Starting phenix.real_space_refine on Sat Jun 28 22:04:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6gve_0071/06_2025/6gve_0071.cif Found real_map, /net/cci-nas-00/data/ceres_data/6gve_0071/06_2025/6gve_0071.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6gve_0071/06_2025/6gve_0071.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6gve_0071/06_2025/6gve_0071.map" model { file = "/net/cci-nas-00/data/ceres_data/6gve_0071/06_2025/6gve_0071.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6gve_0071/06_2025/6gve_0071.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 180 5.16 5 C 20896 2.51 5 N 5880 2.21 5 O 6440 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 33412 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2571 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 324} Chain: "B" Number of atoms: 2533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2533 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 302} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 590 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: G, J, L, H, M, P, E, D, F, I, K, O, N Time building chain proxies: 11.91, per 1000 atoms: 0.36 Number of scatterers: 33412 At special positions: 0 Unit cell: (143.439, 114.123, 213.588, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 180 16.00 P 16 15.00 O 6440 8.00 N 5880 7.00 C 20896 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: 8.07 Conformation dependent library (CDL) restraints added in 4.9 seconds 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7920 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 46 sheets defined 37.5% alpha, 27.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.53 Creating SS restraints... Processing helix chain 'P' and resid 2 through 22 removed outlier: 4.057A pdb=" N GLU P 9 " --> pdb=" O GLU P 5 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N CYS P 19 " --> pdb=" O ALA P 15 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP P 20 " --> pdb=" O HIS P 16 " (cutoff:3.500A) Processing helix chain 'P' and resid 26 through 52 Processing helix chain 'P' and resid 56 through 64 removed outlier: 4.253A pdb=" N ASP P 62 " --> pdb=" O GLN P 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 23 Processing helix chain 'D' and resid 39 through 48 removed outlier: 3.695A pdb=" N ASN D 43 " --> pdb=" O ASP D 39 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA D 44 " --> pdb=" O PRO D 40 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N HIS D 45 " --> pdb=" O ARG D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 86 removed outlier: 3.656A pdb=" N ASN D 85 " --> pdb=" O ASN D 82 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU D 86 " --> pdb=" O PRO D 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 82 through 86' Processing helix chain 'D' and resid 105 through 115 removed outlier: 3.812A pdb=" N LYS D 111 " --> pdb=" O GLU D 107 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N HIS D 112 " --> pdb=" O GLY D 108 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU D 113 " --> pdb=" O ALA D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 170 Proline residue: D 161 - end of helix Processing helix chain 'D' and resid 196 through 200 Processing helix chain 'D' and resid 215 through 222 removed outlier: 4.174A pdb=" N GLY D 219 " --> pdb=" O ALA D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 226 Processing helix chain 'D' and resid 255 through 270 removed outlier: 3.617A pdb=" N VAL D 259 " --> pdb=" O ILE D 255 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN D 260 " --> pdb=" O ALA D 256 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU D 268 " --> pdb=" O LYS D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 288 removed outlier: 3.747A pdb=" N ARG D 288 " --> pdb=" O SER D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 301 No H-bonds generated for 'chain 'D' and resid 299 through 301' Processing helix chain 'D' and resid 319 through 334 Processing helix chain 'A' and resid 10 through 23 Processing helix chain 'A' and resid 39 through 48 removed outlier: 3.695A pdb=" N ASN A 43 " --> pdb=" O ASP A 39 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA A 44 " --> pdb=" O PRO A 40 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N HIS A 45 " --> pdb=" O ARG A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 86 removed outlier: 3.655A pdb=" N ASN A 85 " --> pdb=" O ASN A 82 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU A 86 " --> pdb=" O PRO A 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 82 through 86' Processing helix chain 'A' and resid 105 through 115 removed outlier: 3.811A pdb=" N LYS A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N HIS A 112 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 170 Proline residue: A 161 - end of helix Processing helix chain 'A' and resid 196 through 200 Processing helix chain 'A' and resid 215 through 222 removed outlier: 4.175A pdb=" N GLY A 219 " --> pdb=" O ALA A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 226 Processing helix chain 'A' and resid 255 through 270 removed outlier: 3.618A pdb=" N VAL A 259 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 288 removed outlier: 3.749A pdb=" N ARG A 288 " --> pdb=" O SER A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 301 No H-bonds generated for 'chain 'A' and resid 299 through 301' Processing helix chain 'A' and resid 319 through 334 Processing helix chain 'E' and resid 10 through 23 Processing helix chain 'E' and resid 39 through 48 removed outlier: 3.695A pdb=" N ASN E 43 " --> pdb=" O ASP E 39 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA E 44 " --> pdb=" O PRO E 40 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N HIS E 45 " --> pdb=" O ARG E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 86 removed outlier: 3.656A pdb=" N ASN E 85 " --> pdb=" O ASN E 82 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU E 86 " --> pdb=" O PRO E 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 82 through 86' Processing helix chain 'E' and resid 105 through 115 removed outlier: 3.811A pdb=" N LYS E 111 " --> pdb=" O GLU E 107 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N HIS E 112 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU E 113 " --> pdb=" O ALA E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 170 Proline residue: E 161 - end of helix Processing helix chain 'E' and resid 196 through 200 Processing helix chain 'E' and resid 215 through 222 removed outlier: 4.174A pdb=" N GLY E 219 " --> pdb=" O ALA E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 226 Processing helix chain 'E' and resid 255 through 270 removed outlier: 3.618A pdb=" N VAL E 259 " --> pdb=" O ILE E 255 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN E 260 " --> pdb=" O ALA E 256 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU E 268 " --> pdb=" O LYS E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 288 removed outlier: 3.748A pdb=" N ARG E 288 " --> pdb=" O SER E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 301 No H-bonds generated for 'chain 'E' and resid 299 through 301' Processing helix chain 'E' and resid 319 through 334 Processing helix chain 'F' and resid 10 through 23 Processing helix chain 'F' and resid 39 through 48 removed outlier: 3.696A pdb=" N ASN F 43 " --> pdb=" O ASP F 39 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA F 44 " --> pdb=" O PRO F 40 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N HIS F 45 " --> pdb=" O ARG F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 86 removed outlier: 3.656A pdb=" N ASN F 85 " --> pdb=" O ASN F 82 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU F 86 " --> pdb=" O PRO F 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 82 through 86' Processing helix chain 'F' and resid 105 through 115 removed outlier: 3.812A pdb=" N LYS F 111 " --> pdb=" O GLU F 107 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N HIS F 112 " --> pdb=" O GLY F 108 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU F 113 " --> pdb=" O ALA F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 170 Proline residue: F 161 - end of helix Processing helix chain 'F' and resid 196 through 200 Processing helix chain 'F' and resid 215 through 222 removed outlier: 4.174A pdb=" N GLY F 219 " --> pdb=" O ALA F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 226 Processing helix chain 'F' and resid 255 through 270 removed outlier: 3.617A pdb=" N VAL F 259 " --> pdb=" O ILE F 255 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN F 260 " --> pdb=" O ALA F 256 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU F 268 " --> pdb=" O LYS F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 283 through 288 removed outlier: 3.749A pdb=" N ARG F 288 " --> pdb=" O SER F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 301 No H-bonds generated for 'chain 'F' and resid 299 through 301' Processing helix chain 'F' and resid 319 through 334 Processing helix chain 'I' and resid 10 through 23 Processing helix chain 'I' and resid 39 through 48 removed outlier: 3.695A pdb=" N ASN I 43 " --> pdb=" O ASP I 39 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA I 44 " --> pdb=" O PRO I 40 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N HIS I 45 " --> pdb=" O ARG I 41 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 86 removed outlier: 3.656A pdb=" N ASN I 85 " --> pdb=" O ASN I 82 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU I 86 " --> pdb=" O PRO I 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 82 through 86' Processing helix chain 'I' and resid 105 through 115 removed outlier: 3.812A pdb=" N LYS I 111 " --> pdb=" O GLU I 107 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N HIS I 112 " --> pdb=" O GLY I 108 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU I 113 " --> pdb=" O ALA I 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 153 through 170 Proline residue: I 161 - end of helix Processing helix chain 'I' and resid 196 through 200 Processing helix chain 'I' and resid 215 through 222 removed outlier: 4.175A pdb=" N GLY I 219 " --> pdb=" O ALA I 215 " (cutoff:3.500A) Processing helix chain 'I' and resid 223 through 226 Processing helix chain 'I' and resid 255 through 270 removed outlier: 3.617A pdb=" N VAL I 259 " --> pdb=" O ILE I 255 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN I 260 " --> pdb=" O ALA I 256 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU I 268 " --> pdb=" O LYS I 264 " (cutoff:3.500A) Processing helix chain 'I' and resid 283 through 288 removed outlier: 3.748A pdb=" N ARG I 288 " --> pdb=" O SER I 285 " (cutoff:3.500A) Processing helix chain 'I' and resid 299 through 301 No H-bonds generated for 'chain 'I' and resid 299 through 301' Processing helix chain 'I' and resid 319 through 334 Processing helix chain 'K' and resid 10 through 23 Processing helix chain 'K' and resid 39 through 48 removed outlier: 3.695A pdb=" N ASN K 43 " --> pdb=" O ASP K 39 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA K 44 " --> pdb=" O PRO K 40 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N HIS K 45 " --> pdb=" O ARG K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 86 removed outlier: 3.656A pdb=" N ASN K 85 " --> pdb=" O ASN K 82 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU K 86 " --> pdb=" O PRO K 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 82 through 86' Processing helix chain 'K' and resid 105 through 115 removed outlier: 3.812A pdb=" N LYS K 111 " --> pdb=" O GLU K 107 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N HIS K 112 " --> pdb=" O GLY K 108 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU K 113 " --> pdb=" O ALA K 109 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 170 Proline residue: K 161 - end of helix Processing helix chain 'K' and resid 196 through 200 Processing helix chain 'K' and resid 215 through 222 removed outlier: 4.175A pdb=" N GLY K 219 " --> pdb=" O ALA K 215 " (cutoff:3.500A) Processing helix chain 'K' and resid 223 through 226 Processing helix chain 'K' and resid 255 through 270 removed outlier: 3.617A pdb=" N VAL K 259 " --> pdb=" O ILE K 255 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN K 260 " --> pdb=" O ALA K 256 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU K 268 " --> pdb=" O LYS K 264 " (cutoff:3.500A) Processing helix chain 'K' and resid 283 through 288 removed outlier: 3.748A pdb=" N ARG K 288 " --> pdb=" O SER K 285 " (cutoff:3.500A) Processing helix chain 'K' and resid 299 through 301 No H-bonds generated for 'chain 'K' and resid 299 through 301' Processing helix chain 'K' and resid 319 through 334 Processing helix chain 'N' and resid 10 through 23 Processing helix chain 'N' and resid 39 through 48 removed outlier: 3.695A pdb=" N ASN N 43 " --> pdb=" O ASP N 39 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA N 44 " --> pdb=" O PRO N 40 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N HIS N 45 " --> pdb=" O ARG N 41 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 86 removed outlier: 3.655A pdb=" N ASN N 85 " --> pdb=" O ASN N 82 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU N 86 " --> pdb=" O PRO N 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 82 through 86' Processing helix chain 'N' and resid 105 through 115 removed outlier: 3.812A pdb=" N LYS N 111 " --> pdb=" O GLU N 107 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N HIS N 112 " --> pdb=" O GLY N 108 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU N 113 " --> pdb=" O ALA N 109 " (cutoff:3.500A) Processing helix chain 'N' and resid 153 through 170 Proline residue: N 161 - end of helix Processing helix chain 'N' and resid 196 through 200 Processing helix chain 'N' and resid 215 through 222 removed outlier: 4.174A pdb=" N GLY N 219 " --> pdb=" O ALA N 215 " (cutoff:3.500A) Processing helix chain 'N' and resid 223 through 226 Processing helix chain 'N' and resid 255 through 270 removed outlier: 3.618A pdb=" N VAL N 259 " --> pdb=" O ILE N 255 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN N 260 " --> pdb=" O ALA N 256 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU N 268 " --> pdb=" O LYS N 264 " (cutoff:3.500A) Processing helix chain 'N' and resid 283 through 288 removed outlier: 3.748A pdb=" N ARG N 288 " --> pdb=" O SER N 285 " (cutoff:3.500A) Processing helix chain 'N' and resid 299 through 301 No H-bonds generated for 'chain 'N' and resid 299 through 301' Processing helix chain 'N' and resid 319 through 334 Processing helix chain 'O' and resid 10 through 23 Processing helix chain 'O' and resid 39 through 48 removed outlier: 3.695A pdb=" N ASN O 43 " --> pdb=" O ASP O 39 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA O 44 " --> pdb=" O PRO O 40 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N HIS O 45 " --> pdb=" O ARG O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 82 through 86 removed outlier: 3.656A pdb=" N ASN O 85 " --> pdb=" O ASN O 82 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU O 86 " --> pdb=" O PRO O 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 82 through 86' Processing helix chain 'O' and resid 105 through 115 removed outlier: 3.812A pdb=" N LYS O 111 " --> pdb=" O GLU O 107 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N HIS O 112 " --> pdb=" O GLY O 108 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU O 113 " --> pdb=" O ALA O 109 " (cutoff:3.500A) Processing helix chain 'O' and resid 153 through 170 Proline residue: O 161 - end of helix Processing helix chain 'O' and resid 196 through 200 Processing helix chain 'O' and resid 215 through 222 removed outlier: 4.173A pdb=" N GLY O 219 " --> pdb=" O ALA O 215 " (cutoff:3.500A) Processing helix chain 'O' and resid 223 through 226 Processing helix chain 'O' and resid 255 through 270 removed outlier: 3.617A pdb=" N VAL O 259 " --> pdb=" O ILE O 255 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN O 260 " --> pdb=" O ALA O 256 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU O 268 " --> pdb=" O LYS O 264 " (cutoff:3.500A) Processing helix chain 'O' and resid 283 through 288 removed outlier: 3.748A pdb=" N ARG O 288 " --> pdb=" O SER O 285 " (cutoff:3.500A) Processing helix chain 'O' and resid 299 through 301 No H-bonds generated for 'chain 'O' and resid 299 through 301' Processing helix chain 'O' and resid 319 through 334 Processing helix chain 'J' and resid 22 through 32 removed outlier: 3.900A pdb=" N ARG J 26 " --> pdb=" O SER J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 57 Processing helix chain 'J' and resid 67 through 80 removed outlier: 3.563A pdb=" N TYR J 72 " --> pdb=" O PHE J 68 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS J 79 " --> pdb=" O ILE J 75 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN J 80 " --> pdb=" O LYS J 76 " (cutoff:3.500A) Processing helix chain 'J' and resid 134 through 149 removed outlier: 3.519A pdb=" N LYS J 144 " --> pdb=" O ALA J 140 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU J 149 " --> pdb=" O ARG J 145 " (cutoff:3.500A) Processing helix chain 'J' and resid 156 through 172 removed outlier: 3.708A pdb=" N ASN J 162 " --> pdb=" O ILE J 158 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA J 163 " --> pdb=" O ALA J 159 " (cutoff:3.500A) Proline residue: J 166 - end of helix Processing helix chain 'J' and resid 173 through 176 Processing helix chain 'J' and resid 267 through 275 removed outlier: 3.824A pdb=" N ILE J 273 " --> pdb=" O GLU J 269 