Starting phenix.real_space_refine on Mon Sep 14 21:53:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6gve_0071/09_2026/6gve_0071.cif Found real_map, /net/cci-nas-00/data/ceres_data/6gve_0071/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6gve_0071/09_2026/6gve_0071.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6gve_0071/09_2026/6gve_0071.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6gve_0071/09_2026/6gve_0071.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6gve_0071/09_2026/6gve_0071.cif" model { file = "/net/cci-nas-00/data/ceres_data/6gve_0071/09_2026/6gve_0071.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6gve_0071/09_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-2.2.1-6174/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: 5.46, per 1000 atoms: 0.16 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=8, 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 C 19 " - pdb=" SG CYS C 29 " distance=2.05 Simple disulfide: pdb=" SG CYS H 19 " - pdb=" SG CYS H 29 " distance=2.05 Simple disulfide: pdb=" SG CYS M 19 " - pdb=" SG CYS M 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 61 " - pdb=" SG CYS H 70 " distance=2.02 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: 2.72 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: 1.29 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: 8.50 Time building geometry restraints manager: 3.69 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: 19081 15.12 - 30.24: 1023 30.24 - 45.35: 184 45.35 - 60.47: 24 60.47 - 75.59: 16 Dihedral angle restraints: 20328 sinusoidal: 8004 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 20325 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 4093 0.073 - 0.146: 988 0.146 - 0.218: 99 0.218 - 0.291: 28 0.291 - 0.364: 12 Chirality restraints: 5220 Sorted by residual: chirality pdb=" CB ILE K 148 " pdb=" CA ILE K 148 " pdb=" CG1 ILE K 148 " pdb=" CG2 ILE K 148 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CB ILE F 148 " pdb=" CA ILE F 148 " pdb=" CG1 ILE F 148 " pdb=" CG2 ILE F 148 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CB ILE N 148 " pdb=" CA ILE N 148 " pdb=" CG1 ILE N 148 " pdb=" CG2 ILE N 148 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.27e+00 ... (remaining 5217 not shown) Planarity restraints: 5980 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1D NAD E1001 " -0.013 2.00e-02 2.50e+03 2.63e-02 1.38e+01 pdb=" C2N NAD E1001 " 0.049 2.00e-02 2.50e+03 pdb=" C3N NAD E1001 " 0.006 2.00e-02 2.50e+03 pdb=" C4N NAD E1001 " 0.025 2.00e-02 2.50e+03 pdb=" C5N NAD E1001 " -0.003 2.00e-02 2.50e+03 pdb=" C6N NAD E1001 " -0.027 2.00e-02 2.50e+03 pdb=" C7N NAD E1001 " -0.039 2.00e-02 2.50e+03 pdb=" N1N NAD E1001 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAD A1001 " -0.013 2.00e-02 2.50e+03 2.63e-02 1.38e+01 pdb=" C2N NAD A1001 " 0.049 2.00e-02 2.50e+03 pdb=" C3N NAD A1001 " 0.006 2.00e-02 2.50e+03 pdb=" C4N NAD A1001 " 0.025 2.00e-02 2.50e+03 pdb=" C5N NAD A1001 " -0.003 2.00e-02 2.50e+03 pdb=" C6N NAD A1001 " -0.027 2.00e-02 2.50e+03 pdb=" C7N NAD A1001 " -0.039 2.00e-02 2.50e+03 pdb=" N1N NAD A1001 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAD K1001 " -0.013 2.00e-02 2.50e+03 2.63e-02 1.38e+01 pdb=" C2N NAD K1001 " 0.049 2.00e-02 2.50e+03 pdb=" C3N NAD K1001 " 0.006 2.00e-02 2.50e+03 pdb=" C4N NAD K1001 " 0.025 2.00e-02 2.50e+03 pdb=" C5N NAD K1001 " -0.003 2.00e-02 2.50e+03 pdb=" C6N NAD K1001 " -0.027 2.00e-02 2.50e+03 pdb=" C7N NAD K1001 " -0.039 2.00e-02 2.50e+03 pdb=" N1N NAD K1001 " 0.003 2.00e-02 2.50e+03 ... (remaining 5977 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 426 2.60 - 3.17: 28232 3.17 - 3.75: 53420 3.75 - 4.32: 73497 4.32 - 4.90: 119956 Nonbonded interactions: 275531 Sorted by model distance: nonbonded pdb=" SG CYS J 230 " pdb=" SG CYS J 236 " model vdw 2.020 3.760 nonbonded pdb=" SG CYS G 230 " pdb=" SG CYS G 236 " model vdw 2.020 3.760 nonbonded pdb=" SG CYS L 230 " pdb=" SG CYS L 236 " model vdw 2.020 3.760 nonbonded pdb=" SG CYS B 230 " pdb=" SG CYS B 236 " model vdw 2.021 3.760 nonbonded pdb=" SG CYS G 19 " pdb=" SG CYS G 41 " model vdw 2.029 3.760 ... (remaining 275526 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: 0.12 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: 2.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 30.330 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.080 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.800 ------------------------------------------------------------------------------- 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 34104 Z= 0.442 Angle : 0.987 10.513 46344 Z= 0.530 Chirality : 0.064 0.364 5220 Planarity : 0.008 0.077 5980 Dihedral : 10.072 75.588 12384 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.11 % Allowed : 3.19 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 0.01233 / 0.60 ( 8) SS BOND : angle 2.42448 / 1.52 ( 16) 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 : 1.341 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: 0.2163 time to fit residues: 353.3162 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 : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain L residue 182 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 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 45 HIS M 64 ASN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.108566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.084769 restraints weight = 85435.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.087491 restraints weight = 44970.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.089192 restraints weight = 30100.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.090268 restraints weight = 23640.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.090955 restraints weight = 20391.878| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 34104 Z= 0.132 Angle : 0.628 8.868 46344 Z= 0.333 Chirality : 0.047 0.199 5220 Planarity : 0.006 0.062 5980 Dihedral : 6.406 59.461 4684 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.51 % Allowed : 10.75 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.09 (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 0.006 0.001 ARG D 81 TYR 0.022 0.002 TYR F 321 PHE 0.021 0.002 PHE J 127 TRP 0.011 0.001 TRP E 20 HIS 0.011 0.001 HIS J 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (34096) covalent geometry : angle 0.62756 / 0.33 (46328) SS BOND : bond 0.00584 / 0.29 ( 8) SS BOND : angle 1.48459 / 0.87 ( 16) hydrogen bonds : bond 0.03650 / 2.43 ( 1404) hydrogen bonds : angle 5.50933 / 3.87 ( 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 830 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 741 time to evaluate : 1.342 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: 0.7021 (ttm) cc_final: 0.6177 (tpp) REVERT: P 4 LEU cc_start: 0.8748 (tp) cc_final: 0.8462 (mp) REVERT: P 12 ARG cc_start: 0.8460 (ttt180) cc_final: 0.8144 (ttt180) REVERT: P 33 TRP cc_start: 0.7885 (m100) cc_final: 0.7603 (m100) REVERT: P 39 LEU cc_start: 0.8828 (mp) cc_final: 0.8503 (tp) REVERT: P 47 ARG cc_start: 0.8581 (mmm160) cc_final: 0.8021 (mmm160) REVERT: P 50 GLN cc_start: 0.8251 (tm-30) cc_final: 0.7769 (tm-30) REVERT: P 63 ASP cc_start: 0.7645 (p0) cc_final: 0.7414 (p0) REVERT: D 249 GLN cc_start: 0.7958 (tt0) cc_final: 0.7282 (tt0) REVERT: D 295 ILE cc_start: 0.9393 (mp) cc_final: 0.9051 (mt) REVERT: A 67 CYS cc_start: 0.7822 (m) cc_final: 0.7616 (t) REVERT: A 147 ASP cc_start: 0.8233 (p0) cc_final: 0.7919 (p0) REVERT: A 176 MET cc_start: 0.7504 (mmt) cc_final: 0.7169 (mmt) REVERT: A 302 MET cc_start: 0.7373 (ptp) cc_final: 0.5633 (ptp) REVERT: E 249 GLN cc_start: 0.7740 (tt0) cc_final: 0.7342 (tt0) REVERT: E 295 ILE cc_start: 0.9404 (OUTLIER) cc_final: 0.9130 (mm) REVERT: F 1 MET cc_start: 0.7681 (pmm) cc_final: 0.7309 (ptp) REVERT: F 16 PHE cc_start: 0.9058 (t80) cc_final: 0.8763 (t80) REVERT: F 17 MET cc_start: 0.8565 (tpt) cc_final: 0.8323 (tpt) REVERT: F 20 TRP cc_start: 0.8273 (t60) cc_final: 0.8026 (t60) REVERT: F 40 PRO cc_start: 0.9128 (Cg_exo) cc_final: 0.8906 (Cg_endo) REVERT: F 49 TYR cc_start: 0.9047 (m-80) cc_final: 0.8674 (m-10) REVERT: F 52 MET cc_start: 0.8014 (mmm) cc_final: 0.7703 (mmm) REVERT: F 65 ASP cc_start: 0.8333 (p0) cc_final: 0.7196 (t0) REVERT: F 66 ASP cc_start: 0.8646 (p0) cc_final: 0.8268 (p0) REVERT: F 93 ILE cc_start: 0.8567 (mm) cc_final: 0.8307 (tp) REVERT: F 176 MET cc_start: 0.8015 (mmt) cc_final: 0.7176 (mmt) REVERT: F 284 SER cc_start: 0.9218 (p) cc_final: 0.8895 (p) REVERT: F 302 MET cc_start: 0.7470 (ptp) cc_final: 0.5955 (ptp) REVERT: F 323 GLN cc_start: 0.8978 (mm110) cc_final: 0.8690 (mm-40) REVERT: F 327 ASP cc_start: 0.8579 (m-30) cc_final: 0.8270 (m-30) REVERT: I 249 GLN cc_start: 0.7931 (tt0) cc_final: 0.7104 (tt0) REVERT: I 295 ILE cc_start: 0.9380 (OUTLIER) cc_final: 0.9109 (mm) REVERT: K 20 TRP cc_start: 0.8186 (t60) cc_final: 0.7893 (t60) REVERT: K 22 GLN cc_start: 0.9050 (mt0) cc_final: 0.8806 (tt0) REVERT: K 49 TYR cc_start: 0.8677 (m-80) cc_final: 0.8354 (m-10) REVERT: K 65 ASP cc_start: 0.8298 (p0) cc_final: 0.7191 (t0) REVERT: K 176 MET cc_start: 0.7619 (mmt) cc_final: 0.7209 (mmt) REVERT: K 183 TYR cc_start: 0.9148 (p90) cc_final: 0.8921 (p90) REVERT: K 302 MET cc_start: 0.7165 (ptp) cc_final: 0.5990 (ptp) REVERT: N 196 ASP cc_start: 0.8689 (t0) cc_final: 0.8435 (t0) REVERT: N 240 ASN cc_start: 0.8065 (t0) cc_final: 0.7384 (t0) REVERT: N 295 ILE cc_start: 0.9362 (mp) cc_final: 0.9022 (mt) REVERT: O 20 TRP cc_start: 0.8273 (t60) cc_final: 0.7727 (t60) REVERT: O 21 LEU cc_start: 0.9324 (mt) cc_final: 0.8649 (mt) REVERT: O 65 ASP cc_start: 0.8367 (p0) cc_final: 0.7277 (t0) REVERT: O 159 LEU cc_start: 0.8937 (tp) cc_final: 0.8493 (tp) REVERT: O 174 GLN cc_start: 0.7927 (mm110) cc_final: 0.7360 (mm110) REVERT: O 176 MET cc_start: 0.7287 (mmt) cc_final: 0.6764 (mmt) REVERT: O 323 GLN cc_start: 0.8946 (mm110) cc_final: 0.8586 (mt0) REVERT: O 327 ASP cc_start: 0.8977 (m-30) cc_final: 0.8516 (m-30) REVERT: J 46 HIS cc_start: 0.7557 (m170) cc_final: 0.7266 (m170) REVERT: J 156 ASP cc_start: 0.8192 (t0) cc_final: 0.7715 (t70) REVERT: J 309 GLN cc_start: 0.8959 (mt0) cc_final: 0.8579 (mt0) REVERT: B 116 LEU cc_start: 0.8972 (tp) cc_final: 0.8707 (tt) REVERT: B 279 ASN cc_start: 0.8560 (OUTLIER) cc_final: 0.8305 (t0) REVERT: G 127 PHE cc_start: 0.8079 (t80) cc_final: 0.7506 (t80) REVERT: G 193 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7869 (tm-30) REVERT: L 204 MET cc_start: 0.8736 (ptm) cc_final: 0.8454 (ptm) REVERT: L 279 ASN cc_start: 0.8685 (OUTLIER) cc_final: 0.8212 (t0) REVERT: L 308 PHE cc_start: 0.8923 (m-10) cc_final: 0.8676 (m-10) REVERT: L 309 GLN cc_start: 0.8805 (mt0) cc_final: 0.8295 (mp10) REVERT: C 28 GLN cc_start: 0.9104 (mp-120) cc_final: 0.8770 (mp10) REVERT: C 54 LYS cc_start: 0.7015 (pmmt) cc_final: 0.6233 (tptp) REVERT: C 63 ASP cc_start: 0.7752 (p0) cc_final: 0.7453 (p0) REVERT: H 1 MET cc_start: 0.6880 (ttm) cc_final: 0.6417 (tpp) REVERT: H 28 GLN cc_start: 0.8695 (mp-120) cc_final: 0.8397 (mt0) REVERT: H 60 TYR cc_start: 0.8281 (t80) cc_final: 0.8022 (t80) REVERT: M 12 ARG cc_start: 0.8714 (ttt180) cc_final: 0.8490 (ttt180) REVERT: M 28 GLN cc_start: 0.8727 (mp-120) cc_final: 0.7975 (tm-30) REVERT: M 38 GLU cc_start: 0.9128 (mm-30) cc_final: 0.8824 (mm-30) REVERT: M 42 GLU cc_start: 0.8779 (mm-30) cc_final: 0.8418 (mm-30) REVERT: M 46 GLN cc_start: 0.8496 (tp40) cc_final: 0.8026 (pt0) REVERT: M 47 ARG cc_start: 0.8752 (mmm160) cc_final: 0.8329 (mmm160) REVERT: M 50 GLN cc_start: 0.8755 (tm-30) cc_final: 0.8459 (tm-30) REVERT: M 54 LYS cc_start: 0.7322 (pmmt) cc_final: 0.6729 (tptp) outliers start: 89 outliers final: 59 residues processed: 803 average time/residue: 0.1933 time to fit residues: 263.6836 Evaluate side-chains 626 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 563 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain 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 245 ASP 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 224 THR Chi-restraints excluded: chain L residue 225 ILE Chi-restraints excluded: chain L residue 279 ASN Chi-restraints excluded: chain L residue 292 LEU Chi-restraints excluded: chain C residue 8 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 21 optimal weight: 6.9990 chunk 355 optimal weight: 0.0070 chunk 391 optimal weight: 8.9990 chunk 33 optimal weight: 0.9990 chunk 123 optimal weight: 7.9990 chunk 208 optimal weight: 5.9990 chunk 281 optimal weight: 2.9990 chunk 196 optimal weight: 8.9990 chunk 117 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 29 optimal weight: 0.3980 overall best weight: 1.6804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 16 HIS ** 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 15 ASN 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 O 187 GLN J 184 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN B 295 HIS B 309 GLN G 46 HIS 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 59 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.106539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.082962 restraints weight = 86516.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.085574 restraints weight = 45495.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.087218 restraints weight = 30516.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.088232 restraints weight = 23988.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.088777 restraints weight = 20790.728| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 34104 Z= 0.161 Angle : 0.631 13.446 46344 Z= 0.328 Chirality : 0.048 0.218 5220 Planarity : 0.005 0.057 5980 Dihedral : 6.065 55.611 4684 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.36 % Allowed : 13.37 % Favored : 83.27 % 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: -1.71 (0.12), residues: 4240 helix: -0.37 (0.13), residues: 1460 sheet: -1.64 (0.16), residues: 900 loop : -1.36 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 188 TYR 0.019 0.002 TYR L 217 PHE 0.020 0.001 PHE K 246 TRP 0.023 0.001 TRP E 20 HIS 0.022 0.001 HIS O 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (34096) covalent geometry : angle 0.63016 / 0.33 (46328) SS BOND : bond 0.00701 / 0.34 ( 8) SS BOND : angle 1.61226 / 0.94 ( 16) hydrogen bonds : bond 0.03352 / 2.27 ( 1404) hydrogen bonds : angle 5.25048 / 3.68 ( 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 711 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 592 time to evaluate : 1.378 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 12 ARG cc_start: 0.8505 (ttt180) cc_final: 0.8201 (ttt180) REVERT: P 39 LEU cc_start: 0.8846 (mp) cc_final: 0.8540 (tp) REVERT: P 49 GLU cc_start: 0.8287 (mm-30) cc_final: 0.8068 (mm-30) REVERT: P 54 LYS cc_start: 0.7727 (pmmt) cc_final: 0.6850 (tptp) REVERT: P 63 ASP cc_start: 0.7868 (p0) cc_final: 0.7614 (p0) REVERT: D 142 TYR cc_start: 0.7731 (p90) cc_final: 0.7363 (p90) REVERT: D 240 ASN cc_start: 0.7996 (t0) cc_final: 0.7498 (t0) REVERT: D 295 ILE cc_start: 0.9449 (mp) cc_final: 0.9042 (mt) REVERT: D 332 MET cc_start: 0.8295 (mmp) cc_final: 0.7901 (mmt) REVERT: A 20 TRP cc_start: 0.8192 (t60) cc_final: 0.7642 (t60) REVERT: A 147 ASP cc_start: 0.8400 (p0) cc_final: 0.8026 (p0) REVERT: A 176 MET cc_start: 0.7793 (mmt) cc_final: 0.7183 (mmt) REVERT: A 284 SER cc_start: 0.9268 (OUTLIER) cc_final: 0.8723 (m) REVERT: A 302 MET cc_start: 0.7568 (ptp) cc_final: 0.6318 (ptp) REVERT: A 323 GLN cc_start: 0.8837 (mm-40) cc_final: 0.8528 (mt0) REVERT: A 327 ASP cc_start: 0.8888 (m-30) cc_final: 0.8493 (m-30) REVERT: F 17 MET cc_start: 0.8344 (tpt) cc_final: 0.7852 (tpt) REVERT: F 20 TRP cc_start: 0.8442 (t60) cc_final: 0.7974 (t60) REVERT: F 40 PRO cc_start: 0.9096 (Cg_exo) cc_final: 0.8884 (Cg_endo) REVERT: F 65 ASP cc_start: 0.8343 (p0) cc_final: 0.7277 (t0) REVERT: F 93 ILE cc_start: 0.8648 (mm) cc_final: 0.8417 (tp) REVERT: F 176 MET cc_start: 0.8168 (mmt) cc_final: 0.7324 (mmt) REVERT: F 284 SER cc_start: 0.9245 (p) cc_final: 0.8730 (m) REVERT: F 302 MET cc_start: 0.7354 (ptp) cc_final: 0.5859 (ptp) REVERT: F 323 GLN cc_start: 0.8933 (mm110) cc_final: 0.8589 (mm-40) REVERT: F 327 ASP cc_start: 0.8731 (m-30) cc_final: 0.8380 (m-30) REVERT: I 142 TYR cc_start: 0.7596 (OUTLIER) cc_final: 0.6924 (p90) REVERT: I 284 SER cc_start: 0.9066 (p) cc_final: 0.8570 (m) REVERT: I 295 ILE cc_start: 0.9381 (OUTLIER) cc_final: 0.9051 (mm) REVERT: I 314 TRP cc_start: 0.9458 (m100) cc_final: 0.8953 (m100) REVERT: I 321 TYR cc_start: 0.9054 (t80) cc_final: 0.8831 (t80) REVERT: K 49 TYR cc_start: 0.8782 (m-80) cc_final: 0.8537 (m-10) REVERT: K 65 ASP cc_start: 0.8237 (p0) cc_final: 0.7371 (t0) REVERT: K 174 GLN cc_start: 0.8395 (mm-40) cc_final: 0.7655 (mm-40) REVERT: K 176 MET cc_start: 0.7687 (mmt) cc_final: 0.6939 (mmt) REVERT: K 271 MET cc_start: 0.7676 (mmt) cc_final: 0.7469 (mmp) REVERT: K 284 SER cc_start: 0.9353 (OUTLIER) cc_final: 0.8836 (m) REVERT: K 302 MET cc_start: 0.7131 (ptp) cc_final: 0.6850 (ptp) REVERT: N 207 ILE cc_start: 0.9334 (mt) cc_final: 0.8901 (mt) REVERT: N 240 ASN cc_start: 0.8097 (t0) cc_final: 0.7762 (t0) REVERT: N 295 ILE cc_start: 0.9448 (mp) cc_final: 0.9025 (mt) REVERT: O 20 TRP cc_start: 0.8191 (t60) cc_final: 0.7496 (t60) REVERT: O 65 ASP cc_start: 0.8415 (p0) cc_final: 0.7486 (t0) REVERT: O 159 LEU cc_start: 0.8928 (tp) cc_final: 0.8511 (tp) REVERT: O 284 SER cc_start: 0.9428 (OUTLIER) cc_final: 0.8886 (m) REVERT: O 323 GLN cc_start: 0.8922 (mm110) cc_final: 0.8530 (mm-40) REVERT: O 327 ASP cc_start: 0.8878 (m-30) cc_final: 0.8496 (m-30) REVERT: J 46 HIS cc_start: 0.7791 (m170) cc_final: 0.7403 (m-70) REVERT: J 241 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8419 (tp) REVERT: J 309 GLN cc_start: 0.8980 (mt0) cc_final: 0.8535 (mp10) REVERT: B 67 ASN cc_start: 0.8738 (m110) cc_final: 0.8178 (p0) REVERT: G 46 HIS cc_start: 0.7802 (m170) cc_final: 0.7513 (m-70) REVERT: G 69 ASP cc_start: 0.7742 (OUTLIER) cc_final: 0.7518 (m-30) REVERT: G 70 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8428 (tt) REVERT: G 127 PHE cc_start: 0.8102 (t80) cc_final: 0.7537 (t80) REVERT: G 193 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7904 (tm-30) REVERT: L 279 ASN cc_start: 0.8573 (OUTLIER) cc_final: 0.8308 (t0) REVERT: L 309 GLN cc_start: 0.8897 (mt0) cc_final: 0.8264 (mp10) REVERT: C 28 GLN cc_start: 0.9101 (mp-120) cc_final: 0.8746 (mp10) REVERT: C 54 LYS cc_start: 0.7638 (pmmt) cc_final: 0.6471 (tptp) REVERT: C 63 ASP cc_start: 0.7839 (p0) cc_final: 0.7550 (p0) REVERT: H 1 MET cc_start: 0.7066 (ttm) cc_final: 0.6690 (tpp) REVERT: H 28 GLN cc_start: 0.8787 (mp-120) cc_final: 0.8439 (mt0) REVERT: M 1 MET cc_start: 0.8421 (tpp) cc_final: 0.8091 (tmm) REVERT: M 28 GLN cc_start: 0.8784 (mp-120) cc_final: 0.8018 (tm-30) REVERT: M 47 ARG cc_start: 0.8791 (mmm160) cc_final: 0.7990 (mmm160) REVERT: M 49 GLU cc_start: 0.8339 (mm-30) cc_final: 0.7897 (mm-30) REVERT: M 50 GLN cc_start: 0.8749 (tm-30) cc_final: 0.8382 (tm-30) REVERT: M 54 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.7135 (tptp) REVERT: M 66 ASP cc_start: 0.7792 (t0) cc_final: 0.7442 (t0) outliers start: 119 outliers final: 76 residues processed: 677 average time/residue: 0.1976 time to fit residues: 226.3020 Evaluate side-chains 585 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 499 time to evaluate : 1.341 ------------------------------------------------------------------------------- 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 155 THR 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 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 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 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 247 VAL Chi-restraints excluded: chain O residue 85 ASN Chi-restraints excluded: chain O residue 193 SER Chi-restraints excluded: chain O residue 220 LEU 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 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 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 Chi-restraints excluded: chain M residue 54 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 126 optimal weight: 0.9980 chunk 407 optimal weight: 1.9990 chunk 182 optimal weight: 0.1980 chunk 348 optimal weight: 7.9990 chunk 219 optimal weight: 8.9990 chunk 381 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 220 optimal weight: 3.9990 chunk 356 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 285 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 16 HIS A 15 ASN A 174 GLN ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 7 ASN K 73 HIS K 291 ASN ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 290 HIS J 184 GLN J 279 ASN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 184 GLN L 106 HIS L 184 GLN ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 279 ASN H 28 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.108842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.085618 restraints weight = 85867.