Starting phenix.real_space_refine on Thu Oct 29 18:30:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6gve_0071/10_2026/6gve_0071.cif Found real_map, /net/cci-nas-00/data/ceres_data/6gve_0071/10_2026/6gve_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6gve_0071/10_2026/6gve_0071.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6gve_0071/10_2026/6gve_0071.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6gve_0071/10_2026/6gve_0071.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6gve_0071/10_2026/6gve_0071.map" model { file = "/net/cci-nas-00/data/ceres_data/6gve_0071/10_2026/6gve_0071.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6gve_0071/10_2026/6gve_0071.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33412 Number of models: 1 Model: "" Number of chains: 4 Chain: "P" 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: "D" 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: "J" 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: {'GLU:plan': 3, 'GLN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "D" 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: C, H, M, A, E, F, I, K, N, O, B, G, L Time building chain proxies: 4.51, per 1000 atoms: 0.13 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=16, symmetry=0 Simple disulfide: pdb=" SG CYS P 19 " - pdb=" SG CYS P 29 " distance=2.05 Simple disulfide: pdb=" SG CYS P 61 " - pdb=" SG CYS P 70 " distance=2.02 Simple disulfide: pdb=" SG CYS J 19 " - pdb=" SG CYS J 41 " distance=2.03 Simple disulfide: pdb=" SG CYS J 230 " - pdb=" SG CYS J 236 " distance=2.02 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 41 " distance=2.03 Simple disulfide: pdb=" SG CYS B 230 " - pdb=" SG CYS B 236 " distance=2.02 Simple disulfide: pdb=" SG CYS G 19 " - pdb=" SG CYS G 41 " distance=2.03 Simple disulfide: pdb=" SG CYS G 230 " - pdb=" SG CYS G 236 " distance=2.02 Simple disulfide: pdb=" SG CYS L 19 " - pdb=" SG CYS L 41 " distance=2.03 Simple disulfide: pdb=" SG CYS L 230 " - pdb=" SG CYS L 236 " distance=2.02 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 29 " distance=2.05 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 70 " distance=2.02 Simple disulfide: pdb=" SG CYS H 19 " - pdb=" SG CYS H 29 " distance=2.05 Simple disulfide: pdb=" SG CYS H 61 " - pdb=" SG CYS H 70 " distance=2.02 Simple disulfide: pdb=" SG CYS M 19 " - pdb=" SG CYS M 29 " distance=2.05 Simple disulfide: pdb=" SG CYS M 61 " - pdb=" SG CYS M 70 " distance=2.02 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: 2.70 Conformation dependent library (CDL) restraints added in 1.4 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: 0.91 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: 6.00 Time building geometry restraints manager: 3.68 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: 19093 15.12 - 30.24: 1031 30.24 - 45.35: 184 45.35 - 60.47: 28 60.47 - 75.59: 16 Dihedral angle restraints: 20352 sinusoidal: 8028 harmonic: 12324 Sorted by residual: dihedral pdb=" CB CYS H 19 " pdb=" SG CYS H 19 " pdb=" SG CYS H 29 " pdb=" CB CYS H 29 " ideal model delta sinusoidal sigma weight residual 93.00 19.46 73.54 1 1.00e+01 1.00e-02 6.88e+01 dihedral pdb=" CB CYS P 19 " pdb=" SG CYS P 19 " pdb=" SG CYS P 29 " pdb=" CB CYS P 29 " ideal model delta sinusoidal sigma weight residual 93.00 19.46 73.54 1 1.00e+01 1.00e-02 6.88e+01 dihedral pdb=" CB CYS C 19 " pdb=" SG CYS C 19 " pdb=" SG CYS C 29 " pdb=" CB CYS C 29 " ideal model delta sinusoidal sigma weight residual 93.00 19.46 73.54 1 1.00e+01 1.00e-02 6.88e+01 ... (remaining 20349 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: 2.13 - 2.69: 1179 2.69 - 3.24: 32023 3.24 - 3.79: 56109 3.79 - 4.35: 69876 4.35 - 4.90: 116320 Nonbonded interactions: 275507 Sorted by model distance: nonbonded pdb=" OH TYR C 73 " pdb=" O1A NAD E1001 " model vdw 2.133 3.040 nonbonded pdb=" OG1 THR J 226 " pdb=" OG1 THR G 226 " model vdw 2.252 3.040 nonbonded pdb=" OH TYR M 73 " pdb=" O1A NAD N1001 " model vdw 2.263 3.040 nonbonded pdb=" NH1 ARG E 81 " pdb=" OD2 ASP C 66 " model vdw 2.264 3.120 nonbonded pdb=" OG1 THR B 226 " pdb=" OG1 THR L 226 " model vdw 2.270 3.040 ... (remaining 275502 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.07 Found NCS groups: ncs_group { reference = chain 'P' selection = chain 'C' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'D' selection = chain 'A' selection = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'K' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'J' selection = chain 'B' selection = chain 'G' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 26.200 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 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 34112 Z= 0.442 Angle : 0.988 10.513 46360 Z= 0.530 Chirality : 0.064 0.364 5220 Planarity : 0.008 0.077 5980 Dihedral : 10.072 75.588 12384 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.11 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.009 0.002 ARG G 50 TYR 0.027 0.003 TYR D 315 PHE 0.022 0.003 PHE D 9 TRP 0.027 0.003 TRP J 227 HIS 0.011 0.003 HIS B 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00952 / 0.44 (34096) covalent geometry : angle 0.98630 / 0.53 (46328) SS BOND : bond 0.01029 / 0.66 ( 16) SS BOND : angle 2.10808 / 1.33 ( 32) hydrogen bonds : bond 0.18602 / 12.30 ( 1404) hydrogen bonds : angle 8.61916 / 6.00 ( 4500) *********************** 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 : 1.208 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: 0.8198 (tp-100) REVERT: P 55 THR cc_start: 0.6559 (p) cc_final: 0.6337 (p) REVERT: D 133 TYR cc_start: 0.7991 (m-80) cc_final: 0.7738 (m-80) REVERT: D 173 GLN cc_start: 0.8513 (mt0) cc_final: 0.8059 (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: 0.8107 (ttp) REVERT: D 179 THR cc_start: 0.8018 (t) cc_final: 0.7751 (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: 0.7471 (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: 0.8714 (m110) REVERT: A 147 ASP cc_start: 0.8429 (p0) cc_final: 0.8103 (p0) REVERT: A 176 MET cc_start: 0.8644 (mmt) cc_final: 0.8306 (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: 0.7208 (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: 0.7756 (t) REVERT: E 182 SER cc_start: 0.9270 (p) cc_final: 0.8972 (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: 0.8585 (t) REVERT: E 249 GLN cc_start: 0.7699 (tt0) cc_final: 0.7433 (tt0) REVERT: E 286 ASP cc_start: 0.8372 (m-30) cc_final: 0.7948 (m-30) REVERT: F 20 TRP cc_start: 0.8703 (t60) cc_final: 0.7999 (t60) REVERT: F 67 CYS cc_start: 0.8517 (m) cc_final: 0.7948 (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: 0.8705 (ppp) REVERT: F 284 SER cc_start: 0.8633 (p) cc_final: 0.8370 (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: 0.8543 (mt0) REVERT: F 327 ASP cc_start: 0.8893 (m-30) cc_final: 0.8374 (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: 0.7487 (m-80) REVERT: I 173 GLN cc_start: 0.8427 (mt0) cc_final: 0.8035 (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: 0.8433 (tpt) REVERT: K 20 TRP cc_start: 0.8616 (t60) cc_final: 0.8006 (t60) REVERT: K 93 ILE cc_start: 0.8808 (mm) cc_final: 0.8441 (tp) REVERT: K 129 ASN cc_start: 0.8556 (m-40) cc_final: 0.8183 (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: 0.8685 (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: 0.6221 (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: 0.8490 (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: 0.7123 (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: 0.8686 (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 17 MET cc_start: 0.8815 (tpt) cc_final: 0.8495 (tpt) REVERT: O 21 LEU cc_start: 0.9317 (mt) cc_final: 0.8938 (mp) REVERT: O 93 ILE cc_start: 0.8925 (mm) cc_final: 0.8653 (tp) REVERT: O 129 ASN cc_start: 0.8204 (m-40) cc_final: 0.7644 (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: 0.7655 (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: 0.8475 (mt0) REVERT: O 323 GLN cc_start: 0.9350 (mm-40) cc_final: 0.8462 (mt0) REVERT: O 327 ASP cc_start: 0.8975 (m-30) cc_final: 0.8547 (m-30) REVERT: O 331 HIS cc_start: 0.8510 (t70) cc_final: 0.8026 (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: 0.6643 (m170) REVERT: B 66 ASN cc_start: 0.7612 (m-40) cc_final: 0.7315 (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: 0.8743 (m-10) REVERT: B 309 GLN cc_start: 0.8896 (mt0) cc_final: 0.8462 (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: 0.7158 (m-40) REVERT: G 106 HIS cc_start: 0.7077 (m-70) cc_final: 0.6842 (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: 0.7102 (m170) REVERT: L 116 LEU cc_start: 0.8943 (tp) cc_final: 0.8634 (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: 0.5671 (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: 0.7661 (pp30) 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: 0.2138 time to fit residues: 349.0004 Evaluate side-chains 574 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 570 time to evaluate : 1.326 ------------------------------------------------------------------------------- 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: [197, 388, 215, 20, 132, 261, 248, 207, 401, 155, 244] chunk 197 optimal weight: 20.0000 chunk 388 optimal weight: 0.5980 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.9980 chunk 401 optimal weight: 3.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 ** E 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 N 173 GLN ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 181 HIS N 331 HIS O 45 HIS O 173 GLN O 181 HIS O 290 HIS O 323 GLN O 331 HIS J 114 HIS J 184 GLN J 206 GLN B 184 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN 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 64 ASN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.108444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.084426 restraints weight = 85288.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.087193 restraints weight = 44130.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.088950 restraints weight = 29337.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.090066 restraints weight = 22893.