Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 161 ASN Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 300 TYR Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 326 ASN Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 154 GLU Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 300 TYR Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 105 ASP Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 272 SER Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 326 ASN Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 171 ILE Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 298 LEU Chi-restraints excluded: chain H residue 300 TYR Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 326 ASN Chi-restraints excluded: chain I residue 16 ARG Chi-restraints excluded: chain I residue 132 GLU Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 154 GLU Chi-restraints excluded: chain I residue 171 ILE Chi-restraints excluded: chain I residue 212 GLU Chi-restraints excluded: chain I residue 259 ASP Chi-restraints excluded: chain I residue 300 TYR Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain I residue 326 ASN Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 105 ASP Chi-restraints excluded: chain J residue 161 ASN Chi-restraints excluded: chain J residue 181 ILE Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain J residue 326 ASN Chi-restraints excluded: chain K residue 161 ASN Chi-restraints excluded: chain K residue 179 THR Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 298 LEU Chi-restraints excluded: chain K residue 300 TYR Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain K residue 326 ASN Chi-restraints excluded: chain K residue 343 HIS Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 154 GLU Chi-restraints excluded: chain L residue 171 ILE Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain L residue 224 GLU Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 300 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 469 optimal weight: 7.9990 chunk 14 optimal weight: 0.9980 chunk 169 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 163 optimal weight: 2.9990 chunk 570 optimal weight: 0.2980 chunk 51 optimal weight: 10.0000 chunk 392 optimal weight: 1.9990 chunk 162 optimal weight: 7.9990 chunk 352 optimal weight: 5.9990 chunk 607 optimal weight: 4.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 151 ASN d 151 ASN f 2 GLN i 2 GLN j 151 ASN l 2 GLN A 50 ASN ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 ASN A 295 ASN A 326 ASN A 371 GLN B 161 ASN C 161 ASN D 50 ASN ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 295 ASN D 371 GLN ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 161 ASN ** F 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 326 ASN F 371 GLN G 161 ASN G 295 ASN G 371 GLN H 161 ASN I 37 GLN ** I 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 326 ASN I 371 GLN J 161 ASN J 295 ASN J 371 GLN K 161 ASN L 161 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.118995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.105389 restraints weight = 68637.675| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 1.40 r_work: 0.2863 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 52092 Z= 0.193 Angle : 0.591 10.238 70464 Z= 0.304 Chirality : 0.043 0.335 8040 Planarity : 0.004 0.041 9096 Dihedral : 4.988 31.575 6992 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.75 % Allowed : 7.00 % Favored : 92.25 % Rotamer: Outliers : 3.41 % Allowed : 16.88 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.10), residues: 6396 helix: 1.66 (0.10), residues: 2784 sheet: 0.90 (0.20), residues: 792 loop : -1.94 (0.11), residues: 2820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 116 HIS 0.006 0.001 HIS C 343 PHE 0.011 0.001 PHE K 277 TYR 0.018 0.001 TYR a 88 ARG 0.003 0.000 ARG i 169 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12792 Ramachandran restraints generated. 6396 Oldfield, 0 Emsley, 6396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12792 Ramachandran restraints generated. 6396 Oldfield, 0 Emsley, 6396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1303 residues out of total 5724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 1108 time to evaluate : 5.548 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 41 MET cc_start: 0.8116 (mtt) cc_final: 0.7819 (mtt) REVERT: a 49 GLN cc_start: 0.8765 (tt0) cc_final: 0.8417 (tt0) REVERT: a 96 LYS cc_start: 0.8843 (mttm) cc_final: 0.8357 (mmtt) REVERT: b 2 GLN cc_start: 0.7849 (tt0) cc_final: 0.7608 (tt0) REVERT: b 96 LYS cc_start: 0.8549 (mttp) cc_final: 0.8263 (mmtm) REVERT: c 27 MET cc_start: 0.8713 (mtt) cc_final: 0.8453 (mtt) REVERT: c 165 GLU cc_start: 0.8621 (tp30) cc_final: 0.8377 (mm-30) REVERT: d 8 ASP cc_start: 0.8518 (m-30) cc_final: 0.8236 (m-30) REVERT: d 96 LYS cc_start: 0.8747 (mttm) cc_final: 0.8253 (mmtt) REVERT: e 2 GLN cc_start: 0.8048 (tt0) cc_final: 0.7762 (tt0) REVERT: e 7 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8083 (mp0) REVERT: e 12 TYR cc_start: 0.8687 (t80) cc_final: 0.8212 (t80) REVERT: e 83 GLU cc_start: 0.7177 (mt-10) cc_final: 0.6697 (mp0) REVERT: e 96 LYS cc_start: 0.8554 (mttp) cc_final: 0.8263 (mmtm) REVERT: f 5 THR cc_start: 0.8136 (p) cc_final: 0.7731 (t) REVERT: f 16 LYS cc_start: 0.6505 (OUTLIER) cc_final: 0.5145 (pttp) REVERT: f 27 MET cc_start: 0.8690 (mtt) cc_final: 0.8460 (mtt) REVERT: f 42 ASP cc_start: 0.6507 (t0) cc_final: 0.6270 (t70) REVERT: f 110 GLN cc_start: 0.7734 (tt0) cc_final: 0.7511 (tt0) REVERT: f 167 TYR cc_start: 0.8064 (m-80) cc_final: 0.7825 (m-10) REVERT: g 49 GLN cc_start: 0.8804 (tt0) cc_final: 0.8488 (tt0) REVERT: g 96 LYS cc_start: 0.8716 (mttm) cc_final: 0.8221 (mmtt) REVERT: h 2 GLN cc_start: 0.7964 (tt0) cc_final: 0.7728 (tt0) REVERT: h 96 LYS cc_start: 0.8505 (mttp) cc_final: 0.8235 (mmtm) REVERT: i 5 THR cc_start: 0.8120 (p) cc_final: 0.7740 (t) REVERT: i 16 LYS cc_start: 0.6501 (OUTLIER) cc_final: 0.5285 (pttp) REVERT: i 116 MET cc_start: 0.8541 (tpp) cc_final: 0.8220 (tpp) REVERT: i 167 TYR cc_start: 0.8130 (m-80) cc_final: 0.7854 (m-10) REVERT: j 49 GLN cc_start: 0.8746 (tt0) cc_final: 0.8449 (tt0) REVERT: j 96 LYS cc_start: 0.8703 (mttm) cc_final: 0.7967 (mmtt) REVERT: k 25 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7788 (mm-30) REVERT: k 96 LYS cc_start: 0.8515 (mttp) cc_final: 0.8236 (mmtm) REVERT: l 5 THR cc_start: 0.8231 (p) cc_final: 0.7815 (t) REVERT: l 165 GLU cc_start: 0.8664 (tp30) cc_final: 0.8453 (mm-30) REVERT: A 21 MET cc_start: 0.8102 (mmp) cc_final: 0.7540 (tpt) REVERT: A 368 ASP cc_start: 0.7085 (t0) cc_final: 0.6062 (p0) REVERT: B 21 MET cc_start: 0.7496 (tpt) cc_final: 0.7228 (ttp) REVERT: B 41 LYS cc_start: 0.8558 (mttt) cc_final: 0.8309 (mttt) REVERT: B 79 LYS cc_start: 0.7565 (mtpt) cc_final: 0.6856 (mmmt) REVERT: B 171 ILE cc_start: 0.7967 (OUTLIER) cc_final: 0.7486 (pt) REVERT: B 300 TYR cc_start: 0.8382 (OUTLIER) cc_final: 0.7913 (t80) REVERT: C 79 LYS cc_start: 0.8037 (mmmt) cc_final: 0.7104 (pttt) REVERT: C 152 VAL cc_start: 0.7370 (OUTLIER) cc_final: 0.7105 (t) REVERT: C 171 ILE cc_start: 0.8161 (OUTLIER) cc_final: 0.7449 (pt) REVERT: C 203 VAL cc_start: 0.8958 (m) cc_final: 0.8241 (t) REVERT: C 288 ASN cc_start: 0.8157 (p0) cc_final: 0.7805 (p0) REVERT: D 21 MET cc_start: 0.7947 (mmm) cc_final: 0.7302 (tpt) REVERT: D 26 HIS cc_start: 0.7745 (m90) cc_final: 0.7481 (m170) REVERT: D 79 LYS cc_start: 0.8516 (mmmt) cc_final: 0.8000 (tptp) REVERT: D 148 ILE cc_start: 0.7224 (mm) cc_final: 0.6876 (mm) REVERT: D 275 LEU cc_start: 0.8567 (tt) cc_final: 0.8364 (tt) REVERT: E 43 GLU cc_start: 0.7850 (pm20) cc_final: 0.7636 (pm20) REVERT: E 50 ASN cc_start: 0.9008 (m110) cc_final: 0.8778 (m110) REVERT: E 79 LYS cc_start: 0.7606 (mtpt) cc_final: 0.6909 (mmmt) REVERT: E 151 ARG cc_start: 0.7347 (mtp-110) cc_final: 0.6826 (ttm170) REVERT: E 300 TYR cc_start: 0.8378 (OUTLIER) cc_final: 0.7833 (t80) REVERT: F 79 LYS cc_start: 0.7978 (mmmt) cc_final: 0.7062 (pttt) REVERT: F 152 VAL cc_start: 0.7413 (OUTLIER) cc_final: 0.7152 (t) REVERT: F 171 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7538 (pt) REVERT: G 17 ILE cc_start: 0.8699 (mp) cc_final: 0.8411 (mm) REVERT: G 21 MET cc_start: 0.7936 (mmp) cc_final: 0.7138 (tpp) REVERT: G 105 ASP cc_start: 0.8573 (OUTLIER) cc_final: 0.8246 (m-30) REVERT: G 149 ASN cc_start: 0.7161 (m-40) cc_final: 0.6952 (t0) REVERT: G 189 LYS cc_start: 0.8722 (mtpt) cc_final: 0.8139 (mtpt) REVERT: G 300 TYR cc_start: 0.8138 (m-80) cc_final: 0.7809 (m-80) REVERT: H 43 GLU cc_start: 0.7790 (mp0) cc_final: 0.7589 (mp0) REVERT: H 50 ASN cc_start: 0.8983 (m-40) cc_final: 0.8741 (m110) REVERT: H 79 LYS cc_start: 0.7577 (mtpt) cc_final: 0.6865 (mmmt) REVERT: H 151 ARG cc_start: 0.7524 (mtp-110) cc_final: 0.6949 (ttm170) REVERT: H 171 ILE cc_start: 0.7809 (OUTLIER) cc_final: 0.7300 (pt) REVERT: H 300 TYR cc_start: 0.8375 (OUTLIER) cc_final: 0.7897 (t80) REVERT: I 79 LYS cc_start: 0.8138 (mmmt) cc_final: 0.7138 (pttt) REVERT: I 146 ASN cc_start: 0.6115 (m-40) cc_final: 0.5708 (m110) REVERT: I 152 VAL cc_start: 0.7386 (OUTLIER) cc_final: 0.7103 (t) REVERT: I 171 ILE cc_start: 0.8246 (OUTLIER) cc_final: 0.7543 (pt) REVERT: I 203 VAL cc_start: 0.8924 (m) cc_final: 0.8231 (t) REVERT: I 212 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7132 (mt-10) REVERT: I 275 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8654 (tp) REVERT: J 21 MET cc_start: 0.7965 (mmp) cc_final: 0.7246 (tpt) REVERT: J 31 LYS cc_start: 0.8884 (mttt) cc_final: 0.8430 (mtpt) REVERT: J 119 THR cc_start: 0.8702 (p) cc_final: 0.8458 (p) REVERT: J 271 LYS cc_start: 0.8631 (mmmt) cc_final: 0.8401 (tptt) REVERT: K 26 HIS cc_start: 0.7426 (m90) cc_final: 0.7221 (m90) REVERT: K 31 LYS cc_start: 0.8797 (mttt) cc_final: 0.8399 (mttt) REVERT: K 50 ASN cc_start: 0.9030 (m-40) cc_final: 0.8671 (m110) REVERT: K 79 LYS cc_start: 0.7605 (mtpt) cc_final: 0.6886 (mmmt) REVERT: K 151 ARG cc_start: 0.7593 (mtp-110) cc_final: 0.7110 (ttm170) REVERT: K 171 ILE cc_start: 0.8041 (OUTLIER) cc_final: 0.7561 (pt) REVERT: K 300 TYR cc_start: 0.8440 (OUTLIER) cc_final: 0.7790 (t80) REVERT: L 79 LYS cc_start: 0.8302 (mmmt) cc_final: 0.7145 (pttt) REVERT: L 152 VAL cc_start: 0.7396 (OUTLIER) cc_final: 0.7122 (t) REVERT: L 171 ILE cc_start: 0.8185 (OUTLIER) cc_final: 0.7502 (pt) REVERT: L 212 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7201 (mt-10) outliers start: 195 outliers final: 136 residues processed: 1224 average time/residue: 0.5041 time to fit residues: 1022.1929 Evaluate side-chains 1245 residues out of total 5724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 1088 time to evaluate : 4.