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.088278 restraints weight = 44445.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.089988 restraints weight = 29656.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.091022 restraints weight = 23101.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.091581 restraints weight = 19941.254| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 34104 Z= 0.111 Angle : 0.596 10.596 46344 Z= 0.306 Chirality : 0.046 0.260 5220 Planarity : 0.004 0.054 5980 Dihedral : 5.749 56.348 4684 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.47 % Allowed : 14.87 % Favored : 81.66 % 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: -1.29 (0.12), residues: 4240 helix: -0.05 (0.13), residues: 1468 sheet: -1.32 (0.16), residues: 880 loop : -1.15 (0.14), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 47 TYR 0.018 0.001 TYR G 217 PHE 0.021 0.001 PHE L 68 TRP 0.015 0.001 TRP E 20 HIS 0.013 0.001 HIS K 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (34096) covalent geometry : angle 0.59460 / 0.31 (46328) SS BOND : bond 0.00785 / 0.40 ( 8) SS BOND : angle 1.96587 / 1.15 ( 16) hydrogen bonds : bond 0.03104 / 2.09 ( 1404) hydrogen bonds : angle 5.01746 / 3.53 ( 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 732 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 609 time to evaluate : 1.297 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: P 39 LEU cc_start: 0.8881 (mp) cc_final: 0.8547 (tp) REVERT: P 54 LYS cc_start: 0.7590 (pmmt) cc_final: 0.6652 (tptp) REVERT: P 63 ASP cc_start: 0.7664 (p0) cc_final: 0.7360 (p0) REVERT: D 295 ILE cc_start: 0.9434 (mp) cc_final: 0.9072 (mt) REVERT: A 65 ASP cc_start: 0.8347 (p0) cc_final: 0.7545 (t0) REVERT: A 147 ASP cc_start: 0.8423 (p0) cc_final: 0.8181 (p0) REVERT: A 176 MET cc_start: 0.7727 (mmt) cc_final: 0.7180 (mmt) REVERT: A 284 SER cc_start: 0.9135 (OUTLIER) cc_final: 0.8658 (m) REVERT: A 302 MET cc_start: 0.7622 (ptp) cc_final: 0.6394 (ptp) REVERT: A 323 GLN cc_start: 0.8723 (mm-40) cc_final: 0.8453 (mt0) REVERT: A 327 ASP cc_start: 0.8879 (m-30) cc_final: 0.8490 (m-30) REVERT: E 52 MET cc_start: 0.7179 (mmm) cc_final: 0.6974 (tpt) REVERT: E 246 PHE cc_start: 0.8573 (t80) cc_final: 0.8207 (t80) REVERT: F 1 MET cc_start: 0.7163 (pmm) cc_final: 0.6835 (ptp) REVERT: F 20 TRP cc_start: 0.8357 (t60) cc_final: 0.8008 (t60) REVERT: F 40 PRO cc_start: 0.9058 (Cg_exo) cc_final: 0.8801 (Cg_endo) REVERT: F 48 LYS cc_start: 0.8840 (tttt) cc_final: 0.8416 (tttt) REVERT: F 65 ASP cc_start: 0.8323 (p0) cc_final: 0.7404 (t0) REVERT: F 93 ILE cc_start: 0.8568 (mm) cc_final: 0.8305 (tp) REVERT: F 176 MET cc_start: 0.8165 (mmt) cc_final: 0.7355 (mmt) REVERT: F 284 SER cc_start: 0.9233 (p) cc_final: 0.8783 (m) REVERT: F 302 MET cc_start: 0.7365 (ptp) cc_final: 0.5898 (ptp) REVERT: F 323 GLN cc_start: 0.8923 (mm110) cc_final: 0.8468 (mm-40) REVERT: F 327 ASP cc_start: 0.8639 (m-30) cc_final: 0.8251 (m-30) REVERT: I 142 TYR cc_start: 0.7502 (OUTLIER) cc_final: 0.6707 (p90) REVERT: I 246 PHE cc_start: 0.8664 (t80) cc_final: 0.8420 (t80) REVERT: I 295 ILE cc_start: 0.9369 (OUTLIER) cc_final: 0.9026 (mm) REVERT: I 314 TRP cc_start: 0.9378 (m100) cc_final: 0.9084 (m100) REVERT: I 321 TYR cc_start: 0.8966 (t80) cc_final: 0.8713 (t80) REVERT: K 65 ASP cc_start: 0.8145 (p0) cc_final: 0.7303 (t0) REVERT: K 174 GLN cc_start: 0.8376 (mm-40) cc_final: 0.7705 (mm-40) REVERT: K 271 MET cc_start: 0.7672 (mmt) cc_final: 0.7449 (mmp) REVERT: K 284 SER cc_start: 0.9273 (OUTLIER) cc_final: 0.8837 (m) REVERT: K 302 MET cc_start: 0.7041 (ptp) cc_final: 0.5630 (ptp) REVERT: N 240 ASN cc_start: 0.8019 (t0) cc_final: 0.7721 (t0) REVERT: N 295 ILE cc_start: 0.9413 (mp) cc_final: 0.9032 (mt) REVERT: O 17 MET cc_start: 0.8399 (tpt) cc_final: 0.8158 (tpt) REVERT: O 20 TRP cc_start: 0.8291 (t60) cc_final: 0.7457 (t60) REVERT: O 65 ASP cc_start: 0.8309 (p0) cc_final: 0.7482 (t0) REVERT: O 159 LEU cc_start: 0.8882 (tp) cc_final: 0.8515 (tp) REVERT: O 176 MET cc_start: 0.7554 (mmt) cc_final: 0.6547 (mmt) REVERT: O 284 SER cc_start: 0.9368 (OUTLIER) cc_final: 0.8931 (m) REVERT: O 304 LEU cc_start: 0.8439 (mt) cc_final: 0.7896 (mt) REVERT: O 323 GLN cc_start: 0.8912 (mm110) cc_final: 0.8605 (mm-40) REVERT: O 327 ASP cc_start: 0.8933 (m-30) cc_final: 0.8492 (m-30) REVERT: J 46 HIS cc_start: 0.7650 (m170) cc_final: 0.7309 (m170) REVERT: J 69 ASP cc_start: 0.7550 (m-30) cc_final: 0.6147 (t0) REVERT: J 127 PHE cc_start: 0.7840 (t80) cc_final: 0.6627 (t80) REVERT: B 67 ASN cc_start: 0.8665 (m110) cc_final: 0.8152 (p0) REVERT: B 241 ILE cc_start: 0.8788 (OUTLIER) cc_final: 0.8485 (tp) REVERT: B 270 LEU cc_start: 0.9432 (OUTLIER) cc_final: 0.9187 (tt) REVERT: G 46 HIS cc_start: 0.7644 (m170) cc_final: 0.7248 (m-70) REVERT: G 80 ASN cc_start: 0.6981 (m110) cc_final: 0.6034 (t0) REVERT: G 127 PHE cc_start: 0.8083 (t80) cc_final: 0.7518 (t80) REVERT: G 193 GLU cc_start: 0.8338 (tm-30) cc_final: 0.8062 (tm-30) REVERT: L 241 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8581 (tp) REVERT: C 28 GLN cc_start: 0.9136 (mp-120) cc_final: 0.8782 (mp10) REVERT: C 40 GLN cc_start: 0.9341 (mm-40) cc_final: 0.8937 (mm-40) REVERT: C 63 ASP cc_start: 0.7645 (p0) cc_final: 0.7338 (p0) REVERT: H 1 MET cc_start: 0.7007 (ttm) cc_final: 0.6184 (tpp) REVERT: H 28 GLN cc_start: 0.8672 (mp10) cc_final: 0.8239 (mt0) REVERT: H 36 LEU cc_start: 0.8911 (tt) cc_final: 0.8657 (tp) REVERT: H 63 ASP cc_start: 0.7200 (p0) cc_final: 0.6900 (p0) REVERT: M 46 GLN cc_start: 0.8295 (tp40) cc_final: 0.7925 (pt0) REVERT: M 47 ARG cc_start: 0.8857 (mmm160) cc_final: 0.8127 (mmm160) REVERT: M 50 GLN cc_start: 0.8817 (tm-30) cc_final: 0.8379 (tm-30) REVERT: M 54 LYS cc_start: 0.7538 (pmmt) cc_final: 0.6970 (tptp) REVERT: M 66 ASP cc_start: 0.7942 (t0) cc_final: 0.7673 (t0) outliers start: 123 outliers final: 78 residues processed: 697 average time/residue: 0.1889 time to fit residues: 223.8516 Evaluate side-chains 619 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 533 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain P residue 4 LEU 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 251 GLU Chi-restraints excluded: chain D residue 282 LEU 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 247 VAL Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain F residue 21 LEU 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 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 220 LEU Chi-restraints excluded: chain O residue 245 ASP Chi-restraints excluded: chain O residue 284 SER Chi-restraints excluded: chain O residue 290 HIS Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 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 28 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 270 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 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 257 VAL Chi-restraints excluded: chain G residue 292 LEU Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 182 VAL Chi-restraints excluded: chain L residue 225 ILE Chi-restraints excluded: chain L residue 241 ILE 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: chunk 27 optimal weight: 2.9990 chunk 397 optimal weight: 0.2980 chunk 386 optimal weight: 6.9990 chunk 393 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 chunk 173 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 28 optimal weight: 0.4980 chunk 369 optimal weight: 0.0470 chunk 278 optimal weight: 5.9990 overall best weight: 1.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 16 HIS P 59 GLN ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 240 ASN K 290 HIS N 45 HIS ** N 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 187 GLN O 290 HIS O 323 GLN J 184 GLN ** J 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN B 114 HIS ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 184 GLN G 206 GLN L 106 HIS L 184 GLN ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.107037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.083185 restraints weight = 86731.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.085846 restraints weight = 45744.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.087517 restraints weight = 30890.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.088595 restraints weight = 24336.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.089233 restraints weight = 21029.977| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 34104 Z= 0.131 Angle : 0.616 13.544 46344 Z= 0.314 Chirality : 0.047 0.271 5220 Planarity : 0.004 0.053 5980 Dihedral : 5.672 54.631 4684 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.64 % Allowed : 16.31 % Favored : 80.05 % 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: -1.01 (0.13), residues: 4240 helix: 0.12 (0.14), residues: 1460 sheet: -1.10 (0.16), residues: 880 loop : -0.96 (0.14), residues: 1900 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 0.024 0.001 PHE F 16 TRP 0.028 0.001 TRP K 20 HIS 0.014 0.001 HIS O 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (34096) covalent geometry : angle 0.61431 / 0.31 (46328) SS BOND : bond 0.00796 / 0.37 ( 8) SS BOND : angle 2.85743 / 1.43 ( 16) hydrogen bonds : bond 0.03167 / 2.13 ( 1404) hydrogen bonds : angle 4.97722 / 3.50 ( 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 682 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 553 time to evaluate : 1.388 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: P 12 ARG cc_start: 0.8391 (ttt180) cc_final: 0.8185 (ttt180) REVERT: P 39 LEU cc_start: 0.8888 (mp) cc_final: 0.8605 (tp) REVERT: P 54 LYS cc_start: 0.7742 (pmmt) cc_final: 0.6984 (tptp) REVERT: P 63 ASP cc_start: 0.7595 (p0) cc_final: 0.7289 (p0) REVERT: P 69 GLU cc_start: 0.7664 (mp0) cc_final: 0.7420 (mp0) REVERT: D 142 TYR cc_start: 0.7485 (OUTLIER) cc_final: 0.6911 (p90) REVERT: D 295 ILE cc_start: 0.9444 (mp) cc_final: 0.9079 (mt) REVERT: A 20 TRP cc_start: 0.8133 (t60) cc_final: 0.7178 (t60) REVERT: A 65 ASP cc_start: 0.8317 (p0) cc_final: 0.7689 (t0) REVERT: A 176 MET cc_start: 0.7628 (mmt) cc_final: 0.7180 (mmp) REVERT: A 284 SER cc_start: 0.9105 (OUTLIER) cc_final: 