Starting phenix.real_space_refine on Tue Aug 26 05:01:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6gve_0071/08_2025/6gve_0071.cif Found real_map, /net/cci-nas-00/data/ceres_data/6gve_0071/08_2025/6gve_0071.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6gve_0071/08_2025/6gve_0071.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6gve_0071/08_2025/6gve_0071.map" model { file = "/net/cci-nas-00/data/ceres_data/6gve_0071/08_2025/6gve_0071.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6gve_0071/08_2025/6gve_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-2.0-5787/lib/python3.9/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: 3.88, per 1000 atoms: 0.12 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: 2.77 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.43 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: 8.03 Time building geometry restraints manager: 3.73 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: 19377 15.12 - 30.24: 1087 30.24 - 45.35: 200 45.35 - 60.47: 48 60.47 - 75.59: 16 Dihedral angle restraints: 20728 sinusoidal: 8404 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 20725 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: 0.09 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: 3.720 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: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 27.200 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.067 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 : 10.439 75.588 12784 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.11 % Allowed : 3.19 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren 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 covalent geometry : bond 0.00952 (34096) covalent geometry : angle 0.98630 (46328) SS BOND : bond 0.01233 ( 8) SS BOND : angle 2.42448 ( 16) hydrogen bonds : bond 0.18602 ( 1404) hydrogen bonds : angle 8.61916 ( 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 : 1.006 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: 0.7698 (tt0) cc_final: 0.7433 (tt0) REVERT: E 286 ASP cc_start: 0.8372 (m-30) cc_final: 0.7948 (m-30) REVERT: F 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: 0.7613 (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: 0.1819 time to fit residues: 297.3140 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 : 0.820 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: P 16 HIS P 64 ASN D 173 GLN D 181 HIS A 45 HIS A 173 GLN A 181 HIS A 187 GLN A 323 GLN E 45 HIS E 173 GLN 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 K 323 GLN N 173 GLN ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 181 HIS O 45 HIS O 173 GLN O 181 HIS O 290 HIS O 323 GLN O 331 HIS J 114 HIS J 184 GLN J 206 GLN B 184 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN G 184 GLN ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 114 HIS L 184 GLN L 279 ASN C 10 GLN C 64 ASN H 64 ASN M 64 ASN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.108853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.084368 restraints weight = 86565.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.087088 restraints weight = 46105.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.088832 restraints weight = 31229.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.089927 restraints weight = 24620.