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.090743 restraints weight = 19663.154| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 34112 Z= 0.134 Angle : 0.632 8.776 46360 Z= 0.335 Chirality : 0.047 0.196 5220 Planarity : 0.006 0.062 5980 Dihedral : 6.422 59.536 4684 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.43 % Allowed : 10.86 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.43 (0.12), residues: 4240 helix: -1.10 (0.12), residues: 1444 sheet: -1.98 (0.16), residues: 864 loop : -1.71 (0.13), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 188 TYR 0.021 0.002 TYR F 321 PHE 0.022 0.002 PHE J 127 TRP 0.014 0.001 TRP E 20 HIS 0.010 0.001 HIS J 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (34096) covalent geometry : angle 0.63166 / 0.33 (46328) SS BOND : bond 0.00462 / 0.29 ( 16) SS BOND : angle 1.30286 / 0.86 ( 32) hydrogen bonds : bond 0.03684 / 2.45 ( 1404) hydrogen bonds : angle 5.53658 / 3.89 ( 4500) *********************** 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 831 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 745 time to evaluate : 1.178 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: 0.7070 (ttm) cc_final: 0.6208 (tpp) REVERT: P 4 LEU cc_start: 0.8757 (tp) cc_final: 0.8473 (mp) REVERT: P 12 ARG cc_start: 0.8467 (ttt180) cc_final: 0.8154 (ttt180) REVERT: P 33 TRP cc_start: 0.7892 (m100) cc_final: 0.7591 (m100) REVERT: P 39 LEU cc_start: 0.8833 (mp) cc_final: 0.8504 (tp) REVERT: P 47 ARG cc_start: 0.8579 (mmm160) cc_final: 0.8027 (mmm160) REVERT: P 50 GLN cc_start: 0.8273 (tm-30) cc_final: 0.7798 (tm-30) REVERT: P 54 LYS cc_start: 0.7522 (pmmt) cc_final: 0.6598 (tptp) REVERT: P 63 ASP cc_start: 0.7654 (p0) cc_final: 0.7401 (p0) REVERT: D 249 GLN cc_start: 0.7961 (tt0) cc_final: 0.7327 (tt0) REVERT: D 295 ILE cc_start: 0.9400 (mp) cc_final: 0.9062 (mt) REVERT: A 67 CYS cc_start: 0.7847 (m) cc_final: 0.7626 (t) REVERT: A 147 ASP cc_start: 0.8167 (p0) cc_final: 0.7839 (p0) REVERT: A 176 MET cc_start: 0.7541 (mmt) cc_final: 0.7189 (mmt) REVERT: A 302 MET cc_start: 0.7370 (ptp) cc_final: 0.5636 (ptp) REVERT: A 323 GLN cc_start: 0.9112 (mm110) cc_final: 0.8895 (mm110) REVERT: A 327 ASP cc_start: 0.8773 (m-30) cc_final: 0.8412 (m-30) REVERT: E 249 GLN cc_start: 0.7743 (tt0) cc_final: 0.7344 (tt0) REVERT: E 295 ILE cc_start: 0.9408 (OUTLIER) cc_final: 0.9132 (mm) REVERT: F 1 MET cc_start: 0.7701 (pmm) cc_final: 0.7310 (ptp) REVERT: F 16 PHE cc_start: 0.9073 (t80) cc_final: 0.8756 (t80) REVERT: F 20 TRP cc_start: 0.8339 (t60) cc_final: 0.8085 (t60) REVERT: F 21 LEU cc_start: 0.9421 (mt) cc_final: 0.8950 (mt) REVERT: F 40 PRO cc_start: 0.9135 (Cg_exo) cc_final: 0.8914 (Cg_endo) REVERT: F 49 TYR cc_start: 0.9051 (m-80) cc_final: 0.8680 (m-10) REVERT: F 52 MET cc_start: 0.8039 (mmm) cc_final: 0.7696 (mmm) REVERT: F 65 ASP cc_start: 0.8343 (p0) cc_final: 0.7205 (t0) REVERT: F 66 ASP cc_start: 0.8657 (p0) cc_final: 0.8280 (p0) REVERT: F 93 ILE cc_start: 0.8597 (mm) cc_final: 0.8328 (tp) REVERT: F 176 MET cc_start: 0.8042 (mmt) cc_final: 0.7103 (mmt) REVERT: F 284 SER cc_start: 0.9218 (p) cc_final: 0.8891 (p) REVERT: F 302 MET cc_start: 0.7456 (ptp) cc_final: 0.5984 (ptp) REVERT: F 323 GLN cc_start: 0.8997 (mm110) cc_final: 0.8719 (mm-40) REVERT: F 327 ASP cc_start: 0.8599 (m-30) cc_final: 0.8294 (m-30) REVERT: I 249 GLN cc_start: 0.7934 (tt0) cc_final: 0.7097 (tt0) REVERT: I 295 ILE cc_start: 0.9386 (OUTLIER) cc_final: 0.9109 (mm) REVERT: K 20 TRP cc_start: 0.8200 (t60) cc_final: 0.7890 (t60) REVERT: K 22 GLN cc_start: 0.9068 (mt0) cc_final: 0.8823 (tt0) REVERT: K 49 TYR cc_start: 0.8693 (m-80) cc_final: 0.8360 (m-10) REVERT: K 65 ASP cc_start: 0.8306 (p0) cc_final: 0.7188 (t0) REVERT: K 176 MET cc_start: 0.7635 (mmt) cc_final: 0.7217 (mmt) REVERT: K 183 TYR cc_start: 0.9160 (p90) cc_final: 0.8935 (p90) REVERT: K 302 MET cc_start: 0.7168 (ptp) cc_final: 0.5954 (ptp) REVERT: K 323 GLN cc_start: 0.9081 (mm-40) cc_final: 0.8809 (mt0) REVERT: N 196 ASP cc_start: 0.8702 (t0) cc_final: 0.8447 (t0) REVERT: N 240 ASN cc_start: 0.8070 (t0) cc_final: 0.7388 (t0) REVERT: N 295 ILE cc_start: 0.9368 (mp) cc_final: 0.9027 (mt) REVERT: O 20 TRP cc_start: 0.8302 (t60) cc_final: 0.7738 (t60) REVERT: O 21 LEU cc_start: 0.9332 (mt) cc_final: 0.8660 (mt) REVERT: O 65 ASP cc_start: 0.8376 (p0) cc_final: 0.7276 (t0) REVERT: O 159 LEU cc_start: 0.8939 (tp) cc_final: 0.8499 (tp) REVERT: O 176 MET cc_start: 0.7311 (mmt) cc_final: 0.6763 (mmt) REVERT: O 323 GLN cc_start: 0.8977 (mm110) cc_final: 0.8546 (mt0) REVERT: O 327 ASP cc_start: 0.8996 (m-30) cc_final: 0.8543 (m-30) REVERT: J 46 HIS cc_start: 0.7617 (m170) cc_final: 0.7328 (m170) REVERT: J 156 ASP cc_start: 0.8218 (t0) cc_final: 0.7740 (t70) REVERT: J 309 GLN cc_start: 0.8965 (mt0) cc_final: 0.8582 (mt0) REVERT: B 71 MET cc_start: 0.8528 (ptp) cc_final: 0.8279 (ptp) REVERT: B 116 LEU cc_start: 0.8963 (tp) cc_final: 0.8705 (tt) REVERT: B 279 ASN cc_start: 0.8581 (OUTLIER) cc_final: 0.8264 (t0) REVERT: G 127 PHE cc_start: 0.8085 (t80) cc_final: 0.7488 (t80) REVERT: G 193 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7871 (tm-30) REVERT: L 204 MET cc_start: 0.8726 (ptm) cc_final: 0.8449 (ptm) REVERT: L 279 ASN cc_start: 0.8696 (OUTLIER) cc_final: 0.8203 (t0) REVERT: L 308 PHE cc_start: 0.8925 (m-10) cc_final: 0.8678 (m-10) REVERT: L 309 GLN cc_start: 0.8809 (mt0) cc_final: 0.8291 (mp10) REVERT: C 28 GLN cc_start: 0.9105 (mp-120) cc_final: 0.8779 (mp10) REVERT: C 54 LYS cc_start: 0.6998 (pmmt) cc_final: 0.6199 (tptp) REVERT: C 63 ASP cc_start: 0.7766 (p0) cc_final: 0.7471 (p0) REVERT: H 1 MET cc_start: 0.6928 (ttm) cc_final: 0.6450 (tpp) REVERT: H 28 GLN cc_start: 0.8699 (mp-120) cc_final: 0.8408 (mt0) REVERT: H 63 ASP cc_start: 0.7256 (p0) cc_final: 0.7024 (p0) REVERT: M 12 ARG cc_start: 0.8726 (ttt180) cc_final: 0.8499 (ttt180) REVERT: M 28 GLN cc_start: 0.8731 (mp-120) cc_final: 0.7990 (tm-30) REVERT: M 38 GLU cc_start: 0.9139 (mm-30) cc_final: 0.8835 (mm-30) REVERT: M 42 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8494 (mm-30) REVERT: M 46 GLN cc_start: 0.8495 (tp40) cc_final: 0.8032 (pt0) REVERT: M 47 ARG cc_start: 0.8749 (mmm160) cc_final: 0.8328 (mmm160) REVERT: M 50 GLN cc_start: 0.8755 (tm-30) cc_final: 0.8463 (tm-30) REVERT: M 54 LYS cc_start: 0.7327 (pmmt) cc_final: 0.6751 (tptp) outliers start: 86 outliers final: 56 residues processed: 804 average time/residue: 0.1903 time to fit residues: 259.0245 Evaluate side-chains 621 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 561 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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: [21, 355, 391, 33, 123, 208, 281, 196, 117, 38, 29] chunk 21 optimal weight: 8.9990 chunk 355 optimal weight: 0.0010 chunk 391 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 8.9990 chunk 208 optimal weight: 5.9990 chunk 281 optimal weight: 1.9990 chunk 196 optimal weight: 8.9990 chunk 117 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 overall best weight: 1.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 16 HIS ** P 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 GLN ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 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 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 173 GLN K 258 GLN K 290 HIS ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 187 GLN J 184 GLN B 184 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN B 295 HIS B 309 GLN G 184 GLN ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 279 ASN G 309 GLN L 106 HIS L 184 GLN ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 279 ASN L 295 HIS M 45 HIS M 59 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.106082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.082501 restraints weight = 86344.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.085120 restraints weight = 45496.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.086751 restraints weight = 30514.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.087777 restraints weight = 24054.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.088303 restraints weight = 20819.130| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 34112 Z= 0.177 Angle : 0.637 13.177 46360 Z= 0.332 Chirality : 0.048 0.225 5220 Planarity : 0.005 0.058 5980 Dihedral : 6.136 55.369 4684 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.24 % Allowed : 13.43 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.12), residues: 4240 helix: -0.37 (0.13), residues: 1448 sheet: -1.66 (0.16), residues: 900 loop : -1.32 (0.14), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 188 TYR 0.022 0.002 TYR B 45 PHE 0.020 0.002 PHE K 246 TRP 0.023 0.001 TRP E 20 HIS 0.015 0.001 HIS O 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 (34096) covalent geometry : angle 0.63629 / 0.33 (46328) SS BOND : bond 0.00498 / 0.33 ( 16) SS BOND : angle 1.37592 / 0.93 ( 32) hydrogen bonds : bond 0.03404 / 2.30 ( 1404) hydrogen bonds : angle 5.30347 / 3.72 ( 4500) *********************** 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 691 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 576 time to evaluate : 1.294 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: P 12 ARG cc_start: 0.8490 (ttt180) cc_final: 0.8200 (ttt180) REVERT: P 39 LEU cc_start: 0.8842 (mp) cc_final: 0.8537 (tp) REVERT: P 49 GLU cc_start: 0.8354 (mm-30) cc_final: 0.8073 (mm-30) REVERT: P 54 LYS cc_start: 0.7853 (pmmt) cc_final: 0.7011 (tptp) REVERT: P 63 ASP cc_start: 0.7925 (p0) cc_final: 0.7682 (p0) REVERT: D 142 TYR cc_start: 0.7728 (p90) cc_final: 0.7371 (p90) REVERT: D 240 ASN cc_start: 0.8004 (t0) cc_final: 0.7651 (t0) REVERT: D 295 ILE cc_start: 0.9445 (mp) cc_final: 0.9036 (mt) REVERT: D 332 MET cc_start: 0.8405 (mmp) cc_final: 0.7949 (mmt) REVERT: A 20 TRP cc_start: 0.8201 (t60) cc_final: 0.7665 (t60) REVERT: A 147 ASP cc_start: 0.8418 (p0) cc_final: 0.8042 (p0) REVERT: A 176 MET cc_start: 0.7810 (mmt) cc_final: 0.7121 (mmt) REVERT: A 284 SER cc_start: 0.9281 (OUTLIER) cc_final: 0.8745 (m) REVERT: A 302 MET cc_start: 0.7502 (ptp) cc_final: 0.6167 (ptp) REVERT: A 323 GLN cc_start: 0.9116 (mm110) cc_final: 0.8817 (mm-40) REVERT: A 327 ASP cc_start: 0.8876 (m-30) cc_final: 0.8467 (m-30) REVERT: E 240 ASN cc_start: 0.8217 (t0) cc_final: 0.7919 (t0) REVERT: F 20 TRP cc_start: 0.8389 (t60) cc_final: 0.8005 (t60) REVERT: F 40 PRO cc_start: 0.9100 (Cg_exo) cc_final: 0.8887 (Cg_endo) REVERT: F 65 ASP cc_start: 0.8385 (p0) cc_final: 0.7252 (t0) REVERT: F 93 ILE cc_start: 0.8664 (mm) cc_final: 0.8404 (tp) REVERT: F 176 MET cc_start: 0.8165 (mmt) cc_final: 0.7263 (mmt) REVERT: F 284 SER cc_start: 0.9260 (p) cc_final: 0.8725 (m) REVERT: F 302 MET cc_start: 0.7390 (ptp) cc_final: 0.5791 (ptp) REVERT: F 323 GLN cc_start: 0.8949 (mm110) cc_final: 0.8649 (mm-40) REVERT: F 327 ASP cc_start: 0.8703 (m-30) cc_final: 0.8380 (m-30) REVERT: I 57 GLN cc_start: 0.7344 (pp30) cc_final: 0.6435 (pp30) REVERT: I 142 TYR cc_start: 0.7595 (OUTLIER) cc_final: 0.7052 (p90) REVERT: I 284 SER cc_start: 0.9076 (p) cc_final: 0.8561 (m) REVERT: I 295 ILE cc_start: 0.9382 (OUTLIER) cc_final: 0.9065 (mm) REVERT: I 314 TRP cc_start: 0.9467 (m100) cc_final: 0.8985 (m100) REVERT: I 321 TYR cc_start: 0.9055 (t80) cc_final: 0.8827 (t80) REVERT: K 49 TYR cc_start: 0.8803 (m-80) cc_final: 0.8558 (m-10) REVERT: K 65 ASP cc_start: 0.8268 (p0) cc_final: 0.7390 (t0) REVERT: K 174 GLN cc_start: 0.8435 (mm-40) cc_final: 0.7645 (mm-40) REVERT: K 176 MET cc_start: 0.7635 (mmt) cc_final: 0.7044 (mmt) REVERT: K 284 SER cc_start: 0.9363 (OUTLIER) cc_final: 0.8832 (m) REVERT: K 302 MET cc_start: 0.7123 (ptp) cc_final: 0.6831 (ptp) REVERT: N 133 TYR cc_start: 0.8171 (m-80) cc_final: 0.7891 (m-80) REVERT: N 207 ILE cc_start: 0.9345 (mt) cc_final: 0.8988 (mp) REVERT: N 240 ASN cc_start: 0.8114 (t0) cc_final: 0.7799 (t0) REVERT: N 295 ILE cc_start: 0.9467 (mp) cc_final: 0.9053 (mt) REVERT: O 20 TRP cc_start: 0.8221 (t60) cc_final: 0.7524 (t60) REVERT: O 65 ASP cc_start: 0.8421 (p0) cc_final: 0.7475 (t0) REVERT: O 159 LEU cc_start: 0.8929 (tp) cc_final: 0.8505 (tp) REVERT: O 245 ASP cc_start: 0.8212 (OUTLIER) cc_final: 0.7960 (p0) REVERT: O 284 SER cc_start: 0.9416 (OUTLIER) cc_final: 0.8852 (m) REVERT: O 323 GLN cc_start: 0.8889 (mm110) cc_final: 0.8506 (mm-40) REVERT: O 327 ASP cc_start: 0.8903 (m-30) cc_final: 0.8512 (m-30) REVERT: J 46 HIS cc_start: 0.7793 (m170) cc_final: 0.7479 (m170) REVERT: J 241 ILE cc_start: 0.8781 (OUTLIER) cc_final: 0.8485 (tp) REVERT: J 309 