0.8651 (m) REVERT: A 302 MET cc_start: 0.7628 (ptp) cc_final: 0.6272 (ptp) REVERT: A 323 GLN cc_start: 0.8732 (mm-40) cc_final: 0.8463 (mt0) REVERT: A 327 ASP cc_start: 0.8897 (m-30) cc_final: 0.8415 (m-30) REVERT: E 246 PHE cc_start: 0.8653 (t80) cc_final: 0.8267 (t80) REVERT: F 1 MET cc_start: 0.7311 (pmm) cc_final: 0.6963 (ptp) REVERT: F 20 TRP cc_start: 0.8422 (t60) cc_final: 0.8102 (t60) REVERT: F 40 PRO cc_start: 0.9068 (Cg_exo) cc_final: 0.8817 (Cg_endo) REVERT: F 65 ASP cc_start: 0.8283 (p0) cc_final: 0.7372 (t0) REVERT: F 93 ILE cc_start: 0.8635 (mm) cc_final: 0.8361 (tp) REVERT: F 176 MET cc_start: 0.8239 (mmt) cc_final: 0.7282 (mmt) REVERT: F 284 SER cc_start: 0.9313 (p) cc_final: 0.9075 (p) REVERT: F 302 MET cc_start: 0.7303 (ptp) cc_final: 0.6640 (ptp) REVERT: F 323 GLN cc_start: 0.8909 (mm110) cc_final: 0.8439 (mm-40) REVERT: F 327 ASP cc_start: 0.8536 (m-30) cc_final: 0.8203 (m-30) REVERT: I 142 TYR cc_start: 0.7629 (OUTLIER) cc_final: 0.6495 (p90) REVERT: I 246 PHE cc_start: 0.8743 (t80) cc_final: 0.8492 (t80) REVERT: I 295 ILE cc_start: 0.9396 (OUTLIER) cc_final: 0.9041 (mm) REVERT: I 302 MET cc_start: 0.8152 (ptp) cc_final: 0.7928 (ptp) REVERT: I 314 TRP cc_start: 0.9351 (m100) cc_final: 0.9067 (m100) REVERT: I 321 TYR cc_start: 0.9047 (t80) cc_final: 0.8814 (t80) REVERT: K 65 ASP cc_start: 0.8135 (p0) cc_final: 0.7449 (t0) REVERT: K 174 GLN cc_start: 0.8443 (mm-40) cc_final: 0.7708 (mm-40) REVERT: K 176 MET cc_start: 0.7605 (mmt) cc_final: 0.6900 (mmt) REVERT: K 271 MET cc_start: 0.7710 (mmt) cc_final: 0.7500 (mmp) REVERT: K 284 SER cc_start: 0.9265 (OUTLIER) cc_final: 0.8874 (m) REVERT: K 302 MET cc_start: 0.7083 (ptp) cc_final: 0.6812 (ptp) REVERT: N 205 MET cc_start: 0.8513 (mtp) cc_final: 0.8188 (mtp) REVERT: N 240 ASN cc_start: 0.8066 (t0) cc_final: 0.7842 (t0) REVERT: N 295 ILE cc_start: 0.9446 (mp) cc_final: 0.9064 (mt) REVERT: O 17 MET cc_start: 0.8269 (tpt) cc_final: 0.8009 (tpt) REVERT: O 20 TRP cc_start: 0.8364 (t60) cc_final: 0.7472 (t60) REVERT: O 65 ASP cc_start: 0.8320 (p0) cc_final: 0.7720 (t0) REVERT: O 284 SER cc_start: 0.9368 (OUTLIER) cc_final: 0.8891 (m) REVERT: O 323 GLN cc_start: 0.8891 (mm-40) cc_final: 0.8555 (mm-40) REVERT: O 327 ASP cc_start: 0.8900 (m-30) cc_final: 0.8468 (m-30) REVERT: J 46 HIS cc_start: 0.7731 (m170) cc_final: 0.7396 (m170) REVERT: J 69 ASP cc_start: 0.7645 (m-30) cc_final: 0.6252 (t70) REVERT: J 127 PHE cc_start: 0.7833 (t80) cc_final: 0.7510 (t80) REVERT: B 67 ASN cc_start: 0.8737 (m110) cc_final: 0.8224 (p0) REVERT: B 241 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8435 (tp) REVERT: G 46 HIS cc_start: 0.7603 (m170) cc_final: 0.7177 (m-70) REVERT: G 80 ASN cc_start: 0.7091 (m110) cc_final: 0.6218 (t0) REVERT: G 127 PHE cc_start: 0.8069 (t80) cc_final: 0.7411 (t80) REVERT: G 193 GLU cc_start: 0.8355 (tm-30) cc_final: 0.8095 (tm-30) REVERT: L 69 ASP cc_start: 0.7916 (OUTLIER) cc_final: 0.6776 (t70) REVERT: L 241 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8563 (tp) REVERT: C 28 GLN cc_start: 0.9107 (mp10) cc_final: 0.8672 (mp10) REVERT: C 63 ASP cc_start: 0.7749 (p0) cc_final: 0.7451 (p0) REVERT: C 69 GLU cc_start: 0.7910 (mp0) cc_final: 0.7546 (mp0) REVERT: H 1 MET cc_start: 0.7250 (ttm) cc_final: 0.6530 (tpp) REVERT: H 4 LEU cc_start: 0.8806 (tp) cc_final: 0.8568 (tt) REVERT: H 12 ARG cc_start: 0.8293 (ttt180) cc_final: 0.8001 (ttt180) REVERT: H 28 GLN cc_start: 0.8741 (mp10) cc_final: 0.8314 (mt0) REVERT: M 1 MET cc_start: 0.8746 (tpp) cc_final: 0.8494 (tmm) REVERT: M 28 GLN cc_start: 0.8729 (mp-120) cc_final: 0.7925 (tm-30) REVERT: M 46 GLN cc_start: 0.8275 (tp40) cc_final: 0.7877 (pt0) REVERT: M 47 ARG cc_start: 0.8866 (mmm160) cc_final: 0.8113 (mmm160) REVERT: M 50 GLN cc_start: 0.8875 (tm-30) cc_final: 0.8483 (tm-30) REVERT: M 54 LYS cc_start: 0.7705 (pmmt) cc_final: 0.7056 (tptp) REVERT: M 66 ASP cc_start: 0.8030 (t0) cc_final: 0.7749 (t0) outliers start: 129 outliers final: 86 residues processed: 652 average time/residue: 0.1895 time to fit residues: 210.2991 Evaluate side-chains 603 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 508 time to evaluate : 1.482 ------------------------------------------------------------------------------- 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 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 282 LEU Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 285 SER 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 247 VAL Chi-restraints excluded: chain E residue 302 MET Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 142 TYR Chi-restraints excluded: chain I residue 166 LEU 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 247 VAL Chi-restraints excluded: chain N residue 302 MET Chi-restraints excluded: chain O residue 21 LEU 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 244 VAL Chi-restraints excluded: chain O residue 284 SER 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 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 28 LEU Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 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 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 241 ILE Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 289 THR 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 C residue 8 ILE Chi-restraints excluded: chain M residue 2 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 149 optimal weight: 5.9990 chunk 188 optimal weight: 0.9990 chunk 98 optimal weight: 0.1980 chunk 63 optimal weight: 0.2980 chunk 165 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 376 optimal weight: 2.9990 chunk 267 optimal weight: 7.9990 chunk 309 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 GLN ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 ASN ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 240 ASN K 290 HIS ** N 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 290 HIS J 279 ASN L 91 HIS L 106 HIS ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 28 GLN ** 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 = 0.3745 r_free = 0.3745 target = 0.107758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.084496 restraints weight = 86114.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.087198 restraints weight = 44890.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.088863 restraints weight = 29884.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.089923 restraints weight = 23455.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.090552 restraints weight = 20225.603| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 34104 Z= 0.117 Angle : 0.601 12.378 46344 Z= 0.307 Chirality : 0.046 0.267 5220 Planarity : 0.004 0.051 5980 Dihedral : 5.549 57.889 4684 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.67 % Allowed : 16.73 % Favored : 79.60 % 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: 0.30 (0.14), residues: 1464 sheet: -0.93 (0.16), residues: 888 loop : -0.83 (0.15), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 120 TYR 0.018 0.001 TYR J 217 PHE 0.024 0.001 PHE O 246 TRP 0.046 0.001 TRP K 20 HIS 0.008 0.001 HIS K 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (34096) covalent geometry : angle 0.60067 / 0.31 (46328) SS BOND : bond 0.00225 / 0.11 ( 8) SS BOND : angle 1.65675 / 0.88 ( 16) hydrogen bonds : bond 0.03077 / 2.07 ( 1404) hydrogen bonds : angle 4.85298 / 3.41 ( 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 701 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 571 time to evaluate : 1.599 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: P 12 ARG cc_start: 0.8459 (ttt180) cc_final: 0.8035 (ttt180) REVERT: P 39 LEU cc_start: 0.8871 (mp) cc_final: 0.8531 (tp) REVERT: P 54 LYS cc_start: 0.7840 (pmmt) cc_final: 0.7048 (tptp) REVERT: P 63 ASP cc_start: 0.7692 (p0) cc_final: 0.7358 (p0) REVERT: P 66 ASP cc_start: 0.8073 (t0) cc_final: 0.7825 (t0) REVERT: D 142 TYR cc_start: 0.7410 (OUTLIER) cc_final: 0.6882 (p90) REVERT: D 246 PHE cc_start: 0.8839 (t80) cc_final: 0.8592 (t80) REVERT: D 295 ILE cc_start: 0.9444 (mp) cc_final: 0.9066 (mt) REVERT: A 65 ASP cc_start: 0.8291 (p0) cc_final: 0.7663 (t0) REVERT: A 176 MET cc_start: 0.7608 (mmt) cc_final: 0.7167 (mmt) REVERT: A 284 SER cc_start: 0.9081 (OUTLIER) cc_final: 0.8642 (m) REVERT: A 302 MET cc_start: 0.7555 (ptp) cc_final: 0.6230 (ptp) REVERT: A 323 GLN cc_start: 0.8700 (mm-40) cc_final: 0.8472 (mt0) REVERT: A 327 ASP cc_start: 0.8858 (m-30) cc_final: 0.8424 (m-30) REVERT: E 246 PHE cc_start: 0.8750 (t80) cc_final: 0.8346 (t80) REVERT: E 295 ILE cc_start: 0.9189 (mm) cc_final: 0.8956 (mm) REVERT: E 332 MET cc_start: 0.7989 (mmp) cc_final: 0.7761 (mmp) REVERT: F 1 MET cc_start: 0.7330 (pmm) cc_final: 0.6964 (ptp) REVERT: F 20 TRP cc_start: 0.8360 (t60) cc_final: 0.8115 (t60) REVERT: F 40 PRO cc_start: 0.9073 (Cg_exo) cc_final: 0.8843 (Cg_endo) REVERT: F 65 ASP cc_start: 0.8237 (p0) cc_final: 0.7415 (t0) REVERT: F 93 ILE cc_start: 0.8604 (mm) cc_final: 0.8370 (tp) REVERT: F 129 ASN cc_start: 0.6377 (p0) cc_final: 0.6093 (p0) REVERT: F 176 MET cc_start: 0.8088 (mmt) cc_final: 0.7474 (mmt) REVERT: F 284 SER cc_start: 0.9274 (p) cc_final: 0.9051 (p) REVERT: F 302 MET cc_start: 0.7350 (ptp) cc_final: 0.6641 (ptp) REVERT: F 323 GLN cc_start: 0.8845 (mm110) cc_final: 0.8409 (mm-40) REVERT: F 327 ASP cc_start: 0.8515 (m-30) cc_final: 0.8186 (m-30) REVERT: I 142 TYR cc_start: 0.7540 (OUTLIER) cc_final: 0.6661 (p90) REVERT: I 246 PHE cc_start: 0.8734 (t80) cc_final: 0.8471 (t80) REVERT: I 295 ILE cc_start: 0.9368 (OUTLIER) cc_final: 0.9018 (mm) REVERT: I 321 TYR cc_start: 0.9020 (t80) cc_final: 0.8791 (t80) REVERT: I 332 MET cc_start: 0.8092 (mmp) cc_final: 0.7807 (mmt) REVERT: K 65 ASP cc_start: 0.8087 (p0) cc_final: 0.7525 (t0) REVERT: K 176 MET cc_start: 0.7676 (mmt) cc_final: 0.6792 (mmt) REVERT: K 271 MET cc_start: 0.7733 (mmt) cc_final: 0.7498 (mmp) REVERT: K 284 SER cc_start: 0.9244 (OUTLIER) cc_final: 0.8069 (m) REVERT: K 302 MET cc_start: 0.7206 (ptp) cc_final: 0.5929 (ptp) REVERT: K 314 TRP cc_start: 0.9041 (m100) cc_final: 0.8363 (m100) REVERT: N 226 GLN cc_start: 0.7816 (tm-30) cc_final: 0.7481 (tm-30) REVERT: N 240 ASN cc_start: 0.8040 (t0) cc_final: 0.7739 (t0) REVERT: N 295 ILE cc_start: 0.9440 (mp) cc_final: 0.9046 (mt) REVERT: O 20 TRP cc_start: 0.8316 (t60) cc_final: 0.7457 (t60) REVERT: O 65 ASP cc_start: 0.8279 (p0) cc_final: 0.7747 (t0) REVERT: O 176 MET cc_start: 0.7456 (mmt) cc_final: 0.6379 (mmt) REVERT: O 265 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7660 (tp30) REVERT: O 284 SER cc_start: 0.9375 (OUTLIER) cc_final: 0.8888 (m) REVERT: O 323 GLN cc_start: 0.8897 (mm-40) cc_final: 0.8583 (mm-40) REVERT: O 327 ASP cc_start: 0.8922 (m-30) cc_final: 0.8500 (m-30) REVERT: J 46 HIS cc_start: 0.7641 (m170) cc_final: 0.7304 (m170) REVERT: J 127 PHE cc_start: 0.7684 (t80) cc_final: 0.7471 (t80) REVERT: B 67 ASN cc_start: 0.8768 (m110) cc_final: 0.8280 (p0) REVERT: B 131 LEU cc_start: 0.9383 (tt) cc_final: 0.9085 (mm) REVERT: B 241 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8402 (tp) REVERT: G 46 HIS cc_start: 0.7511 (m170) cc_final: 0.7105 (m-70) REVERT: G 80 ASN cc_start: 0.7250 (m110) cc_final: 0.6384 (t0) REVERT: G 193 GLU cc_start: 0.8383 (tm-30) cc_final: 0.8157 (tm-30) REVERT: G 241 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8435 (tp) REVERT: L 69 ASP cc_start: 0.8009 (OUTLIER) cc_final: 0.7170 (t70) REVERT: L 214 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7562 (mp0) REVERT: L 241 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8587 (tp) REVERT: C 1 MET cc_start: 0.9020 (tpp) cc_final: 0.8137 (tmm) REVERT: C 28 GLN cc_start: 0.9132 (mp10) cc_final: 0.8706 (mp10) REVERT: C 40 GLN cc_start: 0.9284 (mm-40) cc_final: 0.8857 (mm-40) REVERT: C 63 ASP cc_start: 0.7729 (p0) cc_final: 0.7465 (p0) REVERT: H 1 MET cc_start: 0.7015 (ttm) cc_final: 0.6386 (tpp) REVERT: H 63 ASP cc_start: 0.7302 (p0) cc_final: 0.7044 (p0) REVERT: M 28 GLN cc_start: 0.8632 (mp10) cc_final: 0.7860 (tm-30) REVERT: M 39 LEU cc_start: 0.8945 (mp) cc_final: 0.8583 (tp) REVERT: M 42 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8333 (mm-30) REVERT: M 46 GLN cc_start: 0.8305 (tp40) cc_final: 0.7903 (pt0) REVERT: M 47 ARG cc_start: 0.8896 (mmm160) cc_final: 0.8087 (mmm160) REVERT: M 50 GLN cc_start: 0.8902 (tm-30) cc_final: 0.8605 (tm-30) REVERT: M 54 LYS cc_start: 0.7746 (pmmt) cc_final: 0.7080 (tptp) REVERT: M 66 ASP cc_start: 0.7928 (t0) cc_final: 0.7694 (t0) outliers start: 130 outliers final: 89 residues processed: 662 average time/residue: 0.1925 time to fit residues: 217.8648 Evaluate side-chains 628 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 528 time to evaluate : 1.304 ------------------------------------------------------------------------------- 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 282 LEU Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 285 SER 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 208 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 302 MET Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 142 TYR 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 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 K residue 85 ASN Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain K residue 259 VAL Chi-restraints excluded: chain K residue 278 SER Chi-restraints excluded: chain K residue 284 SER Chi-restraints excluded: chain K residue 290 HIS Chi-restraints excluded: chain N residue 4 VAL Chi-restraints excluded: chain N residue 155 THR Chi-restraints excluded: chain N residue 208 VAL Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain O residue 21 LEU 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 220 LEU Chi-restraints excluded: chain O residue 244 VAL 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 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 J residue 279 ASN Chi-restraints excluded: chain J residue 292 LEU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 42 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 225 ILE Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 289 THR Chi-restraints excluded: chain G residue 301 SER Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 69 ASP Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 182 VAL Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 225 ILE Chi-restraints excluded: chain L residue 241 ILE Chi-restraints excluded: chain L residue 257 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 380 optimal weight: 0.4980 chunk 401 optimal weight: 0.5980 chunk 10 optimal weight: 5.9990 chunk 367 optimal weight: 0.0980 chunk 352 optimal weight: 3.9990 chunk 171 optimal weight: 0.9980 chunk 176 optimal weight: 0.1980 chunk 74 optimal weight: 0.8980 chunk 345 optimal weight: 8.9990 chunk 327 optimal weight: 5.9990 chunk 228 optimal weight: 0.7980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 290 HIS ** N 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 15 ASN O 290 HIS ** J 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 279 ASN ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.109492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.085836 restraints weight = 87165.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.088585 restraints weight = 45639.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.090312 restraints weight = 30619.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.091395 restraints weight = 24061.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.091905 restraints weight = 20772.887| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.4511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 34104 Z= 0.106 Angle : 0.621 13.351 46344 Z= 0.312 Chirality : 0.047 0.301 5220 Planarity : 0.004 0.050 5980 Dihedral : 5.472 59.263 4684 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.27 % Allowed : 17.47 % Favored : 79.26 % 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: -0.66 (0.13), residues: 4240 helix: 0.34 (0.14), residues: 1484 sheet: -0.77 (0.17), residues: 888 loop : -0.77 (0.15), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 47 TYR 0.029 0.001 TYR O 49 PHE 0.019 0.001 PHE B 127 TRP 0.069 0.001 TRP K 20 HIS 0.015 0.001 HIS K 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (34096) covalent geometry : angle 0.61965 / 0.31 (46328) SS BOND : bond 0.00552 / 0.24 ( 8) SS BOND : angle 2.44268 / 1.67 ( 16) hydrogen bonds : bond 0.03026 / 2.05 ( 1404) hydrogen bonds : angle 4.80730 / 3.38 ( 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 733 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 617 time to evaluate : 1.360 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: P 37 GLU cc_start: 0.8822 (tp30) cc_final: 0.8617 (tp30) REVERT: P 39 LEU cc_start: 0.8860 (mp) cc_final: 0.8531 (tp) REVERT: P 54 LYS cc_start: 0.7855 (pmmt) cc_final: 0.7063 (tptp) REVERT: P 61 CYS cc_start: 0.4890 (OUTLIER) cc_final: 0.4299 (m) REVERT: P 63 ASP cc_start: 0.7649 (p0) cc_final: 0.7391 (p0) REVERT: D 52 MET cc_start: 0.7157 (tpt) cc_final: 0.6636 (tpt) REVERT: D 142 TYR cc_start: 0.7067 (OUTLIER) cc_final: 0.6778 (p90) REVERT: D 246 PHE cc_start: 0.8790 (t80) cc_final: 0.8498 (t80) REVERT: D 295 ILE cc_start: 0.9437 (mp) cc_final: 0.9061 (mt) REVERT: A 20 TRP cc_start: 0.7924 (t60) cc_final: 0.7483 (t60) REVERT: A 65 ASP cc_start: 0.8156 (p0) cc_final: 0.7713 (t0) REVERT: A 176 MET cc_start: 0.7557 (mmt) cc_final: 0.7056 (mmt) REVERT: A 284 SER cc_start: 0.9004 (OUTLIER) cc_final: 0.8656 (m) REVERT: A 302 MET cc_start: 0.7515 (ptp) cc_final: 0.6140 (ptp) REVERT: A 327 ASP cc_start: 0.8830 (m-30) cc_final: 0.8406 (m-30) REVERT: E 246 PHE cc_start: 0.8751 (t80) cc_final: 0.8480 (t80) REVERT: E 295 ILE cc_start: 0.9183 (mm) cc_final: 0.8930 (mm) REVERT: E 332 MET cc_start: 0.7961 (mmp) cc_final: 0.7494 (mmp) REVERT: F 1 MET cc_start: 0.7330 (pmm) cc_final: 0.7060 (ptp) REVERT: F 20 TRP cc_start: 0.8290 (t60) cc_final: 0.8090 (t60) REVERT: F 40 PRO cc_start: 0.9029 (Cg_exo) cc_final: 0.8786 (Cg_endo) REVERT: F 65 ASP cc_start: 0.8212 (p0) cc_final: 0.7464 (t0) REVERT: F 93 ILE cc_start: 0.8581 (mm) cc_final: 0.8346 (tp) REVERT: F 176 MET cc_start: 0.8220 (mmt) cc_final: 0.7340 (mmt) REVERT: F 284 SER cc_start: 0.9247 (p) cc_final: 0.9022 (p) REVERT: F 302 MET cc_start: 0.7393 (ptp) cc_final: 0.6006 (ptp) REVERT: F 323 GLN cc_start: 0.8849 (mm110) cc_final: 0.8409 (mm-40) REVERT: F 327 ASP cc_start: 0.8533 (m-30) cc_final: 0.8184 (m-30) REVERT: I 29 LEU cc_start: 0.8735 (mt) cc_final: 0.8513 (mt) REVERT: I 142 TYR cc_start: 0.7434 (OUTLIER) cc_final: 0.6383 (p90) REVERT: I 246 PHE cc_start: 0.8775 (t80) cc_final: 0.8543 (t80) REVERT: I 295 ILE cc_start: 0.9341 (OUTLIER) cc_final: 0.8988 (mm) REVERT: I 321 TYR cc_start: 0.9004 (t80) cc_final: 0.8766 (t80) REVERT: I 332 MET cc_start: 0.7929 (mmp) cc_final: 0.7552 (mmt) REVERT: K 65 ASP cc_start: 0.8034 (p0) cc_final: 0.7555 (t0) REVERT: K 176 MET cc_start: 0.7777 (mmt) cc_final: 0.6968 (mmt) REVERT: K 284 SER cc_start: 0.9174 (OUTLIER) cc_final: 0.8071 (m) REVERT: K 302 MET cc_start: 0.7298 (ptp) cc_final: 0.6089 (ptp) REVERT: K 314 TRP cc_start: 0.8937 (m100) cc_final: 0.8436 (m100) REVERT: K 323 GLN cc_start: 0.8719 (mt0) cc_final: 0.8489 (mt0) REVERT: N 226 GLN cc_start: 0.7848 (tm-30) cc_final: 0.7537 (tm-30) REVERT: N 240 ASN cc_start: 0.7933 (t0) cc_final: 0.7723 (t0) REVERT: N 295 ILE cc_start: 0.9412 (mp) cc_final: 0.9024 (mt) REVERT: O 17 MET cc_start: 0.8269 (tpt) cc_final: 0.7708 (tpt) REVERT: O 20 TRP cc_start: 0.8360 (t60) cc_final: 0.7388 (t60) REVERT: O 65 ASP cc_start: 0.8220 (p0) cc_final: 0.7770 (t0) REVERT: O 148 ILE cc_start: 0.8332 (OUTLIER) cc_final: 0.8069 (tt) REVERT: O 176 MET cc_start: 0.7427 (mmt) cc_final: 0.6510 (mmt) REVERT: O 240 ASN cc_start: 0.8275 (t0) cc_final: 0.8021 (t0) REVERT: O 265 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7766 (tp30) REVERT: O 284 SER cc_start: 0.9305 (OUTLIER) cc_final: 0.8812 (m) REVERT: O 290 HIS cc_start: 0.8616 (OUTLIER) cc_final: 0.8305 (t70) REVERT: O 323 GLN cc_start: 0.8880 (mm-40) cc_final: 0.8458 (mt0) REVERT: O 327 ASP cc_start: 0.8938 (m-30) cc_final: 0.8538 (m-30) REVERT: J 46 HIS cc_start: 0.7492 (m170) cc_final: 0.6961 (m170) REVERT: J 316 MET cc_start: 0.9041 (mmt) cc_final: 0.8779 (mmt) REVERT: B 67 ASN cc_start: 0.8777 (m110) cc_final: 0.8284 (p0) REVERT: B 131 LEU cc_start: 0.9364 (tt) cc_final: 0.9073 (mm) REVERT: B 241 ILE cc_start: 0.8686 (OUTLIER) cc_final: 0.8422 (tp) REVERT: G 42 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7768 (mt) REVERT: G 46 HIS cc_start: 0.7367 (m170) cc_final: 0.7011 (m-70) REVERT: G 80 ASN cc_start: 0.7316 (m110) cc_final: 0.6597 (t0) REVERT: L 42 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7628 (mt) REVERT: L 69 ASP cc_start: 0.7759 (m-30) cc_final: 0.7240 (t70) REVERT: L 74 GLN cc_start: 0.8739 (mt0) cc_final: 0.8380 (mt0) REVERT: L 124 LEU cc_start: 0.8467 (tp) cc_final: 0.8163 (tt) REVERT: C 28 GLN cc_start: 0.9127 (mp10) cc_final: 0.8723 (mp10) REVERT: C 40 GLN cc_start: 0.9246 (mm-40) cc_final: 0.8874 (mm-40) REVERT: C 63 ASP cc_start: 0.7669 (p0) cc_final: 0.7416 (p0) REVERT: C 69 GLU cc_start: 0.7809 (mp0) cc_final: 0.7433 (mp0) REVERT: H 12 ARG cc_start: 0.8326 (ttt180) cc_final: 0.8115 (ttt180) REVERT: H 63 ASP cc_start: 0.7353 (p0) cc_final: 0.7043 (p0) REVERT: M 1 MET cc_start: 0.7853 (tmm) cc_final: 0.4147 (mmp) REVERT: M 4 LEU cc_start: 0.8710 (pp) cc_final: 0.7985 (tp) REVERT: M 28 GLN cc_start: 0.8624 (mp10) cc_final: 0.7790 (tm-30) REVERT: M 46 GLN cc_start: 0.8320 (tp40) cc_final: 0.7975 (pt0) REVERT: M 47 ARG cc_start: 0.8918 (mmm160) cc_final: 0.8143 (mmm160) REVERT: M 50 GLN cc_start: 0.8930 (tm-30) cc_final: 0.8718 (tm-30) REVERT: M 54 LYS cc_start: 0.7791 (pmmt) cc_final: 0.7151 (tptp) outliers start: 116 outliers final: 79 residues processed: 701 average time/residue: 0.1953 time to fit residues: 233.0542 Evaluate side-chains 627 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 535 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 4 LEU 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 166 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 285 SER 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 208 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 282 LEU 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 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 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 155 THR Chi-restraints excluded: chain N residue 208 VAL Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain O residue 85 ASN Chi-restraints excluded: chain O residue 148 ILE Chi-restraints excluded: chain O residue 193 SER Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 220 LEU Chi-restraints excluded: chain O residue 244 VAL 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 O residue 326 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 279 ASN Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 225 ILE 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 225 ILE Chi-restraints excluded: chain L residue 257 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 3 optimal weight: 0.9990 chunk 250 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 363 optimal weight: 0.6980 chunk 28 optimal weight: 0.0970 chunk 169 optimal weight: 0.7980 chunk 174 optimal weight: 3.9990 chunk 374 optimal weight: 0.9980 chunk 344 optimal weight: 5.9990 chunk 396 optimal weight: 5.9990 chunk 246 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 GLN ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 ASN ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 157 ASN ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 226 GLN O 290 HIS ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 10 GLN ** M 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.109018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.085913 restraints weight = 86361.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.088643 restraints weight = 44878.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.090333 restraints weight = 29907.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.091398 restraints weight = 23405.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.091965 restraints weight = 20157.915| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.4687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 34104 Z= 0.116 Angle : 0.641 13.252 46344 Z= 0.322 Chirality : 0.047 0.319 5220 Planarity : 0.004 0.048 5980 Dihedral : 5.418 59.768 4684 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.22 % Allowed : 18.28 % Favored : 78.50 % 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: -0.54 (0.13), residues: 4240 helix: 0.39 (0.14), residues: 1484 sheet: -0.69 (0.17), residues: 888 loop : -0.67 (0.15), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 207 TYR 0.023 0.001 TYR J 89 PHE 0.030 0.001 PHE B 68 TRP 0.081 0.001 TRP K 20 HIS 0.009 0.001 HIS P 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (34096) covalent geometry : angle 0.63992 / 0.32 (46328) SS BOND : bond 0.00398 / 0.18 ( 8) SS BOND : angle 1.99691 / 1.00 ( 16) hydrogen bonds : bond 0.03116 / 2.12 ( 1404) hydrogen bonds : angle 4.82252 / 3.39 ( 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 688 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 574 time to evaluate : 1.190 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 12 ARG cc_start: 0.8489 (ttt180) cc_final: 0.8285 (ttt180) REVERT: P 37 GLU cc_start: 0.8823 (tp30) cc_final: 0.8528 (tp30) REVERT: P 39 LEU cc_start: 0.8878 (mp) cc_final: 0.8554 (tp) REVERT: P 54 LYS cc_start: 0.7926 (pmmt) cc_final: 0.7147 (tptp) REVERT: P 63 ASP cc_start: 0.7465 (p0) cc_final: 0.7151 (p0) REVERT: D 142 TYR cc_start: 0.7082 (OUTLIER) cc_final: 0.6736 (p90) REVERT: D 240 ASN cc_start: 0.7945 (t0) cc_final: 0.7295 (t0) REVERT: D 246 PHE cc_start: 0.8822 (t80) cc_final: 0.8509 (t80) REVERT: D 295 ILE cc_start: 0.9443 (mp) cc_final: 0.9065 (mt) REVERT: A 20 TRP cc_start: 0.8056 (t60) cc_final: 0.7673 (t60) REVERT: A 65 ASP cc_start: 0.8100 (p0) cc_final: 0.7654 (t0) REVERT: A 176 MET cc_start: 0.7623 (mmt) cc_final: 0.7106 (mmt) REVERT: A 284 SER cc_start: 0.9032 (OUTLIER) cc_final: 0.8699 (m) REVERT: A 302 MET cc_start: 0.7477 (ptp) cc_final: 0.6139 (ptp) REVERT: A 327 ASP cc_start: 0.8742 (m-30) cc_final: 0.8295 (m-30) REVERT: E 240 ASN cc_start: 0.8144 (OUTLIER) cc_final: 0.7680 (t0) REVERT: E 246 PHE cc_start: 0.8683 (t80) cc_final: 0.8398 (t80) REVERT: E 295 ILE cc_start: 0.9238 (mm) cc_final: 0.8979 (mm) REVERT: E 332 MET cc_start: 0.7990 (mmp) cc_final: 0.7438 (mmp) REVERT: F 1 MET cc_start: 0.7259 (pmm) cc_final: 0.7059 (ptp) REVERT: F 40 PRO cc_start: 0.9042 (Cg_exo) cc_final: 0.8805 (Cg_endo) REVERT: F 65 ASP cc_start: 0.8172 (p0) cc_final: 0.7548 (t0) REVERT: F 93 ILE cc_start: 0.8548 (mm) cc_final: 0.8336 (tp) REVERT: F 176 MET cc_start: 0.8144 (mmt) cc_final: 0.7520 (mmt) REVERT: F 284 SER cc_start: 0.9265 (p) cc_final: 0.9016 (p) REVERT: F 302 MET cc_start: 0.7330 (ptp) cc_final: 0.5932 (ptp) REVERT: F 323 GLN cc_start: 0.8819 (mm110) cc_final: 0.8389 (mm-40) REVERT: F 327 ASP cc_start: 0.8524 (m-30) cc_final: 0.8192 (m-30) REVERT: I 29 LEU cc_start: 0.8709 (mt) cc_final: 0.8486 (mt) REVERT: I 142 TYR cc_start: 0.7412 (OUTLIER) cc_final: 0.6321 (p90) REVERT: I 205 MET cc_start: 0.8403 (mtp) cc_final: 0.8187 (mtp) REVERT: I 246 PHE cc_start: 0.8835 (t80) cc_final: 0.8621 (t80) REVERT: I 295 ILE cc_start: 0.9331 (OUTLIER) cc_final: 0.8946 (mm) REVERT: I 321 TYR cc_start: 0.9021 (t80) cc_final: 0.8788 (t80) REVERT: I 332 MET cc_start: 0.8020 (mmp) cc_final: 0.7760 (mmt) REVERT: K 65 ASP cc_start: 0.7965 (p0) cc_final: 0.7562 (t0) REVERT: K 284 SER cc_start: 0.9207 (OUTLIER) cc_final: 0.8059 (m) REVERT: K 302 MET cc_start: 0.7226 (ptp) cc_final: 0.5985 (ptp) REVERT: K 314 TRP cc_start: 0.8931 (m100) cc_final: 0.8406 (m100) REVERT: N 226 GLN cc_start: 0.7873 (tm-30) cc_final: 0.7583 (tm-30) REVERT: N 240 ASN cc_start: 0.7990 (t0) cc_final: 0.7773 (t0) REVERT: N 295 ILE cc_start: 0.9433 (mp) cc_final: 0.9053 (mt) REVERT: O 65 ASP cc_start: 0.8182 (p0) cc_final: 0.7763 (t0) REVERT: O 176 MET cc_start: 0.7572 (mmt) cc_final: 0.6542 (mmt) REVERT: O 240 ASN cc_start: 0.8254 (t0) cc_final: 0.8021 (t0) REVERT: O 265 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7773 (tp30) REVERT: O 323 GLN cc_start: 0.8890 (mm-40) cc_final: 0.8582 (mm-40) REVERT: O 327 ASP cc_start: 0.8941 (m-30) cc_final: 0.8519 (m-30) REVERT: J 46 HIS cc_start: 0.7511 (m170) cc_final: 0.7181 (m170) REVERT: J 127 PHE cc_start: 0.7996 (t80) cc_final: 0.7575 (t80) REVERT: J 320 TYR cc_start: 0.9117 (t80) cc_final: 0.8771 (t80) REVERT: B 67 ASN cc_start: 0.8749 (m110) cc_final: 0.8177 (p0) REVERT: B 131 LEU cc_start: 0.9366 (tt) cc_final: 0.9076 (mm) REVERT: B 241 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8469 (tp) REVERT: G 42 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7848 (mt) REVERT: G 46 HIS cc_start: 0.7349 (m170) cc_final: 0.6983 (m-70) REVERT: G 80 ASN cc_start: 0.7148 (m110) cc_final: 0.6442 (t0) REVERT: L 42 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7758 (mt) REVERT: L 69 ASP cc_start: 0.7738 (m-30) cc_final: 0.7233 (t70) REVERT: L 74 GLN cc_start: 0.8840 (mt0) cc_final: 0.8517 (mt0) REVERT: C 1 MET cc_start: 0.8715 (tpp) cc_final: 0.7922 (tmm) REVERT: C 28 GLN cc_start: 0.9122 (mp10) cc_final: 0.8725 (mp10) REVERT: C 40 GLN cc_start: 0.9252 (mm-40) cc_final: 0.8966 (mm-40) REVERT: C 63 ASP cc_start: 0.7669 (p0) cc_final: 0.7354 (p0) REVERT: C 69 GLU cc_start: 0.7937 (mp0) cc_final: 0.7614 (mp0) REVERT: H 1 MET cc_start: 0.7076 (ttt) cc_final: 0.6557 (ttm) REVERT: H 12 ARG cc_start: 0.8350 (ttt180) cc_final: 0.8104 (ttt180) REVERT: H 63 ASP cc_start: 0.7350 (p0) cc_final: 0.7010 (p0) REVERT: M 1 MET cc_start: 0.8175 (tmm) cc_final: 0.4825 (mmm) REVERT: M 4 LEU cc_start: 0.8639 (pp) cc_final: 0.8308 (pt) REVERT: M 12 ARG cc_start: 0.8643 (ttt180) cc_final: 0.8422 (ttt180) REVERT: M 28 GLN cc_start: 0.8707 (mp10) cc_final: 0.7805 (tm-30) REVERT: M 39 LEU cc_start: 0.8915 (mp) cc_final: 0.8564 (tp) REVERT: M 46 GLN cc_start: 0.8290 (tp40) cc_final: 0.7935 (pt0) REVERT: M 47 ARG cc_start: 0.8923 (mmm160) cc_final: 0.8145 (mmm160) outliers start: 114 outliers final: 76 residues processed: 658 average time/residue: 0.1843 time to fit residues: 207.1115 Evaluate side-chains 611 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 525 time to evaluate : 1.289 ------------------------------------------------------------------------------- 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 166 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 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 285 SER 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 284 SER Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 142 TYR Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 240 ASN Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 282 LEU 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 251 GLU Chi-restraints excluded: chain I residue 275 