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU J 274 " --> pdb=" O LEU J 270 " (cutoff:3.500A) Processing helix chain 'J' and resid 286 through 294 Processing helix chain 'J' and resid 303 through 325 removed outlier: 3.852A pdb=" N LEU J 307 " --> pdb=" O ASN J 303 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL J 310 " --> pdb=" O GLY J 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 32 removed outlier: 3.899A pdb=" N ARG B 26 " --> pdb=" O SER B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 57 Processing helix chain 'B' and resid 67 through 80 removed outlier: 3.563A pdb=" N TYR B 72 " --> pdb=" O PHE B 68 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS B 79 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN B 80 " --> pdb=" O LYS B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 149 removed outlier: 3.519A pdb=" N LYS B 144 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU B 149 " --> pdb=" O ARG B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 172 removed outlier: 3.707A pdb=" N ASN B 162 " --> pdb=" O ILE B 158 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA B 163 " --> pdb=" O ALA B 159 " (cutoff:3.500A) Proline residue: B 166 - end of helix Processing helix chain 'B' and resid 173 through 176 Processing helix chain 'B' and resid 267 through 275 removed outlier: 3.824A pdb=" N ILE B 273 " --> pdb=" O GLU B 269 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU B 274 " --> pdb=" O LEU B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 294 Processing helix chain 'B' and resid 303 through 325 removed outlier: 3.852A pdb=" N LEU B 307 " --> pdb=" O ASN B 303 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL B 310 " --> pdb=" O GLY B 306 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 32 removed outlier: 3.900A pdb=" N ARG G 26 " --> pdb=" O SER G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 57 Processing helix chain 'G' and resid 67 through 80 removed outlier: 3.563A pdb=" N TYR G 72 " --> pdb=" O PHE G 68 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS G 79 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN G 80 " --> pdb=" O LYS G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 149 removed outlier: 3.519A pdb=" N LYS G 144 " --> pdb=" O ALA G 140 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU G 149 " --> pdb=" O ARG G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 156 through 172 removed outlier: 3.708A pdb=" N ASN G 162 " --> pdb=" O ILE G 158 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA G 163 " --> pdb=" O ALA G 159 " (cutoff:3.500A) Proline residue: G 166 - end of helix Processing helix chain 'G' and resid 173 through 176 Processing helix chain 'G' and resid 267 through 275 removed outlier: 3.824A pdb=" N ILE G 273 " --> pdb=" O GLU G 269 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU G 274 " --> pdb=" O LEU G 270 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 294 Processing helix chain 'G' and resid 303 through 325 removed outlier: 3.851A pdb=" N LEU G 307 " --> pdb=" O ASN G 303 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL G 310 " --> pdb=" O GLY G 306 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 32 removed outlier: 3.900A pdb=" N ARG L 26 " --> pdb=" O SER L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 57 Processing helix chain 'L' and resid 67 through 80 removed outlier: 3.563A pdb=" N TYR L 72 " --> pdb=" O PHE L 68 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS L 79 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN L 80 " --> pdb=" O LYS L 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 149 removed outlier: 3.519A pdb=" N LYS L 144 " --> pdb=" O ALA L 140 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU L 149 " --> pdb=" O ARG L 145 " (cutoff:3.500A) Processing helix chain 'L' and resid 156 through 172 removed outlier: 3.708A pdb=" N ASN L 162 " --> pdb=" O ILE L 158 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA L 163 " --> pdb=" O ALA L 159 " (cutoff:3.500A) Proline residue: L 166 - end of helix Processing helix chain 'L' and resid 173 through 176 Processing helix chain 'L' and resid 267 through 275 removed outlier: 3.824A pdb=" N ILE L 273 " --> pdb=" O GLU L 269 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU L 274 " --> pdb=" O LEU L 270 " (cutoff:3.500A) Processing helix chain 'L' and resid 286 through 294 Processing helix chain 'L' and resid 303 through 325 removed outlier: 3.852A pdb=" N LEU L 307 " --> pdb=" O ASN L 303 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL L 310 " --> pdb=" O GLY L 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 22 removed outlier: 4.057A pdb=" N GLU C 9 " --> pdb=" O GLU C 5 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N CYS C 19 " --> pdb=" O ALA C 15 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP C 20 " --> pdb=" O HIS C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 52 Processing helix chain 'C' and resid 56 through 64 removed outlier: 4.252A pdb=" N ASP C 62 " --> pdb=" O GLN C 58 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 22 removed outlier: 4.057A pdb=" N GLU H 9 " --> pdb=" O GLU H 5 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N CYS H 19 " --> pdb=" O ALA H 15 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP H 20 " --> pdb=" O HIS H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 52 Processing helix chain 'H' and resid 56 through 64 removed outlier: 4.253A pdb=" N ASP H 62 " --> pdb=" O GLN H 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 22 removed outlier: 4.057A pdb=" N GLU M 9 " --> pdb=" O GLU M 5 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N CYS M 19 " --> pdb=" O ALA M 15 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP M 20 " --> pdb=" O HIS M 16 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 52 Processing helix chain 'M' and resid 56 through 64 removed outlier: 4.253A pdb=" N ASP M 62 " --> pdb=" O GLN M 58 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 61 through 63 removed outlier: 9.538A pdb=" N GLU D 30 " --> pdb=" O ALA D 74 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N LYS D 76 " --> pdb=" O GLU D 30 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL D 32 " --> pdb=" O LYS D 76 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL D 78 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE D 34 " --> pdb=" O VAL D 78 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL D 2 " --> pdb=" O GLU D 30 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL D 32 " --> pdb=" O VAL D 2 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N VAL D 4 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE D 34 " --> pdb=" O VAL D 4 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE D 6 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU D 95 " --> pdb=" O ARG D 3 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL D 96 " --> pdb=" O LEU D 121 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N THR D 123 " --> pdb=" O VAL D 96 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N GLU D 98 " --> pdb=" O THR D 123 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 49 through 50 Processing sheet with id=AA3, first strand: chain 'D' and resid 208 through 212 removed outlier: 3.960A pdb=" N THR D 212 " --> pdb=" O GLY D 231 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLY D 231 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN D 174 " --> pdb=" O GLN D 249 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER D 182 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N VAL D 241 " --> pdb=" O SER D 182 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N VAL D 312 " --> pdb=" O ASP D 297 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 208 through 212 removed outlier: 3.960A pdb=" N THR D 212 " --> pdb=" O GLY D 231 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLY D 231 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN D 174 " --> pdb=" O GLN D 249 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER D 182 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N VAL D 241 " --> pdb=" O SER D 182 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 61 through 63 removed outlier: 9.539A pdb=" N GLU A 30 " --> pdb=" O ALA A 74 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N LYS A 76 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL A 32 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N VAL A 78 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE A 34 " --> pdb=" O VAL A 78 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL A 2 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL A 32 " --> pdb=" O VAL A 2 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL A 4 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ILE A 34 " --> pdb=" O VAL A 4 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE A 6 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 95 " --> pdb=" O ARG A 3 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL A 96 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N THR A 123 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N GLU A 98 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 49 through 50 Processing sheet with id=AA7, first strand: chain 'A' and resid 208 through 212 removed outlier: 3.959A pdb=" N THR A 212 " --> pdb=" O GLY A 231 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLY A 231 " --> pdb=" O THR A 212 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN A 174 " --> pdb=" O GLN A 249 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER A 182 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL A 241 " --> pdb=" O SER A 182 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N VAL A 312 " --> pdb=" O ASP A 297 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 208 through 212 removed outlier: 3.959A pdb=" N THR A 212 " --> pdb=" O GLY A 231 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLY A 231 " --> pdb=" O THR A 212 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN A 174 " --> pdb=" O GLN A 249 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER A 182 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL A 241 " --> pdb=" O SER A 182 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 61 through 63 removed outlier: 9.539A pdb=" N GLU E 30 " --> pdb=" O ALA E 74 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N LYS E 76 " --> pdb=" O GLU E 30 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL E 32 " --> pdb=" O LYS E 76 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N VAL E 78 " --> pdb=" O VAL E 32 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE E 34 " --> pdb=" O VAL E 78 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL E 2 " --> pdb=" O GLU E 30 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL E 32 " --> pdb=" O VAL E 2 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL E 4 " --> pdb=" O VAL E 32 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE E 34 " --> pdb=" O VAL E 4 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE E 6 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU E 95 " --> pdb=" O ARG E 3 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL E 96 " --> pdb=" O LEU E 121 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N THR E 123 " --> pdb=" O VAL E 96 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N GLU E 98 " --> pdb=" O THR E 123 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 49 through 50 Processing sheet with id=AB2, first strand: chain 'E' and resid 208 through 212 removed outlier: 3.959A pdb=" N THR E 212 " --> pdb=" O GLY E 231 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLY E 231 " --> pdb=" O THR E 212 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN E 174 " --> pdb=" O GLN E 249 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER E 182 " --> pdb=" O VAL E 241 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL E 241 " --> pdb=" O SER E 182 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N VAL E 312 " --> pdb=" O ASP E 297 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 208 through 212 removed outlier: 3.959A pdb=" N THR E 212 " --> pdb=" O GLY E 231 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLY E 231 " --> pdb=" O THR E 212 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN E 174 " --> pdb=" O GLN E 249 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER E 182 " --> pdb=" O VAL E 241 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL E 241 " --> pdb=" O SER E 182 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 61 through 63 removed outlier: 9.539A pdb=" N GLU F 30 " --> pdb=" O ALA F 74 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N LYS F 76 " --> pdb=" O GLU F 30 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL F 32 " --> pdb=" O LYS F 76 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL F 78 " --> pdb=" O VAL F 32 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE F 34 " --> pdb=" O VAL F 78 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL F 2 " --> pdb=" O GLU F 30 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL F 32 " --> pdb=" O VAL F 2 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N VAL F 4 " --> pdb=" O VAL F 32 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE F 34 " --> pdb=" O VAL F 4 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE F 6 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU F 95 " --> pdb=" O ARG F 3 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL F 96 " --> pdb=" O LEU F 121 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N THR F 123 " --> pdb=" O VAL F 96 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N GLU F 98 " --> pdb=" O THR F 123 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 49 through 50 Processing sheet with id=AB6, first strand: chain 'F' and resid 208 through 212 removed outlier: 3.959A pdb=" N THR F 212 " --> pdb=" O GLY F 231 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLY F 231 " --> pdb=" O THR F 212 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN F 174 " --> pdb=" O GLN F 249 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER F 182 " --> pdb=" O VAL F 241 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N VAL F 241 " --> pdb=" O SER F 182 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N VAL F 312 " --> pdb=" O ASP F 297 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 208 through 212 removed outlier: 3.959A pdb=" N THR F 212 " --> pdb=" O GLY F 231 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLY F 231 " --> pdb=" O THR F 212 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN F 174 " --> pdb=" O GLN F 249 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER F 182 " --> pdb=" O VAL F 241 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N VAL F 241 " --> pdb=" O SER F 182 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 61 through 63 removed outlier: 9.539A pdb=" N GLU I 30 " --> pdb=" O ALA I 74 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N LYS I 76 " --> pdb=" O GLU I 30 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL I 32 " --> pdb=" O LYS I 76 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N VAL I 78 " --> pdb=" O VAL I 32 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE I 34 " --> pdb=" O VAL I 78 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL I 2 " --> pdb=" O GLU I 30 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL I 32 " --> pdb=" O VAL I 2 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL I 4 " --> pdb=" O VAL I 32 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE I 34 " --> pdb=" O VAL I 4 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE I 6 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU I 95 " --> pdb=" O ARG I 3 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL I 96 " --> pdb=" O LEU I 121 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N THR I 123 " --> pdb=" O VAL I 96 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N GLU I 98 " --> pdb=" O THR I 123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 49 through 50 Processing sheet with id=AC1, first strand: chain 'I' and resid 208 through 212 removed outlier: 3.958A pdb=" N THR I 212 " --> pdb=" O GLY I 231 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLY I 231 " --> pdb=" O THR I 212 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN I 174 " --> pdb=" O GLN I 249 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER I 182 " --> pdb=" O VAL I 241 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N VAL I 241 " --> pdb=" O SER I 182 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N VAL I 312 " --> pdb=" O ASP I 297 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 208 through 212 removed outlier: 3.958A pdb=" N THR I 212 " --> pdb=" O GLY I 231 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLY I 231 " --> pdb=" O THR I 212 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN I 174 " --> pdb=" O GLN I 249 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER I 182 " --> pdb=" O VAL I 241 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N VAL I 241 " --> pdb=" O SER I 182 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 61 through 63 removed outlier: 9.538A pdb=" N GLU K 30 " --> pdb=" O ALA K 74 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N LYS K 76 " --> pdb=" O GLU K 30 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL K 32 " --> pdb=" O LYS K 76 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL K 78 " --> pdb=" O VAL K 32 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE K 34 " --> pdb=" O VAL K 78 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL K 2 " --> pdb=" O GLU K 30 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL K 32 " --> pdb=" O VAL K 2 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL K 4 " --> pdb=" O VAL K 32 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ILE K 34 " --> pdb=" O VAL K 4 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE K 6 " --> pdb=" O ILE K 34 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU K 95 " --> pdb=" O ARG K 3 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL K 96 " --> pdb=" O LEU K 121 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N THR K 123 " --> pdb=" O VAL K 96 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N GLU K 98 " --> pdb=" O THR K 123 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 49 through 50 Processing sheet with id=AC5, first strand: chain 'K' and resid 208 through 212 removed outlier: 3.959A pdb=" N THR K 212 " --> pdb=" O GLY K 231 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLY K 231 " --> pdb=" O THR K 212 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN K 174 " --> pdb=" O GLN K 249 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER K 182 " --> pdb=" O VAL K 241 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N VAL K 241 " --> pdb=" O SER K 182 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N VAL K 312 " --> pdb=" O ASP K 297 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 208 through 212 removed outlier: 3.959A pdb=" N THR K 212 " --> pdb=" O GLY K 231 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLY K 231 " --> pdb=" O THR K 212 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN K 174 " --> pdb=" O GLN K 249 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER K 182 " --> pdb=" O VAL K 241 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N VAL K 241 " --> pdb=" O SER K 182 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'N' and resid 61 through 63 removed outlier: 9.539A pdb=" N GLU N 30 " --> pdb=" O ALA N 74 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N LYS N 76 " --> pdb=" O GLU N 30 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL N 32 " --> pdb=" O LYS N 76 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL N 78 " --> pdb=" O VAL N 32 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE N 34 " --> pdb=" O VAL N 78 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N VAL N 2 " --> pdb=" O GLU N 30 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL N 32 " --> pdb=" O VAL N 2 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL N 4 " --> pdb=" O VAL N 32 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE N 34 " --> pdb=" O VAL N 4 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE N 6 " --> pdb=" O ILE N 34 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU N 95 " --> pdb=" O ARG N 3 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL N 96 " --> pdb=" O LEU N 121 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N THR N 123 " --> pdb=" O VAL N 96 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N GLU N 98 " --> pdb=" O THR N 123 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 49 through 50 Processing sheet with id=AC9, first strand: chain 'N' and resid 208 through 212 removed outlier: 3.959A pdb=" N THR N 212 " --> pdb=" O GLY N 231 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLY N 231 " --> pdb=" O THR N 212 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN N 174 " --> pdb=" O GLN N 249 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER N 182 " --> pdb=" O VAL N 241 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL N 241 " --> pdb=" O SER N 182 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N VAL N 312 " --> pdb=" O ASP N 297 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 208 through 212 removed outlier: 3.959A pdb=" N THR N 212 " --> pdb=" O GLY N 231 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLY N 231 " --> pdb=" O THR N 212 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN N 174 " --> pdb=" O GLN N 249 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER N 182 " --> pdb=" O VAL N 241 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL N 241 " --> pdb=" O SER N 182 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 61 through 63 removed outlier: 9.539A pdb=" N GLU O 30 " --> pdb=" O ALA O 74 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N LYS O 76 " --> pdb=" O GLU O 30 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL O 32 " --> pdb=" O LYS O 76 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL O 78 " --> pdb=" O VAL O 32 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE O 34 " --> pdb=" O VAL O 78 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL O 2 " --> pdb=" O GLU O 30 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL O 32 " --> pdb=" O VAL O 2 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N VAL O 4 " --> pdb=" O VAL O 32 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ILE O 34 " --> pdb=" O VAL O 4 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE O 6 " --> pdb=" O ILE O 34 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU O 95 " --> pdb=" O ARG O 3 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL O 96 " --> pdb=" O LEU O 121 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N THR O 123 " --> pdb=" O VAL O 96 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N GLU O 98 " --> pdb=" O THR O 123 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 49 through 50 Processing sheet with id=AD4, first strand: chain 'O' and resid 208 through 212 removed outlier: 3.959A pdb=" N THR O 212 " --> pdb=" O GLY O 231 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLY O 231 " --> pdb=" O THR O 212 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN O 174 " --> pdb=" O GLN O 249 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER O 182 " --> pdb=" O VAL O 241 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N VAL O 241 " --> pdb=" O SER O 182 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N VAL O 312 " --> pdb=" O ASP O 297 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'O' and resid 208 through 212 removed outlier: 3.959A pdb=" N THR O 212 " --> pdb=" O GLY O 231 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLY O 231 " --> pdb=" O THR O 212 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN O 174 " --> pdb=" O GLN O 249 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER O 182 " --> pdb=" O VAL O 241 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N VAL O 241 " --> pdb=" O SER O 182 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 37 through 38 removed outlier: 3.531A pdb=" N VAL J 181 " --> pdb=" O SER J 128 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU J 258 " --> pdb=" O MET J 204 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN J 206 " --> pdb=" O SER J 256 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 84 through 89 removed outlier: 6.528A pdb=" N ILE J 84 " --> pdb=" O LYS J 101 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LYS J 101 " --> pdb=" O ILE J 84 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LYS J 86 " --> pdb=" O PRO J 99 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE J 88 " --> pdb=" O ASP J 97 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 217 through 218 Processing sheet with id=AD9, first strand: chain 'J' and resid 223 through 231 Processing sheet with id=AE1, first strand: chain 'B' and resid 37 through 38 removed outlier: 3.532A pdb=" N VAL B 181 " --> pdb=" O SER B 128 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU B 258 " --> pdb=" O MET B 204 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN B 206 " --> pdb=" O SER B 256 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 84 through 89 removed outlier: 6.528A pdb=" N ILE B 84 " --> pdb=" O LYS B 101 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LYS B 101 " --> pdb=" O ILE B 84 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LYS B 86 " --> pdb=" O PRO B 99 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE B 88 " --> pdb=" O ASP B 97 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 217 through 218 Processing sheet with id=AE4, first strand: chain 'B' and resid 223 through 231 Processing sheet with id=AE5, first strand: chain 'G' and resid 37 through 38 removed outlier: 3.532A pdb=" N VAL G 181 " --> pdb=" O SER G 128 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU G 258 " --> pdb=" O MET G 204 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN G 206 " --> pdb=" O SER G 256 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 84 through 89 removed outlier: 6.527A pdb=" N ILE G 84 " --> pdb=" O LYS G 101 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LYS G 101 " --> pdb=" O ILE G 84 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LYS G 86 " --> pdb=" O PRO G 99 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE G 88 " --> pdb=" O ASP G 97 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 217 through 218 Processing sheet with id=AE8, first strand: chain 'L' and resid 37 through 38 removed outlier: 3.532A pdb=" N VAL L 181 " --> pdb=" O SER L 128 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU L 258 " --> pdb=" O MET L 204 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN L 206 " --> pdb=" O SER L 256 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 84 through 89 removed outlier: 6.528A pdb=" N ILE L 84 " --> pdb=" O LYS L 101 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LYS L 101 " --> pdb=" O ILE L 84 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N LYS L 86 " --> pdb=" O PRO L 99 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE L 88 " --> pdb=" O ASP L 97 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 217 through 218 1612 hydrogen bonds defined for protein. 4500 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: 20.14 Time building geometry restraints manager: 9.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10572 1.33 - 1.45: 5793 1.45 - 1.57: 17411 1.57 - 1.69: 32 1.69 - 1.81: 288 Bond restraints: 34096 Sorted by residual: bond pdb=" O3 NAD K1001 " pdb=" PA NAD K1001 " ideal model delta sigma weight residual 1.653 1.593 0.060 2.00e-02 2.50e+03 8.91e+00 bond pdb=" O3 NAD N1001 " pdb=" PA NAD N1001 " ideal model delta sigma weight residual 1.653 1.594 0.059 2.00e-02 2.50e+03 8.85e+00 bond pdb=" O3 NAD I1001 " pdb=" PA NAD I1001 " ideal model delta sigma weight residual 1.653 1.594 0.059 2.00e-02 2.50e+03 8.85e+00 bond pdb=" O3 NAD A1001 " pdb=" PA NAD A1001 " ideal model delta sigma weight residual 1.653 1.594 0.059 2.00e-02 2.50e+03 8.82e+00 bond pdb=" O3 NAD D1001 " pdb=" PA NAD D1001 " ideal model delta sigma weight residual 1.653 1.594 0.059 2.00e-02 2.50e+03 8.81e+00 ... (remaining 34091 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 44141 2.10 - 4.21: 1853 4.21 - 6.31: 286 6.31 - 8.41: 36 8.41 - 10.51: 12 Bond angle restraints: 46328 Sorted by residual: angle pdb=" C TYR J 154 " pdb=" N GLU J 155 " pdb=" CA GLU J 155 " ideal model delta sigma weight residual 121.54 132.05 -10.51 1.91e+00 2.74e-01 3.03e+01 angle pdb=" C TYR G 154 " pdb=" N GLU G 155 " pdb=" CA GLU G 155 " ideal model delta sigma weight residual 121.54 132.03 -10.49 1.91e+00 2.74e-01 3.02e+01 angle pdb=" C TYR B 154 " pdb=" N GLU B 155 " pdb=" CA GLU B 155 " ideal model delta sigma weight residual 121.54 132.00 -10.46 1.91e+00 2.74e-01 3.00e+01 angle pdb=" C TYR L 154 " pdb=" N GLU L 155 " pdb=" CA GLU L 155 " ideal model delta sigma weight residual 121.54 131.99 -10.45 1.91e+00 2.74e-01 2.99e+01 angle pdb=" C LEU L 218 " pdb=" N PHE L 219 " pdb=" CA PHE L 219 " ideal model delta sigma weight residual 121.54 129.55 -8.01 1.91e+00 2.74e-01 1.76e+01 ... (remaining 46323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.12: 19373 15.12 - 30.24: 1075 30.24 - 45.35: 196 45.35 - 60.47: 48 60.47 - 75.59: 12 Dihedral angle restraints: 20704 sinusoidal: 8380 harmonic: 12324 Sorted by residual: dihedral pdb=" CA ARG J 165 " pdb=" C ARG J 165 " pdb=" N PRO J 166 " pdb=" CA PRO J 166 " ideal model delta harmonic sigma weight residual -180.00 -154.65 -25.35 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA ARG L 165 " pdb=" C ARG L 165 " pdb=" N PRO L 166 " pdb=" CA PRO L 166 " ideal model delta harmonic sigma weight residual -180.00 -154.66 -25.34 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA ARG G 165 " pdb=" C ARG G 165 " pdb=" N PRO G 166 " pdb=" CA PRO G 166 " ideal model delta harmonic sigma weight residual -180.00 -154.70 -25.30 0 5.00e+00 4.00e-02 2.56e+01 ... (remaining 20701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 4093 0.073 - 0.146: 988 0.146 - 0.218: 99 0.218 - 0.291: 28 0.291 - 0.364: 12 Chirality restraints: 5220 Sorted by residual: chirality pdb=" CB ILE K 148 " pdb=" CA ILE K 148 " pdb=" CG1 ILE K 148 " pdb=" CG2 ILE K 148 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CB ILE F 148 " pdb=" CA ILE F 148 " pdb=" CG1 ILE F 148 " pdb=" CG2 ILE F 148 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CB ILE N 148 " pdb=" CA ILE N 148 " pdb=" CG1 ILE N 148 " pdb=" CG2 ILE N 148 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.27e+00 ... (remaining 5217 not shown) Planarity restraints: 5980 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1D NAD E1001 " -0.013 2.00e-02 2.50e+03 2.63e-02 1.38e+01 pdb=" C2N NAD E1001 " 0.049 2.00e-02 2.50e+03 pdb=" C3N NAD E1001 " 0.006 2.00e-02 2.50e+03 pdb=" C4N NAD E1001 " 0.025 2.00e-02 2.50e+03 pdb=" C5N NAD E1001 " -0.003 2.00e-02 2.50e+03 pdb=" C6N NAD E1001 " -0.027 2.00e-02 2.50e+03 pdb=" C7N NAD E1001 " -0.039 2.00e-02 2.50e+03 pdb=" N1N NAD E1001 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAD A1001 " -0.013 2.00e-02 2.50e+03 2.63e-02 1.38e+01 pdb=" C2N NAD A1001 " 0.049 2.00e-02 2.50e+03 pdb=" C3N NAD A1001 " 0.006 2.00e-02 2.50e+03 pdb=" C4N NAD A1001 " 0.025 2.00e-02 2.50e+03 pdb=" C5N NAD A1001 " -0.003 2.00e-02 2.50e+03 pdb=" C6N NAD A1001 " -0.027 2.00e-02 2.50e+03 pdb=" C7N NAD A1001 " -0.039 2.00e-02 2.50e+03 pdb=" N1N NAD A1001 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAD K1001 " -0.013 2.00e-02 2.50e+03 2.63e-02 1.38e+01 pdb=" C2N NAD K1001 " 0.049 2.00e-02 2.50e+03 pdb=" C3N NAD K1001 " 0.006 2.00e-02 2.50e+03 pdb=" C4N NAD K1001 " 0.025 2.00e-02 2.50e+03 pdb=" C5N NAD K1001 " -0.003 2.00e-02 2.50e+03 pdb=" C6N NAD K1001 " -0.027 2.00e-02 2.50e+03 pdb=" C7N NAD K1001 " -0.039 2.00e-02 2.50e+03 pdb=" N1N NAD K1001 " 0.003 2.00e-02 2.50e+03 ... (remaining 5977 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 434 2.60 - 3.17: 28248 3.17 - 3.75: 53420 3.75 - 4.32: 73497 4.32 - 4.90: 119956 Nonbonded interactions: 275555 Sorted by model distance: nonbonded pdb=" SG CYS J 230 " pdb=" SG CYS J 236 " model vdw 2.020 3.760 nonbonded pdb=" SG CYS G 230 " pdb=" SG CYS G 236 " model vdw 2.020 3.760 nonbonded pdb=" SG CYS L 230 " pdb=" SG CYS L 236 " model vdw 2.020 3.760 nonbonded pdb=" SG CYS B 230 " pdb=" SG CYS B 236 " model vdw 2.021 3.760 nonbonded pdb=" SG CYS C 61 " pdb=" SG CYS C 70 " model vdw 2.022 3.760 ... (remaining 275550 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: 0.26 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'M' selection = chain 'P' } ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'D' selection = chain 'F' selection = chain 'I' selection = chain 'K' selection = chain 'O' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.190 Check model and map are aligned: 0.250 Set scattering table: 0.290 Process input model: 78.590 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.480 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:4.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 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 : 0.010 0.067 34096 Z= 0.442 Angle : 0.986 10.513 46328 Z= 0.530 Chirality : 0.064 0.364 5220 Planarity : 0.008 0.077 5980 Dihedral : 10.439 75.588 12784 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.11 % Allowed : 3.19 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -3.72 (0.10), residues: 4240 helix: -2.67 (0.10), residues: 1412 sheet: -2.27 (0.15), residues: 896 loop : -2.26 (0.12), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP J 227 HIS 0.011 0.003 HIS B 295 PHE 0.022 0.003 PHE D 9 TYR 0.027 0.003 TYR D 315 ARG 0.009 0.002 ARG G 50 Details of bonding type rmsd hydrogen bonds : bond 0.18602 ( 1404) hydrogen bonds : angle 8.61916 ( 4500) covalent geometry : bond 0.00952 (34096) covalent geometry : angle 0.98630 (46328) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1010 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 1006 time to evaluate : 3.