GLN cc_start: 0.9000 (mt0) cc_final: 0.8531 (mp10) REVERT: B 67 ASN cc_start: 0.8598 (m110) cc_final: 0.8007 (p0) REVERT: G 70 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8503 (tt) REVERT: G 127 PHE cc_start: 0.8116 (t80) cc_final: 0.7532 (t80) REVERT: G 193 GLU cc_start: 0.8249 (tm-30) cc_final: 0.7950 (tm-30) REVERT: L 111 GLU cc_start: 0.7205 (pp20) cc_final: 0.6960 (pp20) REVERT: L 279 ASN cc_start: 0.8596 (OUTLIER) cc_final: 0.8330 (t0) REVERT: L 309 GLN cc_start: 0.8914 (mt0) cc_final: 0.8255 (mp10) REVERT: C 28 GLN cc_start: 0.9101 (mp-120) cc_final: 0.8758 (mp10) REVERT: C 54 LYS cc_start: 0.7559 (pmmt) cc_final: 0.6406 (tptp) REVERT: C 63 ASP cc_start: 0.7837 (p0) cc_final: 0.7554 (p0) REVERT: H 1 MET cc_start: 0.7097 (ttm) cc_final: 0.6695 (tpp) REVERT: H 28 GLN cc_start: 0.8796 (mp-120) cc_final: 0.8472 (mt0) REVERT: H 63 ASP cc_start: 0.7340 (p0) cc_final: 0.7097 (p0) REVERT: M 1 MET cc_start: 0.8448 (tpp) cc_final: 0.8244 (tmm) REVERT: M 12 ARG cc_start: 0.8744 (ttt180) cc_final: 0.8543 (ttt180) REVERT: M 28 GLN cc_start: 0.8790 (mp-120) cc_final: 0.8025 (tm-30) REVERT: M 46 GLN cc_start: 0.8423 (tp40) cc_final: 0.7990 (pt0) REVERT: M 47 ARG cc_start: 0.8797 (mmm160) cc_final: 0.8206 (mmm160) REVERT: M 50 GLN cc_start: 0.8810 (tm-30) cc_final: 0.8464 (tm-30) REVERT: M 54 LYS cc_start: 0.7757 (pmmt) cc_final: 0.7192 (tptp) REVERT: M 66 ASP cc_start: 0.7726 (t0) cc_final: 0.7453 (t0) outliers start: 115 outliers final: 78 residues processed: 658 average time/residue: 0.1919 time to fit residues: 213.2662 Evaluate side-chains 585 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 498 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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 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 247 VAL 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 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 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 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 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 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 28 LEU 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 204 MET Chi-restraints excluded: chain J residue 225 ILE Chi-restraints excluded: chain J residue 241 ILE Chi-restraints excluded: chain J residue 289 THR 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 B residue 257 VAL Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 70 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 69 ASP 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: [126, 407, 182, 348, 219, 381, 10, 220, 356, 104, 285] chunk 126 optimal weight: 2.9990 chunk 407 optimal weight: 7.9990 chunk 182 optimal weight: 0.0050 chunk 348 optimal weight: 7.9990 chunk 219 optimal weight: 4.9990 chunk 381 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 220 optimal weight: 3.9990 chunk 356 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 285 optimal weight: 0.7980 overall best weight: 1.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 16 HIS P 59 GLN A 174 GLN ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 GLN ** I 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 7 ASN K 15 ASN ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 290 HIS J 279 ASN B 91 HIS ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 106 HIS ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 279 ASN ** M 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.105487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.081360 restraints weight = 86864.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.083944 restraints weight = 46321.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.085596 restraints weight = 31528.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.086630 restraints weight = 25031.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.087243 restraints weight = 21743.384| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 34112 Z= 0.161 Angle : 0.625 10.267 46360 Z= 0.323 Chirality : 0.047 0.243 5220 Planarity : 0.005 0.056 5980 Dihedral : 5.958 53.224 4684 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.84 % Allowed : 14.73 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.13), residues: 4240 helix: -0.04 (0.14), residues: 1460 sheet: -1.39 (0.16), residues: 900 loop : -1.17 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 47 TYR 0.020 0.002 TYR F 321 PHE 0.022 0.002 PHE J 127 TRP 0.018 0.001 TRP E 20 HIS 0.009 0.001 HIS K 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (34096) covalent geometry : angle 0.62348 / 0.32 (46328) SS BOND : bond 0.00512 / 0.34 ( 16) SS BOND : angle 1.49952 / 1.01 ( 32) hydrogen bonds : bond 0.03293 / 2.21 ( 1404) hydrogen bonds : angle 5.17967 / 3.63 ( 4500) *********************** 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 682 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 546 time to evaluate : 1.227 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: P 12 ARG cc_start: 0.8520 (ttt180) cc_final: 0.8248 (ttt180) REVERT: P 39 LEU cc_start: 0.8893 (mp) cc_final: 0.8521 (tp) REVERT: P 54 LYS cc_start: 0.7736 (pmmt) cc_final: 0.7022 (tptp) REVERT: P 63 ASP cc_start: 0.7765 (p0) cc_final: 0.7454 (p0) REVERT: D 142 TYR cc_start: 0.7654 (p90) cc_final: 0.7195 (p90) REVERT: D 295 ILE cc_start: 0.9466 (mp) cc_final: 0.9057 (mt) REVERT: D 332 MET cc_start: 0.8312 (mmp) cc_final: 0.7870 (mmt) REVERT: A 20 TRP cc_start: 0.8107 (t60) cc_final: 0.7550 (t60) REVERT: A 65 ASP cc_start: 0.8396 (p0) cc_final: 0.7653 (t0) REVERT: A 147 ASP cc_start: 0.8437 (p0) cc_final: 0.8133 (p0) REVERT: A 176 MET cc_start: 0.7822 (mmt) cc_final: 0.7269 (mmt) REVERT: A 302 MET cc_start: 0.7633 (ptp) cc_final: 0.6358 (ptp) REVERT: A 323 GLN cc_start: 0.9123 (mm110) cc_final: 0.8492 (tt0) REVERT: A 327 ASP cc_start: 0.8932 (m-30) cc_final: 0.8546 (m-30) REVERT: E 240 ASN cc_start: 0.8202 (t0) cc_final: 0.7836 (t0) REVERT: E 246 PHE cc_start: 0.8603 (t80) cc_final: 0.8233 (t80) REVERT: F 1 MET cc_start: 0.7336 (pmm) cc_final: 0.6757 (pmm) REVERT: F 20 TRP cc_start: 0.8379 (t60) cc_final: 0.8014 (t60) REVERT: F 40 PRO cc_start: 0.9110 (Cg_exo) cc_final: 0.8851 (Cg_endo) REVERT: F 65 ASP cc_start: 0.8342 (p0) cc_final: 0.7316 (t0) REVERT: F 93 ILE cc_start: 0.8653 (mm) cc_final: 0.8418 (tp) REVERT: F 176 MET cc_start: 0.8247 (mmt) cc_final: 0.7263 (mmt) REVERT: F 284 SER cc_start: 0.9288 (p) cc_final: 0.9015 (p) REVERT: F 302 MET cc_start: 0.7387 (ptp) cc_final: 0.5785 (ptp) REVERT: F 323 GLN cc_start: 0.8894 (mm110) cc_final: 0.8557 (mm-40) REVERT: F 327 ASP cc_start: 0.8667 (m-30) cc_final: 0.8310 (m-30) REVERT: I 142 TYR cc_start: 0.7515 (OUTLIER) cc_final: 0.6882 (p90) REVERT: I 295 ILE cc_start: 0.9416 (OUTLIER) cc_final: 0.9094 (mm) REVERT: I 314 TRP cc_start: 0.9457 (m100) cc_final: 0.9078 (m100) REVERT: I 321 TYR cc_start: 0.9076 (t80) cc_final: 0.8856 (t80) REVERT: K 65 ASP cc_start: 0.8241 (p0) cc_final: 0.7329 (t0) REVERT: K 174 GLN cc_start: 0.8385 (mm-40) cc_final: 0.7626 (mm-40) REVERT: K 284 SER cc_start: 0.9337 (OUTLIER) cc_final: 0.8830 (m) REVERT: K 302 MET cc_start: 0.7108 (ptp) cc_final: 0.6847 (ptp) REVERT: N 240 ASN cc_start: 0.8097 (t0) cc_final: 0.7893 (t0) REVERT: N 295 ILE cc_start: 0.9442 (mp) cc_final: 0.9072 (mt) REVERT: O 17 MET cc_start: 0.8428 (tpt) cc_final: 0.8201 (tpt) REVERT: O 20 TRP cc_start: 0.8316 (t60) cc_final: 0.7502 (t60) REVERT: O 65 ASP cc_start: 0.8409 (p0) cc_final: 0.7585 (t0) REVERT: O 284 SER cc_start: 0.9403 (OUTLIER) cc_final: 0.8856 (m) REVERT: O 323 GLN cc_start: 0.8885 (mm110) cc_final: 0.8530 (mm-40) REVERT: O 327 ASP cc_start: 0.8881 (m-30) cc_final: 0.8487 (m-30) REVERT: J 46 HIS cc_start: 0.7756 (m170) cc_final: 0.7424 (m170) REVERT: J 241 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8473 (tp) REVERT: J 309 GLN cc_start: 0.9044 (mt0) cc_final: 0.8565 (mp10) REVERT: B 67 ASN cc_start: 0.8857 (m110) cc_final: 0.8177 (p0) REVERT: G 70 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8406 (tt) REVERT: G 127 PHE cc_start: 0.8201 (t80) cc_final: 0.7680 (t80) REVERT: G 193 GLU cc_start: 0.8379 (tm-30) cc_final: 0.8072 (tm-30) REVERT: L 180 ASP cc_start: 0.8177 (m-30) cc_final: 0.7807 (m-30) REVERT: L 309 GLN cc_start: 0.8906 (mt0) cc_final: 0.8159 (mp10) REVERT: C 28 GLN cc_start: 0.9062 (mp-120) cc_final: 0.8778 (mp10) REVERT: C 63 ASP cc_start: 0.7846 (p0) cc_final: 0.7552 (p0) REVERT: H 1 MET cc_start: 0.7098 (ttm) cc_final: 0.6295 (tpp) REVERT: H 28 GLN cc_start: 0.8867 (mp-120) cc_final: 0.8498 (mt0) REVERT: H 63 ASP cc_start: 0.7464 (p0) cc_final: 0.7071 (p0) REVERT: M 12 ARG cc_start: 0.8708 (ttt180) cc_final: 0.8498 (ttt180) REVERT: M 28 GLN cc_start: 0.8809 (mp-120) cc_final: 0.8010 (tm-30) REVERT: M 46 GLN cc_start: 0.8357 (tp40) cc_final: 0.7984 (pt0) REVERT: M 47 ARG cc_start: 0.8834 (mmm160) cc_final: 0.8153 (mmm160) REVERT: M 50 GLN cc_start: 0.8805 (tm-30) cc_final: 0.8446 (tm-30) REVERT: M 66 ASP cc_start: 0.7982 (t0) cc_final: 0.7718 (t0) outliers start: 136 outliers final: 93 residues processed: 648 average time/residue: 0.1900 time to fit residues: 208.9698 Evaluate side-chains 583 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 484 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 4 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 282 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 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 247 VAL Chi-restraints excluded: chain E residue 275 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 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 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 21 LEU 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 28 LEU 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 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 28 LEU Chi-restraints excluded: chain B residue 42 LEU 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 292 LEU Chi-restraints excluded: chain B residue 314 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 224 THR Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 236 CYS 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 110 ILE Chi-restraints excluded: chain L residue 182 VAL 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 M residue 2 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: [27, 397, 386, 393, 77, 70, 173, 169, 28, 369, 278] chunk 27 optimal weight: 5.9990 chunk 397 optimal weight: 0.0060 chunk 386 optimal weight: 6.9990 chunk 393 optimal weight: 0.2980 chunk 77 optimal weight: 0.9990 chunk 70 optimal weight: 9.9990 chunk 173 optimal weight: 5.9990 chunk 169 optimal weight: 0.5980 chunk 28 optimal weight: 5.9990 chunk 369 optimal weight: 10.0000 chunk 278 optimal weight: 0.7980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 59 GLN A 15 ASN ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 ASN F 7 ASN ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 240 ASN ** 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 249 GLN O 290 HIS O 323 GLN ** J 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN B 184 GLN L 91 HIS L 106 HIS ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 GLN H 28 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.107939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.084642 restraints weight = 85306.