ILE Chi-restraints excluded: chain I residue 295 ILE Chi-restraints excluded: chain I residue 302 MET Chi-restraints excluded: chain K residue 85 ASN Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain K residue 259 VAL Chi-restraints excluded: chain K residue 278 SER Chi-restraints excluded: chain K residue 284 SER Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 137 VAL Chi-restraints excluded: chain N residue 208 VAL Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain O residue 85 ASN Chi-restraints excluded: chain O residue 193 SER Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 220 LEU Chi-restraints excluded: chain O residue 244 VAL 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 O residue 326 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 97 ASP Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 225 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 97 ASP Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 182 VAL Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 225 ILE Chi-restraints excluded: chain L residue 257 VAL Chi-restraints excluded: chain C residue 36 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 90 optimal weight: 0.9980 chunk 219 optimal weight: 0.9990 chunk 384 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 293 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 214 optimal weight: 6.9990 chunk 337 optimal weight: 10.0000 chunk 139 optimal weight: 7.9990 chunk 256 optimal weight: 6.9990 chunk 333 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 129 ASN ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** N 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 15 ASN ** J 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 HIS ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 ASN ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.104496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.081221 restraints weight = 86719.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.083728 restraints weight = 45861.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.085339 restraints weight = 31075.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.086314 restraints weight = 24471.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.086922 restraints weight = 21264.262| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.4676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 34104 Z= 0.217 Angle : 0.726 12.999 46344 Z= 0.369 Chirality : 0.050 0.325 5220 Planarity : 0.005 0.095 5980 Dihedral : 5.730 58.378 4684 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.19 % Allowed : 18.99 % Favored : 77.82 % 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: -0.58 (0.13), residues: 4240 helix: 0.38 (0.14), residues: 1464 sheet: -0.74 (0.17), residues: 872 loop : -0.69 (0.15), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 207 TYR 0.024 0.002 TYR E 315 PHE 0.030 0.002 PHE B 68 TRP 0.082 0.002 TRP K 20 HIS 0.011 0.001 HIS B 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.22 (34096) covalent geometry : angle 0.72339 / 0.37 (46328) SS BOND : bond 0.00640 / 0.30 ( 8) SS BOND : angle 3.16638 / 2.19 ( 16) hydrogen bonds : bond 0.03534 / 2.39 ( 1404) hydrogen bonds : angle 5.12417 / 3.60 ( 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 633 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 520 time to evaluate : 1.344 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: P 37 GLU cc_start: 0.8732 (tp30) cc_final: 0.8468 (tp30) REVERT: P 39 LEU cc_start: 0.8906 (mp) cc_final: 0.8478 (tp) REVERT: P 54 LYS cc_start: 0.8247 (pmmt) cc_final: 0.7590 (tptp) REVERT: P 63 ASP cc_start: 0.7686 (p0) cc_final: 0.7328 (p0) REVERT: D 142 TYR cc_start: 0.7473 (OUTLIER) cc_final: 0.6921 (p90) REVERT: D 295 ILE cc_start: 0.9506 (mp) cc_final: 0.9090 (mt) REVERT: D 321 TYR cc_start: 0.9141 (t80) cc_final: 0.8931 (t80) REVERT: A 20 TRP cc_start: 0.8136 (t60) cc_final: 0.7647 (t60) REVERT: A 65 ASP cc_start: 0.8289 (p0) cc_final: 0.7753 (t0) REVERT: A 176 MET cc_start: 0.7787 (mmt) cc_final: 0.7014 (mmt) REVERT: A 302 MET cc_start: 0.7492 (ptp) cc_final: 0.6044 (ptp) REVERT: A 327 ASP cc_start: 0.8815 (m-30) cc_final: 0.8409 (m-30) REVERT: E 246 PHE cc_start: 0.8751 (t80) cc_final: 0.8335 (t80) REVERT: F 65 ASP cc_start: 0.8246 (p0) cc_final: 0.7665 (t0) REVERT: F 93 ILE cc_start: 0.8673 (mm) cc_final: 0.8398 (tp) REVERT: F 176 MET cc_start: 0.8267 (mmt) cc_final: 0.7402 (mmt) REVERT: F 265 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.6946 (mp0) REVERT: F 284 SER cc_start: 0.9339 (p) cc_final: 0.9071 (p) REVERT: F 302 MET cc_start: 0.7306 (ptp) cc_final: 0.5962 (ptp) REVERT: F 323 GLN cc_start: 0.8763 (mm110) cc_final: 0.8452 (mm-40) REVERT: F 327 ASP cc_start: 0.8511 (m-30) cc_final: 0.8255 (m-30) REVERT: I 142 TYR cc_start: 0.7540 (OUTLIER) cc_final: 0.6306 (p90) REVERT: I 205 MET cc_start: 0.8556 (mtp) cc_final: 0.8346 (mtp) REVERT: I 246 PHE cc_start: 0.8870 (t80) cc_final: 0.8646 (t80) REVERT: I 285 SER cc_start: 0.8658 (t) cc_final: 0.8382 (p) REVERT: I 295 ILE cc_start: 0.9360 (OUTLIER) cc_final: 0.9028 (mm) REVERT: I 321 TYR cc_start: 0.9144 (t80) cc_final: 0.8928 (t80) REVERT: K 65 ASP cc_start: 0.8019 (p0) cc_final: 0.7603 (t0) REVERT: K 176 MET cc_start: 0.7971 (mmt) cc_final: 0.7309 (mmt) REVERT: K 302 MET cc_start: 0.7109 (ptp) cc_final: 0.6909 (ptp) REVERT: N 226 GLN cc_start: 0.8052 (tm-30) cc_final: 0.7757 (tm-30) REVERT: N 295 ILE cc_start: 0.9471 (mp) cc_final: 0.9144 (mt) REVERT: O 65 ASP cc_start: 0.8245 (p0) cc_final: 0.7763 (t0) REVERT: O 290 HIS cc_start: 0.8900 (OUTLIER) cc_final: 0.8286 (t-90) REVERT: O 323 GLN cc_start: 0.8903 (mm-40) cc_final: 0.8436 (tt0) REVERT: O 327 ASP cc_start: 0.8836 (m-30) cc_final: 0.8501 (m-30) REVERT: J 37 MET cc_start: 0.8469 (tmm) cc_final: 0.8197 (tpp) REVERT: J 46 HIS cc_start: 0.7390 (m170) cc_final: 0.7185 (m90) REVERT: J 127 PHE cc_start: 0.7889 (t80) cc_final: 0.7380 (t80) REVERT: J 233 LYS cc_start: 0.8790 (mmtt) cc_final: 0.8533 (mptt) REVERT: B 56 MET cc_start: 0.6391 (ptp) cc_final: 0.6137 (ptp) REVERT: B 67 ASN cc_start: 0.8838 (m110) cc_final: 0.8228 (p0) REVERT: B 131 LEU cc_start: 0.9459 (tt) cc_final: 0.9119 (mm) REVERT: B 269 GLU cc_start: 0.8446 (pp20) cc_final: 0.7788 (pp20) REVERT: G 46 HIS cc_start: 0.7594 (m170) cc_final: 0.7355 (m-70) REVERT: G 80 ASN cc_start: 0.6872 (m110) cc_final: 0.6183 (t0) REVERT: L 42 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8233 (mt) REVERT: L 78 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8445 (mm) REVERT: L 131 LEU cc_start: 0.9421 (tt) cc_final: 0.9066 (mp) REVERT: C 1 MET cc_start: 0.8908 (tpp) cc_final: 0.8566 (tmm) REVERT: C 25 THR cc_start: 0.8288 (p) cc_final: 0.8055 (p) REVERT: C 28 GLN cc_start: 0.9146 (mp10) cc_final: 0.8862 (mp10) REVERT: C 47 ARG cc_start: 0.8820 (tpp80) cc_final: 0.8190 (tpp80) REVERT: C 50 GLN cc_start: 0.8199 (mm110) cc_final: 0.7975 (mm110) REVERT: C 54 LYS cc_start: 0.7751 (pmmt) cc_final: 0.6649 (tptp) REVERT: C 63 ASP cc_start: 0.7870 (p0) cc_final: 0.7642 (p0) REVERT: C 69 GLU cc_start: 0.8017 (mp0) cc_final: 0.7699 (mp0) REVERT: H 1 MET cc_start: 0.6743 (ttt) cc_final: 0.6258 (ttm) REVERT: H 54 LYS cc_start: 0.8142 (pmmt) cc_final: 0.7695 (ptpt) REVERT: H 63 ASP cc_start: 0.7537 (p0) cc_final: 0.7226 (p0) REVERT: H 69 GLU cc_start: 0.7999 (mp0) cc_final: 0.7756 (mp0) REVERT: M 1 MET cc_start: 0.8089 (tmm) cc_final: 0.5084 (mmm) REVERT: M 4 LEU cc_start: 0.8647 (pp) cc_final: 0.8371 (pt) REVERT: M 39 LEU cc_start: 0.8987 (mp) cc_final: 0.8585 (tp) REVERT: M 42 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8516 (mm-30) REVERT: M 46 GLN cc_start: 0.8380 (tp40) cc_final: 0.8061 (pt0) outliers start: 113 outliers final: 82 residues processed: 604 average time/residue: 0.1939 time to fit residues: 200.5651 Evaluate side-chains 571 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 482 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 25 THR 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 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 208 VAL Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain F residue 17 MET Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 142 TYR Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 265 GLU Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 142 TYR Chi-restraints excluded: chain I residue 158 CYS Chi-restraints excluded: chain I residue 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 251 GLU Chi-restraints excluded: chain I residue 295 ILE Chi-restraints excluded: chain I residue 302 MET Chi-restraints excluded: chain K residue 85 ASN Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain K residue 259 VAL Chi-restraints excluded: chain K residue 278 SER Chi-restraints excluded: chain K residue 284 SER Chi-restraints excluded: chain 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 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 149 VAL Chi-restraints excluded: chain O residue 193 SER Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 220 LEU Chi-restraints excluded: chain O residue 244 VAL 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 110 ILE Chi-restraints excluded: chain J residue 131 LEU 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 97 ASP Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 301 SER Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 182 VAL Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 225 ILE Chi-restraints excluded: chain L residue 257 VAL Chi-restraints excluded: chain C residue 36 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 72 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 172 optimal weight: 7.9990 chunk 179 optimal weight: 0.9980 chunk 413 optimal weight: 3.9990 chunk 195 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 296 optimal weight: 2.9990 chunk 323 optimal weight: 2.9990 chunk 264 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 323 GLN K 335 HIS ** N 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 240 ASN O 290 HIS ** J 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 284 HIS ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 HIS ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 206 GLN ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 HIS ** M 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.107208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.083280 restraints weight = 87697.