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 46 GLN cc_start: 0.8488 (tp40) cc_final: 0.8199 (tp-100) REVERT: P 55 THR cc_start: 0.6559 (p) cc_final: 0.6336 (p) REVERT: D 133 TYR cc_start: 0.7991 (m-80) cc_final: 0.7737 (m-80) REVERT: D 173 GLN cc_start: 0.8513 (mt0) cc_final: 0.8058 (mp10) REVERT: D 174 GLN cc_start: 0.8065 (mm-40) cc_final: 0.7837 (mt0) REVERT: D 177 MET cc_start: 0.8419 (ppp) cc_final: 0.8106 (ttp) REVERT: D 179 THR cc_start: 0.8018 (t) cc_final: 0.7752 (t) REVERT: D 238 THR cc_start: 0.9143 (p) cc_final: 0.8715 (t) REVERT: D 249 GLN cc_start: 0.7833 (tt0) cc_final: 0.7269 (tt0) REVERT: D 261 GLN cc_start: 0.8956 (tp40) cc_final: 0.8735 (tp40) REVERT: D 286 ASP cc_start: 0.8199 (m-30) cc_final: 0.7469 (m-30) REVERT: D 295 ILE cc_start: 0.9289 (mp) cc_final: 0.8840 (mm) REVERT: A 85 ASN cc_start: 0.9007 (m-40) cc_final: 0.8713 (m110) REVERT: A 147 ASP cc_start: 0.8429 (p0) cc_final: 0.8102 (p0) REVERT: A 176 MET cc_start: 0.8644 (mmt) cc_final: 0.8307 (mmt) REVERT: A 177 MET cc_start: 0.9024 (ppp) cc_final: 0.8705 (ppp) REVERT: A 225 LEU cc_start: 0.9202 (mt) cc_final: 0.8982 (tp) REVERT: A 271 MET cc_start: 0.7575 (mmt) cc_final: 0.7209 (mmp) REVERT: A 302 MET cc_start: 0.7533 (ptp) cc_final: 0.6180 (ptp) REVERT: A 323 GLN cc_start: 0.9434 (mm-40) cc_final: 0.8925 (mt0) REVERT: A 331 HIS cc_start: 0.8489 (t70) cc_final: 0.8188 (t-90) REVERT: E 133 TYR cc_start: 0.8229 (m-80) cc_final: 0.8021 (m-80) REVERT: E 173 GLN cc_start: 0.8704 (mt0) cc_final: 0.8371 (mp10) REVERT: E 179 THR cc_start: 0.7981 (t) cc_final: 0.7757 (t) REVERT: E 182 SER cc_start: 0.9270 (p) cc_final: 0.8970 (t) REVERT: E 188 ARG cc_start: 0.8049 (mmm-85) cc_final: 0.7626 (mmm-85) REVERT: E 238 THR cc_start: 0.9060 (p) cc_final: 0.8586 (t) REVERT: E 249 GLN cc_start: 0.7698 (tt0) cc_final: 0.7433 (tt0) REVERT: E 286 ASP cc_start: 0.8372 (m-30) cc_final: 0.7948 (m-30) REVERT: F 17 MET cc_start: 0.8857 (tpt) cc_final: 0.8587 (tpt) REVERT: F 20 TRP cc_start: 0.8703 (t60) cc_final: 0.7961 (t60) REVERT: F 67 CYS cc_start: 0.8517 (m) cc_final: 0.7953 (p) REVERT: F 69 TYR cc_start: 0.8545 (m-80) cc_final: 0.8323 (m-80) REVERT: F 129 ASN cc_start: 0.8249 (m-40) cc_final: 0.7753 (p0) REVERT: F 176 MET cc_start: 0.8886 (mmt) cc_final: 0.7736 (mmt) REVERT: F 177 MET cc_start: 0.9187 (ppp) cc_final: 0.8706 (ppp) REVERT: F 284 SER cc_start: 0.8633 (p) cc_final: 0.8368 (p) REVERT: F 302 MET cc_start: 0.7437 (ptp) cc_final: 0.6977 (ptp) REVERT: F 323 GLN cc_start: 0.9307 (mm-40) cc_final: 0.8544 (mt0) REVERT: F 327 ASP cc_start: 0.8893 (m-30) cc_final: 0.8372 (m-30) REVERT: I 86 LEU cc_start: 0.9155 (mt) cc_final: 0.8817 (mt) REVERT: I 133 TYR cc_start: 0.7996 (m-80) cc_final: 0.7486 (m-80) REVERT: I 173 GLN cc_start: 0.8427 (mt0) cc_final: 0.8034 (mp10) REVERT: I 176 MET cc_start: 0.8516 (mmt) cc_final: 0.8248 (mmt) REVERT: I 238 THR cc_start: 0.8844 (p) cc_final: 0.8446 (t) REVERT: I 249 GLN cc_start: 0.7821 (tt0) cc_final: 0.7204 (tt0) REVERT: K 17 MET cc_start: 0.8794 (tpt) cc_final: 0.8426 (tpt) REVERT: K 20 TRP cc_start: 0.8616 (t60) cc_final: 0.7993 (t60) REVERT: K 93 ILE cc_start: 0.8808 (mm) cc_final: 0.8442 (tp) REVERT: K 129 ASN cc_start: 0.8556 (m-40) cc_final: 0.8184 (m-40) REVERT: K 183 TYR cc_start: 0.8956 (p90) cc_final: 0.8471 (p90) REVERT: K 246 PHE cc_start: 0.9048 (t80) cc_final: 0.8684 (t80) REVERT: K 258 GLN cc_start: 0.8960 (tt0) cc_final: 0.8646 (mt0) REVERT: K 302 MET cc_start: 0.7478 (ptp) cc_final: 0.6220 (ptp) REVERT: K 323 GLN cc_start: 0.9273 (mm-40) cc_final: 0.8518 (mt0) REVERT: K 327 ASP cc_start: 0.8789 (m-30) cc_final: 0.8491 (m-30) REVERT: N 43 ASN cc_start: 0.8107 (p0) cc_final: 0.7893 (p0) REVERT: N 55 ILE cc_start: 0.8793 (mt) cc_final: 0.8557 (mt) REVERT: N 142 TYR cc_start: 0.7480 (p90) cc_final: 0.7124 (p90) REVERT: N 179 THR cc_start: 0.7923 (t) cc_final: 0.7707 (t) REVERT: N 238 THR cc_start: 0.9098 (p) cc_final: 0.8687 (t) REVERT: N 286 ASP cc_start: 0.8260 (m-30) cc_final: 0.7844 (m-30) REVERT: N 295 ILE cc_start: 0.9275 (mp) cc_final: 0.8824 (mm) REVERT: O 21 LEU cc_start: 0.9317 (mt) cc_final: 0.8960 (mt) REVERT: O 93 ILE cc_start: 0.8925 (mm) cc_final: 0.8652 (tp) REVERT: O 129 ASN cc_start: 0.8204 (m-40) cc_final: 0.7643 (p0) REVERT: O 159 LEU cc_start: 0.8964 (tp) cc_final: 0.8648 (tp) REVERT: O 176 MET cc_start: 0.8664 (mmt) cc_final: 0.7654 (mmt) REVERT: O 249 GLN cc_start: 0.8640 (tt0) cc_final: 0.8340 (tm-30) REVERT: O 258 GLN cc_start: 0.8777 (tt0) cc_final: 0.8503 (mt0) REVERT: O 323 GLN cc_start: 0.9350 (mm-40) cc_final: 0.8464 (mt0) REVERT: O 327 ASP cc_start: 0.8975 (m-30) cc_final: 0.8548 (m-30) REVERT: O 331 HIS cc_start: 0.8510 (t70) cc_final: 0.8025 (t-90) REVERT: J 309 GLN cc_start: 0.9077 (mt0) cc_final: 0.8681 (mp10) REVERT: B 46 HIS cc_start: 0.7146 (m170) cc_final: 0.6639 (m170) REVERT: B 66 ASN cc_start: 0.7613 (m-40) cc_final: 0.7309 (m-40) REVERT: B 233 LYS cc_start: 0.8918 (mtpp) cc_final: 0.8703 (mmtp) REVERT: B 308 PHE cc_start: 0.9021 (m-10) cc_final: 0.8745 (m-10) REVERT: B 309 GLN cc_start: 0.8896 (mt0) cc_final: 0.8461 (mt0) REVERT: G 46 HIS cc_start: 0.7543 (m170) cc_final: 0.7162 (m170) REVERT: G 66 ASN cc_start: 0.7588 (m-40) cc_final: 0.7159 (m-40) REVERT: G 106 HIS cc_start: 0.7077 (m-70) cc_final: 0.6844 (m170) REVERT: G 116 LEU cc_start: 0.9050 (tp) cc_final: 0.8720 (tp) REVERT: G 127 PHE cc_start: 0.8252 (t80) cc_final: 0.7880 (t80) REVERT: G 309 GLN cc_start: 0.9029 (mt0) cc_final: 0.8708 (mt0) REVERT: L 106 HIS cc_start: 0.7392 (m-70) cc_final: 0.7101 (m170) REVERT: L 116 LEU cc_start: 0.8943 (tp) cc_final: 0.8633 (tp) REVERT: L 204 MET cc_start: 0.7705 (ptm) cc_final: 0.7473 (ptm) REVERT: L 308 PHE cc_start: 0.9096 (m-10) cc_final: 0.8753 (m-10) REVERT: L 309 GLN cc_start: 0.8927 (mt0) cc_final: 0.8296 (mp10) REVERT: C 28 GLN cc_start: 0.8841 (mp-120) cc_final: 0.8617 (mp10) REVERT: C 63 ASP cc_start: 0.6752 (p0) cc_final: 0.6539 (p0) REVERT: H 1 MET cc_start: 0.5974 (ttm) cc_final: 0.5669 (tpp) REVERT: H 28 GLN cc_start: 0.8450 (mp-120) cc_final: 0.8043 (mt0) REVERT: M 28 GLN cc_start: 0.8317 (mp-120) cc_final: 0.7735 (tm-30) REVERT: M 46 GLN cc_start: 0.8524 (tp40) cc_final: 0.8250 (tp40) outliers start: 4 outliers final: 4 residues processed: 1010 average time/residue: 0.4633 time to fit residues: 752.7627 Evaluate side-chains 577 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 573 time to evaluate : 3.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain L residue 182 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 351 optimal weight: 0.9980 chunk 315 optimal weight: 3.9990 chunk 174 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 212 optimal weight: 10.0000 chunk 168 optimal weight: 3.9990 chunk 326 optimal weight: 7.9990 chunk 126 optimal weight: 0.9990 chunk 198 optimal weight: 1.9990 chunk 242 optimal weight: 3.9990 chunk 377 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 16 HIS P 64 ASN D 173 GLN D 181 HIS A 45 HIS A 173 GLN A 181 HIS A 187 GLN A 323 GLN E 45 HIS E 181 HIS F 45 HIS F 181 HIS F 323 GLN I 173 GLN I 181 HIS I 240 ASN K 45 HIS K 173 GLN K 181 HIS K 187 GLN K 290 HIS N 173 GLN ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 181 HIS O 45 HIS O 173 GLN O 181 HIS O 290 HIS O 323 GLN O 331 HIS J 114 HIS ** J 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 184 GLN ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 114 HIS L 184 GLN L 279 ASN C 10 GLN C 64 ASN H 64 ASN M 45 HIS M 64 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.108046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.083432 restraints weight = 86949.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.086124 restraints weight = 46934.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.087798 restraints weight = 31966.494| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 34096 Z= 0.146 Angle : 0.632 8.983 46328 Z= 0.335 Chirality : 0.047 0.197 5220 Planarity : 0.006 0.062 5980 Dihedral : 7.185 58.936 5084 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.54 % Allowed : 10.89 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -2.37 (0.12), residues: 4240 helix: -1.06 (0.12), residues: 1436 sheet: -1.92 (0.16), residues: 880 loop : -1.67 (0.13), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 20 HIS 0.010 0.001 HIS J 46 PHE 0.022 0.002 PHE L 68 TYR 0.021 0.002 TYR O 49 ARG 0.007 0.001 ARG D 81 Details of bonding type rmsd hydrogen bonds : bond 0.03615 ( 1404) hydrogen bonds : angle 5.45728 ( 4500) covalent geometry : bond 0.00317 (34096) covalent geometry : angle 0.63246 (46328) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 825 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 735 time to evaluate : 3.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 1 MET cc_start: 0.7445 (ttm) cc_final: 0.6399 (tpp) REVERT: P 4 LEU cc_start: 0.8822 (tp) cc_final: 0.8510 (mp) REVERT: P 12 ARG cc_start: 0.8509 (ttt180) cc_final: 0.8176 (ttt180) REVERT: P 33 TRP cc_start: 0.7858 (m100) cc_final: 0.7650 (m100) REVERT: P 39 LEU cc_start: 0.8860 (mp) cc_final: 0.8521 (tp) REVERT: P 47 ARG cc_start: 0.8628 (mmm160) cc_final: 0.8065 (mmm160) REVERT: P 50 GLN cc_start: 0.8225 (tm-30) cc_final: 0.7751 (tm-30) REVERT: P 59 GLN cc_start: 0.7743 (mm110) cc_final: 0.7510 (mm110) REVERT: D 249 GLN cc_start: 0.7992 (tt0) cc_final: 0.7438 (tt0) REVERT: D 295 ILE cc_start: 0.9399 (mp) cc_final: 0.9092 (mt) REVERT: A 67 CYS cc_start: 0.7926 (m) cc_final: 0.7674 (t) REVERT: A 147 ASP cc_start: 0.8337 (p0) cc_final: 0.8021 (p0) REVERT: A 176 MET cc_start: 0.7553 (mmt) cc_final: 0.7203 (mmt) REVERT: A 302 MET cc_start: 0.7399 (ptp) cc_final: 0.5590 (ptp) REVERT: A 327 ASP cc_start: 0.8829 (m-30) cc_final: 0.8458 (m-30) REVERT: E 295 ILE cc_start: 0.9423 (OUTLIER) cc_final: 0.9143 (mm) REVERT: E 302 MET cc_start: 0.8209 (ptp) cc_final: 0.8008 (ptp) REVERT: F 1 MET cc_start: 0.7822 (pmm) cc_final: 0.7325 (ptp) REVERT: F 16 PHE cc_start: 0.9074 (t80) cc_final: 0.8831 (t80) REVERT: F 20 TRP cc_start: 0.8270 (t60) cc_final: 0.7890 (t60) REVERT: F 40 PRO cc_start: 0.9129 (Cg_exo) cc_final: 0.8906 (Cg_endo) REVERT: F 49 TYR cc_start: 0.9026 (m-80) cc_final: 0.8649 (m-10) REVERT: F 52 MET cc_start: 0.8056 (mmm) cc_final: 0.7756 (mmm) REVERT: F 65 ASP cc_start: 0.8428 (p0) cc_final: 0.7289 (t0) REVERT: F 66 ASP cc_start: 0.8703 (p0) cc_final: 0.8310 (p0) REVERT: F 93 ILE cc_start: 0.8706 (mm) cc_final: 0.8419 (tp) REVERT: F 176 MET cc_start: 0.8043 (mmt) cc_final: 0.7145 (mmt) REVERT: F 284 SER cc_start: 0.9240 (p) cc_final: 0.8643 (m) REVERT: F 302 MET cc_start: 0.7415 (ptp) cc_final: 0.5850 (ptp) REVERT: F 323 GLN cc_start: 0.8955 (mm110) cc_final: 0.8668 (mm-40) REVERT: F 327 ASP cc_start: 0.8614 (m-30) cc_final: 0.8323 (m-30) REVERT: I 295 ILE cc_start: 0.9404 (OUTLIER) cc_final: 0.9116 (mm) REVERT: K 20 TRP cc_start: 0.8242 (t60) cc_final: 0.7927 (t60) REVERT: K 22 GLN cc_start: 0.9089 (mt0) cc_final: 0.8837 (tt0) REVERT: K 49 TYR cc_start: 0.8688 (m-80) cc_final: 0.8366 (m-10) REVERT: K 65 ASP cc_start: 0.8407 (p0) cc_final: 0.7301 (t0) REVERT: K 176 MET cc_start: 0.7674 (mmt) cc_final: 0.7243 (mmt) REVERT: K 302 MET cc_start: 0.7168 (ptp) cc_final: 0.6007 (ptp) REVERT: N 142 TYR cc_start: 0.7179 (p90) cc_final: 0.6845 (p90) REVERT: N 196 ASP cc_start: 0.8732 (t0) cc_final: 0.8490 (t0) REVERT: N 205 MET cc_start: 0.8236 (mtp) cc_final: 0.7944 (mtp) REVERT: N 240 ASN cc_start: 0.8089 (t0) cc_final: 0.7439 (t0) REVERT: N 249 GLN cc_start: 0.7982 (tt0) cc_final: 0.7627 (tt0) REVERT: N 295 ILE cc_start: 0.9380 (mp) cc_final: 0.9015 (mt) REVERT: O 20 TRP cc_start: 0.8241 (t60) cc_final: 0.7621 (t60) REVERT: O 65 ASP cc_start: 0.8480 (p0) cc_final: 0.7402 (t0) REVERT: O 159 LEU cc_start: 0.8943 (tp) cc_final: 0.8500 (tp) REVERT: O 174 GLN cc_start: 0.7988 (mm110) cc_final: 0.7383 (mm110) REVERT: O 176 MET cc_start: 0.7356 (mmt) cc_final: 0.6736 (mmt) REVERT: O 323 GLN cc_start: 0.8961 (mm110) cc_final: 0.8612 (mt0) REVERT: O 327 ASP cc_start: 0.9023 (m-30) cc_final: 0.8628 (m-30) REVERT: J 46 HIS cc_start: 0.7664 (m170) cc_final: 0.7352 (m170) REVERT: B 45 TYR cc_start: 0.7516 (m-80) cc_final: 0.7152 (m-80) REVERT: B 46 HIS cc_start: 0.7226 (m170) cc_final: 0.6667 (m170) REVERT: B 116 LEU cc_start: 0.9024 (tp) cc_final: 0.8741 (tt) REVERT: B 279 ASN cc_start: 0.8572 (OUTLIER) cc_final: 0.8304 (t0) REVERT: G 127 PHE cc_start: 0.8101 (t80) cc_final: 0.7521 (t80) REVERT: G 193 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7964 (tm-30) REVERT: L 127 PHE cc_start: 0.7761 (t80) cc_final: 0.7558 (t80) REVERT: L 204 MET cc_start: 0.8722 (ptm) cc_final: 0.8434 (ptm) REVERT: L 279 ASN cc_start: 0.8682 (OUTLIER) cc_final: 0.8212 (t0) REVERT: L 308 PHE cc_start: 0.8967 (m-10) cc_final: 0.8688 (m-10) REVERT: L 309 GLN cc_start: 0.8822 (mt0) cc_final: 0.8324 (mp10) REVERT: C 6 LYS cc_start: 0.8512 (mtmm) cc_final: 0.8245 (ptpp) REVERT: C 28 GLN cc_start: 0.9105 (mp-120) cc_final: 0.8847 (mp10) REVERT: C 54 LYS cc_start: 0.6896 (pmmt) cc_final: 0.6169 (tptp) REVERT: C 63 ASP cc_start: 0.7877 (p0) cc_final: 0.7583 (p0) REVERT: H 1 MET cc_start: 0.7152 (ttm) cc_final: 0.6573 (tpp) REVERT: H 28 GLN cc_start: 0.8720 (mp-120) cc_final: 0.8433 (mt0) REVERT: M 12 ARG cc_start: 0.8784 (ttt180) cc_final: 0.8558 (ttt180) REVERT: M 28 GLN cc_start: 0.8814 (mp-120) cc_final: 0.7947 (pp30) REVERT: M 38 GLU cc_start: 0.9142 (mm-30) cc_final: 0.8838 (mm-30) REVERT: M 42 GLU cc_start: 0.8821 (mm-30) cc_final: 0.8466 (mm-30) REVERT: M 46 GLN cc_start: 0.8439 (tp40) cc_final: 0.7957 (pt0) REVERT: M 47 ARG cc_start: 0.8773 (mmm160) cc_final: 0.8342 (mmm160) REVERT: M 50 GLN cc_start: 0.8731 (tm-30) cc_final: 0.8431 (tm-30) REVERT: M 54 LYS cc_start: 0.7184 (pmmt) cc_final: 0.6723 (tptp) outliers start: 90 outliers final: 60 residues processed: 798 average time/residue: 0.4133 time to fit residues: 554.6770 Evaluate side-chains 631 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 567 time to evaluate : 3.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 295 ILE Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 228 LYS Chi-restraints excluded: chain I residue 245 ASP Chi-restraints excluded: chain I residue 295 ILE Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 85 ASN Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 290 HIS Chi-restraints excluded: chain N residue 4 VAL Chi-restraints excluded: chain N residue 155 THR Chi-restraints excluded: chain N residue 208 VAL Chi-restraints excluded: chain N residue 282 LEU Chi-restraints excluded: chain O residue 85 ASN Chi-restraints excluded: chain O residue 193 SER Chi-restraints excluded: chain O residue 245 ASP Chi-restraints excluded: chain O residue 284 SER Chi-restraints excluded: chain O residue 290 HIS Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 225 ILE Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 224 THR Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 292 LEU Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 182 VAL Chi-restraints excluded: chain L residue 225 ILE Chi-restraints excluded: chain L residue 279 ASN Chi-restraints excluded: chain L residue 292 LEU Chi-restraints excluded: chain C residue 8 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 343 optimal weight: 0.6980 chunk 215 optimal weight: 8.9990 chunk 134 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 194 optimal weight: 0.0770 chunk 69 optimal weight: 10.0000 chunk 340 optimal weight: 0.0870 chunk 174 optimal weight: 2.9990 chunk 412 optimal weight: 9.9990 chunk 221 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 overall best weight: 0.9718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 16 HIS ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 7 ASN ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 45 HIS I 129 ASN ** I 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 240 ASN K 15 ASN K 258 GLN ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 173 GLN O 187 GLN J 184 GLN ** J 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 309 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 GLN G 184 GLN ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 279 ASN G 309 GLN ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 279 ASN L 295 HIS M 59 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.108382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.084135 restraints weight = 87262.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.086805 restraints weight = 46505.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.088460 restraints weight = 31586.150| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34096 Z= 0.130 Angle : 0.602 14.306 46328 Z= 0.313 Chirality : 0.047 0.199 5220 Planarity : 0.005 0.057 5980 Dihedral : 6.716 56.459 5084 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.96 % Allowed : 13.57 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.12), residues: 4240 helix: -0.33 (0.13), residues: 1456 sheet: -1.60 (0.16), residues: 900 loop : -1.31 (0.14), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 20 HIS 0.018 0.001 HIS O 290 PHE 0.019 0.001 PHE K 246 TYR 0.018 0.002 TYR F 321 ARG 0.005 0.000 ARG E 188 Details of bonding type rmsd hydrogen bonds : bond 0.03216 ( 1404) hydrogen bonds : angle 5.10639 ( 4500) covalent geometry : bond 0.00282 (34096) covalent geometry : angle 0.60161 (46328) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 631 time to evaluate : 3.