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.087332 restraints weight = 44530.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.089049 restraints weight = 29692.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.090049 restraints weight = 23154.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.090725 restraints weight = 20050.466| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 34112 Z= 0.108 Angle : 0.599 11.623 46360 Z= 0.307 Chirality : 0.047 0.258 5220 Planarity : 0.004 0.055 5980 Dihedral : 5.713 54.580 4684 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.22 % Allowed : 16.31 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.13), residues: 4240 helix: 0.18 (0.14), residues: 1452 sheet: -1.12 (0.16), residues: 880 loop : -0.95 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 47 TYR 0.019 0.001 TYR J 217 PHE 0.018 0.001 PHE F 16 TRP 0.032 0.001 TRP K 20 HIS 0.018 0.001 HIS O 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (34096) covalent geometry : angle 0.59686 / 0.31 (46328) SS BOND : bond 0.00478 / 0.32 ( 16) SS BOND : angle 2.12607 / 1.46 ( 32) hydrogen bonds : bond 0.03045 / 2.06 ( 1404) hydrogen bonds : angle 4.96334 / 3.48 ( 4500) *********************** 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 733 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 619 time to evaluate : 1.300 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: P 28 GLN cc_start: 0.8814 (mp10) cc_final: 0.8608 (mp10) REVERT: P 39 LEU cc_start: 0.8877 (mp) cc_final: 0.8548 (tp) REVERT: P 54 LYS cc_start: 0.7878 (OUTLIER) cc_final: 0.7070 (tptp) REVERT: P 63 ASP cc_start: 0.7613 (p0) cc_final: 0.7306 (p0) REVERT: P 69 GLU cc_start: 0.7584 (mp0) cc_final: 0.7234 (mp0) REVERT: D 142 TYR cc_start: 0.7532 (OUTLIER) cc_final: 0.6942 (p90) REVERT: D 246 PHE cc_start: 0.8855 (t80) cc_final: 0.8614 (t80) REVERT: D 295 ILE cc_start: 0.9419 (mp) cc_final: 0.9048 (mt) REVERT: D 332 MET cc_start: 0.8248 (mmp) cc_final: 0.7972 (mmt) REVERT: A 1 MET cc_start: 0.7214 (ppp) cc_final: 0.6905 (ptm) REVERT: A 65 ASP cc_start: 0.8314 (p0) cc_final: 0.7649 (t0) REVERT: A 176 MET cc_start: 0.7615 (mmt) cc_final: 0.7282 (mmt) REVERT: A 284 SER cc_start: 0.9078 (OUTLIER) cc_final: 0.8641 (m) REVERT: A 302 MET cc_start: 0.7611 (ptp) cc_final: 0.6327 (ptp) REVERT: A 323 GLN cc_start: 0.9095 (mm110) cc_final: 0.8516 (tt0) REVERT: A 327 ASP cc_start: 0.8871 (m-30) cc_final: 0.8477 (m-30) REVERT: E 240 ASN cc_start: 0.8192 (OUTLIER) cc_final: 0.7824 (t0) REVERT: E 246 PHE cc_start: 0.8606 (t80) cc_final: 0.8255 (t80) REVERT: E 332 MET cc_start: 0.8006 (mmp) cc_final: 0.7627 (mmm) REVERT: F 1 MET cc_start: 0.7244 (pmm) cc_final: 0.6853 (ptp) REVERT: F 20 TRP cc_start: 0.8388 (t60) cc_final: 0.8081 (t60) REVERT: F 40 PRO cc_start: 0.9054 (Cg_exo) cc_final: 0.8817 (Cg_endo) REVERT: F 65 ASP cc_start: 0.8286 (p0) cc_final: 0.7450 (t0) REVERT: F 93 ILE cc_start: 0.8592 (mm) cc_final: 0.8382 (tp) REVERT: F 176 MET cc_start: 0.8093 (mmt) cc_final: 0.7344 (mmt) REVERT: F 284 SER cc_start: 0.9294 (p) cc_final: 0.9075 (p) REVERT: F 302 MET cc_start: 0.7340 (ptp) cc_final: 0.6549 (ptp) REVERT: F 323 GLN cc_start: 0.8844 (mm110) cc_final: 0.8399 (mm-40) REVERT: F 327 ASP cc_start: 0.8629 (m-30) cc_final: 0.8253 (m-30) REVERT: I 142 TYR cc_start: 0.7617 (OUTLIER) cc_final: 0.6845 (p90) REVERT: I 246 PHE cc_start: 0.8691 (t80) cc_final: 0.8406 (t80) REVERT: I 295 ILE cc_start: 0.9358 (OUTLIER) cc_final: 0.9018 (mm) REVERT: I 302 MET cc_start: 0.8115 (ptp) cc_final: 0.7903 (ptp) REVERT: I 321 TYR cc_start: 0.8959 (t80) cc_final: 0.8718 (t80) REVERT: K 17 MET cc_start: 0.8264 (tpt) cc_final: 0.8015 (tpt) REVERT: K 65 ASP cc_start: 0.8081 (p0) cc_final: 0.7459 (t0) REVERT: K 174 GLN cc_start: 0.8399 (mm-40) cc_final: 0.7647 (mm-40) REVERT: K 176 MET cc_start: 0.7585 (mmt) cc_final: 0.6879 (mmt) REVERT: K 271 MET cc_start: 0.7698 (mmt) cc_final: 0.7450 (mmp) REVERT: K 284 SER cc_start: 0.9265 (OUTLIER) cc_final: 0.8864 (m) REVERT: K 302 MET cc_start: 0.7267 (ptp) cc_final: 0.5939 (ptp) REVERT: N 240 ASN cc_start: 0.7997 (t0) cc_final: 0.7758 (t0) REVERT: N 295 ILE cc_start: 0.9446 (mp) cc_final: 0.9085 (mt) REVERT: O 17 MET cc_start: 0.8166 (tpt) cc_final: 0.7681 (tpt) REVERT: O 20 TRP cc_start: 0.8337 (t60) cc_final: 0.7513 (t60) REVERT: O 65 ASP cc_start: 0.8356 (p0) cc_final: 0.7568 (t0) REVERT: O 176 MET cc_start: 0.7383 (mmt) cc_final: 0.6457 (mmt) REVERT: O 284 SER cc_start: 0.9355 (p) cc_final: 0.8981 (m) REVERT: O 323 GLN cc_start: 0.8888 (mm-40) cc_final: 0.8561 (mm-40) REVERT: O 327 ASP cc_start: 0.8923 (m-30) cc_final: 0.8482 (m-30) REVERT: J 46 HIS cc_start: 0.7701 (m170) cc_final: 0.7400 (m170) REVERT: J 127 PHE cc_start: 0.7868 (t80) cc_final: 0.6601 (t80) REVERT: B 67 ASN cc_start: 0.8795 (m110) cc_final: 0.8197 (p0) REVERT: B 131 LEU cc_start: 0.9387 (tt) cc_final: 0.9036 (mm) REVERT: B 241 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8360 (tp) REVERT: G 67 ASN cc_start: 0.8162 (p0) cc_final: 0.7890 (p0) REVERT: G 70 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8332 (tt) REVERT: G 80 ASN cc_start: 0.6883 (m110) cc_final: 0.6063 (t0) REVERT: G 127 PHE cc_start: 0.8069 (t80) cc_final: 0.7553 (t80) REVERT: G 193 GLU cc_start: 0.8317 (tm-30) cc_final: 0.8064 (tm-30) REVERT: L 69 ASP cc_start: 0.7855 (m-30) cc_final: 0.6787 (t70) REVERT: L 110 ILE cc_start: 0.8657 (OUTLIER) cc_final: 0.8195 (tt) REVERT: L 127 PHE cc_start: 0.7323 (t80) cc_final: 0.6587 (t80) REVERT: L 131 LEU cc_start: 0.9368 (tt) cc_final: 0.9026 (mp) REVERT: L 180 ASP cc_start: 0.7990 (m-30) cc_final: 0.7646 (m-30) REVERT: L 241 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8446 (tp) REVERT: C 28 GLN cc_start: 0.9095 (mp10) cc_final: 0.8637 (mp10) REVERT: C 63 ASP cc_start: 0.7687 (p0) cc_final: 0.7397 (p0) REVERT: H 1 MET cc_start: 0.6876 (ttm) cc_final: 0.6214 (tpp) REVERT: H 12 ARG cc_start: 0.8329 (ttt180) cc_final: 0.8000 (ttt180) REVERT: H 63 ASP cc_start: 0.7283 (p0) cc_final: 0.6758 (p0) REVERT: M 1 MET cc_start: 0.8799 (tpp) cc_final: 0.8279 (tmm) REVERT: M 12 ARG cc_start: 0.8668 (ttt180) cc_final: 0.8454 (ttt180) REVERT: M 28 GLN cc_start: 0.8807 (mp-120) cc_final: 0.7975 (tm-30) REVERT: M 46 GLN cc_start: 0.8348 (tp40) cc_final: 0.7960 (pt0) REVERT: M 47 ARG cc_start: 0.8870 (mmm160) cc_final: 0.8133 (mmm160) REVERT: M 49 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7731 (mm-30) REVERT: M 50 GLN cc_start: 0.8825 (tm-30) cc_final: 0.8519 (tm-30) REVERT: M 66 ASP cc_start: 0.8007 (t0) cc_final: 0.7742 (t0) outliers start: 114 outliers final: 75 residues processed: 698 average time/residue: 0.1957 time to fit residues: 230.8783 Evaluate side-chains 624 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 538 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 54 LYS Chi-restraints excluded: chain D residue 4 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 245 ASP Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain A residue 122 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 240 ASN Chi-restraints excluded: chain E residue 247 VAL 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 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 244 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 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 247 VAL Chi-restraints excluded: chain O residue 22 GLN 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 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 182 VAL Chi-restraints excluded: chain J residue 204 MET Chi-restraints excluded: chain J residue 225 ILE Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 42 LEU 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 236 CYS 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 B residue 314 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 224 THR Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 236 CYS Chi-restraints excluded: chain G residue 241 ILE 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 241 ILE 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: [149, 188, 98, 63, 165, 100, 132, 37, 376, 267, 309] chunk 149 optimal weight: 1.9990 chunk 188 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 165 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 132 optimal weight: 0.8980 chunk 37 optimal weight: 0.3980 chunk 376 optimal weight: 3.9990 chunk 267 optimal weight: 10.0000 chunk 309 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 59 GLN A 323 GLN ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 ASN ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 290 HIS N 45 HIS ** N 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 187 GLN J 279 ASN B 184 GLN G 206 GLN L 106 HIS ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.107355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.083954 restraints weight = 85748.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.086643 restraints weight = 44910.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.088332 restraints weight = 30054.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.089373 restraints weight = 23516.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.089954 restraints weight = 20310.523| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 34112 Z= 0.125 Angle : 0.605 12.350 46360 Z= 0.310 Chirality : 0.047 0.285 5220 Planarity : 0.004 0.053 5980 Dihedral : 5.599 59.533 4684 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.92 % Allowed : 16.96 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.13), residues: 4240 helix: 0.32 (0.14), residues: 1452 sheet: -0.95 (0.16), residues: 888 loop : -0.81 (0.15), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 3 TYR 0.024 0.001 TYR F 49 PHE 0.027 0.002 PHE N 170 TRP 0.043 0.001 TRP K 20 HIS 0.010 0.001 HIS K 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (34096) covalent geometry : angle 0.60422 / 0.31 (46328) SS BOND : bond 0.00196 / 0.13 ( 16) SS BOND : angle 1.32500 / 1.03 ( 32) hydrogen bonds : bond 0.03070 / 2.08 ( 1404) hydrogen bonds : angle 4.90351 / 3.44 ( 4500) *********************** 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 696 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 557 time to evaluate : 1.365 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: P 39 LEU cc_start: 0.8878 (mp) cc_final: 0.8622 (tp) REVERT: P 54 LYS cc_start: 0.7970 (pmmt) cc_final: 0.7141 (tptp) REVERT: P 63 ASP cc_start: 0.7558 (p0) cc_final: 0.7260 (p0) REVERT: D 142 TYR cc_start: 0.7486 (OUTLIER) cc_final: 0.6845 (p90) REVERT: D 246 PHE cc_start: 0.8860 (t80) cc_final: 0.8608 (t80) REVERT: D 295 ILE cc_start: 0.9449 (mp) cc_final: 0.9084 (mt) REVERT: D 332 MET cc_start: 0.8135 (mmp) cc_final: 0.7868 (mmt) REVERT: A 65 ASP cc_start: 0.8261 (p0) cc_final: 0.7761 (t0) REVERT: A 176 MET cc_start: 0.7619 (mmt) cc_final: 0.7163 (mmp) REVERT: A 284 SER cc_start: 0.9102 (OUTLIER) cc_final: 0.8653 (m) REVERT: A 302 MET cc_start: 0.7592 (ptp) cc_final: 0.6253 (ptp) REVERT: A 323 GLN cc_start: 0.9132 (mm-40) cc_final: 0.8497 (mt0) REVERT: A 327 ASP cc_start: 0.8905 (m-30) cc_final: 0.8444 (m-30) REVERT: E 240 ASN cc_start: 0.8278 (OUTLIER) cc_final: 0.7873 (t0) REVERT: E 246 PHE cc_start: 0.8770 (t80) cc_final: 0.8346 (t80) REVERT: E 295 ILE cc_start: 0.9267 (mm) cc_final: 0.9011 (mm) REVERT: F 1 MET