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.090568 restraints weight = 21330.165| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 34104 Z= 0.132 Angle : 0.628 8.915 46344 Z= 0.332 Chirality : 0.047 0.197 5220 Planarity : 0.006 0.062 5980 Dihedral : 7.146 58.004 5084 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.43 % Allowed : 10.98 % Favored : 86.60 % 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 aren not related in a simple way. whole: -2.44 (0.11), residues: 4240 helix: -1.12 (0.12), residues: 1452 sheet: -1.99 (0.16), residues: 864 loop : -1.71 (0.13), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 81 TYR 0.021 0.002 TYR F 321 PHE 0.022 0.002 PHE J 127 TRP 0.012 0.001 TRP E 20 HIS 0.009 0.001 HIS J 46 Details of bonding type rmsd covalent geometry : bond 0.00288 (34096) covalent geometry : angle 0.62752 (46328) SS BOND : bond 0.00579 ( 8) SS BOND : angle 1.42302 ( 16) hydrogen bonds : bond 0.03641 ( 1404) hydrogen bonds : angle 5.49262 ( 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 836 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 750 time to evaluate : 1.235 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 1 MET cc_start: 0.7156 (ttm) cc_final: 0.6232 (tpp) REVERT: P 4 LEU cc_start: 0.8783 (tp) cc_final: 0.8485 (mp) REVERT: P 12 ARG cc_start: 0.8471 (ttt180) cc_final: 0.8235 (ttt180) REVERT: P 33 TRP cc_start: 0.7907 (m100) cc_final: 0.7599 (m100) REVERT: P 39 LEU cc_start: 0.8846 (mp) cc_final: 0.8513 (tp) REVERT: P 54 LYS cc_start: 0.7520 (pmmt) cc_final: 0.6606 (tptp) REVERT: P 63 ASP cc_start: 0.7652 (p0) cc_final: 0.7413 (p0) REVERT: D 52 MET cc_start: 0.7706 (tpp) cc_final: 0.7154 (tpt) REVERT: D 249 GLN cc_start: 0.7935 (tt0) cc_final: 0.7265 (tt0) REVERT: D 295 ILE cc_start: 0.9397 (mp) cc_final: 0.9066 (mt) REVERT: A 67 CYS cc_start: 0.7821 (m) cc_final: 0.7610 (t) REVERT: A 147 ASP cc_start: 0.8245 (p0) cc_final: 0.7966 (p0) REVERT: A 176 MET cc_start: 0.7502 (mmt) cc_final: 0.7168 (mmt) REVERT: A 302 MET cc_start: 0.7363 (ptp) cc_final: 0.5621 (ptp) REVERT: A 323 GLN cc_start: 0.9102 (mm110) cc_final: 0.8850 (mm-40) REVERT: A 327 ASP cc_start: 0.8776 (m-30) cc_final: 0.8377 (m-30) REVERT: E 245 ASP cc_start: 0.7732 (t70) cc_final: 0.6937 (t0) REVERT: E 249 GLN cc_start: 0.7718 (tt0) cc_final: 0.7329 (tt0) REVERT: E 295 ILE cc_start: 0.9412 (OUTLIER) cc_final: 0.9126 (mm) REVERT: F 1 MET cc_start: 0.7715 (pmm) cc_final: 0.7220 (ptp) REVERT: F 16 PHE cc_start: 0.9056 (t80) cc_final: 0.8739 (t80) REVERT: F 20 TRP cc_start: 0.8298 (t60) cc_final: 0.8016 (t60) REVERT: F 21 LEU cc_start: 0.9422 (mt) cc_final: 0.8966 (mt) REVERT: F 40 PRO cc_start: 0.9129 (Cg_exo) cc_final: 0.8904 (Cg_endo) REVERT: F 49 TYR cc_start: 0.9047 (m-80) cc_final: 0.8618 (m-10) REVERT: F 52 MET cc_start: 0.8038 (mmm) cc_final: 0.7674 (mmm) REVERT: F 65 ASP cc_start: 0.8345 (p0) cc_final: 0.7211 (t0) REVERT: F 66 ASP cc_start: 0.8641 (p0) cc_final: 0.8265 (p0) REVERT: F 176 MET cc_start: 0.8019 (mmt) cc_final: 0.7096 (mmt) REVERT: F 284 SER cc_start: 0.9219 (p) cc_final: 0.8917 (p) REVERT: F 302 MET cc_start: 0.7465 (ptp) cc_final: 0.5971 (ptp) REVERT: F 323 GLN cc_start: 0.8973 (mm110) cc_final: 0.8695 (mm-40) REVERT: F 327 ASP cc_start: 0.8596 (m-30) cc_final: 0.8283 (m-30) REVERT: I 249 GLN cc_start: 0.7923 (tt0) cc_final: 0.6831 (tt0) REVERT: I 295 ILE cc_start: 0.9383 (OUTLIER) cc_final: 0.9110 (mm) REVERT: K 20 TRP cc_start: 0.8181 (t60) cc_final: 