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 12 ARG cc_start: 0.8508 (ttt180) cc_final: 0.8299 (ttt180) REVERT: P 39 LEU cc_start: 0.8885 (mp) cc_final: 0.8584 (tp) REVERT: P 49 GLU cc_start: 0.8280 (mm-30) cc_final: 0.8027 (mm-30) REVERT: D 142 TYR cc_start: 0.7706 (p90) cc_final: 0.7348 (p90) REVERT: D 277 TYR cc_start: 0.8406 (t80) cc_final: 0.8174 (t80) REVERT: D 295 ILE cc_start: 0.9441 (mp) cc_final: 0.9063 (mt) REVERT: D 332 MET cc_start: 0.8276 (mmp) cc_final: 0.8064 (mmt) REVERT: A 147 ASP cc_start: 0.8409 (p0) cc_final: 0.8007 (p0) REVERT: A 176 MET cc_start: 0.7764 (mmt) cc_final: 0.7127 (mmt) REVERT: A 284 SER cc_start: 0.9132 (OUTLIER) cc_final: 0.8612 (m) REVERT: A 302 MET cc_start: 0.7567 (ptp) cc_final: 0.6284 (ptp) REVERT: A 323 GLN cc_start: 0.9006 (mm110) cc_final: 0.8241 (mt0) REVERT: A 327 ASP cc_start: 0.8913 (m-30) cc_final: 0.8543 (m-30) REVERT: F 1 MET cc_start: 0.7777 (pmm) cc_final: 0.7482 (ptm) REVERT: F 20 TRP cc_start: 0.8316 (t60) cc_final: 0.7808 (t60) REVERT: F 40 PRO cc_start: 0.9060 (Cg_exo) cc_final: 0.8833 (Cg_endo) REVERT: F 65 ASP cc_start: 0.8400 (p0) cc_final: 0.7343 (t0) REVERT: F 93 ILE cc_start: 0.8681 (mm) cc_final: 0.8412 (tp) REVERT: F 176 MET cc_start: 0.8131 (mmt) cc_final: 0.7286 (mmt) REVERT: F 284 SER cc_start: 0.9238 (p) cc_final: 0.8693 (m) REVERT: F 302 MET cc_start: 0.7367 (ptp) cc_final: 0.5922 (ptp) REVERT: F 323 GLN cc_start: 0.8965 (mm110) cc_final: 0.8619 (mm-40) REVERT: F 327 ASP cc_start: 0.8740 (m-30) cc_final: 0.8381 (m-30) REVERT: I 142 TYR cc_start: 0.7582 (OUTLIER) cc_final: 0.7062 (p90) REVERT: I 246 PHE cc_start: 0.8782 (t80) cc_final: 0.8490 (t80) REVERT: I 284 SER cc_start: 0.8959 (p) cc_final: 0.8475 (m) REVERT: I 295 ILE cc_start: 0.9393 (OUTLIER) cc_final: 0.9067 (mm) REVERT: I 314 TRP cc_start: 0.9385 (m100) cc_final: 0.8927 (m100) REVERT: I 321 TYR cc_start: 0.8989 (t80) cc_final: 0.8776 (t80) REVERT: K 49 TYR cc_start: 0.8692 (m-80) cc_final: 0.8456 (m-80) REVERT: K 65 ASP cc_start: 0.8290 (p0) cc_final: 0.7410 (t0) REVERT: K 174 GLN cc_start: 0.8393 (mm-40) cc_final: 0.7637 (mm-40) REVERT: K 176 MET cc_start: 0.7655 (mmt) cc_final: 0.7062 (mmt) REVERT: K 284 SER cc_start: 0.9327 (OUTLIER) cc_final: 0.8812 (m) REVERT: K 302 MET cc_start: 0.7103 (ptp) cc_final: 0.6820 (ptp) REVERT: N 196 ASP cc_start: 0.8760 (t0) cc_final: 0.8549 (t0) REVERT: N 240 ASN cc_start: 0.7984 (t0) cc_final: 0.7638 (t0) REVERT: N 295 ILE cc_start: 0.9448 (mp) cc_final: 0.8963 (mt) REVERT: O 17 MET cc_start: 0.8327 (tpt) cc_final: 0.7747 (tpt) REVERT: O 20 TRP cc_start: 0.8211 (t60) cc_final: 0.7366 (t60) REVERT: O 65 ASP cc_start: 0.8439 (p0) cc_final: 0.7515 (t0) REVERT: O 159 LEU cc_start: 0.8915 (tp) cc_final: 0.8496 (tp) REVERT: O 284 SER cc_start: 0.9395 (OUTLIER) cc_final: 0.8878 (m) REVERT: O 323 GLN cc_start: 0.8878 (mm110) cc_final: 0.8555 (mm-40) REVERT: O 327 ASP cc_start: 0.8955 (m-30) cc_final: 0.8606 (m-30) REVERT: J 46 HIS cc_start: 0.7789 (m170) cc_final: 0.7263 (m170) REVERT: J 53 ARG cc_start: 0.8292 (mtt180) cc_final: 0.8076 (mtt-85) REVERT: J 127 PHE cc_start: 0.7841 (t80) cc_final: 0.7547 (t80) REVERT: J 241 ILE cc_start: 0.8701 (OUTLIER) cc_final: 0.8433 (tp) REVERT: B 67 ASN cc_start: 0.8773 (m110) cc_final: 0.8115 (p0) REVERT: B 69 ASP cc_start: 0.7745 (OUTLIER) cc_final: 0.7512 (m-30) REVERT: G 46 HIS cc_start: 0.7923 (m-70) cc_final: 0.7538 (m-70) REVERT: G 127 PHE cc_start: 0.8081 (t80) cc_final: 0.7492 (t80) REVERT: G 193 GLU cc_start: 0.8320 (tm-30) cc_final: 0.8013 (tm-30) REVERT: L 127 PHE cc_start: 0.7733 (t80) cc_final: 0.7521 (t80) REVERT: L 279 ASN cc_start: 0.8593 (OUTLIER) cc_final: 0.8330 (t0) REVERT: L 309 GLN cc_start: 0.8833 (mt0) cc_final: 0.8225 (mp10) REVERT: C 6 LYS cc_start: 0.8494 (mtmm) cc_final: 0.8263 (ptpp) REVERT: C 28 GLN cc_start: 0.9064 (mp-120) cc_final: 0.8810 (mp10) REVERT: C 63 ASP cc_start: 0.7932 (p0) cc_final: 0.7662 (p0) REVERT: C 66 ASP cc_start: 0.7977 (t0) cc_final: 0.7755 (t0) REVERT: H 1 MET cc_start: 0.7228 (ttm) cc_final: 0.6722 (tpp) REVERT: H 28 GLN cc_start: 0.8758 (mp-120) cc_final: 0.8454 (mt0) REVERT: H 63 ASP cc_start: 0.7310 (p0) cc_final: 0.7055 (p0) REVERT: M 12 ARG cc_start: 0.8808 (ttt180) cc_final: 0.8606 (ttt180) REVERT: M 28 GLN cc_start: 0.8765 (mp-120) cc_final: 0.7957 (pp30) REVERT: M 46 GLN cc_start: 0.8469 (tp40) cc_final: 0.7965 (pt0) REVERT: M 47 ARG cc_start: 0.8823 (mmm160) cc_final: 0.8185 (mmm160) REVERT: M 50 GLN cc_start: 0.8791 (tm-30) cc_final: 0.8471 (tm-30) REVERT: M 54 LYS cc_start: 0.7017 (pmmt) cc_final: 0.6378 (tptp) REVERT: M 66 ASP cc_start: 0.8035 (t0) cc_final: 0.7762 (t0) outliers start: 105 outliers final: 66 residues processed: 702 average time/residue: 0.4181 time to fit residues: 491.5107 Evaluate side-chains 596 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 522 time to evaluate : 3.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 142 TYR Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 228 LYS Chi-restraints excluded: chain I residue 245 ASP Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 295 ILE Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain K residue 85 ASN Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain K residue 259 VAL Chi-restraints excluded: chain K residue 284 SER Chi-restraints excluded: chain N residue 4 VAL Chi-restraints excluded: chain N residue 155 THR Chi-restraints excluded: chain N residue 166 LEU Chi-restraints excluded: chain N residue 208 VAL Chi-restraints excluded: chain N residue 245 ASP Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain O residue 85 ASN Chi-restraints excluded: chain O residue 193 SER Chi-restraints excluded: chain O residue 245 ASP Chi-restraints excluded: chain O residue 284 SER Chi-restraints excluded: chain O residue 290 HIS Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 225 ILE Chi-restraints excluded: chain J residue 241 ILE Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 224 THR Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 279 ASN Chi-restraints excluded: chain G residue 289 THR Chi-restraints excluded: chain G residue 292 LEU Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 182 VAL Chi-restraints excluded: chain L residue 225 ILE Chi-restraints excluded: chain L residue 279 ASN Chi-restraints excluded: chain L residue 292 LEU Chi-restraints excluded: chain H residue 8 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 405 optimal weight: 5.9990 chunk 73 optimal weight: 10.0000 chunk 189 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 155 optimal weight: 0.7980 chunk 208 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 268 optimal weight: 10.0000 chunk 277 optimal weight: 0.8980 chunk 325 optimal weight: 4.9990 chunk 336 optimal weight: 10.0000 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 16 HIS ** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 331 HIS ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 ASN ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 7 ASN K 290 HIS K 323 GLN N 45 HIS ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 290 HIS ** O 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 184 GLN J 206 GLN J 279 ASN B 184 GLN G 206 GLN L 106 HIS L 184 GLN ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 279 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.103324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.078947 restraints weight = 88365.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.081474 restraints weight = 48000.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.083059 restraints weight = 33035.335| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 34096 Z= 0.236 Angle : 0.682 10.241 46328 Z= 0.353 Chirality : 0.049 0.191 5220 Planarity : 0.005 0.058 5980 Dihedral : 7.102 59.369 5084 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 4.46 % Allowed : 14.93 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.12), residues: 4240 helix: -0.01 (0.14), residues: 1444 sheet: -1.31 (0.17), residues: 816 loop : -1.28 (0.14), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP K 20 HIS 0.006 0.001 HIS P 16 PHE 0.024 0.002 PHE L 68 TYR 0.021 0.002 TYR F 321 ARG 0.005 0.001 ARG B 317 Details of bonding type rmsd hydrogen bonds : bond 0.03545 ( 1404) hydrogen bonds : angle 5.30286 ( 4500) covalent geometry : bond 0.00516 (34096) covalent geometry : angle 0.68198 (46328) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 520 time to evaluate : 3.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 12 ARG cc_start: 0.8552 (ttt180) cc_final: 0.8274 (ttt180) REVERT: P 28 GLN cc_start: 0.8896 (mp10) cc_final: 0.8548 (mp10) REVERT: P 39 LEU cc_start: 0.8990 (mp) cc_final: 0.8596 (tp) REVERT: P 54 LYS cc_start: 0.7310 (pmmt) cc_final: 0.6626 (tppt) REVERT: D 142 TYR cc_start: 0.7637 (OUTLIER) cc_final: 0.7155 (p90) REVERT: D 177 MET cc_start: 0.7060 (tmm) cc_final: 0.6845 (tmm) REVERT: D 240 ASN cc_start: 0.8061 (t0) cc_final: 0.7615 (t0) REVERT: D 295 ILE cc_start: 0.9467 (mp) cc_final: 0.9052 (mt) REVERT: A 49 TYR cc_start: 0.8636 (m-80) cc_final: 0.8404 (m-10) REVERT: A 65 ASP cc_start: 0.8461 (p0) cc_final: 0.7741 (t0) REVERT: A 147 ASP cc_start: 0.8538 (p0) cc_final: 0.8243 (p0) REVERT: A 176 MET cc_start: 0.7939 (mmt) cc_final: 0.7270 (mmt) REVERT: A 302 MET cc_start: 0.7549 (ptp) cc_final: 0.5939 (ptp) REVERT: A 323 GLN cc_start: 0.8981 (mm110) cc_final: 0.8452 (mt0) REVERT: A 327 ASP cc_start: 0.8966 (m-30) cc_final: 0.8566 (m-30) REVERT: E 205 MET cc_start: 0.8485 (mtp) cc_final: 0.8258 (mtp) REVERT: E 240 ASN cc_start: 0.8364 (OUTLIER) cc_final: 0.8055 (t0) REVERT: F 1 MET cc_start: 0.7813 (pmm) cc_final: 0.7598 (pmm) REVERT: F 20 TRP cc_start: 0.8467 (t60) cc_final: 0.7894 (t60) REVERT: F 40 PRO cc_start: 0.9124 (Cg_exo) cc_final: 0.8890 (Cg_endo) REVERT: F 93 ILE cc_start: 0.8700 (mm) cc_final: 0.8368 (tp) REVERT: F 176 MET cc_start: 0.8237 (mmt) cc_final: 0.7038 (mmt) REVERT: F 284 SER cc_start: 0.9350 (p) cc_final: 0.9069 (p) REVERT: F 302 MET cc_start: 0.7474 (ptp) cc_final: 0.5981 (ptp) REVERT: F 323 GLN cc_start: 0.8887 (mm110) cc_final: 0.8588 (mm-40) REVERT: F 327 ASP cc_start: 0.8719 (m-30) cc_final: 0.8407 (m-30) REVERT: I 142 TYR cc_start: 0.7730 (OUTLIER) cc_final: 0.7028 (p90) REVERT: I 240 ASN cc_start: 0.7930 (t0) cc_final: 0.7595 (t0) REVERT: I 295 ILE cc_start: 0.9408 (OUTLIER) cc_final: 0.9122 (mm) REVERT: K 65 ASP cc_start: 0.8328 (p0) cc_final: 0.7536 (t0) REVERT: K 176 MET cc_start: 0.7510 (mmt) cc_final: 0.7230 (mmt) REVERT: K 284 SER cc_start: 0.9363 (OUTLIER) cc_final: 0.8873 (m) REVERT: K 302 MET cc_start: 0.7119 (ptp) cc_final: 0.5592 (ptp) REVERT: N 295 ILE cc_start: 0.9473 (mp) cc_final: 0.9249 (mm) REVERT: O 20 TRP cc_start: 0.8374 (t60) cc_final: 0.7595 (t60) REVERT: O 65 ASP cc_start: 0.8432 (p0) cc_final: 0.7666 (t0) REVERT: O 176 MET cc_start: 0.7752 (mmt) cc_final: 0.6735 (mmt) REVERT: O 323 GLN cc_start: 0.8919 (mm110) cc_final: 0.8620 (mm-40) REVERT: O 327 ASP cc_start: 0.8895 (m-30) cc_final: 0.8531 (m-30) REVERT: J 46 HIS cc_start: 0.7792 (m170) cc_final: 0.7131 (m90) REVERT: J 53 ARG cc_start: 0.8280 (mtt180) cc_final: 0.7929 (mtt-85) REVERT: J 241 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8522 (tp) REVERT: J 309 GLN cc_start: 0.8925 (mt0) cc_final: 0.8397 (mp10) REVERT: B 67 ASN cc_start: 0.8880 (m110) cc_final: 0.8214 (p0) REVERT: B 69 ASP cc_start: 0.7842 (OUTLIER) cc_final: 0.7496 (m-30) REVERT: G 46 HIS cc_start: 0.8142 (m-70) cc_final: 0.7703 (m-70) REVERT: G 70 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8476 (tt) REVERT: G 127 PHE cc_start: 0.8211 (t80) cc_final: 0.7721 (t80) REVERT: G 130 TYR cc_start: 0.8573 (t80) cc_final: 0.8300 (t80) REVERT: G 193 GLU cc_start: 0.8486 (tm-30) cc_final: 0.8147 (tm-30) REVERT: L 78 LEU cc_start: 0.8542 (mm) cc_final: 0.8264 (mm) REVERT: L 127 PHE cc_start: 0.7905 (t80) cc_final: 0.7673 (t80) REVERT: C 28 GLN cc_start: 0.9040 (mp-120) cc_final: 0.8798 (mp10) REVERT: C 63 ASP cc_start: 0.8167 (p0) cc_final: 0.7932 (p0) REVERT: H 1 MET cc_start: 0.7393 (ttm) cc_final: 0.6429 (tpp) REVERT: H 28 GLN cc_start: 0.8821 (mp-120) cc_final: 0.8593 (mt0) REVERT: H 52 ASP cc_start: 0.7877 (t0) cc_final: 0.7238 (p0) REVERT: H 63 ASP cc_start: 0.7772 (p0) cc_final: 0.7510 (p0) REVERT: H 70 CYS cc_start: 0.8125 (p) cc_final: 0.7593 (p) REVERT: M 36 LEU cc_start: 0.9315 (tp) cc_final: 0.9060 (tp) REVERT: M 42 GLU cc_start: 0.8964 (mm-30) cc_final: 0.8542 (mm-30) REVERT: M 46 GLN cc_start: 0.8369 (tp40) cc_final: 0.7949 (pt0) REVERT: M 47 ARG cc_start: 0.8806 (mmm160) cc_final: 0.8086 (mmm160) REVERT: M 49 GLU cc_start: 0.8365 (mm-30) cc_final: 0.7998 (mm-30) REVERT: M 50 GLN cc_start: 0.8754 (tm-30) cc_final: 0.8389 (tm-30) REVERT: M 66 ASP cc_start: 0.8045 (t0) cc_final: 0.7765 (t0) outliers start: 158 outliers final: 101 residues processed: 632 average time/residue: 0.3992 time to fit residues: 430.1858 Evaluate side-chains 570 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 461 time to evaluate : 4.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 142 TYR Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 228 LYS Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 240 ASN Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain F residue 85 ASN Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 142 TYR Chi-restraints excluded: chain I residue 158 CYS Chi-restraints excluded: chain I residue 168 GLU Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 228 LYS Chi-restraints excluded: chain I residue 245 ASP Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 251 GLU Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain I residue 295 ILE Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain I residue 325 VAL Chi-restraints excluded: chain K residue 85 ASN Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain K residue 259 VAL Chi-restraints excluded: chain K residue 284 SER Chi-restraints excluded: chain K residue 290 HIS Chi-restraints excluded: chain N residue 4 VAL Chi-restraints excluded: chain N residue 155 THR Chi-restraints excluded: chain N residue 208 VAL Chi-restraints excluded: chain N residue 218 VAL Chi-restraints excluded: chain N residue 245 ASP Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain O residue 85 ASN Chi-restraints excluded: chain O residue 193 SER Chi-restraints excluded: chain O residue 244 VAL Chi-restraints excluded: chain O residue 245 ASP Chi-restraints excluded: chain O residue 284 SER Chi-restraints excluded: chain O residue 290 HIS Chi-restraints excluded: chain J residue 69 ASP Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 204 MET Chi-restraints excluded: chain J residue 225 ILE Chi-restraints excluded: chain J residue 241 ILE Chi-restraints excluded: chain J residue 257 VAL Chi-restraints excluded: chain J residue 279 ASN Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 134 SER Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 206 GLN Chi-restraints excluded: chain G residue 224 THR Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 289 THR Chi-restraints excluded: chain G residue 292 LEU Chi-restraints excluded: chain G residue 301 SER Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 69 ASP Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 182 VAL Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 225 ILE Chi-restraints excluded: chain L residue 241 ILE Chi-restraints excluded: chain L residue 257 VAL Chi-restraints excluded: chain L residue 292 LEU Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain M residue 2 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 108 optimal weight: 0.9990 chunk 368 optimal weight: 7.9990 chunk 67 optimal weight: 7.9990 chunk 274 optimal weight: 10.0000 chunk 28 optimal weight: 0.9980 chunk 405 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 327 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 109 optimal weight: 10.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 16 HIS P 59 GLN A 174 GLN ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 ASN ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 290 HIS O 323 GLN J 279 ASN B 284 HIS ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 106 HIS ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.103958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.080644 restraints weight = 86598.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.083199 restraints weight = 45611.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.084827 restraints weight = 30705.679| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 34096 Z= 0.174 Angle : 0.633 13.550 46328 Z= 0.327 Chirality : 0.048 0.234 5220 Planarity : 0.005 0.054 5980 Dihedral : 6.924 59.458 5084 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 4.20 % Allowed : 16.06 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.13), residues: 4240 helix: 0.13 (0.14), residues: 1436 sheet: -1.28 (0.16), residues: 876 loop : -1.11 (0.14), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP K 20 HIS 0.009 0.001 HIS K 290 PHE 0.022 0.002 PHE G 308 TYR 0.019 0.002 TYR G 217 ARG 0.005 0.000 ARG H 47 Details of bonding type rmsd hydrogen bonds : bond 0.03303 ( 1404) hydrogen bonds : angle 5.16742 ( 4500) covalent geometry : bond 0.00385 (34096) covalent geometry : angle 0.63294 (46328) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 526 time to evaluate : 4.