cc_start: 0.7355 (pmm) cc_final: 0.6973 (pmm) REVERT: F 7 ASN cc_start: 0.8181 (t0) cc_final: 0.7856 (t0) REVERT: F 20 TRP cc_start: 0.8387 (t60) cc_final: 0.8100 (t60) REVERT: F 40 PRO cc_start: 0.9074 (Cg_exo) cc_final: 0.8846 (Cg_endo) REVERT: F 65 ASP cc_start: 0.8260 (p0) cc_final: 0.7456 (t0) REVERT: F 93 ILE cc_start: 0.8620 (mm) cc_final: 0.8376 (tp) REVERT: F 176 MET cc_start: 0.8214 (mmt) cc_final: 0.7351 (mmt) REVERT: F 284 SER cc_start: 0.9281 (p) cc_final: 0.9052 (p) REVERT: F 302 MET cc_start: 0.7329 (ptp) cc_final: 0.6675 (ptp) REVERT: F 323 GLN cc_start: 0.8811 (mm110) cc_final: 0.8408 (mm-40) REVERT: F 327 ASP cc_start: 0.8594 (m-30) cc_final: 0.8234 (m-30) REVERT: I 142 TYR cc_start: 0.7625 (OUTLIER) cc_final: 0.6682 (p90) REVERT: I 246 PHE cc_start: 0.8683 (t80) cc_final: 0.8453 (t80) REVERT: I 295 ILE cc_start: 0.9332 (OUTLIER) cc_final: 0.9018 (mm) REVERT: I 321 TYR cc_start: 0.9045 (t80) cc_final: 0.8749 (t80) REVERT: K 65 ASP cc_start: 0.8093 (p0) cc_final: 0.7515 (t0) REVERT: K 176 MET cc_start: 0.7631 (mmt) cc_final: 0.6858 (mmt) REVERT: K 271 MET cc_start: 0.7792 (mmt) cc_final: 0.7558 (mmp) REVERT: K 284 SER cc_start: 0.9272 (OUTLIER) cc_final: 0.8868 (m) REVERT: K 302 MET cc_start: 0.7234 (ptp) cc_final: 0.5867 (ptp) REVERT: N 226 GLN cc_start: 0.7825 (tm-30) cc_final: 0.7473 (tm-30) REVERT: N 295 ILE cc_start: 0.9431 (mp) cc_final: 0.9047 (mt) REVERT: O 20 TRP cc_start: 0.8245 (t60) cc_final: 0.7335 (t60) REVERT: O 65 ASP cc_start: 0.8270 (p0) cc_final: 0.7742 (t0) REVERT: O 176 MET cc_start: 0.7471 (mmt) cc_final: 0.6452 (mmt) REVERT: O 265 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7680 (tp30) REVERT: O 284 SER cc_start: 0.9384 (OUTLIER) cc_final: 0.9113 (p) REVERT: O 323 GLN cc_start: 0.8856 (mm-40) cc_final: 0.8542 (mm-40) REVERT: O 327 ASP cc_start: 0.8873 (m-30) cc_final: 0.8450 (m-30) REVERT: J 46 HIS cc_start: 0.7657 (m170) cc_final: 0.7357 (m170) REVERT: J 127 PHE cc_start: 0.7808 (t80) cc_final: 0.7501 (t80) REVERT: B 67 ASN cc_start: 0.8774 (m110) cc_final: 0.8244 (p0) REVERT: B 131 LEU cc_start: 0.9379 (tt) cc_final: 0.9072 (mm) REVERT: B 241 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8384 (tp) REVERT: G 70 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8273 (tt) REVERT: G 80 ASN cc_start: 0.7056 (m110) cc_final: 0.6063 (t0) REVERT: G 110 ILE cc_start: 0.8707 (OUTLIER) cc_final: 0.8122 (tp) REVERT: G 127 PHE cc_start: 0.7993 (t80) cc_final: 0.7495 (t80) REVERT: G 193 GLU cc_start: 0.8370 (tm-30) cc_final: 0.8139 (tm-30) REVERT: L 69 ASP cc_start: 0.7834 (m-30) cc_final: 0.6803 (t70) REVERT: L 124 LEU cc_start: 0.8476 (tp) cc_final: 0.8177 (tt) REVERT: L 131 LEU cc_start: 0.9366 (tt) cc_final: 0.8996 (mp) REVERT: L 241 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8513 (tp) REVERT: C 1 MET cc_start: 0.8979 (tpp) cc_final: 0.7819 (tmm) REVERT: C 28 GLN cc_start: 0.9160 (mp10) cc_final: 0.8733 (mp10) REVERT: C 63 ASP cc_start: 0.7746 (p0) cc_final: 0.7482 (p0) REVERT: H 1 MET cc_start: 0.7056 (ttm) cc_final: 0.6484 (tpp) REVERT: H 63 ASP cc_start: 0.7255 (p0) cc_final: 0.6807 (p0) REVERT: M 12 ARG cc_start: 0.8695 (ttt180) cc_final: 0.8493 (ttt180) REVERT: M 28 GLN cc_start: 0.8727 (mp-120) cc_final: 0.7909 (tm-30) REVERT: M 39 LEU cc_start: 0.8941 (mp) cc_final: 0.8360 (tp) REVERT: M 46 GLN cc_start: 0.8352 (tp40) cc_final: 0.7925 (pt0) REVERT: M 47 ARG cc_start: 0.8896 (mmm160) cc_final: 0.8097 (mmm160) REVERT: M 50 GLN cc_start: 0.8872 (tm-30) cc_final: 0.8495 (tm-30) REVERT: M 54 LYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7194 (tptp) REVERT: M 66 ASP cc_start: 0.8067 (t0) cc_final: 0.7817 (t0) outliers start: 139 outliers final: 92 residues processed: 654 average time/residue: 0.1899 time to fit residues: 212.0106 Evaluate side-chains 628 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 523 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 4 VAL 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 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 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 166 LEU Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 240 ASN Chi-restraints excluded: chain E residue 247 VAL 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 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 244 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 301 THR 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 284 SER 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 247 VAL Chi-restraints excluded: chain O residue 85 ASN Chi-restraints excluded: chain O residue 158 CYS 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 265 GLU Chi-restraints excluded: chain O residue 284 SER 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 182 VAL 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 B residue 42 LEU Chi-restraints excluded: chain B residue 97 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 236 CYS Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 314 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 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 236 CYS 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 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 C residue 8 ILE Chi-restraints excluded: chain C residue 36 LEU 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: [380, 401, 10, 367, 352, 171, 176, 74, 345, 327, 228] chunk 380 optimal weight: 4.9990 chunk 401 optimal weight: 0.6980 chunk 10 optimal weight: 7.9990 chunk 367 optimal weight: 0.4980 chunk 352 optimal weight: 0.4980 chunk 171 optimal weight: 0.6980 chunk 176 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 345 optimal weight: 1.9990 chunk 327 optimal weight: 6.9990 chunk 228 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 59 GLN ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 ASN ** E 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 240 ASN ** N 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 157 ASN ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 240 ASN ** N 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 15 ASN ** J 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 GLN B 284 HIS ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 206 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.108486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.085107 restraints weight = 86112.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.087820 restraints weight = 45059.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.089514 restraints weight = 30085.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.090573 restraints weight = 23546.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.091148 restraints weight = 20349.672| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.4442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 34112 Z= 0.111 Angle : 0.614 13.177 46360 Z= 0.310 Chirality : 0.047 0.308 5220 Planarity : 0.004 0.052 5980 Dihedral : 5.509 59.833 4684 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.58 % Allowed : 18.00 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.13), residues: 4240 helix: 0.36 (0.14), residues: 1460 sheet: -0.91 (0.17), residues: 864 loop : -0.68 (0.15), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 47 TYR 0.019 0.001 TYR J 217 PHE 0.022 0.001 PHE L 68 TRP 0.061 0.001 TRP K 20 HIS 0.014 0.001 HIS B 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (34096) covalent geometry : angle 0.61257 / 0.31 (46328) SS BOND : bond 0.00409 / 0.33 ( 16) SS BOND : angle 1.43227 / 0.96 ( 32) hydrogen bonds : bond 0.03005 / 2.03 ( 1404) hydrogen bonds : angle 4.82650 / 3.39 ( 4500) *********************** 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 713 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 586 time to evaluate : 1.261 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 12 ARG cc_start: 0.8597 (ttt180) cc_final: 0.8133 (ttt180) REVERT: P 39 LEU cc_start: 0.8872 (mp) cc_final: 0.8563 (tp) REVERT: P 54 LYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7082 (tptp) REVERT: P 63 ASP cc_start: 0.7586 (p0) cc_final: 0.7310 (p0) REVERT: D 142 TYR cc_start: 0.7439 (OUTLIER) cc_final: 0.6844 (p90) REVERT: D 176 MET cc_start: 0.7753 (mtp) cc_final: 0.7490 (mtp) REVERT: D 246 PHE cc_start: 0.8830 (t80) cc_final: 0.8529 (t80) REVERT: D 295 ILE cc_start: 0.9433 (mp) cc_final: 0.9048 (mt) REVERT: D 314 TRP cc_start: 0.9229 (m100) cc_final: 0.8574 (m100) REVERT: D 332 MET cc_start: 0.8065 (mmp) cc_final: 0.7845 (mmt) REVERT: A 20 TRP cc_start: 0.7849 (t60) cc_final: 0.7318 (t60) REVERT: A 65 ASP cc_start: 0.8214 (p0) cc_final: 0.7778 (t0) REVERT: A 176 MET cc_start: 0.7583 (mmt) cc_final: 0.7219 (mmt) REVERT: A 284 SER cc_start: 0.9048 (OUTLIER) cc_final: 0.8635 (m) REVERT: A 302 MET cc_start: 0.7561 (ptp) cc_final: 0.6258 (ptp) REVERT: A 323 GLN cc_start: 0.9124 (mm-40) cc_final: 0.8502 (tt0) REVERT: A 327 ASP cc_start: 0.8857 (m-30) cc_final: 0.8427 (m-30) REVERT: E 246 PHE cc_start: 0.8735 (t80) cc_final: 0.8301 (t80) REVERT: E 295 ILE cc_start: 0.9258 (mm) cc_final: 0.8981 (mm) REVERT: F 1 MET cc_start: 0.7294 (pmm) cc_final: 0.6917 (pmm) REVERT: F 7 ASN cc_start: 0.8150 (t0) cc_final: 0.7843 (t0) REVERT: F 20 TRP cc_start: 0.8393 (t60) cc_final: 0.8173 (t60) REVERT: F 40 PRO cc_start: 0.9069 (Cg_exo) cc_final: 0.8836 (Cg_endo) REVERT: F 65 ASP cc_start: 0.8226 (p0) cc_final: 0.7615 (t0) REVERT: F 93 ILE cc_start: 0.8596 (mm) cc_final: 0.8364 (tp) REVERT: F 176 MET cc_start: 0.8110 (mmt) cc_final: 0.7406 (mmt) REVERT: F 205 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.8059 (mtp) REVERT: F 284 SER cc_start: 0.9258 (p) cc_final: 0.9018 (p) REVERT: F 302 MET cc_start: 0.7358 (ptp) cc_final: 0.6645 (ptp) REVERT: F 323 GLN cc_start: 0.8815 (mm110) cc_final: 0.8437 (mm-40) REVERT: F 327 ASP cc_start: 0.8602 (m-30) cc_final: 0.8230 (m-30) REVERT: I 142 TYR cc_start: 0.7528 (OUTLIER) cc_final: 0.6442 (p90) REVERT: I 246 PHE cc_start: 0.8786 (t80) cc_final: 0.8538 (t80) REVERT: I 295 ILE cc_start: 0.9323 (OUTLIER) cc_final: 0.8986 (mm) REVERT: I 321 TYR cc_start: 0.8979 (t80) cc_final: 0.8672 (t80) REVERT: K 65 ASP cc_start: 0.8062 (p0) cc_final: 0.7561 (t0) REVERT: K 176 MET cc_start: 0.7695 (mmt) cc_final: 0.6806 (mmt) REVERT: K 284 SER cc_start: 0.9254 (OUTLIER) cc_final: 0.8104 (m) REVERT: K 302 MET cc_start: 0.7300 (ptp) cc_final: 0.5999 (ptp) REVERT: K 314 TRP cc_start: 0.9021 (m100) cc_final: 0.8407 (m100) REVERT: N 226 GLN cc_start: 0.7872 (tm-30) cc_final: 0.7538 (tm-30) REVERT: N 240 ASN cc_start: 0.8042 (t0) cc_final: 0.7799 (t0) REVERT: N 295 ILE cc_start: 0.9404 (mp) cc_final: 0.8993 (mt) REVERT: O 20 TRP cc_start: 0.8287 (t60) cc_final: 0.7920 (t60) REVERT: O 65 ASP cc_start: 0.8244 (p0) cc_final: 0.7758 (t0) REVERT: O 176 MET cc_start: 0.7448 (mmt) cc_final: 0.6531 (mmt) REVERT: O 240 ASN cc_start: 0.8349 (t0) cc_final: 0.8089 (t0) REVERT: O 265 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7711 (tp30) REVERT: O 284 SER cc_start: 0.9338 (OUTLIER) cc_final: 0.8876 (m) REVERT: O 323 GLN cc_start: 0.8856 (mm-40) cc_final: 0.8565 (mm-40) REVERT: O 327 ASP cc_start: 0.8897 (m-30) cc_final: 0.8455 (m-30) REVERT: J 46 HIS cc_start: 0.7620 (m170) cc_final: 0.7294 (m170) REVERT: J 127 PHE cc_start: 0.7768 (t80) cc_final: 0.7495 (t80) REVERT: B 67 ASN cc_start: 0.8795 (m110) cc_final: 0.8216 (p0) REVERT: B 131 LEU cc_start: 0.9371 (tt) cc_final: 0.9071 (mm) REVERT: B 241 ILE cc_start: 0.8639 (OUTLIER) cc_final: 0.8372 (tp) REVERT: G 67 ASN cc_start: 0.8102 (p0) cc_final: 0.7829 (p0) REVERT: G 69 ASP cc_start: 0.7945 (m-30) cc_final: 0.7191 (t70) REVERT: G 70 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8192 (tt) REVERT: G 80 ASN cc_start: 0.6984 (m110) cc_final: 0.6181 (t0) REVERT: G 127 PHE cc_start: 0.8028 (t80) cc_final: 0.7503 (t80) REVERT: G 193 GLU cc_start: 0.8363 (tm-30) cc_final: 0.8141 (tm-30) REVERT: L 69 ASP cc_start: 0.7954 (m-30) cc_final: 0.7126 (t70) REVERT: L 74 GLN cc_start: 0.8708 (mt0) cc_final: 0.8332 (mt0) REVERT: L 124 LEU cc_start: 0.8493 (tp) cc_final: 0.8185 (tt) REVERT: L 131 LEU cc_start: 0.9373 (tt) cc_final: 0.9018 (mp) REVERT: L 241 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8553 (tp) REVERT: C 28 GLN cc_start: 0.9045 (mp10) cc_final: 0.8670 (mp10) REVERT: C 40 GLN cc_start: 0.9282 (mm-40) cc_final: 0.8903 (mm-40) REVERT: C 63 ASP cc_start: 0.7635 (p0) cc_final: 0.7388 (p0) REVERT: C 69 GLU cc_start: 0.7880 (mp0) cc_final: 0.7584 (mp0) REVERT: H 1 MET cc_start: 0.7095 (ttm) cc_final: 0.6539 (tpp) REVERT: H 63 ASP cc_start: 0.7212 (p0) cc_final: 0.6771 (p0) REVERT: M 12 ARG cc_start: 0.8715 (ttt180) cc_final: 0.8350 (ttt180) REVERT: M 28 GLN cc_start: 0.8765 (mp-120) cc_final: 0.7846 (tm-30) REVERT: M 39 LEU cc_start: 0.8928 (mp) cc_final: 0.8349 (tp) REVERT: M 42 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8332 (mm-30) REVERT: M 46 GLN cc_start: 0.8336 (tp40) cc_final: 0.7969 (pt0) REVERT: M 47 ARG cc_start: 0.8908 (mmm160) cc_final: 0.8120 (mmm160) REVERT: M 50 GLN cc_start: 0.8892 (tm-30) cc_final: 0.8592 (tm-30) outliers start: 127 outliers final: 95 residues processed: 674 average time/residue: 0.1869 time to fit residues: 216.0963 Evaluate side-chains 645 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 538 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 54 LYS Chi-restraints excluded: chain P residue 61 CYS Chi-restraints excluded: chain D residue 4 VAL 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 205 MET 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 247 VAL Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 280 LEU 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 166 LEU 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 325 VAL Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 205 MET 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 142 TYR Chi-restraints excluded: chain I residue 166 LEU Chi-restraints excluded: chain I residue 182 SER 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 244 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 301 THR 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 284 SER 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 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 265 GLU Chi-restraints excluded: chain O residue 284 SER Chi-restraints excluded: chain O residue 290 HIS Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 182 VAL 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 B residue 28 LEU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 97 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 236 CYS 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 B residue 314 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 70 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 236 CYS 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 42 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 206 GLN 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 C residue 36 LEU 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: [3, 250, 103, 363, 28, 169, 174, 374, 344, 396, 246] chunk 3 optimal weight: 7.9990 chunk 250 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 363 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 chunk 169 optimal weight: 0.3980 chunk 174 optimal weight: 6.9990 chunk 374 optimal weight: 3.9990 chunk 344 optimal weight: 0.6980 chunk 396 optimal weight: 0.5980 chunk 246 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 ASN ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 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 249 GLN ** J 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 279 ASN B 114 HIS B 184 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 HIS ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 16 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.107802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.084456 restraints weight = 86302.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.087150 restraints weight = 45237.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.088851 restraints weight = 30215.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.089892 restraints weight = 23635.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.090453 restraints weight = 20458.125| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.4576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 34112 Z= 0.129 Angle : 0.642 13.033 46360 Z= 0.323 Chirality : 0.048 0.315 5220 Planarity : 0.004 0.051 5980 Dihedral : 5.470 59.195 4684 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.58 % Allowed : 18.23 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.13), residues: 4240 helix: 0.41 (0.14), residues: 1480 sheet: -0.81 (0.17), residues: 856 loop : -0.71 (0.15), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 47 TYR 0.019 0.001 TYR J 217 PHE 0.028 0.002 PHE B 68 TRP 0.076 0.001 TRP K 20 HIS 0.010 0.001 HIS B 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (34096) covalent geometry : angle 0.64075 / 0.32 (46328) SS BOND : bond 0.00342 / 0.27 ( 16) SS BOND : angle 1.58449 / 0.97 ( 32) hydrogen bonds : bond 0.03145 / 2.11 ( 1404) hydrogen bonds : angle 4.87172 / 3.41 ( 4500) *********************** 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 685 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 558 time to evaluate : 0.985 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: P 39 LEU cc_start: 0.8864 (mp) cc_final: 0.8494 (tp) REVERT: P 54 LYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7195 (tptp) REVERT: P 63 ASP cc_start: 0.7555 (p0) cc_final: 0.7254 (p0) REVERT: D 142 TYR cc_start: 0.7345 (OUTLIER) cc_final: 0.6388 (p90) REVERT: D 176 MET cc_start: 0.7913 (mtp) cc_final: 0.7558 (mtp) REVERT: D 246 PHE cc_start: 0.8824 (t80) cc_final: 0.8563 (t80) REVERT: D 295 ILE cc_start: 0.9450 (mp) cc_final: 0.9040 (mt) REVERT: D 314 TRP cc_start: 0.9239 (m100) cc_final: 0.8616 (m100) REVERT: A 20 TRP cc_start: 0.7959 (t60) cc_final: 0.7493 (t60) REVERT: A 65 ASP cc_start: 0.8208 (p0) cc_final: 0.7762 (t0) REVERT: A 176 MET cc_start: 0.7602 (mmt) cc_final: 0.7093 (mmp) REVERT: A 302 MET cc_start: 0.7523 (ptp) cc_final: 0.6182 (ptp) REVERT: A 323 GLN cc_start: 0.9125 (mm-40) cc_final: 0.8535 (mt0) REVERT: A 327 ASP cc_start: 0.8907 (m-30) cc_final: 0.8413 (m-30) REVERT: E 246 PHE cc_start: 0.8739 (t80) cc_final: 0.8280 (t80) REVERT: F 1 MET cc_start: 0.7281 (pmm) cc_final: 0.6947 (pmm) REVERT: F 20 TRP cc_start: 0.8404 (t60) cc_final: 0.8128 (t60) REVERT: F 40 PRO cc_start: 0.9071 (Cg_exo) cc_final: 0.8826 (Cg_endo) REVERT: F 65 ASP cc_start: 0.8197 (p0) cc_final: 0.7630 (t0) REVERT: F 93 ILE cc_start: 0.8603 (mm) cc_final: 0.8378 (tp) REVERT: F 176 MET cc_start: 0.8249 (mmt) cc_final: 0.7371 (mmt) REVERT: F 205 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.8158 (mtp) REVERT: F 284 SER cc_start: 0.9278 (p) cc_final: 0.9035 (p) REVERT: F 302 MET cc_start: 0.7315 (ptp) cc_final: 0.6683 (ptp) REVERT: F 323 GLN cc_start: 0.8818 (mm110) cc_final: 0.8410 (mm-40) REVERT: F 327 ASP cc_start: 0.8614 (m-30) cc_final: 0.8259 (m-30) REVERT: I 142 TYR cc_start: 0.7435 (OUTLIER) cc_final: 0.6265 (p90) REVERT: I 246 PHE cc_start: 0.8839 (t80) cc_final: 0.8621 (t80) REVERT: I 295 ILE cc_start: 0.9335 (OUTLIER) cc_final: 0.8996 (mm) REVERT: I 321 TYR cc_start: 0.9036 (t80) cc_final: 0.8748 (t80) REVERT: K 65 ASP cc_start: 0.7984 (p0) cc_final: 0.7540 (t0) REVERT: K 176 MET cc_start: 0.7735 (mmt) cc_final: 0.6911 (mmt) REVERT: K 284 SER cc_start: 0.9293 (OUTLIER) cc_final: 0.8916 (m) REVERT: K 302 MET cc_start: 0.7184 (ptp) cc_final: 0.5899 (ptp) REVERT: N 226 GLN cc_start: 0.7902 (tm-30) cc_final: 0.7573 (tm-30) REVERT: N 295 ILE cc_start: 0.9444 (mp) cc_final: 0.9063 (mt) REVERT: O 20 TRP cc_start: 0.8231 (t60) cc_final: 0.7946 (t60) REVERT: O 65 ASP cc_start: 0.8243 (p0) cc_final: 0.7777 (t0) REVERT: O 176 MET cc_start: 0.7625 (mmt) cc_final: 0.6627 (mmt) REVERT: O 265 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7746 (tp30) REVERT: O 323 GLN cc_start: 0.8867 (mm-40) cc_final: 0.8565 (mm-40) REVERT: O 327 ASP cc_start: 0.8903 (m-30) cc_final: 0.8474 (m-30) REVERT: J 46 HIS cc_start: 0.7571 (m170) cc_final: 0.7184 (m170) REVERT: J 127 PHE cc_start: 0.7710 (t80) cc_final: 0.7470 (t80) REVERT: B 67 ASN cc_start: 0.8823 (m110) cc_final: 0.8252 (p0) REVERT: B 131 LEU cc_start: 0.9380 (tt) cc_final: 0.9084 (mm) REVERT: B 241 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8428 (tp) REVERT: G 67 ASN cc_start: 0.8176 (p0) cc_final: 0.7820 (p0) REVERT: G 70 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8154 (tt) REVERT: G 80 ASN cc_start: 0.7185 (m110) cc_final: 0.6631 (t0) REVERT: G 127 PHE cc_start: 0.8065 (t80) cc_final: 0.7512 (t80) REVERT: G 193 GLU cc_start: 0.8406 (tm-30) cc_final: 0.8174 (tm-30) REVERT: L 69 ASP cc_start: 0.7727 (m-30) cc_final: 0.7258 (t70) REVERT: L 124 LEU cc_start: 0.8485 (tp) cc_final: 0.8184 (tt) REVERT: L 131 LEU cc_start: 0.9392 (tt) cc_final: 0.9026 (mp) REVERT: C 1 MET cc_start: 0.8759 (tpp) cc_final: 0.7516 (tmm) REVERT: C 28 GLN cc_start: 0.9047 (mp10) cc_final: 0.8695 (mp10) REVERT: C 63 ASP cc_start: 0.7681 (p0) cc_final: 0.7423 (p0) REVERT: H 1 MET cc_start: 0.7100 (ttm) cc_final: 0.6479 (tpp) REVERT: H 63 ASP cc_start: 0.7358 (p0) cc_final: 0.6909 (p0) REVERT: M 10 GLN cc_start: 0.8864 (mt0) cc_final: 0.8638 (mt0) REVERT: M 12 ARG cc_start: 0.8698 (ttt180) cc_final: 0.8448 (ttt180) REVERT: M 39 LEU cc_start: 0.8949 (mp) cc_final: 0.8387 (tp) REVERT: M 46 GLN cc_start: 0.8281 (tp40) cc_final: 0.7881 (pt0) REVERT: M 47 ARG cc_start: 0.8916 (mmm160) cc_final: 0.8129 (mmm160) REVERT: M 50 GLN cc_start: 0.8937 (tm-30) cc_final: 0.8697 (tm-30) REVERT: M 54 LYS cc_start: 0.7792 (OUTLIER) cc_final: 0.7577 (pttm) outliers start: 127 outliers final: 96 residues processed: 647 average time/residue: 0.1847 time to fit residues: 203.9527 Evaluate side-chains 622 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 516 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 54 LYS Chi-restraints excluded: chain D residue 4 VAL 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 205 MET 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 247 VAL Chi-restraints excluded: chain D residue 251 GLU 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 166 LEU 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 325 VAL Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 205 MET 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 166 LEU Chi-restraints excluded: chain I residue 168 GLU Chi-restraints excluded: chain I residue 182 SER 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 244 VAL 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 301 THR 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 N residue 4 VAL Chi-restraints excluded: chain N residue 37 THR 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 247 VAL Chi-restraints excluded: chain O residue 34 ILE Chi-restraints excluded: chain O residue 85 ASN Chi-restraints excluded: chain O residue 158 CYS 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 265 GLU Chi-restraints excluded: chain O residue 284 SER Chi-restraints excluded: chain O residue 290 HIS Chi-restraints excluded: chain J residue 28 LEU 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 182 VAL 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 B residue 42 LEU Chi-restraints excluded: chain B residue 97 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 236 CYS 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 B residue 314 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 70 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 225 ILE Chi-restraints excluded: chain G residue 236 CYS 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 42 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 257 VAL Chi-restraints excluded: chain C residue 36 LEU 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: [90, 219, 384, 86, 293, 30, 214, 337, 139, 256, 333] chunk 90 optimal weight: 6.9990 chunk 219 optimal weight: 0.9990 chunk 384 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 293 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 214 optimal weight: 8.9990 chunk 337 optimal weight: 9.9990 chunk 139 optimal weight: 8.9990 chunk 256 optimal weight: 8.9990 chunk 333 optimal weight: 5.