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 35 ILE Chi-restraints excluded: chain a residue 110 GLN Chi-restraints excluded: chain a residue 147 VAL Chi-restraints excluded: chain a residue 156 ILE Chi-restraints excluded: chain a residue 159 HIS Chi-restraints excluded: chain a residue 166 VAL Chi-restraints excluded: chain b residue 63 SER Chi-restraints excluded: chain b residue 141 THR Chi-restraints excluded: chain b residue 156 ILE Chi-restraints excluded: chain c residue 1 MET Chi-restraints excluded: chain c residue 66 SER Chi-restraints excluded: chain c residue 69 SER Chi-restraints excluded: chain c residue 70 VAL Chi-restraints excluded: chain c residue 98 ASN Chi-restraints excluded: chain c residue 141 THR Chi-restraints excluded: chain c residue 156 ILE Chi-restraints excluded: chain d residue 69 SER Chi-restraints excluded: chain d residue 147 VAL Chi-restraints excluded: chain d residue 156 ILE Chi-restraints excluded: chain d residue 159 HIS Chi-restraints excluded: chain d residue 166 VAL Chi-restraints excluded: chain e residue 63 SER Chi-restraints excluded: chain e residue 70 VAL Chi-restraints excluded: chain e residue 141 THR Chi-restraints excluded: chain e residue 156 ILE Chi-restraints excluded: chain f residue 16 LYS Chi-restraints excluded: chain f residue 66 SER Chi-restraints excluded: chain f residue 69 SER Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 98 ASN Chi-restraints excluded: chain f residue 105 ASP Chi-restraints excluded: chain f residue 141 THR Chi-restraints excluded: chain f residue 156 ILE Chi-restraints excluded: chain g residue 69 SER Chi-restraints excluded: chain g residue 110 GLN Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 156 ILE Chi-restraints excluded: chain g residue 159 HIS Chi-restraints excluded: chain h residue 63 SER Chi-restraints excluded: chain h residue 109 THR Chi-restraints excluded: chain h residue 156 ILE Chi-restraints excluded: chain h residue 166 VAL Chi-restraints excluded: chain i residue 1 MET Chi-restraints excluded: chain i residue 16 LYS Chi-restraints excluded: chain i residue 63 SER Chi-restraints excluded: chain i residue 66 SER Chi-restraints excluded: chain i residue 69 SER Chi-restraints excluded: chain i residue 70 VAL Chi-restraints excluded: chain i residue 98 ASN Chi-restraints excluded: chain i residue 141 THR Chi-restraints excluded: chain i residue 156 ILE Chi-restraints excluded: chain j residue 7 GLU Chi-restraints excluded: chain j residue 35 ILE Chi-restraints excluded: chain j residue 69 SER Chi-restraints excluded: chain j residue 156 ILE Chi-restraints excluded: chain j residue 159 HIS Chi-restraints excluded: chain j residue 166 VAL Chi-restraints excluded: chain k residue 63 SER Chi-restraints excluded: chain k residue 156 ILE Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 42 ASP Chi-restraints excluded: chain l residue 70 VAL Chi-restraints excluded: chain l residue 98 ASN Chi-restraints excluded: chain l residue 141 THR Chi-restraints excluded: chain l residue 156 ILE Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 161 ASN Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 182 ASP Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 300 TYR Chi-restraints excluded: chain C residue 326 ASN Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 300 TYR Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 300 TYR Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 105 ASP Chi-restraints excluded: chain G residue 161 ASN Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 272 SER Chi-restraints excluded: chain G residue 298 LEU Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 161 ASN Chi-restraints excluded: chain H residue 171 ILE Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 275 LEU Chi-restraints excluded: chain H residue 298 LEU Chi-restraints excluded: chain H residue 300 TYR Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain I residue 16 ARG Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain I residue 132 GLU Chi-restraints excluded: chain I residue 152 VAL Chi-restraints excluded: chain I residue 154 GLU Chi-restraints excluded: chain I residue 171 ILE Chi-restraints excluded: chain I residue 212 GLU Chi-restraints excluded: chain I residue 259 ASP Chi-restraints excluded: chain I residue 275 LEU Chi-restraints excluded: chain I residue 300 TYR Chi-restraints excluded: chain I residue 326 ASN Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 105 ASP Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain J residue 181 ILE Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain K residue 119 THR Chi-restraints excluded: chain K residue 171 ILE Chi-restraints excluded: chain K residue 179 THR Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 300 TYR Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain K residue 343 HIS Chi-restraints excluded: chain L residue 105 ASP Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 154 GLU Chi-restraints excluded: chain L residue 171 ILE Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain L residue 214 LEU Chi-restraints excluded: chain L residue 224 GLU Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 300 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 36 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 525 optimal weight: 4.9990 chunk 604 optimal weight: 7.9990 chunk 86 optimal weight: 0.0170 chunk 272 optimal weight: 0.9980 chunk 310 optimal weight: 6.9990 chunk 371 optimal weight: 5.9990 chunk 342 optimal weight: 8.9990 chunk 321 optimal weight: 2.9990 chunk 249 optimal weight: 5.9990 overall best weight: 2.8024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 151 ASN d 151 ASN e 132 HIS f 2 GLN i 2 GLN j 110 GLN j 151 ASN l 2 GLN ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 ASN A 371 GLN B 161 ASN ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 371 GLN ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 161 ASN ** F 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 326 ASN F 371 GLN G 161 ASN G 371 GLN H 161 ASN ** I 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 326 ASN I 371 