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 12 ARG cc_start: 0.8482 (ttt180) cc_final: 0.8187 (ttt180) REVERT: P 28 GLN cc_start: 0.8903 (mp10) cc_final: 0.8586 (mp10) REVERT: P 54 LYS cc_start: 0.7476 (pmmt) cc_final: 0.6750 (tppt) REVERT: D 240 ASN cc_start: 0.7969 (t0) cc_final: 0.7663 (t0) REVERT: D 295 ILE cc_start: 0.9470 (mp) cc_final: 0.9070 (mt) REVERT: A 20 TRP cc_start: 0.8179 (t60) cc_final: 0.7297 (t60) REVERT: A 49 TYR cc_start: 0.8692 (m-80) cc_final: 0.8161 (m-10) REVERT: A 65 ASP cc_start: 0.8428 (p0) cc_final: 0.7648 (t0) REVERT: A 147 ASP cc_start: 0.8427 (p0) cc_final: 0.8109 (p0) REVERT: A 176 MET cc_start: 0.7897 (mmt) cc_final: 0.7320 (mmt) REVERT: A 302 MET cc_start: 0.7713 (ptp) cc_final: 0.6224 (ptp) REVERT: E 240 ASN cc_start: 0.8237 (t0) cc_final: 0.7950 (t0) REVERT: E 246 PHE cc_start: 0.8619 (t80) cc_final: 0.8192 (t80) REVERT: E 249 GLN cc_start: 0.7436 (tt0) cc_final: 0.7035 (tt0) REVERT: F 20 TRP cc_start: 0.8450 (t60) cc_final: 0.7858 (t60) REVERT: F 65 ASP cc_start: 0.8359 (p0) cc_final: 0.7495 (t0) REVERT: F 93 ILE cc_start: 0.8691 (mm) cc_final: 0.8414 (tp) REVERT: F 176 MET cc_start: 0.8220 (mmt) cc_final: 0.7251 (mmt) REVERT: F 284 SER cc_start: 0.9331 (p) cc_final: 0.9094 (p) REVERT: F 302 MET cc_start: 0.7442 (ptp) cc_final: 0.5990 (ptp) REVERT: F 323 GLN cc_start: 0.8855 (mm110) cc_final: 0.8546 (mm-40) REVERT: F 327 ASP cc_start: 0.8607 (m-30) cc_final: 0.8303 (m-30) REVERT: I 142 TYR cc_start: 0.7638 (OUTLIER) cc_final: 0.6950 (p90) REVERT: I 240 ASN cc_start: 0.7882 (t0) cc_final: 0.7467 (t0) REVERT: I 246 PHE cc_start: 0.8755 (t80) cc_final: 0.8489 (t80) REVERT: I 295 ILE cc_start: 0.9395 (OUTLIER) cc_final: 0.9094 (mm) REVERT: I 314 TRP cc_start: 0.9381 (m100) cc_final: 0.9009 (m100) REVERT: K 65 ASP cc_start: 0.8243 (p0) cc_final: 0.7665 (t0) REVERT: K 271 MET cc_start: 0.7816 (mmt) cc_final: 0.7542 (mmp) REVERT: K 284 SER cc_start: 0.9325 (OUTLIER) cc_final: 0.8902 (m) REVERT: K 302 MET cc_start: 0.7182 (ptp) cc_final: 0.6740 (ptp) REVERT: N 295 ILE cc_start: 0.9451 (mp) cc_final: 0.9230 (mm) REVERT: O 20 TRP cc_start: 0.8297 (t60) cc_final: 0.7483 (t60) REVERT: O 65 ASP cc_start: 0.8401 (p0) cc_final: 0.7695 (t0) REVERT: O 207 ILE cc_start: 0.9507 (mp) cc_final: 0.9303 (mp) REVERT: J 46 HIS cc_start: 0.7715 (m170) cc_final: 0.7273 (m-70) REVERT: J 127 PHE cc_start: 0.8146 (t80) cc_final: 0.7916 (t80) REVERT: B 67 ASN cc_start: 0.8816 (m110) cc_final: 0.8159 (p0) REVERT: B 131 LEU cc_start: 0.9434 (tt) cc_final: 0.9101 (mm) REVERT: G 46 HIS cc_start: 0.8040 (m-70) cc_final: 0.7589 (m-70) REVERT: G 67 ASN cc_start: 0.8309 (p0) cc_final: 0.8097 (p0) REVERT: G 127 PHE cc_start: 0.8217 (t80) cc_final: 0.7703 (t80) REVERT: G 131 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9207 (mp) REVERT: G 193 GLU cc_start: 0.8454 (tm-30) cc_final: 0.8161 (tm-30) REVERT: L 78 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8185 (mm) REVERT: L 131 LEU cc_start: 0.9445 (tt) cc_final: 0.9048 (mp) REVERT: C 6 LYS cc_start: 0.8642 (mtmm) cc_final: 0.8249 (ptpp) REVERT: C 28 GLN cc_start: 0.9047 (mp-120) cc_final: 0.8794 (mp10) REVERT: C 54 LYS cc_start: 0.7349 (pmmt) cc_final: 0.6310 (tptp) REVERT: C 63 ASP cc_start: 0.8384 (p0) cc_final: 0.8116 (p0) REVERT: H 1 MET cc_start: 0.7226 (ttm) cc_final: 0.6422 (tpp) REVERT: H 28 GLN cc_start: 0.8871 (mp-120) cc_final: 0.8671 (mp10) REVERT: M 28 GLN cc_start: 0.8900 (mp10) cc_final: 0.8544 (mp10) REVERT: M 39 LEU cc_start: 0.9096 (mp) cc_final: 0.8549 (tp) REVERT: M 47 ARG cc_start: 0.8882 (mmm160) cc_final: 0.8002 (mmm160) REVERT: M 50 GLN cc_start: 0.8902 (tm-30) cc_final: 0.8418 (tm-30) REVERT: M 66 ASP cc_start: 0.8001 (t0) cc_final: 0.7668 (t0) outliers start: 149 outliers final: 102 residues processed: 634 average time/residue: 0.5416 time to fit residues: 580.3666 Evaluate side-chains 592 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 485 time to evaluate : 4.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 228 LYS Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 302 MET Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 142 TYR Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 228 LYS Chi-restraints excluded: chain I residue 245 ASP Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 251 GLU Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain I residue 295 ILE Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain I residue 325 VAL Chi-restraints excluded: chain K residue 85 ASN Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain K residue 259 VAL Chi-restraints excluded: chain K residue 278 SER Chi-restraints excluded: chain K residue 284 SER Chi-restraints excluded: chain K residue 290 HIS Chi-restraints excluded: chain N residue 4 VAL Chi-restraints excluded: chain N residue 155 THR Chi-restraints excluded: chain N residue 208 VAL Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain O residue 85 ASN Chi-restraints excluded: chain O residue 193 SER Chi-restraints excluded: chain O residue 244 VAL Chi-restraints excluded: chain O residue 245 ASP Chi-restraints excluded: chain O residue 284 SER Chi-restraints excluded: chain O residue 290 HIS Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 225 ILE Chi-restraints excluded: chain J residue 257 VAL Chi-restraints excluded: chain J residue 279 ASN Chi-restraints excluded: chain J residue 288 VAL Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 134 SER Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 224 THR Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 289 THR Chi-restraints excluded: chain G residue 292 LEU Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 69 ASP Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 182 VAL Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 225 ILE Chi-restraints excluded: chain L residue 236 CYS Chi-restraints excluded: chain L residue 241 ILE Chi-restraints excluded: chain L residue 257 VAL Chi-restraints excluded: chain L residue 292 LEU Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain M residue 2 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 118 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 113 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 318 optimal weight: 5.9990 chunk 304 optimal weight: 4.9990 chunk 261 optimal weight: 0.7980 chunk 214 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 317 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 16 HIS P 59 GLN ** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 GLN ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 290 HIS ** N 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 187 GLN O 290 HIS J 279 ASN ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 59 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.103179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.080020 restraints weight = 86817.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.082568 restraints weight = 45643.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.084196 restraints weight = 30618.971| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 34096 Z= 0.195 Angle : 0.655 11.804 46328 Z= 0.335 Chirality : 0.048 0.257 5220 Planarity : 0.005 0.055 5980 Dihedral : 6.976 59.699 5084 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 4.37 % Allowed : 16.68 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.13), residues: 4240 helix: 0.25 (0.14), residues: 1452 sheet: -1.02 (0.17), residues: 824 loop : -1.12 (0.14), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP K 20 HIS 0.013 0.001 HIS O 290 PHE 0.024 0.002 PHE J 68 TYR 0.021 0.002 TYR D 133 ARG 0.005 0.000 ARG H 47 Details of bonding type rmsd hydrogen bonds : bond 0.03356 ( 1404) hydrogen bonds : angle 5.19227 ( 4500) covalent geometry : bond 0.00432 (34096) covalent geometry : angle 0.65478 (46328) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 514 time to evaluate : 3.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 28 GLN cc_start: 0.8932 (mp10) cc_final: 0.8621 (mp10) REVERT: P 39 LEU cc_start: 0.8951 (mp) cc_final: 0.8540 (tp) REVERT: D 142 TYR cc_start: 0.7606 (OUTLIER) cc_final: 0.6990 (p90) REVERT: D 240 ASN cc_start: 0.8071 (t0) cc_final: 0.7600 (t0) REVERT: D 295 ILE cc_start: 0.9454 (mp) cc_final: 0.9042 (mt) REVERT: A 20 TRP cc_start: 0.8186 (t60) cc_final: 0.7490 (t60) REVERT: A 65 ASP cc_start: 0.8388 (p0) cc_final: 0.7709 (t0) REVERT: A 147 ASP cc_start: 0.8443 (p0) cc_final: 0.8120 (p0) REVERT: A 176 MET cc_start: 0.7863 (mmt) cc_final: 0.7336 (mmt) REVERT: A 302 MET cc_start: 0.7710 (ptp) cc_final: 0.6238 (ptp) REVERT: E 240 ASN cc_start: 0.8296 (t0) cc_final: 0.8055 (t0) REVERT: E 246 PHE cc_start: 0.8725 (t80) cc_final: 0.8270 (t80) REVERT: E 295 ILE cc_start: 0.9309 (mm) cc_final: 0.9077 (mm) REVERT: F 20 TRP cc_start: 0.8465 (t60) cc_final: 0.7841 (t60) REVERT: F 65 ASP cc_start: 0.8382 (p0) cc_final: 0.7631 (t0) REVERT: F 93 ILE cc_start: 0.8715 (mm) cc_final: 0.8439 (tp) REVERT: F 176 MET cc_start: 0.8298 (mmt) cc_final: 0.7134 (mmt) REVERT: F 284 SER cc_start: 0.9359 (p) cc_final: 0.9094 (p) REVERT: F 302 MET cc_start: 0.7383 (ptp) cc_final: 0.5990 (ptp) REVERT: F 323 GLN cc_start: 0.8844 (mm110) cc_final: 0.8533 (mm-40) REVERT: F 327 ASP cc_start: 0.8599 (m-30) cc_final: 0.8317 (m-30) REVERT: I 142 TYR cc_start: 0.7556 (OUTLIER) cc_final: 0.6860 (p90) REVERT: I 246 PHE cc_start: 0.8897 (t80) cc_final: 0.8512 (t80) REVERT: I 295 ILE cc_start: 0.9407 (OUTLIER) cc_final: 0.9088 (mm) REVERT: I 314 TRP cc_start: 0.9381 (m100) cc_final: 0.8985 (m100) REVERT: K 65 ASP cc_start: 0.8266 (p0) cc_final: 0.7675 (t0) REVERT: K 271 MET cc_start: 0.7883 (mmt) cc_final: 0.7628 (mmp) REVERT: K 302 MET cc_start: 0.7242 (ptp) cc_final: 0.5771 (ptp) REVERT: N 295 ILE cc_start: 0.9435 (mp) cc_final: 0.9073 (mt) REVERT: N 302 MET cc_start: 0.8137 (ptp) cc_final: 0.7923 (ptp) REVERT: O 17 MET cc_start: 0.8484 (tpt) cc_final: 0.8254 (tpt) REVERT: O 20 TRP cc_start: 0.8341 (t60) cc_final: 0.7444 (t60) REVERT: O 65 ASP cc_start: 0.8410 (p0) cc_final: 0.7731 (t0) REVERT: O 176 MET cc_start: 0.7616 (mmt) cc_final: 0.6415 (mmt) REVERT: O 261 GLN cc_start: 0.8436 (tm-30) cc_final: 0.8101 (pp30) REVERT: O 327 ASP cc_start: 0.8908 (m-30) cc_final: 0.8517 (m-30) REVERT: J 46 HIS cc_start: 0.7591 (m170) cc_final: 0.7296 (m170) REVERT: J 131 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9005 (mp) REVERT: B 67 ASN cc_start: 0.8719 (m110) cc_final: 0.8101 (p0) REVERT: B 131 LEU cc_start: 0.9420 (tt) cc_final: 0.9109 (mm) REVERT: B 298 TYR cc_start: 0.8459 (OUTLIER) cc_final: 0.7845 (m-10) REVERT: G 46 HIS cc_start: 0.8004 (m-70) cc_final: 0.7544 (m170) REVERT: G 127 PHE cc_start: 0.8244 (t80) cc_final: 0.7642 (t80) REVERT: G 131 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.9168 (mp) REVERT: G 193 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8167 (tm-30) REVERT: L 78 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8199 (mm) REVERT: L 131 LEU cc_start: 0.9457 (tt) cc_final: 0.9045 (mp) REVERT: L 180 ASP cc_start: 0.8349 (m-30) cc_final: 0.7885 (m-30) REVERT: L 214 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7799 (mp0) REVERT: L 298 TYR cc_start: 0.8550 (OUTLIER) cc_final: 0.7505 (m-10) REVERT: C 6 LYS cc_start: 0.8594 (mtmm) cc_final: 0.8267 (ptpp) REVERT: C 28 GLN cc_start: 0.9088 (mp-120) cc_final: 0.8848 (mp10) REVERT: C 54 LYS cc_start: 0.7375 (pmmt) cc_final: 0.6323 (tptp) REVERT: C 63 ASP cc_start: 0.8437 (p0) cc_final: 0.8207 (p0) REVERT: H 1 MET cc_start: 0.7224 (ttm) cc_final: 0.6452 (tpp) REVERT: H 28 GLN cc_start: 0.8901 (mp-120) cc_final: 0.8696 (mp10) REVERT: H 50 GLN cc_start: 0.8608 (tm-30) cc_final: 0.8407 (tm-30) REVERT: H 54 LYS cc_start: 0.7473 (pmmt) cc_final: 0.7272 (pttt) REVERT: M 28 GLN cc_start: 0.8829 (mp10) cc_final: 0.8470 (mp10) REVERT: M 36 LEU cc_start: 0.9267 (tp) cc_final: 0.8999 (tp) REVERT: M 37 GLU cc_start: 0.8798 (tp30) cc_final: 0.8572 (tp30) REVERT: M 39 LEU cc_start: 0.9103 (mp) cc_final: 0.8569 (tp) REVERT: M 42 GLU cc_start: 0.8883 (mm-30) cc_final: 0.8637 (mm-30) REVERT: M 47 ARG cc_start: 0.8897 (mmm160) cc_final: 0.7946 (mmm160) REVERT: M 50 GLN cc_start: 0.8915 (tm-30) cc_final: 0.8390 (tm-30) REVERT: M 66 ASP cc_start: 0.7951 (t0) cc_final: 0.7563 (t0) outliers start: 155 outliers final: 126 residues processed: 627 average time/residue: 0.4258 time to fit residues: 452.7458 Evaluate side-chains 617 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 483 time to evaluate : 3.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain P residue 8 ILE Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 142 TYR Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 228 LYS Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 302 MET Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain I residue 142 TYR Chi-restraints excluded: chain I residue 205 MET Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 228 LYS Chi-restraints excluded: chain I residue 243 VAL Chi-restraints excluded: chain I residue 245 ASP Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 251 GLU Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain I residue 295 ILE Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain I residue 325 VAL Chi-restraints excluded: chain I residue 332 MET Chi-restraints excluded: chain K residue 17 MET Chi-restraints excluded: chain K residue 85 ASN Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain K residue 259 VAL Chi-restraints excluded: chain K residue 278 SER Chi-restraints excluded: chain K residue 284 SER Chi-restraints excluded: chain K residue 290 HIS Chi-restraints excluded: chain N residue 4 VAL Chi-restraints excluded: chain N residue 155 THR Chi-restraints excluded: chain N residue 208 VAL Chi-restraints excluded: chain N residue 218 VAL Chi-restraints excluded: chain N residue 243 VAL Chi-restraints excluded: chain N residue 245 ASP Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain O residue 34 ILE Chi-restraints excluded: chain O residue 85 ASN Chi-restraints excluded: chain O residue 149 VAL Chi-restraints excluded: chain O residue 193 SER Chi-restraints excluded: chain O residue 244 VAL Chi-restraints excluded: chain O residue 245 ASP Chi-restraints excluded: chain O residue 284 SER Chi-restraints excluded: chain O residue 290 HIS Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 204 MET Chi-restraints excluded: chain J residue 225 ILE Chi-restraints excluded: chain J residue 257 VAL Chi-restraints excluded: chain J residue 279 ASN Chi-restraints excluded: chain J residue 288 VAL Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 236 CYS Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 298 TYR Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 134 SER Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 200 LEU Chi-restraints excluded: chain G residue 206 GLN Chi-restraints excluded: chain G residue 224 THR Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 289 THR Chi-restraints excluded: chain G residue 301 SER Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 69 ASP Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 182 VAL Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 225 ILE Chi-restraints excluded: chain L residue 236 CYS Chi-restraints excluded: chain L residue 241 ILE Chi-restraints excluded: chain L residue 257 VAL Chi-restraints excluded: chain L residue 292 LEU Chi-restraints excluded: chain L residue 298 TYR Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain M residue 2 SER Chi-restraints excluded: chain M residue 54 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 369 optimal weight: 0.9980 chunk 3 optimal weight: 9.9990 chunk 212 optimal weight: 10.0000 chunk 151 optimal weight: 3.9990 chunk 145 optimal weight: 9.9990 chunk 179 optimal weight: 2.9990 chunk 316 optimal weight: 9.9990 chunk 400 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 325 optimal weight: 1.9990 chunk 395 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 290 HIS ** J 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 295 HIS ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.103234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.079019 restraints weight = 88506.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.081543 restraints weight = 47896.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.083121 restraints weight = 32904.739| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.4393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 34096 Z= 0.211 Angle : 0.669 12.310 46328 Z= 0.343 Chirality : 0.049 0.278 5220 Planarity : 0.005 0.056 5980 Dihedral : 7.039 58.768 5084 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 4.54 % Allowed : 16.87 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.94 (0.13), residues: 4240 helix: 0.27 (0.14), residues: 1452 sheet: -0.94 (0.17), residues: 824 loop : -1.08 (0.14), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.081 0.002 TRP K 20 HIS 0.011 0.001 HIS K 290 PHE 0.026 0.002 PHE L 127 TYR 0.022 0.002 TYR D 133 ARG 0.006 0.000 ARG H 47 Details of bonding type rmsd hydrogen bonds : bond 0.03368 ( 1404) hydrogen bonds : angle 5.20820 ( 4500) covalent geometry : bond 0.00464 (34096) covalent geometry : angle 0.66900 (46328) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 503 time to evaluate : 3.