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.085958 restraints weight = 46507.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.087634 restraints weight = 31505.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.088663 restraints weight = 24883.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.089259 restraints weight = 21629.515| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.4868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 34104 Z= 0.137 Angle : 0.688 13.663 46344 Z= 0.346 Chirality : 0.048 0.311 5220 Planarity : 0.004 0.063 5980 Dihedral : 5.563 58.784 4684 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.02 % Allowed : 19.95 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.56 (0.13), residues: 4240 helix: 0.39 (0.14), residues: 1492 sheet: -0.81 (0.17), residues: 856 loop : -0.65 (0.15), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 207 TYR 0.035 0.002 TYR F 49 PHE 0.033 0.002 PHE B 68 TRP 0.070 0.002 TRP K 20 HIS 0.014 0.001 HIS J 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (34096) covalent geometry : angle 0.68588 / 0.35 (46328) SS BOND : bond 0.00786 / 0.35 ( 8) SS BOND : angle 2.72330 / 1.54 ( 16) hydrogen bonds : bond 0.03244 / 2.20 ( 1404) hydrogen bonds : angle 4.96175 / 3.48 ( 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 643 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 536 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 28 GLN cc_start: 0.8765 (mp10) cc_final: 0.8435 (mp10) REVERT: P 37 GLU cc_start: 0.8740 (tp30) cc_final: 0.8493 (tp30) REVERT: P 39 LEU cc_start: 0.8891 (mp) cc_final: 0.8491 (tp) REVERT: P 47 ARG cc_start: 0.8387 (tpp-160) cc_final: 0.8160 (ttt180) REVERT: P 54 LYS cc_start: 0.8314 (pmmt) cc_final: 0.7603 (tptp) REVERT: P 63 ASP cc_start: 0.7615 (p0) cc_final: 0.7371 (p0) REVERT: P 70 CYS cc_start: 0.5413 (p) cc_final: 0.5151 (p) REVERT: D 142 TYR cc_start: 0.7257 (OUTLIER) cc_final: 0.6918 (p90) REVERT: D 295 ILE cc_start: 0.9471 (mp) cc_final: 0.9075 (mt) REVERT: A 65 ASP cc_start: 0.8229 (p0) cc_final: 0.7746 (t0) REVERT: A 176 MET cc_start: 0.7733 (mmt) cc_final: 0.7118 (mmt) REVERT: A 226 GLN cc_start: 0.8686 (tp-100) cc_final: 0.8340 (mt0) REVERT: A 302 MET cc_start: 0.7504 (ptp) cc_final: 0.6165 (ptp) REVERT: A 327 ASP cc_start: 0.8744 (m-30) cc_final: 0.8317 (m-30) REVERT: E 246 PHE cc_start: 0.8771 (t80) cc_final: 0.8368 (t80) REVERT: E 295 ILE cc_start: 0.9322 (mm) cc_final: 0.9060 (mm) REVERT: F 40 PRO cc_start: 0.9075 (Cg_exo) cc_final: 0.8861 (Cg_endo) REVERT: F 65 ASP cc_start: 0.8232 (p0) cc_final: 0.7756 (t0) REVERT: F 93 ILE cc_start: 0.8550 (mm) cc_final: 0.8287 (tp) REVERT: F 176 MET cc_start: 0.8181 (mmt) cc_final: 0.7276 (mmt) REVERT: F 265 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.6930 (mp0) REVERT: F 284 SER cc_start: 0.9265 (p) cc_final: 0.8995 (p) REVERT: F 302 MET cc_start: 0.7297 (ptp) cc_final: 0.5676 (ptp) REVERT: F 323 GLN cc_start: 0.8853 (mm-40) cc_final: 0.8366 (mm-40) REVERT: F 327 ASP cc_start: 0.8543 (m-30) cc_final: 0.8206 (m-30) REVERT: I 142 TYR cc_start: 0.7461 (OUTLIER) cc_final: 0.6162 (p90) REVERT: I 246 PHE cc_start: 0.8934 (t80) cc_final: 0.8721 (t80) REVERT: I 285 SER cc_start: 0.8527 (t) cc_final: 0.8236 (p) REVERT: I 295 ILE cc_start: 0.9376 (OUTLIER) cc_final: 0.8975 (mm) REVERT: I 321 TYR cc_start: 0.9050 (t80) cc_final: 0.8761 (t80) REVERT: K 65 ASP cc_start: 0.7976 (p0) cc_final: 0.7608 (t0) REVERT: K 176 MET cc_start: 0.7893 (mmt) cc_final: 0.7201 (mmt) REVERT: K 284 SER cc_start: 0.9308 (OUTLIER) cc_final: 0.8958 (m) REVERT: K 302 MET cc_start: 0.7162 (ptp) cc_final: 0.5863 (ptp) REVERT: N 295 ILE cc_start: 0.9426 (mp) cc_final: 0.8969 (mt) REVERT: N 314 TRP cc_start: 0.9233 (m100) cc_final: 0.8725 (m100) REVERT: O 65 ASP cc_start: 0.8217 (p0) cc_final: 0.7707 (t0) REVERT: O 176 MET cc_start: 0.7685 (mmt) cc_final: 0.6471 (mmt) REVERT: O 323 GLN cc_start: 0.8904 (mm-40) cc_final: 0.8413 (mt0) REVERT: O 327 ASP cc_start: 0.8870 (m-30) cc_final: 0.8477 (m-30) REVERT: J 42 LEU cc_start: 0.8452 (mm) cc_final: 0.8234 (mt) REVERT: J 46 HIS cc_start: 0.7335 (m170) cc_final: 0.7077 (m90) REVERT: J 127 PHE cc_start: 0.7967 (t80) cc_final: 0.7414 (t80) REVERT: J 233 LYS cc_start: 0.8765 (mmtt) cc_final: 0.8524 (mptt) REVERT: B 56 MET cc_start: 0.6486 (ptp) cc_final: 0.6215 (ptp) REVERT: B 67 ASN cc_start: 0.8965 (m110) cc_final: 0.8264 (p0) REVERT: B 131 LEU cc_start: 0.9433 (tt) cc_final: 0.9092 (mm) REVERT: G 46 HIS cc_start: 0.7518 (m170) cc_final: 0.7265 (m-70) REVERT: G 74 GLN cc_start: 0.8994 (mt0) cc_final: 0.8618 (mt0) REVERT: G 78 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8041 (mt) REVERT: G 80 ASN cc_start: 0.7056 (m110) cc_final: 0.6573 (t0) REVERT: G 127 PHE cc_start: 0.7803 (t80) cc_final: 0.7347 (t80) REVERT: L 42 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8226 (mt) REVERT: L 69 ASP cc_start: 0.7767 (m-30) cc_final: 0.7179 (t70) REVERT: L 71 MET cc_start: 0.8654 (mpp) cc_final: 0.7947 (mpp) REVERT: L 131 LEU cc_start: 0.9390 (tt) cc_final: 0.9052 (mp) REVERT: L 241 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8525 (tp) REVERT: C 28 GLN cc_start: 0.9187 (mp10) cc_final: 0.8897 (mp10) REVERT: C 40 GLN cc_start: 0.9253 (mm-40) cc_final: 0.9008 (mm110) REVERT: C 47 ARG cc_start: 0.8887 (tpp80) cc_final: 0.8252 (tpp80) REVERT: C 50 GLN cc_start: 0.8119 (mm110) cc_final: 0.7913 (mm110) REVERT: C 54 LYS cc_start: 0.7628 (pmmt) cc_final: 0.6554 (tptp) REVERT: C 63 ASP cc_start: 0.7763 (p0) cc_final: 0.7515 (p0) REVERT: C 69 GLU cc_start: 0.7826 (mp0) cc_final: 0.7448 (mp0) REVERT: H 1 MET cc_start: 0.7258 (ttt) cc_final: 0.6574 (ttt) REVERT: H 63 ASP cc_start: 0.7355 (p0) cc_final: 0.6957 (p0) REVERT: H 69 GLU cc_start: 0.7860 (mp0) cc_final: 0.7423 (mp0) REVERT: M 1 MET cc_start: 0.8072 (tmm) cc_final: 0.5288 (mmm) REVERT: M 4 LEU cc_start: 0.8654 (pp) cc_final: 0.8272 (pt) REVERT: M 39 LEU cc_start: 0.8977 (mp) cc_final: 0.8622 (tp) REVERT: M 42 GLU cc_start: 0.8831 (mm-30) cc_final: 0.8525 (mm-30) REVERT: M 46 GLN cc_start: 0.8379 (tp40) cc_final: 0.8096 (pt0) REVERT: M 47 ARG cc_start: 0.8840 (mmm160) cc_final: 0.8562 (mmm160) outliers start: 107 outliers final: 84 residues processed: 613 average time/residue: 0.1971 time to fit residues: 205.5520 Evaluate side-chains 597 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 505 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 37 THR 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 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 284 SER Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 142 TYR Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 142 TYR Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 265 GLU 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 251 GLU Chi-restraints excluded: chain I residue 275 ILE Chi-restraints excluded: chain I residue 295 ILE Chi-restraints excluded: chain I residue 302 MET Chi-restraints excluded: chain K residue 85 ASN Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 193 SER 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 37 THR Chi-restraints excluded: chain N residue 137 VAL Chi-restraints excluded: chain N residue 208 VAL Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain O residue 85 ASN Chi-restraints excluded: chain O residue 193 SER Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 220 LEU Chi-restraints excluded: chain O residue 244 VAL 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 110 ILE Chi-restraints excluded: chain J residue 131 LEU 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 97 ASP Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 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 78 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 257 VAL Chi-restraints excluded: chain G residue 301 SER Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 182 VAL Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 225 ILE Chi-restraints excluded: chain L residue 241 ILE Chi-restraints excluded: chain L residue 257 VAL Chi-restraints excluded: chain 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: chunk 364 optimal weight: 7.9990 chunk 236 optimal weight: 0.6980 chunk 309 optimal weight: 4.9990 chunk 258 optimal weight: 0.9980 chunk 179 optimal weight: 5.9990 chunk 331 optimal weight: 0.6980 chunk 278 optimal weight: 0.0870 chunk 288 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 367 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 57 GLN ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 181 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 290 HIS ** J 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 284 HIS ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 GLN M 10 GLN ** M 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.108640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.085510 restraints weight = 86040.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.088228 restraints weight = 44884.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.089891 restraints weight = 29919.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.090845 restraints weight = 23503.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.091534 restraints weight = 20454.714| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.5074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 34104 Z= 0.122 Angle : 0.686 15.122 46344 Z= 0.344 Chirality : 0.048 0.357 5220 Planarity : 0.004 0.055 5980 Dihedral : 5.462 59.344 4684 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.62 % Allowed : 20.57 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.53 (0.13), residues: 4240 helix: 0.37 (0.14), residues: 1496 sheet: -0.76 (0.17), residues: 856 loop : -0.61 (0.15), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 207 TYR 0.033 0.001 TYR F 49 PHE 0.033 0.002 PHE B 68 TRP 0.094 0.002 TRP K 20 HIS 0.011 0.001 HIS P 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (34096) covalent geometry : angle 0.68297 / 0.34 (46328) SS BOND : bond 0.00290 / 0.13 ( 8) SS BOND : angle 3.73588 / 2.72 ( 16) hydrogen bonds : bond 0.03159 / 2.15 ( 1404) hydrogen bonds : angle 4.90686 / 3.45 ( 4500) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6599.72 seconds wall clock time: 115 minutes 10.15 seconds (6910.15 seconds total)