GLN J 161 ASN J 371 GLN K 161 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.115690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.102008 restraints weight = 68571.739| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 1.42 r_work: 0.2820 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 52092 Z= 0.286 Angle : 0.653 12.891 70464 Z= 0.333 Chirality : 0.045 0.338 8040 Planarity : 0.004 0.041 9096 Dihedral : 5.188 32.871 6992 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.66 % Allowed : 7.00 % Favored : 92.34 % Rotamer: Outliers : 3.55 % Allowed : 16.79 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.10), residues: 6396 helix: 1.50 (0.10), residues: 2784 sheet: 0.58 (0.19), residues: 864 loop : -2.04 (0.11), residues: 2748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 116 HIS 0.007 0.002 HIS F 343 PHE 0.013 0.002 PHE B 157 TYR 0.027 0.002 TYR d 88 ARG 0.003 0.000 ARG I 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12792 Ramachandran restraints generated. 6396 Oldfield, 0 Emsley, 6396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12792 Ramachandran restraints generated. 6396 Oldfield, 0 Emsley, 6396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1300 residues out of total 5724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 203 poor density : 1097 time to evaluate : 6.204 Fit side-chains revert: symmetry clash REVERT: a 49 GLN cc_start: 0.8794 (tt0) cc_final: 0.8440 (tt0) REVERT: a 96 LYS cc_start: 0.8849 (mttm) cc_final: 0.8322 (mmtt) REVERT: b 2 GLN cc_start: 0.7831 (tt0) cc_final: 0.7587 (tt0) REVERT: b 96 LYS cc_start: 0.8544 (mttp) cc_final: 0.8257 (mmtm) REVERT: d 8 ASP cc_start: 0.8441 (m-30) cc_final: 0.8140 (m-30) REVERT: d 96 LYS cc_start: 0.8755 (mttm) cc_final: 0.8248 (mmtt) REVERT: e 2 GLN cc_start: 0.8045 (tt0) cc_final: 0.7715 (tt0) REVERT: e 7 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8041 (mp0) REVERT: e 12 TYR cc_start: 0.8678 (t80) cc_final: 0.8095 (t80) REVERT: e 83 GLU cc_start: 0.7135 (mt-10) cc_final: 0.6646 (mp0) REVERT: e 96 LYS cc_start: 0.8569 (mttp) cc_final: 0.8267 (mmtm) REVERT: f 16 LYS cc_start: 0.6488 (OUTLIER) cc_final: 0.5108 (pttp) REVERT: f 42 ASP cc_start: 0.6673 (t0) cc_final: 0.6437 (t70) REVERT: f 110 GLN cc_start: 0.7790 (tt0) cc_final: 0.7549 (tt0) REVERT: g 49 GLN cc_start: 0.8835 (tt0) cc_final: 0.8478 (tt0) REVERT: g 96 LYS cc_start: 0.8747 (mttm) cc_final: 0.8232 (mmtt) REVERT: g 118 GLU cc_start: 0.7570 (mp0) cc_final: 0.7129 (mp0) REVERT: h 2 GLN cc_start: 0.7996 (tt0) cc_final: 0.7748 (tt0) REVERT: h 96 LYS cc_start: 0.8579 (mttp) cc_final: 0.8273 (mmtm) REVERT: i 16 LYS cc_start: 0.6500 (OUTLIER) cc_final: 0.5267 (pttp) REVERT: j 49 GLN cc_start: 0.8850 (tt0) cc_final: 0.8487 (tt0) REVERT: j 96 LYS cc_start: 0.8728 (mttm) cc_final: 0.7984 (mmtt) REVERT: j 118 GLU cc_start: 0.7531 (mp0) cc_final: 0.7071 (mp0) REVERT: k 25 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7826 (mm-30) REVERT: k 96 LYS cc_start: 0.8570 (mttp) cc_final: 0.8260 (mmtm) REVERT: k 110 GLN cc_start: 0.7628 (mt0) cc_final: 0.7128 (mt0) REVERT: l 165 GLU cc_start: 0.8686 (tp30) cc_final: 0.8480 (mm-30) REVERT: A 21 MET cc_start: 0.8083 (mmp) cc_final: 0.7543 (tpt) REVERT: A 79 LYS cc_start: 0.8442 (mmmt) cc_final: 0.8007 (tptp) REVERT: A 149 ASN cc_start: 0.6865 (t0) cc_final: 0.6523 (t0) REVERT: A 368 ASP cc_start: 0.7223 (t0) cc_final: 0.6190 (p0) REVERT: B 21 MET cc_start: 0.7596 (tpt) cc_final: 0.7305 (ttp) REVERT: B 41 LYS cc_start: 0.8675 (mttt) cc_final: 0.8429 (mttt) REVERT: B 79 LYS cc_start: 0.7553 (mtpt) cc_final: 0.6824 (mmmt) REVERT: B 151 ARG cc_start: 0.7653 (mtp-110) cc_final: 0.6983 (ttm170) REVERT: B 214 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8435 (pp) REVERT: B 300 TYR cc_start: 0.8438 (OUTLIER) cc_final: 0.7876 (t80) REVERT: C 171 ILE cc_start: 0.8150 (OUTLIER) cc_final: 0.7411 (pt) REVERT: C 203 VAL cc_start: 0.8995 (m) cc_final: 0.8342 (t) REVERT: D 21 MET cc_start: 0.8005 (mmm) cc_final: 0.7318 (tpt) REVERT: D 26 HIS cc_start: 0.7759 (m90) cc_final: 0.7506 (m90) REVERT: D 79 LYS cc_start: 0.8516 (mmmt) cc_final: 0.8010 (tptp) REVERT: D 255 SER cc_start: 0.8669 (m) cc_final: 0.8273 (p) REVERT: E 43 GLU cc_start: 0.8019 (pm20) cc_final: 0.7801 (pm20) REVERT: E 50 ASN cc_start: 0.9077 (m110) cc_final: 0.8836 (m110) REVERT: E 79 LYS cc_start: 0.7569 (mtpt) cc_final: 0.6855 (mmmt) REVERT: E 151 ARG cc_start: 0.7586 (mtp-110) cc_final: 0.6900 (ttm170) REVERT: E 300 TYR cc_start: 0.8481 (OUTLIER) cc_final: 0.7863 (t80) REVERT: F 79 LYS cc_start: 0.7958 (mmmt) cc_final: 0.7012 (pttt) REVERT: G 21 MET cc_start: 0.7990 (mmp) cc_final: 0.7198 (tpp) REVERT: G 105 ASP cc_start: 0.8605 (OUTLIER) cc_final: 0.8351 (m-30) REVERT: G 300 TYR cc_start: 0.8100 (m-80) cc_final: 0.7514 (m-80) REVERT: H 43 GLU cc_start: 0.7844 (mp0) cc_final: 0.7615 (mp0) REVERT: H 50 ASN cc_start: 0.9063 (m-40) cc_final: 0.8798 (m110) REVERT: H 79 LYS cc_start: 0.7568 (mtpt) cc_final: 0.6837 (mmmt) REVERT: H 130 GLN cc_start: 0.8057 (tt0) cc_final: 0.7813 (tt0) REVERT: H 151 ARG cc_start: 0.7652 (mtp-110) cc_final: 0.6812 (ttm170) REVERT: H 214 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8417 (pp) REVERT: H 300 TYR cc_start: 0.8435 (OUTLIER) cc_final: 0.7899 (t80) REVERT: I 79 LYS cc_start: 0.8141 (mmmt) cc_final: 0.7114 (pttt) REVERT: I 171 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.7619 (pt) REVERT: I 203 VAL cc_start: 0.8947 (m) cc_final: 0.8322 (t) REVERT: I 212 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7198 (mt-10) REVERT: I 263 LYS cc_start: 0.8739 (ttpt) cc_final: 0.8499 (tttm) REVERT: I 275 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8714 (tp) REVERT: J 21 MET cc_start: 0.8117 (mmp) cc_final: 0.7302 (tpt) REVERT: J 31 LYS cc_start: 0.8884 (mttt) cc_final: 0.8437 (mtpt) REVERT: J 105 ASP cc_start: 0.8530 (OUTLIER) cc_final: 0.8156 (m-30) REVERT: J 119 THR cc_start: 0.8845 (p) cc_final: 0.8574 (p) REVERT: J 255 SER cc_start: 0.8675 (m) cc_final: 0.8284 (p) REVERT: J 271 LYS cc_start: 0.8660 (mmmt) cc_final: 0.8409 (tptt) REVERT: K 15 GLN cc_start: 0.8470 (tp-100) cc_final: 0.8183 (tp-100) REVERT: K 26 HIS cc_start: 0.7443 (m90) cc_final: 0.7183 (m90) REVERT: K 31 LYS cc_start: 0.8801 (mttt) cc_final: 0.8399 (mttt) REVERT: K 50 ASN cc_start: 0.9100 (m-40) cc_final: 0.8664 (m110) REVERT: K 74 ASN cc_start: 0.6896 (OUTLIER) cc_final: 0.6491 (m-40) REVERT: K 79 LYS cc_start: 0.7573 (mtpt) cc_final: 0.6832 (mmmt) REVERT: K 130 GLN cc_start: 0.8139 (tt0) cc_final: 0.7883 (tt0) REVERT: K 151 ARG cc_start: 0.7670 (mtp-110) cc_final: 0.6870 (ttm170) REVERT: K 214 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8405 (pp) REVERT: K 300 TYR cc_start: 0.8489 (OUTLIER) cc_final: 0.7868 (t80) REVERT: L 79 LYS cc_start: 0.8272 (mmmt) cc_final: 0.7163 (pttt) REVERT: L 171 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7454 (pt) REVERT: L 203 VAL cc_start: 0.8995 (m) cc_final: 0.8329 (t) REVERT: L 212 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7138 (mt-10) outliers start: 203 outliers final: 159 residues processed: 1213 average time/residue: 0.5249 time to fit residues: 1056.9347 Evaluate side-chains 1256 residues out of total 5724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 1079 time to evaluate : 4.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 35 ILE Chi-restraints excluded: chain a residue 69 SER Chi-restraints excluded: chain a residue 110 GLN Chi-restraints excluded: chain a residue 147 VAL Chi-restraints excluded: chain a residue 156 ILE Chi-restraints excluded: chain a residue 159 HIS Chi-restraints excluded: chain a residue 166 VAL Chi-restraints excluded: chain b residue 20 LEU Chi-restraints excluded: chain b residue 63 SER Chi-restraints excluded: chain b residue 141 THR Chi-restraints excluded: chain b residue 156 ILE Chi-restraints excluded: chain c residue 1 MET Chi-restraints excluded: chain c residue 66 SER Chi-restraints excluded: chain c residue 69 SER Chi-restraints excluded: chain c residue 70 VAL Chi-restraints excluded: chain c residue 98 ASN Chi-restraints excluded: chain c residue 105 ASP Chi-restraints excluded: chain c residue 109 THR Chi-restraints excluded: chain c residue 141 THR Chi-restraints excluded: chain c residue 156 ILE Chi-restraints excluded: chain d residue 69 SER Chi-restraints excluded: chain d residue 73 MET Chi-restraints excluded: chain d residue 145 GLU Chi-restraints excluded: chain d residue 147 VAL Chi-restraints excluded: chain d residue 156 ILE Chi-restraints excluded: chain d residue 159 HIS Chi-restraints excluded: chain d residue 166 VAL Chi-restraints excluded: chain e residue 63 SER Chi-restraints excluded: chain e residue 70 VAL Chi-restraints excluded: chain e residue 141 THR Chi-restraints excluded: chain e residue 156 ILE Chi-restraints excluded: chain f residue 16 LYS Chi-restraints excluded: chain f residue 66 SER Chi-restraints excluded: chain f residue 69 SER Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 98 ASN Chi-restraints excluded: chain f residue 105 ASP Chi-restraints excluded: chain f residue 141 THR Chi-restraints excluded: chain f residue 156 ILE Chi-restraints excluded: chain g residue 63 SER Chi-restraints excluded: chain g residue 69 SER Chi-restraints excluded: chain g residue 110 GLN Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 145 GLU Chi-restraints excluded: chain g residue 156 ILE Chi-restraints excluded: chain g residue 159 HIS Chi-restraints excluded: chain h residue 63 SER Chi-restraints excluded: chain h residue 109 THR Chi-restraints excluded: chain h residue 156 ILE Chi-restraints excluded: chain h residue 166 VAL Chi-restraints excluded: chain i residue 1 MET Chi-restraints excluded: chain i residue 16 LYS Chi-restraints excluded: chain i residue 63 SER Chi-restraints excluded: chain i residue 66 SER Chi-restraints excluded: chain i residue 69 SER Chi-restraints excluded: chain i residue 70 VAL Chi-restraints excluded: chain i residue 98 ASN Chi-restraints excluded: chain i residue 105 ASP Chi-restraints excluded: chain i residue 141 THR Chi-restraints excluded: chain i residue 156 ILE Chi-restraints excluded: chain j residue 35 ILE Chi-restraints excluded: chain j residue 69 SER Chi-restraints excluded: chain j residue 145 GLU Chi-restraints excluded: chain j residue 156 ILE Chi-restraints excluded: chain j residue 159 HIS Chi-restraints excluded: chain j residue 166 VAL Chi-restraints excluded: chain k residue 63 SER Chi-restraints excluded: chain k residue 156 ILE Chi-restraints excluded: chain k residue 166 VAL Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 42 ASP Chi-restraints excluded: chain l residue 66 SER Chi-restraints excluded: chain l residue 70 VAL Chi-restraints excluded: chain l residue 98 ASN Chi-restraints excluded: chain l residue 141 THR Chi-restraints excluded: chain l residue 156 ILE Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 161 ASN Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 182 ASP Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 300 TYR Chi-restraints excluded: chain C residue 326 ASN Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 161 ASN Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 