0.7886 (t60) REVERT: K 22 GLN cc_start: 0.9038 (mt0) cc_final: 0.8796 (tt0) REVERT: K 49 TYR cc_start: 0.8655 (m-80) cc_final: 0.8319 (m-10) REVERT: K 65 ASP cc_start: 0.8300 (p0) cc_final: 0.7304 (t0) REVERT: K 176 MET cc_start: 0.7608 (mmt) cc_final: 0.7211 (mmt) REVERT: K 183 TYR cc_start: 0.9148 (p90) cc_final: 0.8937 (p90) REVERT: K 302 MET cc_start: 0.7158 (ptp) cc_final: 0.5946 (ptp) REVERT: K 323 GLN cc_start: 0.9022 (mm110) cc_final: 0.8815 (mt0) REVERT: N 196 ASP cc_start: 0.8682 (t0) cc_final: 0.8428 (t0) REVERT: N 249 GLN cc_start: 0.7937 (tt0) cc_final: 0.7580 (tt0) REVERT: N 295 ILE cc_start: 0.9379 (mp) cc_final: 0.9047 (mt) REVERT: O 20 TRP cc_start: 0.8293 (t60) cc_final: 0.7739 (t60) REVERT: O 21 LEU cc_start: 0.9329 (mt) cc_final: 0.8654 (mt) REVERT: O 65 ASP cc_start: 0.8382 (p0) cc_final: 0.7295 (t0) REVERT: O 159 LEU cc_start: 0.8931 (tp) cc_final: 0.8487 (tp) REVERT: O 176 MET cc_start: 0.7282 (mmt) cc_final: 0.6654 (mmt) REVERT: O 323 GLN cc_start: 0.8951 (mm110) cc_final: 0.8553 (mt0) REVERT: O 327 ASP cc_start: 0.8983 (m-30) cc_final: 0.8512 (m-30) REVERT: J 46 HIS cc_start: 0.7655 (m170) cc_final: 0.7335 (m170) REVERT: J 156 ASP cc_start: 0.8194 (t0) cc_final: 0.7738 (t70) REVERT: J 309 GLN cc_start: 0.8949 (mt0) cc_final: 0.8602 (mt0) REVERT: B 45 TYR cc_start: 0.7381 (m-80) cc_final: 0.7003 (m-80) REVERT: B 46 HIS cc_start: 0.7142 (m170) cc_final: 0.6652 (m170) REVERT: B 71 MET cc_start: 0.8534 (ptp) cc_final: 0.8325 (ptp) REVERT: B 116 LEU cc_start: 0.8979 (tp) cc_final: 0.8706 (tt) REVERT: B 279 ASN cc_start: 0.8557 (OUTLIER) cc_final: 0.8317 (t0) REVERT: G 127 PHE cc_start: 0.8067 (t80) cc_final: 0.7475 (t80) REVERT: G 193 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7871 (tm-30) REVERT: G 309 GLN cc_start: 0.8892 (mt0) cc_final: 0.8577 (mt0) REVERT: L 204 MET cc_start: 0.8719 (ptm) cc_final: 0.8454 (ptm) REVERT: L 279 ASN cc_start: 0.8681 (OUTLIER) cc_final: 0.8226 (t0) REVERT: L 308 PHE cc_start: 0.8918 (m-10) cc_final: 0.8673 (m-10) REVERT: L 309 GLN cc_start: 0.8798 (mt0) cc_final: 0.8290 (mp10) REVERT: C 28 GLN cc_start: 0.9108 (mp-120) cc_final: 0.8784 (mp10) REVERT: C 54 LYS cc_start: 0.7015 (pmmt) cc_final: 0.6235 (tptp) REVERT: C 63 ASP cc_start: 0.7754 (p0) cc_final: 0.7460 (p0) REVERT: H 1 MET cc_start: 0.6984 (ttm) cc_final: 0.6485 (tpp) REVERT: H 28 GLN cc_start: 0.8702 (mp-120) cc_final: 0.8418 (mt0) REVERT: H 63 ASP cc_start: 0.7257 (p0) cc_final: 0.7033 (p0) REVERT: M 12 ARG cc_start: 0.8752 (ttt180) cc_final: 0.8531 (ttt180) REVERT: M 28 GLN cc_start: 0.8757 (mp-120) cc_final: 0.7986 (tm-30) REVERT: M 38 GLU cc_start: 0.9138 (mm-30) cc_final: 0.8848 (mm-30) REVERT: M 42 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8476 (mm-30) REVERT: M 46 GLN cc_start: 0.8496 (tp40) cc_final: 0.8007 (pt0) REVERT: M 47 ARG cc_start: 0.8763 (mmm160) cc_final: 0.8333 (mmm160) REVERT: M 50 GLN cc_start: 0.8744 (tm-30) cc_final: 0.8453 (tm-30) REVERT: M 54 LYS cc_start: 0.7325 (pmmt) cc_final: 0.6757 (tptp) outliers start: 86 outliers final: 57 residues processed: 810 average time/residue: 0.1599 time to fit residues: 220.2354 Evaluate side-chains 616 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 555 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 295 ILE Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 228 LYS Chi-restraints excluded: chain I residue 245 ASP Chi-restraints