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 ASN ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 249 GLN K 331 HIS ** N 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 15 ASN ** J 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 HIS L 90 ASN L 206 GLN H 16 HIS M 16 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.106871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.083516 restraints weight = 86153.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.086179 restraints weight = 45408.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.087802 restraints weight = 30431.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.088818 restraints weight = 24024.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.089451 restraints weight = 20815.885| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34112 Z= 0.149 Angle : 0.667 13.448 46360 Z= 0.337 Chirality : 0.048 0.330 5220 Planarity : 0.004 0.074 5980 Dihedral : 5.509 57.924 4684 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.58 % Allowed : 18.45 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.13), residues: 4240 helix: 0.39 (0.14), residues: 1492 sheet: -0.79 (0.17), residues: 856 loop : -0.67 (0.15), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 207 TYR 0.021 0.001 TYR F 49 PHE 0.031 0.002 PHE J 68 TRP 0.099 0.002 TRP K 20 HIS 0.011 0.001 HIS P 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (34096) covalent geometry : angle 0.66540 / 0.34 (46328) SS BOND : bond 0.00418 / 0.27 ( 16) SS BOND : angle 1.63542 / 1.11 ( 32) hydrogen bonds : bond 0.03207 / 2.16 ( 1404) hydrogen bonds : angle 4.92684 / 3.44 ( 4500) *********************** 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 663 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 536 time to evaluate : 1.332 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 37 GLU cc_start: 0.8820 (tp30) cc_final: 0.8507 (tp30) REVERT: P 39 LEU cc_start: 0.8872 (mp) cc_final: 0.8496 (tp) REVERT: P 54 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7261 (tptp) REVERT: P 63 ASP cc_start: 0.7533 (p0) cc_final: 0.7233 (p0) REVERT: D 142 TYR cc_start: 0.7263 (OUTLIER) cc_final: 0.6930 (p90) REVERT: D 176 MET cc_start: 0.7910 (mtp) cc_final: 0.7668 (mtp) REVERT: D 240 ASN cc_start: 0.7988 (t0) cc_final: 0.7679 (t0) REVERT: D 295 ILE cc_start: 0.9445 (mp) cc_final: 0.9015 (mt) REVERT: A 20 TRP cc_start: 0.7950 (t60) cc_final: 0.7478 (t60) REVERT: A 65 ASP cc_start: 0.8188 (p0) cc_final: 0.7785 (t0) REVERT: A 176 MET cc_start: 0.7677 (mmt) cc_final: 0.7156 (mmp) REVERT: A 302 MET cc_start: 0.7560 (ptp) cc_final: 0.6215 (ptp) REVERT: A 323 GLN cc_start: 0.9106 (mm-40) cc_final: 0.8530 (mt0) REVERT: A 327 ASP cc_start: 0.8897 (m-30) cc_final: 0.8478 (m-30) REVERT: E 240 ASN cc_start: 0.8268 (t0) cc_final: 0.7938 (t0) REVERT: E 246 PHE cc_start: 0.8736 (t80) cc_final: 0.8300 (t80) REVERT: F 20 TRP cc_start: 0.8435 (t60) cc_final: 0.8144 (t60) REVERT: F 40 PRO cc_start: 0.9090 (Cg_exo) cc_final: 0.8864 (Cg_endo) REVERT: F 65 ASP cc_start: 0.8212 (p0) cc_final: 0.7664 (t0) REVERT: F 93 ILE cc_start: 0.8602 (mm) cc_final: 0.8394 (tp) REVERT: F 176 MET cc_start: 0.8167 (mmt) cc_final: 0.7335 (mmt) REVERT: F 284 SER cc_start: 0.9296 (p) cc_final: 0.9037 (p) REVERT: F 302 MET cc_start: 0.7304 (ptp) cc_final: 0.6760 (ptp) REVERT: F 323 GLN cc_start: 0.8783 (mm110) cc_final: 0.8412 (mm-40) REVERT: F 327 ASP cc_start: 0.8625 (m-30) cc_final: 0.8269 (m-30) REVERT: I 142 TYR cc_start: 0.7433 (OUTLIER) cc_final: 0.6227 (p90) REVERT: I 228 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8422 (mtmm) REVERT: I 246 PHE cc_start: 0.8858 (t80) cc_final: 0.8605 (t80) REVERT: I 295 ILE cc_start: 0.9370 (OUTLIER) cc_final: 0.9016 (mm) REVERT: I 321 TYR cc_start: 0.9070 (t80) cc_final: 0.8772 (t80) REVERT: K 65 ASP cc_start: 0.7954 (p0) cc_final: 0.7565 (t0) REVERT: K 176 MET cc_start: 0.7763 (mmt) cc_final: 0.6909 (mmt) REVERT: K 284 SER cc_start: 0.9292 (OUTLIER) cc_final: 0.8880 (m) REVERT: K 302 MET cc_start: 0.7120 (ptp) cc_final: 0.6823 (ptp) REVERT: N 226 GLN cc_start: 0.7988 (tm-30) cc_final: 0.7682 (tm-30) REVERT: N 295 ILE cc_start: 0.9451 (mp) cc_final: 0.9080 (mt) REVERT: O 20 TRP cc_start: 0.8178 (t60) cc_final: 0.7750 (t60) REVERT: O 65 ASP cc_start: 0.8195 (p0) cc_final: 0.7697 (t0) REVERT: O 265 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7763 (tp30) REVERT: O 323 GLN cc_start: 0.8867 (mm-40) cc_final: 0.8354 (mt0) REVERT: O 327 ASP cc_start: 0.8888 (m-30) cc_final: 0.8495 (m-30) REVERT: J 46 HIS cc_start: 0.7465 (m170) cc_final: 0.7174 (m170) REVERT: J 85 MET cc_start: 0.8256 (tpt) cc_final: 0.7919 (tpt) REVERT: J 233 LYS cc_start: 0.8760 (mmtt) cc_final: 0.8359 (mttp) REVERT: J 316 MET cc_start: 0.9016 (mmt) cc_final: 0.8725 (mmt) REVERT: J 320 TYR cc_start: 0.9141 (t80) cc_final: 0.8772 (t80) REVERT: B 67 ASN cc_start: 0.8796 (m110) cc_final: 0.8208 (p0) REVERT: B 131 LEU cc_start: 0.9397 (tt) cc_final: 0.9084 (mm) REVERT: B 204 MET cc_start: 0.8899 (ptm) cc_final: 0.7991 (ppp) REVERT: B 241 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8433 (tp) REVERT: G 46 HIS cc_start: 0.7766 (m-70) cc_final: 0.7335 (m-70) REVERT: G 67 ASN cc_start: 0.8144 (p0) cc_final: 0.7738 (p0) REVERT: G 69 ASP cc_start: 0.7874 (m-30) cc_final: 0.7186 (t0) REVERT: G 70 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8073 (tt) REVERT: G 80 ASN cc_start: 0.6975 (m110) cc_final: 0.6307 (t0) REVERT: G 85 MET cc_start: 0.8357 (tpt) cc_final: 0.8026 (tpt) REVERT: G 127 PHE cc_start: 0.8096 (t80) cc_final: 0.7634 (t80) REVERT: G 193 GLU cc_start: 0.8387 (tm-30) cc_final: 0.8174 (tm-30) REVERT: L 69 ASP cc_start: 0.7808 (m-30) cc_final: 0.7206 (t70) REVERT: L 78 LEU cc_start: 0.8712 (mm) cc_final: 0.8509 (mm) REVERT: L 124 LEU cc_start: 0.8494 (tp) cc_final: 0.8196 (tt) REVERT: L 131 LEU cc_start: 0.9403 (tt) cc_final: 0.9027 (mp) REVERT: C 1 MET cc_start: 0.8883 (tpp) cc_final: 0.7761 (tmm) REVERT: C 28 GLN cc_start: 0.9076 (mp10) cc_final: 0.8728 (mp10) REVERT: C 47 ARG cc_start: 0.8800 (tpp80) cc_final: 0.8180 (tpp80) REVERT: C 63 ASP cc_start: 0.7720 (p0) cc_final: 0.7451 (p0) REVERT: C 69 GLU cc_start: 0.7970 (mp0) cc_final: 0.7691 (mp0) REVERT: H 1 MET cc_start: 0.7118 (ttm) cc_final: 0.6117 (tpp) REVERT: H 4 LEU cc_start: 0.8499 (tp) cc_final: 0.8177 (tp) REVERT: H 7 GLN cc_start: 0.8052 (mt0) cc_final: 0.7754 (mp10) REVERT: H 28 GLN cc_start: 0.8843 (mp10) cc_final: 0.8612 (mp10) REVERT: H 63 ASP cc_start: 0.7402 (p0) cc_final: 0.6952 (p0) REVERT: M 12 ARG cc_start: 0.8770 (ttt180) cc_final: 0.8542 (ttt180) REVERT: M 39 LEU cc_start: 0.8962 (mp) cc_final: 0.8374 (mp) REVERT: M 46 GLN cc_start: 0.8304 (tp40) cc_final: 0.7901 (pt0) REVERT: M 47 ARG cc_start: 0.8913 (mmm160) cc_final: 0.8028 (mmm160) REVERT: M 50 GLN cc_start: 0.8955 (tm-30) cc_final: 0.8655 (tm-30) REVERT: M 54 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7700 (pttm) REVERT: M 69 GLU cc_start: 0.7965 (mp0) cc_final: 0.7647 (mp0) outliers start: 127 outliers final: 94 residues processed: 621 average time/residue: 0.1879 time to fit residues: 198.2855 Evaluate side-chains 620 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 516 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain P residue 54 LYS Chi-restraints excluded: chain D residue 4 VAL 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 205 MET 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 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 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 166 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 247 VAL 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 I residue 4 VAL Chi-restraints excluded: chain I residue 142 TYR Chi-restraints excluded: chain I residue 182 SER 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 247 VAL Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain I residue 295 ILE Chi-restraints excluded: chain I residue 301 THR 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 N residue 4 VAL Chi-restraints excluded: chain N residue 37 THR 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 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 158 CYS 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 265 GLU Chi-restraints excluded: chain O residue 284 SER Chi-restraints excluded: chain O residue 290 HIS Chi-restraints excluded: chain J residue 28 LEU 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 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 B residue 42 LEU Chi-restraints excluded: chain B residue 97 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 236 CYS 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 B residue 314 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 70 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 224 THR Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 236 CYS 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 42 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 206 GLN Chi-restraints excluded: chain L residue 225 ILE Chi-restraints excluded: chain L residue 257 VAL Chi-restraints excluded: chain L residue 293 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: [72, 83, 172, 179, 413, 195, 31, 296, 323, 264, 128] chunk 72 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 172 optimal weight: 10.0000 chunk 179 optimal weight: 6.9990 chunk 413 optimal weight: 0.9990 chunk 195 optimal weight: 0.0270 chunk 31 optimal weight: 1.9990 chunk 296 optimal weight: 1.9990 chunk 323 optimal weight: 0.9980 chunk 264 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 GLN E 57 GLN ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 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** ** J 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 HIS G 46 HIS L 206 GLN H 59 GLN M 10 GLN M 16 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.108795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.085612 restraints weight = 86425.