300 TYR Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 154 GLU Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 300 TYR Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 105 ASP Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 272 SER Chi-restraints excluded: chain G residue 298 LEU Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 161 ASN Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 214 LEU Chi-restraints excluded: chain H residue 275 LEU Chi-restraints excluded: chain H residue 298 LEU Chi-restraints excluded: chain H residue 300 TYR Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain I residue 16 ARG Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 105 ASP Chi-restraints excluded: chain I residue 132 GLU Chi-restraints excluded: chain I residue 154 GLU Chi-restraints excluded: chain I residue 171 ILE Chi-restraints excluded: chain I residue 212 GLU Chi-restraints excluded: chain I residue 224 GLU Chi-restraints excluded: chain I residue 259 ASP Chi-restraints excluded: chain I residue 275 LEU Chi-restraints excluded: chain I residue 300 TYR Chi-restraints excluded: chain I residue 326 ASN Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 105 ASP Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain J residue 181 ILE Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain K residue 74 ASN Chi-restraints excluded: chain K residue 119 THR Chi-restraints excluded: chain K residue 161 ASN Chi-restraints excluded: chain K residue 179 THR Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 214 LEU Chi-restraints excluded: chain K residue 300 TYR Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain K residue 326 ASN Chi-restraints excluded: chain K residue 343 HIS Chi-restraints excluded: chain L residue 105 ASP Chi-restraints excluded: chain L residue 154 GLU Chi-restraints excluded: chain L residue 171 ILE Chi-restraints excluded: chain L residue 182 ASP Chi-restraints excluded: chain L residue 210 THR Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain L residue 214 LEU Chi-restraints excluded: chain L residue 224 GLU Chi-restraints excluded: chain L residue 259 ASP Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 300 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 518 optimal weight: 0.8980 chunk 517 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 251 optimal weight: 2.9990 chunk 581 optimal weight: 0.9980 chunk 382 optimal weight: 5.9990 chunk 264 optimal weight: 0.5980 chunk 188 optimal weight: 0.2980 chunk 240 optimal weight: 0.9980 chunk 599 optimal weight: 7.9990 chunk 602 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 151 ASN d 151 ASN f 2 GLN h 110 GLN i 2 GLN j 151 ASN l 2 GLN A 149 ASN A 326 ASN A 371 GLN B 161 ASN B 326 ASN C 326 ASN ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 326 ASN D 371 GLN ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 161 ASN E 326 ASN F 130 GLN F 326 ASN G 149 ASN G 161 ASN G 326 ASN G 371 GLN H 161 ASN H 326 ASN I 130 GLN I 253 GLN ** I 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 371 GLN J 161 ASN J 326 ASN J 371 GLN K 161 ASN K 326 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.120442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.106699 restraints weight = 68452.696| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.43 r_work: 0.2886 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 52092 Z= 0.159 Angle : 0.580 11.526 70464 Z= 0.299 Chirality : 0.042 0.314 8040 Planarity : 0.004 0.040 9096 Dihedral : 4.947 30.313 6992 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.53 % Allowed : 7.27 % Favored : 92.20 % Rotamer: Outliers : 2.73 % Allowed : 17.65 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.11), residues: 6396 helix: 1.69 (0.10), residues: 2784 sheet: 0.87 (0.20), residues: 792 loop : -1.93 (0.11), residues: 2820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP f 131 HIS 0.005 0.001 HIS C 343 PHE 0.010 0.001 PHE A 197 TYR 0.026 0.001 TYR J 150 ARG 0.004 0.000 ARG i 169 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12792 Ramachandran restraints generated. 6396 Oldfield, 0 Emsley, 6396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12792 Ramachandran restraints generated. 6396 Oldfield, 0 Emsley, 6396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1255 residues out of total 5724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 1099 time to evaluate : 4.623 Fit side-chains revert: symmetry clash REVERT: a 41 MET cc_start: 0.8065 (mtt) cc_final: 0.7744 (mtt) REVERT: a 49 GLN cc_start: 0.8747 (tt0) cc_final: 0.8401 (tt0) REVERT: a 96 LYS cc_start: 0.8830 (mttm) cc_final: 0.8298 (mmtt) REVERT: b 2 GLN cc_start: 0.7975 (tt0) cc_final: 0.7710 (tt0) REVERT: b 96 LYS cc_start: 0.8490 (mttp) cc_final: 0.8201 (mmtm) REVERT: b 118 GLU cc_start: 0.7594 (mp0) cc_final: 0.7200 (mp0) REVERT: c 21 GLU cc_start: 0.6482 (mp0) cc_final: 0.5630 (tt0) REVERT: c 27 MET cc_start: 0.8659 (mtt) cc_final: 0.8373 (mtt) REVERT: d 8 ASP cc_start: 0.8467 (m-30) cc_final: 0.8177 (m-30) REVERT: d 96 LYS cc_start: 0.8774 (mttm) cc_final: 0.8250 (mmtt) REVERT: e 2 GLN cc_start: 0.8040 (tt0) cc_final: 0.7776 (tt0) REVERT: e 7 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8025 (mp0) REVERT: e 12 TYR cc_start: 0.8634 (t80) cc_final: 0.8150 (t80) REVERT: e 83 GLU cc_start: 0.7164 (mt-10) cc_final: 0.6692 (mp0) REVERT: e 96 LYS cc_start: 0.8513 (mttp) cc_final: 0.8242 (mmtm) REVERT: f 16 LYS cc_start: 0.6437 (OUTLIER) cc_final: 0.5104 (pttp) REVERT: f 110 GLN cc_start: 0.7719 (tt0) cc_final: 0.7487 (tt0) REVERT: g 49 GLN cc_start: 0.8757 (tt0) cc_final: 0.8449 (tt0) REVERT: g 96 LYS cc_start: 0.8723 (mttm) cc_final: 0.8192 (mmtt) REVERT: g 118 GLU cc_start: 0.7532 (mp0) cc_final: 0.7099 (mp0) REVERT: h 2 GLN cc_start: 0.8034 (tt0) cc_final: 0.7787 (tt0) REVERT: h 7 GLU cc_start: 0.8398 (mt-10) cc_final: 0.7858 (mp0) REVERT: h 96 LYS cc_start: 0.8531 (mttp) cc_final: 0.8259 (mmtm) REVERT: i 16 LYS cc_start: 0.6442 (OUTLIER) cc_final: 0.5238 (pttp) REVERT: i 165 GLU cc_start: 0.8501 (mm-30) cc_final: 0.7865 (mm-30) REVERT: j 49 GLN cc_start: 0.8812 (tt0) cc_final: 0.8469 (tt0) REVERT: j 83 GLU cc_start: 0.6545 (mp0) cc_final: 0.6284 (mp0) REVERT: j 96 LYS cc_start: 0.8692 (mttm) cc_final: 0.7950 (mmtt) REVERT: j 118 GLU cc_start: 0.7422 (mp0) cc_final: 0.7030 (mp0) REVERT: k 25 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7723 (mm-30) REVERT: k 96 LYS cc_start: 0.8571 (mttp) cc_final: 0.8264 (mmtm) REVERT: k 118 GLU cc_start: 0.7717 (mp0) cc_final: 0.7055 (mp0) REVERT: l 27 MET cc_start: 0.8637 (mtt) cc_final: 0.8362 (mtt) REVERT: l 165 GLU cc_start: 0.8670 (tp30) cc_final: 0.8455 (mm-30) REVERT: A 21 MET cc_start: 0.8056 (mmp) cc_final: 0.7523 (tpt) REVERT: A 79 LYS cc_start: 0.8399 (mmmt) cc_final: 0.7957 (tptp) REVERT: A 149 ASN cc_start: 0.7139 (OUTLIER) cc_final: 0.6620 (t0) REVERT: A 368 ASP cc_start: 0.7238 (t0) cc_final: 0.6231 (p0) REVERT: B 21 MET cc_start: 0.7629 (tpt) cc_final: 0.7388 (ttp) REVERT: B 41 LYS cc_start: 0.8531 (mttt) cc_final: 0.8293 (mttt) REVERT: B 79 LYS cc_start: 0.7508 (mtpt) cc_final: 0.6774 (mmmt) REVERT: B 151 ARG cc_start: 0.7464 (mtp-110) cc_final: 0.6765 (ttm170) REVERT: B 214 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8274 (pp) REVERT: B 300 TYR cc_start: 0.8336 (OUTLIER) cc_final: 0.7817 (t80) REVERT: C 79 LYS cc_start: 0.7953 (mmmt) cc_final: 0.7050 (pttt) REVERT: C 171 ILE cc_start: 0.8062 (OUTLIER) cc_final: 0.7348 (pt) REVERT: D 21 MET cc_start: 0.7952 (mmm) cc_final: 0.7296 (tpt) REVERT: D 26 HIS cc_start: 0.7704 (m90) cc_final: 0.7400 (m170) REVERT: D 79 LYS cc_start: 0.8500 (mmmt) cc_final: 0.7977 (tptp) REVERT: D 154 GLU cc_start: 0.8633 (pt0) cc_final: 0.8327 (pm20) REVERT: E 50 ASN cc_start: 0.8983 (m110) cc_final: 0.8756 (m110) REVERT: E 79 LYS cc_start: 0.7529 (mtpt) cc_final: 0.6783 (mmmt) REVERT: E 151 ARG cc_start: 0.7395 (mtp-110) cc_final: 0.6804 (ttm170) REVERT: E 300 TYR cc_start: 0.8347 (OUTLIER) cc_final: 0.7789 (t80) REVERT: F 79 LYS cc_start: 0.7955 (mmmt) cc_final: 0.7005 (pttt) REVERT: F 271 LYS cc_start: 0.7951 (tptt) cc_final: 0.7629 (mmtt) REVERT: G 17 ILE cc_start: 0.8579 (mp) cc_final: 0.8278 (mm) REVERT: G 21 MET cc_start: 0.7983 (mmp) cc_final: 0.7379 (tpt) REVERT: G 300 TYR cc_start: 0.8099 (m-80) cc_final: 0.7715 (m-80) REVERT: H 50 ASN cc_start: 0.8970 (m-40) cc_final: 0.8728 (m110) REVERT: H 79 LYS cc_start: 0.7498 (mtpt) cc_final: 0.6743 (mmmt) REVERT: H 151 ARG cc_start: 0.7448 (mtp-110) cc_final: 0.6755 (ttm170) REVERT: H 171 ILE cc_start: 0.7861 (OUTLIER) cc_final: 0.7381 (pt) REVERT: H 214 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8231 (pp) REVERT: H 300 TYR cc_start: 0.8357 (OUTLIER) cc_final: 0.7743 (t80) REVERT: I 79 LYS cc_start: 0.8109 (mmmt) cc_final: 0.7091 (pttt) REVERT: I 171 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7389 (pt) REVERT: I 212 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7184 (mt-10) REVERT: I 275 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8579 (tp) REVERT: J 21 MET cc_start: 0.8084 (mmp) cc_final: 0.7473 (tpt) REVERT: J 31 LYS cc_start: 0.8866 (mttt) cc_final: 0.8380 (mtpt) REVERT: J 119 THR cc_start: 0.8657 (p) cc_final: 0.8404 (p) REVERT: J 271 LYS cc_start: 0.8616 (mmmt) cc_final: 0.8327 (tptt) REVERT: K 26 HIS cc_start: 0.7396 (m90) cc_final: 0.7168 (m90) REVERT: K 31 LYS cc_start: 0.8767 (mttt) cc_final: 0.8353 (mttt) REVERT: K 50 ASN cc_start: 0.9047 (m-40) cc_final: 0.8676 (m110) REVERT: K 74 ASN cc_start: 0.6907 (OUTLIER) cc_final: 0.6676 (m-40) REVERT: K 79 LYS cc_start: 0.7506 (mtpt) cc_final: 0.6759 (mmmt) REVERT: K 151 ARG cc_start: 0.7433 (mtp-110) cc_final: 0.6807 (ttm170) REVERT: K 171 ILE cc_start: 0.8002 (OUTLIER) cc_final: 0.7501 (pt) REVERT: K 214 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8196 (pp) REVERT: K 272 SER cc_start: 0.9180 (t) cc_final: 0.8893 (p) REVERT: K 300 TYR cc_start: 0.8397 (OUTLIER) cc_final: 0.7674 (t80) REVERT: L 79 LYS cc_start: 0.8245 (mmmt) cc_final: 0.7096 (pttt) REVERT: L 171 ILE cc_start: 0.8175 (OUTLIER) cc_final: 0.7467 (pt) outliers start: 156 outliers final: 113 residues processed: 1188 average time/residue: 0.5097 time to fit residues: 1001.9565 Evaluate side-chains 1198 residues out of total 5724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 1067 time to evaluate : 4.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 35 ILE Chi-restraints excluded: chain a residue 147 VAL Chi-restraints excluded: chain a residue 156 ILE Chi-restraints excluded: chain a residue 159 HIS Chi-restraints excluded: chain a residue 166 VAL Chi-restraints excluded: chain b residue 20 LEU Chi-restraints excluded: chain b residue 141 THR Chi-restraints excluded: chain b residue 156 ILE Chi-restraints excluded: chain c residue 70 VAL Chi-restraints excluded: chain c residue 98 ASN Chi-restraints excluded: chain c residue 141 THR Chi-restraints excluded: chain c residue 156 ILE Chi-restraints excluded: chain d residue 69 SER Chi-restraints excluded: chain d residue 147 VAL Chi-restraints excluded: chain d residue 156 ILE Chi-restraints excluded: chain d residue 159 HIS Chi-restraints excluded: chain e residue 70 VAL Chi-restraints