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 1 MET cc_start: 0.7195 (tmm) cc_final: 0.6742 (tmm) REVERT: P 28 GLN cc_start: 0.8944 (mp10) cc_final: 0.8647 (mp10) REVERT: P 46 GLN cc_start: 0.8474 (mm-40) cc_final: 0.8117 (tt0) REVERT: D 142 TYR cc_start: 0.7512 (OUTLIER) cc_final: 0.6946 (p90) REVERT: D 228 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8334 (mtmm) REVERT: D 240 ASN cc_start: 0.7977 (t0) cc_final: 0.7738 (t0) REVERT: D 295 ILE cc_start: 0.9459 (mp) cc_final: 0.9056 (mt) REVERT: A 20 TRP cc_start: 0.8210 (t60) cc_final: 0.7515 (t60) REVERT: A 65 ASP cc_start: 0.8413 (p0) cc_final: 0.7758 (t0) REVERT: A 147 ASP cc_start: 0.8398 (p0) cc_final: 0.8052 (p0) REVERT: A 176 MET cc_start: 0.7883 (mmt) cc_final: 0.7355 (mmt) REVERT: A 302 MET cc_start: 0.7719 (ptp) cc_final: 0.6265 (ptp) REVERT: A 327 ASP cc_start: 0.8936 (m-30) cc_final: 0.8530 (m-30) REVERT: E 240 ASN cc_start: 0.8280 (t0) cc_final: 0.8048 (t0) REVERT: E 246 PHE cc_start: 0.8708 (t80) cc_final: 0.8270 (t80) REVERT: F 20 TRP cc_start: 0.8475 (t60) cc_final: 0.7899 (t60) REVERT: F 65 ASP cc_start: 0.8398 (p0) cc_final: 0.7578 (t0) REVERT: F 93 ILE cc_start: 0.8669 (mm) cc_final: 0.8390 (tp) REVERT: F 176 MET cc_start: 0.8272 (mmt) cc_final: 0.7283 (mmt) REVERT: F 284 SER cc_start: 0.9360 (p) cc_final: 0.9099 (p) REVERT: F 290 HIS cc_start: 0.8757 (OUTLIER) cc_final: 0.7496 (t-90) REVERT: F 302 MET cc_start: 0.7449 (ptp) cc_final: 0.6084 (ptp) REVERT: F 323 GLN cc_start: 0.8821 (mm110) cc_final: 0.8507 (mm-40) REVERT: F 327 ASP cc_start: 0.8585 (m-30) cc_final: 0.8294 (m-30) REVERT: I 142 TYR cc_start: 0.7536 (OUTLIER) cc_final: 0.6911 (p90) REVERT: I 246 PHE cc_start: 0.8881 (t80) cc_final: 0.8444 (t80) REVERT: I 295 ILE cc_start: 0.9376 (OUTLIER) cc_final: 0.9113 (mm) REVERT: K 65 ASP cc_start: 0.8272 (p0) cc_final: 0.7673 (t0) REVERT: K 176 MET cc_start: 0.7945 (mmt) cc_final: 0.7681 (mtt) REVERT: K 302 MET cc_start: 0.7246 (ptp) cc_final: 0.6861 (ptp) REVERT: N 295 ILE cc_start: 0.9455 (mp) cc_final: 0.9108 (mt) REVERT: O 17 MET cc_start: 0.8446 (tpt) cc_final: 0.8091 (tpt) REVERT: O 20 TRP cc_start: 0.8417 (t60) cc_final: 0.7559 (t60) REVERT: O 65 ASP cc_start: 0.8389 (p0) cc_final: 0.7732 (t0) REVERT: J 46 HIS cc_start: 0.7569 (m170) cc_final: 0.7017 (m-70) REVERT: J 53 ARG cc_start: 0.8344 (mtt180) cc_final: 0.8094 (mtt-85) REVERT: J 127 PHE cc_start: 0.8199 (t80) cc_final: 0.7901 (t80) REVERT: J 131 LEU cc_start: 0.9420 (OUTLIER) cc_final: 0.8989 (mp) REVERT: B 48 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7221 (tp) REVERT: B 67 ASN cc_start: 0.8807 (m110) cc_final: 0.8161 (p0) REVERT: B 131 LEU cc_start: 0.9424 (tt) cc_final: 0.9107 (mm) REVERT: G 46 HIS cc_start: 0.8089 (m-70) cc_final: 0.7646 (m170) REVERT: G 69 ASP cc_start: 0.8157 (m-30) cc_final: 0.7295 (t70) REVERT: G 127 PHE cc_start: 0.8232 (t80) cc_final: 0.7524 (t80) REVERT: G 131 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9169 (mp) REVERT: G 193 GLU cc_start: 0.8547 (tm-30) cc_final: 0.8244 (tm-30) REVERT: L 42 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8366 (mp) REVERT: L 78 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8216 (mm) REVERT: L 131 LEU cc_start: 0.9466 (tt) cc_final: 0.9074 (mp) REVERT: L 214 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7731 (mp0) REVERT: C 6 LYS cc_start: 0.8601 (mtmm) cc_final: 0.8231 (ptpp) REVERT: C 54 LYS cc_start: 0.7437 (pmmt) cc_final: 0.6381 (tptp) REVERT: H 1 MET cc_start: 0.7069 (ttm) cc_final: 0.6316 (tpp) REVERT: H 50 GLN cc_start: 0.8553 (tm-30) cc_final: 0.8341 (tm-30) REVERT: H 54 LYS cc_start: 0.7649 (pmmt) cc_final: 0.7391 (pttm) REVERT: M 28 GLN cc_start: 0.8950 (mp10) cc_final: 0.8612 (mp10) REVERT: M 36 LEU cc_start: 0.9304 (tp) cc_final: 0.9040 (tp) REVERT: M 37 GLU cc_start: 0.8840 (tp30) cc_final: 0.8608 (tp30) REVERT: M 39 LEU cc_start: 0.9137 (mp) cc_final: 0.8615 (tp) REVERT: M 42 GLU cc_start: 0.8897 (mm-30) cc_final: 0.8623 (mm-30) REVERT: M 47 ARG cc_start: 0.8905 (mmm160) cc_final: 0.7987 (mmm160) REVERT: M 50 GLN cc_start: 0.8929 (tm-30) cc_final: 0.8411 (tm-30) REVERT: M 54 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7702 (pttp) REVERT: M 66 ASP cc_start: 0.7979 (t0) cc_final: 0.7679 (t0) outliers start: 161 outliers final: 123 residues processed: 624 average time/residue: 0.5637 time to fit residues: 599.5702 Evaluate side-chains 607 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 473 time to evaluate : 3.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 8 ILE Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 142 TYR Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 228 LYS Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 142 TYR Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 302 MET Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain F residue 85 ASN Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 290 HIS Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 142 TYR Chi-restraints excluded: chain I residue 168 GLU Chi-restraints excluded: chain I residue 205 MET Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 228 LYS Chi-restraints excluded: chain I residue 243 VAL Chi-restraints excluded: chain I residue 245 ASP Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 251 GLU Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain I residue 295 ILE Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain I residue 325 VAL Chi-restraints excluded: chain I residue 332 MET Chi-restraints excluded: chain K residue 17 MET Chi-restraints excluded: chain K residue 85 ASN Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain K residue 259 VAL Chi-restraints excluded: chain K residue 278 SER Chi-restraints excluded: chain K residue 284 SER Chi-restraints excluded: chain K residue 290 HIS Chi-restraints excluded: chain N residue 4 VAL Chi-restraints excluded: chain N residue 137 VAL Chi-restraints excluded: chain N residue 155 THR Chi-restraints excluded: chain N residue 208 VAL Chi-restraints excluded: chain N residue 218 VAL Chi-restraints excluded: chain N residue 243 VAL Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain O residue 34 ILE Chi-restraints excluded: chain O residue 85 ASN Chi-restraints excluded: chain O residue 149 VAL Chi-restraints excluded: chain O residue 193 SER Chi-restraints excluded: chain O residue 244 VAL Chi-restraints excluded: chain O residue 245 ASP Chi-restraints excluded: chain O residue 284 SER Chi-restraints excluded: chain O residue 290 HIS Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 204 MET Chi-restraints excluded: chain J residue 225 ILE Chi-restraints excluded: chain J residue 257 VAL Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 236 CYS Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 134 SER Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 200 LEU Chi-restraints excluded: chain G residue 206 GLN Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 289 THR Chi-restraints excluded: chain G residue 301 SER Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 69 ASP Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 182 VAL Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 225 ILE Chi-restraints excluded: chain L residue 236 CYS Chi-restraints excluded: chain L residue 241 ILE Chi-restraints excluded: chain L residue 257 VAL Chi-restraints excluded: chain L residue 292 LEU Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain M residue 2 SER Chi-restraints excluded: chain M residue 54 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 150 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 361 optimal weight: 3.9990 chunk 126 optimal weight: 0.8980 chunk 177 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 chunk 292 optimal weight: 0.6980 chunk 151 optimal weight: 0.0060 chunk 98 optimal weight: 1.9990 chunk 238 optimal weight: 10.0000 overall best weight: 1.5200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 GLN ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 7 ASN ** N 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 157 ASN ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 261 GLN O 290 HIS J 279 ASN ** J 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 ASN ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.104901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.081240 restraints weight = 86885.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.083849 restraints weight = 45949.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.085515 restraints weight = 31000.680| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.4561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 34096 Z= 0.148 Angle : 0.645 14.089 46328 Z= 0.329 Chirality : 0.048 0.294 5220 Planarity : 0.004 0.054 5980 Dihedral : 6.794 60.096 5084 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.12 % Allowed : 18.09 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.13), residues: 4240 helix: 0.35 (0.14), residues: 1456 sheet: -0.93 (0.17), residues: 888 loop : -0.93 (0.15), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.001 TRP K 20 HIS 0.011 0.001 HIS O 290 PHE 0.031 0.002 PHE J 68 TYR 0.020 0.002 TYR D 133 ARG 0.006 0.000 ARG H 47 Details of bonding type rmsd hydrogen bonds : bond 0.03216 ( 1404) hydrogen bonds : angle 5.05517 ( 4500) covalent geometry : bond 0.00331 (34096) covalent geometry : angle 0.64487 (46328) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 527 time to evaluate : 3.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 1 MET cc_start: 0.6935 (tmm) cc_final: 0.6487 (tmm) REVERT: P 28 GLN cc_start: 0.8933 (mp10) cc_final: 0.8624 (mp10) REVERT: P 46 GLN cc_start: 0.8422 (mm-40) cc_final: 0.8052 (tt0) REVERT: D 142 TYR cc_start: 0.7397 (OUTLIER) cc_final: 0.7091 (p90) REVERT: D 228 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8324 (mtmm) REVERT: D 240 ASN cc_start: 0.7905 (t0) cc_final: 0.7534 (t0) REVERT: D 295 ILE cc_start: 0.9444 (mp) cc_final: 0.9044 (mt) REVERT: A 20 TRP cc_start: 0.8146 (t60) cc_final: 0.7416 (t60) REVERT: A 65 ASP cc_start: 0.8344 (p0) cc_final: 0.7737 (t0) REVERT: A 147 ASP cc_start: 0.8409 (p0) cc_final: 0.8088 (p0) REVERT: A 176 MET cc_start: 0.7680 (mmt) cc_final: 0.7269 (mmt) REVERT: A 302 MET cc_start: 0.7705 (ptp) cc_final: 0.6318 (ptp) REVERT: A 327 ASP cc_start: 0.8927 (m-30) cc_final: 0.8506 (m-30) REVERT: E 240 ASN cc_start: 0.8250 (t0) cc_final: 0.8029 (t0) REVERT: E 246 PHE cc_start: 0.8776 (t80) cc_final: 0.8369 (t80) REVERT: E 295 ILE cc_start: 0.9224 (mm) cc_final: 0.8987 (mm) REVERT: F 20 TRP cc_start: 0.8432 (t60) cc_final: 0.7919 (t60) REVERT: F 65 ASP cc_start: 0.8318 (p0) cc_final: 0.7721 (t0) REVERT: F 93 ILE cc_start: 0.8499 (mm) cc_final: 0.8260 (tp) REVERT: F 176 MET cc_start: 0.8273 (mmt) cc_final: 0.7110 (mmt) REVERT: F 284 SER cc_start: 0.9313 (p) cc_final: 0.9027 (p) REVERT: F 302 MET cc_start: 0.7419 (ptp) cc_final: 0.6749 (ptp) REVERT: F 323 GLN cc_start: 0.8790 (mm110) cc_final: 0.8456 (mm-40) REVERT: F 327 ASP cc_start: 0.8587 (m-30) cc_final: 0.8303 (m-30) REVERT: I 142 TYR cc_start: 0.7520 (OUTLIER) cc_final: 0.6756 (p90) REVERT: I 246 PHE cc_start: 0.8912 (t80) cc_final: 0.8420 (t80) REVERT: I 295 ILE cc_start: 0.9425 (OUTLIER) cc_final: 0.9120 (mm) REVERT: I 314 TRP cc_start: 0.9298 (m100) cc_final: 0.9009 (m100) REVERT: K 65 ASP cc_start: 0.8221 (p0) cc_final: 0.7746 (t0) REVERT: K 271 MET cc_start: 0.7956 (mmt) cc_final: 0.7756 (mmp) REVERT: K 302 MET cc_start: 0.7240 (ptp) cc_final: 0.5843 (ptp) REVERT: N 295 ILE cc_start: 0.9440 (mp) cc_final: 0.9077 (mt) REVERT: O 20 TRP cc_start: 0.8464 (t60) cc_final: 0.7436 (t60) REVERT: O 65 ASP cc_start: 0.8341 (p0) cc_final: 0.7663 (t0) REVERT: O 176 MET cc_start: 0.7590 (mmt) cc_final: 0.6434 (mmt) REVERT: O 327 ASP cc_start: 0.8890 (m-30) cc_final: 0.8506 (m-30) REVERT: J 46 HIS cc_start: 0.7453 (m170) cc_final: 0.7184 (m-70) REVERT: J 127 PHE cc_start: 0.8192 (t80) cc_final: 0.7266 (t80) REVERT: J 131 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.8981 (mp) REVERT: J 316 MET cc_start: 0.9038 (OUTLIER) cc_final: 0.8777 (mmt) REVERT: B 67 ASN cc_start: 0.8738 (m110) cc_final: 0.8048 (p0) REVERT: B 131 LEU cc_start: 0.9399 (tt) cc_final: 0.9092 (mm) REVERT: G 46 HIS cc_start: 0.8067 (m-70) cc_final: 0.7664 (m170) REVERT: G 69 ASP cc_start: 0.8129 (m-30) cc_final: 0.7284 (t70) REVERT: G 80 ASN cc_start: 0.7137 (m110) cc_final: 0.6218 (t0) REVERT: G 127 PHE cc_start: 0.8234 (t80) cc_final: 0.7526 (t80) REVERT: G 131 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9163 (mp) REVERT: G 193 GLU cc_start: 0.8515 (tm-30) cc_final: 0.8236 (tm-30) REVERT: L 42 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8308 (mp) REVERT: L 69 ASP cc_start: 0.7948 (m-30) cc_final: 0.6867 (t70) REVERT: L 78 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8246 (mm) REVERT: L 131 LEU cc_start: 0.9457 (tt) cc_final: 0.9076 (mp) REVERT: L 180 ASP cc_start: 0.8244 (m-30) cc_final: 0.7873 (m-30) REVERT: L 214 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7687 (mp0) REVERT: C 1 MET cc_start: 0.9037 (tpp) cc_final: 0.8540 (tmm) REVERT: C 39 LEU cc_start: 0.8817 (mp) cc_final: 0.8348 (tp) REVERT: H 1 MET cc_start: 0.6990 (ttm) cc_final: 0.6376 (tpp) REVERT: M 1 MET cc_start: 0.6175 (tpt) cc_final: 0.5075 (mmp) REVERT: M 4 LEU cc_start: 0.9044 (mp) cc_final: 0.8811 (pt) REVERT: M 10 GLN cc_start: 0.8972 (mt0) cc_final: 0.8643 (mt0) REVERT: M 28 GLN cc_start: 0.8790 (mp10) cc_final: 0.8445 (mp10) REVERT: M 36 LEU cc_start: 0.9299 (tp) cc_final: 0.9048 (tp) REVERT: M 37 GLU cc_start: 0.8797 (tp30) cc_final: 0.8564 (tp30) REVERT: M 39 LEU cc_start: 0.9099 (mp) cc_final: 0.8557 (tp) REVERT: M 42 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8625 (mm-30) REVERT: M 47 ARG cc_start: 0.8900 (mmm160) cc_final: 0.7954 (mmm160) REVERT: M 50 GLN cc_start: 0.8971 (tm-30) cc_final: 0.8493 (tm-30) REVERT: M 54 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7800 (pttp) REVERT: M 66 ASP cc_start: 0.7975 (t0) cc_final: 0.7624 (t0) outliers start: 146 outliers final: 108 residues processed: 631 average time/residue: 0.3965 time to fit residues: 422.6537 Evaluate side-chains 601 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 483 time to evaluate : 3.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 142 TYR Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 228 LYS Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 142 TYR Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 302 MET Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain I residue 142 TYR Chi-restraints excluded: chain I residue 168 GLU Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 228 LYS Chi-restraints excluded: chain I residue 245 ASP Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 251 GLU Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain I residue 295 ILE Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain I residue 332 MET Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 85 ASN Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain K residue 259 VAL Chi-restraints excluded: chain K residue 284 SER Chi-restraints excluded: chain N residue 4 VAL Chi-restraints excluded: chain N residue 137 VAL Chi-restraints excluded: chain N residue 155 THR Chi-restraints excluded: chain N residue 208 VAL Chi-restraints excluded: chain N residue 218 VAL Chi-restraints excluded: chain N residue 243 VAL Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain O residue 34 ILE Chi-restraints excluded: chain O residue 85 ASN Chi-restraints excluded: chain O residue 193 SER Chi-restraints excluded: chain O residue 244 VAL Chi-restraints excluded: chain O residue 245 ASP Chi-restraints excluded: chain O residue 261 GLN Chi-restraints excluded: chain O residue 284 SER Chi-restraints excluded: chain O residue 290 HIS Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 204 MET Chi-restraints excluded: chain J residue 225 ILE Chi-restraints excluded: chain J residue 257 VAL Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 316 MET Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 134 SER Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 200 LEU Chi-restraints excluded: chain G residue 224 THR Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 301 SER Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 182 VAL Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 224 THR Chi-restraints excluded: chain L residue 225 ILE Chi-restraints excluded: chain L residue 236 CYS Chi-restraints excluded: chain L residue 241 ILE Chi-restraints excluded: chain L residue 257 VAL Chi-restraints excluded: chain L residue 292 LEU Chi-restraints excluded: chain M residue 2 SER Chi-restraints excluded: chain M residue 54 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 289 optimal weight: 4.9990 chunk 201 optimal weight: 0.9980 chunk 340 optimal weight: 0.0170 chunk 191 optimal weight: 0.6980 chunk 311 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 384 optimal weight: 0.8980 chunk 110 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 307 optimal weight: 0.7980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 59 GLN E 157 ASN ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 ASN ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 335 HIS ** N 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 290 HIS J 295 HIS ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.106589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.083623 restraints weight = 86062.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.086300 restraints weight = 44720.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.087985 restraints weight = 29686.733| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.4765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34096 Z= 0.118 Angle : 0.646 14.710 46328 Z= 0.329 Chirality : 0.047 0.311 5220 Planarity : 0.004 0.053 5980 Dihedral : 6.487 59.295 5084 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.27 % Allowed : 18.62 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.73 (0.13), residues: 4240 helix: 0.32 (0.13), residues: 1496 sheet: -0.78 (0.17), residues: 880 loop : -0.89 (0.15), residues: 1864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.001 TRP K 20 HIS 0.013 0.001 HIS O 290 PHE 0.032 0.001 PHE B 68 TYR 0.018 0.001 TYR D 133 ARG 0.007 0.000 ARG B 164 Details of bonding type rmsd hydrogen bonds : bond 0.03124 ( 1404) hydrogen bonds : angle 4.94648 ( 4500) covalent geometry : bond 0.00267 (34096) covalent geometry : angle 0.64602 (46328) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 560 time to evaluate : 5.