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.088316 restraints weight = 45090.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.090008 restraints weight = 30116.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.091058 restraints weight = 23612.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.091595 restraints weight = 20375.612| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.4870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 34112 Z= 0.118 Angle : 0.663 14.039 46360 Z= 0.334 Chirality : 0.047 0.305 5220 Planarity : 0.004 0.067 5980 Dihedral : 5.440 58.878 4684 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.22 % Allowed : 19.10 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.13), residues: 4240 helix: 0.39 (0.14), residues: 1492 sheet: -0.73 (0.17), residues: 856 loop : -0.62 (0.15), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 207 TYR 0.018 0.001 TYR N 142 PHE 0.032 0.002 PHE G 68 TRP 0.088 0.001 TRP K 20 HIS 0.011 0.001 HIS P 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (34096) covalent geometry : angle 0.66118 / 0.33 (46328) SS BOND : bond 0.00395 / 0.28 ( 16) SS BOND : angle 1.88251 / 1.52 ( 32) hydrogen bonds : bond 0.03147 / 2.13 ( 1404) hydrogen bonds : angle 4.85569 / 3.40 ( 4500) ********************** 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 690 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 576 time to evaluate : 1.299 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: P 37 GLU cc_start: 0.8801 (tp30) cc_final: 0.8493 (tp30) REVERT: P 39 LEU cc_start: 0.8872 (mp) cc_final: 0.8541 (tp) REVERT: P 54 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7240 (tptp) REVERT: P 61 CYS cc_start: 0.4937 (p) cc_final: 0.4249 (m) REVERT: P 63 ASP cc_start: 0.7443 (p0) cc_final: 0.7179 (p0) REVERT: D 142 TYR cc_start: 0.7159 (OUTLIER) cc_final: 0.6946 (p90) REVERT: D 176 MET cc_start: 0.7836 (mtp) cc_final: 0.7559 (mtp) REVERT: D 295 ILE cc_start: 0.9407 (mp) cc_final: 0.9000 (mt) REVERT: D 314 TRP cc_start: 0.9222 (m100) cc_final: 0.8563 (m100) REVERT: D 332 MET cc_start: 0.7601 (mmp) cc_final: 0.7370 (mmp) REVERT: A 65 ASP cc_start: 0.8118 (p0) cc_final: 0.7738 (t0) REVERT: A 176 MET cc_start: 0.7687 (mmt) cc_final: 0.7122 (mmt) REVERT: A 284 SER cc_start: 0.9144 (OUTLIER) cc_final: 0.8753 (m) REVERT: A 302 MET cc_start: 0.7439 (ptp) cc_final: 0.6104 (ptp) REVERT: A 323 GLN cc_start: 0.9118 (mm-40) cc_final: 0.8529 (mt0) REVERT: A 327 ASP cc_start: 0.8878 (m-30) cc_final: 0.8382 (m-30) REVERT: E 65 ASP cc_start: 0.8494 (p0) cc_final: 0.7526 (t0) REVERT: E 240 ASN cc_start: 0.8213 (t0) cc_final: 0.7894 (t0) REVERT: E 246 PHE cc_start: 0.8735 (t80) cc_final: 0.8319 (t80) REVERT: F 1 MET cc_start: 0.7442 (pmm) cc_final: 0.7164 (ptm) REVERT: F 20 TRP cc_start: 0.8390 (t60) cc_final: 0.8150 (t60) REVERT: F 40 PRO cc_start: 0.9043 (Cg_exo) cc_final: 0.8807 (Cg_endo) REVERT: F 65 ASP cc_start: 0.8158 (p0) cc_final: 0.7636 (t0) REVERT: F 176 MET cc_start: 0.8111 (mmt) cc_final: 0.7144 (mmt) REVERT: F 284 SER cc_start: 0.9259 (p) cc_final: 0.9030 (p) REVERT: F 302 MET cc_start: 0.7256 (ptp) cc_final: 0.6654 (ptp) REVERT: F 323 GLN cc_start: 0.8772 (mm110) cc_final: 0.8384 (mm-40) REVERT: F 327 ASP cc_start: 0.8543 (m-30) cc_final: 0.8210 (m-30) REVERT: I 142 TYR cc_start: 0.7345 (OUTLIER) cc_final: 0.6249 (p90) REVERT: I 285 SER cc_start: 0.8440 (t) cc_final: 0.8195 (p) REVERT: I 295 ILE cc_start: 0.9353 (OUTLIER) cc_final: 0.8966 (mm) REVERT: I 321 TYR cc_start: 0.8997 (t80) cc_final: 0.8655 (t80) REVERT: K 65 ASP cc_start: 0.7916 (p0) cc_final: 0.7585 (t0) REVERT: K 176 MET cc_start: 0.7728 (mmt) cc_final: 0.6848 (mmt) REVERT: K 284 SER cc_start: 0.9243 (OUTLIER) cc_final: 0.8861 (m) REVERT: N 226 GLN cc_start: 0.7949 (tm-30) cc_final: 0.7626 (tm-30) REVERT: N 295 ILE cc_start: 0.9415 (mp) cc_final: 0.8993 (mt) REVERT: N 314 TRP cc_start: 0.9245 (m100) cc_final: 0.8712 (m100) REVERT: O 20 TRP cc_start: 0.8115 (t60) cc_final: 0.6982 (t60) REVERT: O 65 ASP cc_start: 0.8092 (p0) cc_final: 0.7853 (t0) REVERT: O 323 GLN cc_start: 0.8864 (mm-40) cc_final: 0.8395 (mt0) REVERT: O 327 ASP cc_start: 0.8895 (m-30) cc_final: 0.8488 (m-30) REVERT: J 42 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8084 (mt) REVERT: J 46 HIS cc_start: 0.7280 (m170) cc_final: 0.6805 (m170) REVERT: J 85 MET cc_start: 0.8218 (tpt) cc_final: 0.7799 (tpt) REVERT: J 127 PHE cc_start: 0.8011 (t80) cc_final: 0.7665 (t80) REVERT: J 233 LYS cc_start: 0.8708 (mmtt) cc_final: 0.8308 (mttp) REVERT: B 67 ASN cc_start: 0.8874 (m110) cc_final: 0.8224 (p0) REVERT: B 131 LEU cc_start: 0.9372 (tt) cc_final: 0.9084 (mm) REVERT: B 204 MET cc_start: 0.8865 (ptm) cc_final: 0.7965 (ppp) REVERT: B 241 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8370 (tp) REVERT: G 67 ASN cc_start: 0.8036 (p0) cc_final: 0.7640 (p0) REVERT: G 69 ASP cc_start: 0.7801 (m-30) cc_final: 0.7181 (t0) REVERT: G 70 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8059 (tt) REVERT: G 80 ASN cc_start: 0.6987 (m110) cc_final: 0.6628 (t0) REVERT: G 85 MET cc_start: 0.8200 (tpt) cc_final: 0.7920 (tpt) REVERT: G 127 PHE cc_start: 0.8040 (t80) cc_final: 0.7559 (t80) REVERT: G 193 GLU cc_start: 0.8378 (tm-30) cc_final: 0.8163 (tm-30) REVERT: G 241 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8292 (tp) REVERT: L 69 ASP cc_start: 0.7734 (m-30) cc_final: 0.7209 (t70) REVERT: L 71 MET cc_start: 0.8673 (mpp) cc_final: 0.8278 (mpp) REVERT: L 110 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8216 (tt) REVERT: L 131 LEU cc_start: 0.9395 (tt) cc_final: 0.9010 (mp) REVERT: C 1 MET cc_start: 0.8840 (tpp) cc_final: 0.7853 (tmm) REVERT: C 28 GLN cc_start: 0.9180 (mp10) cc_final: 0.8881 (mp10) REVERT: C 47 ARG cc_start: 0.8819 (tpp80) cc_final: 0.8163 (tpp80) REVERT: C 63 ASP cc_start: 0.7739 (p0) cc_final: 0.7494 (p0) REVERT: H 1 MET cc_start: 0.7189 (ttm) cc_final: 0.6734 (tpp) REVERT: H 7 GLN cc_start: 0.8119 (mt0) cc_final: 0.7834 (mp10) REVERT: H 54 LYS cc_start: 0.8489 (pttm) cc_final: 0.8133 (pttm) REVERT: H 63 ASP cc_start: 0.7291 (p0) cc_final: 0.6916 (p0) REVERT: M 1 MET cc_start: 0.8656 (tpp) cc_final: 0.5750 (mmt) REVERT: M 46 GLN cc_start: 0.8365 (tp40) cc_final: 0.8061 (pt0) REVERT: M 47 ARG cc_start: 0.8929 (mmm160) cc_final: 0.7985 (mmm160) REVERT: M 50 GLN cc_start: 0.8910 (tm-30) cc_final: 0.8632 (tm-30) REVERT: M 69 GLU cc_start: 0.8101 (mp0) cc_final: 0.7839 (mp0) outliers start: 114 outliers final: 87 residues processed: 655 average time/residue: 0.1851 time to fit residues: 207.5332 Evaluate side-chains 631 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 533 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain P residue 54 LYS Chi-restraints excluded: chain D residue 4 VAL 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 245 ASP Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain A residue 148 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 142 TYR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 247 VAL 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 I residue 4 VAL Chi-restraints excluded: chain I residue 142 TYR Chi-restraints excluded: chain I residue 182 SER 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 247 VAL Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain I residue 295 ILE 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 N residue 4 VAL Chi-restraints excluded: chain N residue 37 THR 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 247 VAL Chi-restraints excluded: chain O residue 34 ILE Chi-restraints excluded: chain O residue 85 ASN Chi-restraints excluded: chain O residue 137 VAL Chi-restraints excluded: chain O residue 158 CYS 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 284 SER Chi-restraints excluded: chain O residue 290 HIS Chi-restraints excluded: chain J residue 28 LEU 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 182 VAL 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 B residue 42 LEU Chi-restraints excluded: chain B residue 97 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 236 CYS 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 B residue 314 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 70 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 225 ILE Chi-restraints excluded: chain G residue 236 CYS 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 42 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 206 GLN Chi-restraints excluded: chain L residue 225 ILE Chi-restraints excluded: chain L residue 257 VAL Chi-restraints excluded: chain L residue 293 LEU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain H residue 36 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: [364, 236, 309, 258, 179, 331, 278, 288, 26, 367, 99] chunk 364 optimal weight: 5.9990 chunk 236 optimal weight: 0.9980 chunk 309 optimal weight: 8.9990 chunk 258 optimal weight: 0.7980 chunk 179 optimal weight: 0.7980 chunk 331 optimal weight: 0.3980 chunk 278 optimal weight: 10.0000 chunk 288 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 367 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 240 ASN E 57 GLN ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 ASN ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 249 GLN ** K 261 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 240 ASN O 226 GLN ** J 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 46 HIS L 206 GLN H 16 HIS ** 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 = 0.3764 r_free = 0.3764 target = 0.109050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.085754 restraints weight = 86050.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.088469 restraints weight = 45314.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.090149 restraints weight = 30298.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.091183 restraints weight = 23800.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.091810 restraints weight = 20591.755| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.5005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 34112 Z= 0.122 Angle : 0.682 14.249 46360 Z= 0.343 Chirality : 0.048 0.331 5220 Planarity : 0.004 0.055 5980 Dihedral : 5.406 59.233 4684 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.02 % Allowed : 19.64 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.13), residues: 4240 helix: 0.39 (0.14), residues: 1496 sheet: -0.69 (0.17), residues: 856 loop : -0.59 (0.15), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 207 TYR 0.024 0.001 TYR J 89 PHE 0.036 0.002 PHE L 308 TRP 0.079 0.001 TRP K 20 HIS 0.012 0.001 HIS P 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (34096) covalent geometry : angle 0.67781 / 0.34 (46328) SS BOND : bond 0.00209 / 0.13 ( 16) SS BOND : angle 3.07414 / 2.24 ( 32) hydrogen bonds : bond 0.03151 / 2.13 ( 1404) hydrogen bonds : angle 4.83669 / 3.39 ( 4500) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6525.32 seconds wall clock time: 113 minutes 26.05 seconds (6806.05 seconds total)