excluded: chain e residue 141 THR Chi-restraints excluded: chain e residue 156 ILE Chi-restraints excluded: chain f residue 16 LYS Chi-restraints excluded: chain f residue 69 SER Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 98 ASN Chi-restraints excluded: chain f residue 141 THR Chi-restraints excluded: chain f residue 156 ILE Chi-restraints excluded: chain g residue 63 SER Chi-restraints excluded: chain g residue 69 SER Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 156 ILE Chi-restraints excluded: chain g residue 159 HIS Chi-restraints excluded: chain h residue 109 THR Chi-restraints excluded: chain h residue 156 ILE Chi-restraints excluded: chain i residue 16 LYS Chi-restraints excluded: chain i residue 42 ASP Chi-restraints excluded: chain i residue 63 SER Chi-restraints excluded: chain i residue 98 ASN Chi-restraints excluded: chain i residue 141 THR Chi-restraints excluded: chain i residue 156 ILE Chi-restraints excluded: chain j residue 35 ILE Chi-restraints excluded: chain j residue 69 SER Chi-restraints excluded: chain j residue 156 ILE Chi-restraints excluded: chain j residue 159 HIS Chi-restraints excluded: chain k residue 156 ILE Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 98 ASN Chi-restraints excluded: chain l residue 141 THR Chi-restraints excluded: chain l residue 156 ILE Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain B residue 161 ASN Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 326 ASN Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 182 ASP Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 300 TYR Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 326 ASN Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 300 TYR Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain F residue 130 GLN Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 300 TYR Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 326 ASN Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 161 ASN Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 272 SER Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain H residue 171 ILE Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 214 LEU Chi-restraints excluded: chain H residue 275 LEU Chi-restraints excluded: chain H residue 298 LEU Chi-restraints excluded: chain H residue 300 TYR Chi-restraints excluded: chain H residue 326 ASN Chi-restraints excluded: chain I residue 16 ARG Chi-restraints excluded: chain I residue 105 ASP Chi-restraints excluded: chain I residue 130 GLN Chi-restraints excluded: chain I residue 132 GLU Chi-restraints excluded: chain I residue 154 GLU Chi-restraints excluded: chain I residue 171 ILE Chi-restraints excluded: chain I residue 212 GLU Chi-restraints excluded: chain I residue 259 ASP Chi-restraints excluded: chain I residue 275 LEU Chi-restraints excluded: chain I residue 300 TYR Chi-restraints excluded: chain I residue 326 ASN Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain J residue 181 ILE Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain J residue 326 ASN Chi-restraints excluded: chain K residue 74 ASN Chi-restraints excluded: chain K residue 119 THR Chi-restraints excluded: chain K residue 171 ILE Chi-restraints excluded: chain K residue 179 THR Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 214 LEU Chi-restraints excluded: chain K residue 298 LEU Chi-restraints excluded: chain K residue 300 TYR Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain K residue 326 ASN Chi-restraints excluded: chain K residue 343 HIS Chi-restraints excluded: chain L residue 154 GLU Chi-restraints excluded: chain L residue 171 ILE Chi-restraints excluded: chain L residue 182 ASP Chi-restraints excluded: chain L residue 224 GLU Chi-restraints excluded: chain L residue 300 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 313 optimal weight: 4.9990 chunk 521 optimal weight: 0.5980 chunk 15 optimal weight: 4.9990 chunk 386 optimal weight: 0.9990 chunk 577 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 581 optimal weight: 0.3980 chunk 194 optimal weight: 6.9990 chunk 414 optimal weight: 5.9990 chunk 359 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 151 ASN d 151 ASN h 110 GLN i 2 GLN j 151 ASN A 149 ASN A 371 GLN B 161 ASN B 326 ASN ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 371 GLN ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 161 ASN E 326 ASN F 130 GLN F 371 GLN G 149 ASN G 161 ASN G 371 GLN H 161 ASN H 326 ASN ** I 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 371 GLN K 161 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.118311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.104645 restraints weight = 68545.257| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 1.43 r_work: 0.2865 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 52092 Z= 0.226 Angle : 0.609 11.611 70464 Z= 0.312 Chirality : 0.043 0.315 8040 Planarity : 0.004 0.039 9096 Dihedral : 4.956 30.214 6992 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.59 % Allowed : 7.05 % Favored : 92.35 % Rotamer: Outliers : 2.83 % Allowed : 17.65 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.10), residues: 6396 helix: 1.64 (0.10), residues: 2784 sheet: 0.87 (0.20), residues: 792 loop : -1.95 (0.11), residues: 2820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 116 HIS 0.006 0.001 HIS C 343 PHE 0.010 0.001 PHE c 113 TYR 0.023 0.001 TYR g 88 ARG 0.005 0.000 ARG d 161 =============================================================================== Job complete usr+sys time: 23041.55 seconds wall clock time: 396 minutes 33.48 seconds (23793.48 seconds total)