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 1 MET cc_start: 0.6876 (tmm) cc_final: 0.6518 (tmm) REVERT: P 28 GLN cc_start: 0.8906 (mp10) cc_final: 0.8595 (mp10) REVERT: P 39 LEU cc_start: 0.8851 (mp) cc_final: 0.8329 (tp) REVERT: P 46 GLN cc_start: 0.8439 (mm-40) cc_final: 0.8121 (tt0) REVERT: D 228 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8318 (mtmm) REVERT: D 240 ASN cc_start: 0.7739 (t0) cc_final: 0.7432 (t0) REVERT: D 295 ILE cc_start: 0.9429 (mp) cc_final: 0.9078 (mt) REVERT: D 321 TYR cc_start: 0.9011 (t80) cc_final: 0.8787 (t80) REVERT: A 20 TRP cc_start: 0.8071 (t60) cc_final: 0.7315 (t60) REVERT: A 65 ASP cc_start: 0.8279 (p0) cc_final: 0.7722 (t0) REVERT: A 147 ASP cc_start: 0.8418 (p0) cc_final: 0.8138 (p0) REVERT: A 176 MET cc_start: 0.7689 (mmt) cc_final: 0.7304 (mmt) REVERT: A 302 MET cc_start: 0.7584 (ptp) cc_final: 0.6274 (ptp) REVERT: A 327 ASP cc_start: 0.8899 (m-30) cc_final: 0.8455 (m-30) REVERT: E 246 PHE cc_start: 0.8739 (t80) cc_final: 0.8315 (t80) REVERT: E 295 ILE cc_start: 0.9266 (mm) cc_final: 0.8964 (mm) REVERT: F 20 TRP cc_start: 0.8359 (t60) cc_final: 0.7896 (t60) REVERT: F 65 ASP cc_start: 0.8298 (p0) cc_final: 0.7827 (t0) REVERT: F 176 MET cc_start: 0.8144 (mmt) cc_final: 0.7498 (mmt) REVERT: F 284 SER cc_start: 0.9261 (p) cc_final: 0.8993 (p) REVERT: F 290 HIS cc_start: 0.8744 (OUTLIER) cc_final: 0.7414 (t-90) REVERT: F 302 MET cc_start: 0.7400 (ptp) cc_final: 0.6709 (ptp) REVERT: F 323 GLN cc_start: 0.8797 (mm110) cc_final: 0.8414 (mm-40) REVERT: F 327 ASP cc_start: 0.8647 (m-30) cc_final: 0.8363 (m-30) REVERT: I 142 TYR cc_start: 0.7577 (OUTLIER) cc_final: 0.6623 (p90) REVERT: I 246 PHE cc_start: 0.8883 (t80) cc_final: 0.8683 (t80) REVERT: I 295 ILE cc_start: 0.9383 (OUTLIER) cc_final: 0.9046 (mm) REVERT: K 65 ASP cc_start: 0.8134 (p0) cc_final: 0.7773 (t0) REVERT: K 284 SER cc_start: 0.9202 (OUTLIER) cc_final: 0.8883 (m) REVERT: K 302 MET cc_start: 0.7250 (ptp) cc_final: 0.5969 (ptp) REVERT: N 226 GLN cc_start: 0.7922 (tm-30) cc_final: 0.7646 (tm-30) REVERT: N 295 ILE cc_start: 0.9388 (mp) cc_final: 0.9143 (mm) REVERT: N 314 TRP cc_start: 0.9190 (m100) cc_final: 0.8822 (m100) REVERT: O 20 TRP cc_start: 0.8365 (t60) cc_final: 0.7381 (t60) REVERT: O 65 ASP cc_start: 0.8242 (p0) cc_final: 0.7865 (t0) REVERT: O 176 MET cc_start: 0.7463 (mmt) cc_final: 0.6395 (mmt) REVERT: O 323 GLN cc_start: 0.8738 (mm-40) cc_final: 0.8209 (mt0) REVERT: O 327 ASP cc_start: 0.8885 (m-30) cc_final: 0.8555 (m-30) REVERT: J 42 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8145 (mt) REVERT: J 46 HIS cc_start: 0.7311 (m170) cc_final: 0.7011 (m170) REVERT: J 85 MET cc_start: 0.8209 (tpt) cc_final: 0.7891 (tpt) REVERT: J 127 PHE cc_start: 0.8145 (t80) cc_final: 0.7399 (t80) REVERT: J 131 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9066 (mp) REVERT: J 233 LYS cc_start: 0.8845 (mmtt) cc_final: 0.8620 (mptt) REVERT: J 316 MET cc_start: 0.9022 (OUTLIER) cc_final: 0.8796 (mmt) REVERT: B 67 ASN cc_start: 0.8695 (m110) cc_final: 0.8023 (p0) REVERT: B 131 LEU cc_start: 0.9413 (tt) cc_final: 0.9082 (mm) REVERT: G 46 HIS cc_start: 0.8015 (m-70) cc_final: 0.7697 (m170) REVERT: G 69 ASP cc_start: 0.7942 (m-30) cc_final: 0.7207 (t0) REVERT: G 80 ASN cc_start: 0.7149 (m110) cc_final: 0.6440 (t0) REVERT: G 127 PHE cc_start: 0.8225 (t80) cc_final: 0.7710 (t80) REVERT: G 193 GLU cc_start: 0.8477 (tm-30) cc_final: 0.8204 (tm-30) REVERT: L 42 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8044 (mt) REVERT: L 69 ASP cc_start: 0.7885 (m-30) cc_final: 0.6848 (t70) REVERT: L 78 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8166 (mm) REVERT: L 110 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8135 (tp) REVERT: L 131 LEU cc_start: 0.9442 (tt) cc_final: 0.9072 (mp) REVERT: L 180 ASP cc_start: 0.8274 (m-30) cc_final: 0.7990 (m-30) REVERT: C 4 LEU cc_start: 0.8645 (pp) cc_final: 0.8116 (tp) REVERT: C 33 TRP cc_start: 0.8208 (m100) cc_final: 0.7592 (m100) REVERT: C 47 ARG cc_start: 0.8864 (tpp80) cc_final: 0.8300 (tpp80) REVERT: C 54 LYS cc_start: 0.7183 (pmmt) cc_final: 0.6134 (tptp) REVERT: H 1 MET cc_start: 0.7077 (ttm) cc_final: 0.6644 (tpp) REVERT: M 1 MET cc_start: 0.5865 (tpt) cc_final: 0.4889 (mmp) REVERT: M 4 LEU cc_start: 0.9080 (mp) cc_final: 0.8829 (pt) REVERT: M 28 GLN cc_start: 0.8769 (mp10) cc_final: 0.8433 (mp10) REVERT: M 36 LEU cc_start: 0.9275 (tp) cc_final: 0.9049 (tp) REVERT: M 37 GLU cc_start: 0.8749 (tp30) cc_final: 0.8515 (tp30) REVERT: M 39 LEU cc_start: 0.9059 (mp) cc_final: 0.8528 (tp) REVERT: M 42 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8612 (mm-30) REVERT: M 47 ARG cc_start: 0.8933 (mmm160) cc_final: 0.8016 (mmm160) REVERT: M 50 GLN cc_start: 0.8968 (tm-30) cc_final: 0.8642 (tm-30) REVERT: M 54 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7739 (pttp) outliers start: 116 outliers final: 87 residues processed: 637 average time/residue: 0.4494 time to fit residues: 488.7855 Evaluate side-chains 610 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 511 time to evaluate : 4.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 228 LYS Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 142 TYR Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 290 HIS Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain I residue 142 TYR Chi-restraints excluded: chain I residue 166 LEU Chi-restraints excluded: chain I residue 168 GLU Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 228 LYS Chi-restraints excluded: chain I residue 245 ASP Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 251 GLU Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain I residue 295 ILE Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 332 MET Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 85 ASN Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain K residue 259 VAL Chi-restraints excluded: chain K residue 284 SER Chi-restraints excluded: chain N residue 4 VAL Chi-restraints excluded: chain N residue 137 VAL Chi-restraints excluded: chain N residue 208 VAL Chi-restraints excluded: chain N residue 241 VAL Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain O residue 34 ILE Chi-restraints excluded: chain O residue 85 ASN Chi-restraints excluded: chain O residue 132 THR Chi-restraints excluded: chain O residue 149 VAL Chi-restraints excluded: chain O residue 193 SER Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 244 VAL Chi-restraints excluded: chain O residue 245 ASP Chi-restraints excluded: chain O residue 259 VAL Chi-restraints excluded: chain O residue 290 HIS Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 225 ILE Chi-restraints excluded: chain J residue 316 MET Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 224 THR Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 301 SER Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 182 VAL Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 224 THR Chi-restraints excluded: chain L residue 225 ILE Chi-restraints excluded: chain L residue 241 ILE Chi-restraints excluded: chain L residue 292 LEU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain M residue 54 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 117 optimal weight: 9.9990 chunk 385 optimal weight: 1.9990 chunk 35 optimal weight: 0.3980 chunk 70 optimal weight: 4.9990 chunk 196 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 276 optimal weight: 0.1980 chunk 112 optimal weight: 5.9990 chunk 208 optimal weight: 6.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 GLN ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 GLN ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 240 ASN O 290 HIS ** J 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.104690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.080644 restraints weight = 87678.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.083203 restraints weight = 47461.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.084827 restraints weight = 32566.120| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.4813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 34096 Z= 0.186 Angle : 0.705 16.364 46328 Z= 0.356 Chirality : 0.049 0.372 5220 Planarity : 0.004 0.054 5980 Dihedral : 6.705 59.997 5084 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.47 % Allowed : 19.50 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.67 (0.13), residues: 4240 helix: 0.36 (0.14), residues: 1476 sheet: -0.70 (0.18), residues: 824 loop : -0.86 (0.15), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.093 0.002 TRP K 20 HIS 0.013 0.001 HIS P 16 PHE 0.034 0.002 PHE B 68 TYR 0.030 0.002 TYR D 142 ARG 0.008 0.000 ARG L 207 Details of bonding type rmsd hydrogen bonds : bond 0.03341 ( 1404) hydrogen bonds : angle 5.04607 ( 4500) covalent geometry : bond 0.00417 (34096) covalent geometry : angle 0.70457 (46328) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 503 time to evaluate : 3.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 1 MET cc_start: 0.7069 (tmm) cc_final: 0.6791 (tmm) REVERT: P 28 GLN cc_start: 0.8921 (mp10) cc_final: 0.8612 (mp10) REVERT: P 46 GLN cc_start: 0.8399 (mm-40) cc_final: 0.8042 (tt0) REVERT: D 228 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8372 (mtmm) REVERT: D 240 ASN cc_start: 0.8006 (t0) cc_final: 0.7668 (t0) REVERT: D 295 ILE cc_start: 0.9453 (mp) cc_final: 0.9041 (mt) REVERT: D 321 TYR cc_start: 0.9078 (t80) cc_final: 0.8795 (t80) REVERT: D 332 MET cc_start: 0.8096 (mmp) cc_final: 0.7790 (mmp) REVERT: A 20 TRP cc_start: 0.8146 (t60) cc_final: 0.7381 (t60) REVERT: A 65 ASP cc_start: 0.8351 (p0) cc_final: 0.7752 (t0) REVERT: A 147 ASP cc_start: 0.8422 (p0) cc_final: 0.8144 (p0) REVERT: A 176 MET cc_start: 0.7792 (mmt) cc_final: 0.7171 (mmp) REVERT: A 302 MET cc_start: 0.7626 (ptp) cc_final: 0.6230 (ptp) REVERT: A 327 ASP cc_start: 0.8907 (m-30) cc_final: 0.8511 (m-30) REVERT: E 246 PHE cc_start: 0.8764 (t80) cc_final: 0.8353 (t80) REVERT: E 295 ILE cc_start: 0.9313 (mm) cc_final: 0.9040 (mm) REVERT: F 20 TRP cc_start: 0.8463 (t60) cc_final: 0.7991 (t60) REVERT: F 65 ASP cc_start: 0.8295 (p0) cc_final: 0.7824 (t0) REVERT: F 176 MET cc_start: 0.8303 (mmt) cc_final: 0.7164 (mmt) REVERT: F 284 SER cc_start: 0.9313 (p) cc_final: 0.8999 (p) REVERT: F 290 HIS cc_start: 0.8812 (OUTLIER) cc_final: 0.7461 (t-90) REVERT: F 302 MET cc_start: 0.7383 (ptp) cc_final: 0.6892 (ptp) REVERT: F 323 GLN cc_start: 0.8738 (mm110) cc_final: 0.8418 (mm-40) REVERT: F 327 ASP cc_start: 0.8641 (m-30) cc_final: 0.8367 (m-30) REVERT: I 142 TYR cc_start: 0.7557 (OUTLIER) cc_final: 0.6569 (p90) REVERT: I 240 ASN cc_start: 0.7876 (t0) cc_final: 0.7492 (t0) REVERT: I 246 PHE cc_start: 0.8833 (t80) cc_final: 0.8604 (t80) REVERT: I 295 ILE cc_start: 0.9367 (OUTLIER) cc_final: 0.8996 (mm) REVERT: K 65 ASP cc_start: 0.8074 (p0) cc_final: 0.7714 (t0) REVERT: K 261 GLN cc_start: 0.8524 (mm-40) cc_final: 0.7967 (tp40) REVERT: K 302 MET cc_start: 0.7189 (ptp) cc_final: 0.6855 (ptp) REVERT: N 226 GLN cc_start: 0.7970 (tm-30) cc_final: 0.7718 (tm-30) REVERT: N 295 ILE cc_start: 0.9460 (mp) cc_final: 0.9043 (mt) REVERT: O 20 TRP cc_start: 0.8386 (t60) cc_final: 0.7445 (t60) REVERT: O 65 ASP cc_start: 0.8300 (p0) cc_final: 0.7849 (t0) REVERT: O 327 ASP cc_start: 0.8848 (m-30) cc_final: 0.8525 (m-30) REVERT: J 42 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8356 (mp) REVERT: J 46 HIS cc_start: 0.7227 (m170) cc_final: 0.6978 (m170) REVERT: J 85 MET cc_start: 0.8185 (tpt) cc_final: 0.7872 (tpt) REVERT: J 127 PHE cc_start: 0.8128 (t80) cc_final: 0.7340 (t80) REVERT: J 131 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.8984 (mp) REVERT: J 316 MET cc_start: 0.9023 (OUTLIER) cc_final: 0.8809 (mmt) REVERT: B 67 ASN cc_start: 0.8918 (m110) cc_final: 0.8096 (p0) REVERT: B 131 LEU cc_start: 0.9437 (tt) cc_final: 0.9118 (mm) REVERT: G 46 HIS cc_start: 0.8036 (m-70) cc_final: 0.7756 (m170) REVERT: G 80 ASN cc_start: 0.7019 (m110) cc_final: 0.6407 (t0) REVERT: G 85 MET cc_start: 0.8202 (tpt) cc_final: 0.7965 (tpt) REVERT: G 127 PHE cc_start: 0.8187 (t80) cc_final: 0.7568 (t80) REVERT: G 193 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8229 (tm-30) REVERT: G 279 ASN cc_start: 0.8719 (t0) cc_final: 0.8478 (t0) REVERT: L 42 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8359 (mt) REVERT: L 78 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8240 (mm) REVERT: L 127 PHE cc_start: 0.7745 (t80) cc_final: 0.7471 (t80) REVERT: L 131 LEU cc_start: 0.9464 (tt) cc_final: 0.9078 (mp) REVERT: L 180 ASP cc_start: 0.8375 (m-30) cc_final: 0.7977 (m-30) REVERT: C 4 LEU cc_start: 0.8655 (pp) cc_final: 0.8146 (tp) REVERT: C 47 ARG cc_start: 0.8884 (tpp80) cc_final: 0.8290 (tpp80) REVERT: C 54 LYS cc_start: 0.7299 (pmmt) cc_final: 0.6292 (tptp) REVERT: H 1 MET cc_start: 0.7138 (ttm) cc_final: 0.6634 (tpp) REVERT: M 1 MET cc_start: 0.5926 (tpt) cc_final: 0.5231 (mmt) REVERT: M 4 LEU cc_start: 0.9141 (mp) cc_final: 0.8837 (pt) REVERT: M 10 GLN cc_start: 0.8965 (mt0) cc_final: 0.8664 (mt0) REVERT: M 28 GLN cc_start: 0.8796 (mp10) cc_final: 0.8471 (mp10) REVERT: M 36 LEU cc_start: 0.9327 (tp) cc_final: 0.9078 (tp) REVERT: M 37 GLU cc_start: 0.8796 (tp30) cc_final: 0.8571 (tp30) REVERT: M 39 LEU cc_start: 0.9110 (mp) cc_final: 0.8552 (tp) REVERT: M 42 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8613 (mm-30) REVERT: M 47 ARG cc_start: 0.8947 (mmm160) cc_final: 0.8020 (mmm160) REVERT: M 50 GLN cc_start: 0.8946 (tm-30) cc_final: 0.8573 (tm-30) REVERT: M 54 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7793 (pttp) outliers start: 123 outliers final: 103 residues processed: 590 average time/residue: 0.4163 time to fit residues: 417.3144 Evaluate side-chains 611 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 498 time to evaluate : 3.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 228 LYS Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 57 GLN Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 142 TYR Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain F residue 85 ASN Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 290 HIS Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain I residue 142 TYR Chi-restraints excluded: chain I residue 168 GLU Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 228 LYS Chi-restraints excluded: chain I residue 245 ASP Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 251 GLU Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain I residue 295 ILE Chi-restraints excluded: chain I residue 304 LEU Chi-restraints excluded: chain I residue 332 MET Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 85 ASN Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain K residue 259 VAL Chi-restraints excluded: chain K residue 278 SER Chi-restraints excluded: chain K residue 284 SER Chi-restraints excluded: chain K residue 325 VAL Chi-restraints excluded: chain N residue 4 VAL Chi-restraints excluded: chain N residue 137 VAL Chi-restraints excluded: chain N residue 208 VAL Chi-restraints excluded: chain N residue 241 VAL Chi-restraints excluded: chain N residue 243 VAL Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain O residue 34 ILE Chi-restraints excluded: chain O residue 85 ASN Chi-restraints excluded: chain O residue 132 THR Chi-restraints excluded: chain O residue 149 VAL Chi-restraints excluded: chain O residue 193 SER Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 244 VAL Chi-restraints excluded: chain O residue 245 ASP Chi-restraints excluded: chain O residue 290 HIS Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 225 ILE Chi-restraints excluded: chain J residue 288 VAL Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 316 MET Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 206 GLN Chi-restraints excluded: chain G residue 224 THR Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 301 SER Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 182 VAL Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 225 ILE Chi-restraints excluded: chain L residue 236 CYS Chi-restraints excluded: chain L residue 241 ILE Chi-restraints excluded: chain L residue 292 LEU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain M residue 54 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 177 optimal weight: 0.4980 chunk 129 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 167 optimal weight: 0.9980 chunk 318 optimal weight: 0.9990 chunk 375 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 147 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 GLN ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 206 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.104918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.080831 restraints weight = 87795.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.083398 restraints weight = 47647.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.084995 restraints weight = 32751.155| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.4832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.145 34096 Z= 0.190 Angle : 0.784 59.140 46328 Z= 0.414 Chirality : 0.048 0.342 5220 Planarity : 0.004 0.054 5980 Dihedral : 6.708 59.984 5084 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.39 % Allowed : 19.86 % Favored : 76.75 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.44 % 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: -0.66 (0.13), residues: 4240 helix: 0.38 (0.14), residues: 1476 sheet: -0.70 (0.18), residues: 824 loop : -0.86 (0.15), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.083 0.002 TRP K 20 HIS 0.077 0.001 HIS O 290 PHE 0.026 0.002 PHE B 68 TYR 0.024 0.002 TYR D 142 ARG 0.009 0.000 ARG P 12 Details of bonding type rmsd hydrogen bonds : bond 0.03329 ( 1404) hydrogen bonds : angle 5.04938 ( 4500) covalent geometry : bond 0.00425 (34096) covalent geometry : angle 0.78449 (46328) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13053.60 seconds wall clock time: 235 minutes 53.53 seconds (14153.53 seconds total)