excluded: chain I residue 295 ILE Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 85 ASN Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 290 HIS Chi-restraints excluded: chain N residue 4 VAL Chi-restraints excluded: chain N residue 155 THR Chi-restraints excluded: chain N residue 208 VAL Chi-restraints excluded: chain N residue 282 LEU 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: 0.0020 chunk 391 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 chunk 123 optimal weight: 8.9990 chunk 208 optimal weight: 6.9990 chunk 281 optimal weight: 5.9990 chunk 196 optimal weight: 8.9990 chunk 117 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 overall best weight: 2.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 16 HIS ** P 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 ASN ** 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** K 173 GLN K 258 GLN K 290 HIS ** K 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 187 GLN J 184 GLN J 279 ASN B 184 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN B 295 HIS B 309 GLN G 184 GLN ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 279 ASN L 106 HIS L 184 GLN ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 279 ASN L 295 HIS M 45 HIS M 59 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.104619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.080891 restraints weight = 87184.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.083395 restraints weight = 46262.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.085018 restraints weight = 31443.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.086003 restraints weight = 24793.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.086531 restraints weight = 21549.701| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 34104 Z= 0.219 Angle : 0.674 13.237 46344 Z= 0.350 Chirality : 0.049 0.221 5220 Planarity : 0.005 0.062 5980 Dihedral : 7.140 59.952 5084 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.70 % Allowed : 13.71 % Favored : 82.59 % 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 aren not related in a simple way. whole: -1.76 (0.12), residues: 4240 helix: -0.41 (0.13), residues: 1456 sheet: -1.71 (0.16), residues: 872 loop : -1.38 (0.13), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 188 TYR 0.019 0.002 TYR B 217 PHE 0.020 0.002 PHE K 246 TRP 0.024 0.002 TRP E 20 HIS 0.015 0.001 HIS O 290 Details of bonding type rmsd covalent geometry : bond 0.00483 (34096) covalent geometry : angle 0.67339 (46328) SS BOND : bond 0.00740 ( 8) SS BOND : angle 1.79187 ( 16) hydrogen bonds : bond 0.03541 ( 1404) hydrogen bonds : angle 5.37637 ( 4500) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 560 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 12 ARG cc_start: 0.8460 (ttt180) cc_final: 0.8182 (ttt180) REVERT: P 33 TRP cc_start: 0.7870 (m100) cc_final: 0.7538 (m100) REVERT: P 49 GLU cc_start: 0.8385 (mm-30) cc_final: 0.8088 (mm-30) REVERT: P 54 LYS cc_start: 0.7842 (pmmt) cc_final: 0.7077 (tptp) REVERT: P 63 ASP cc_start: 0.7826 (p0) cc_final: 0.7580 (p0) REVERT: D 142 TYR cc_start: 0.7740 (p90) cc_final: 0.7386 (p90) REVERT: D 295 ILE cc_start: 0.9432 (mp) cc_final: 0.9159 (mm) REVERT: D 332 MET cc_start: 0.8460 (mmp) cc_final: 0.7966 (mmt) REVERT: A 20 TRP cc_start: 0.8200 (t60) cc_final: 0.7738 (t60) REVERT: A 49 TYR cc_start: 0.8647 (m-80) cc_final: 0.8409 (m-10) REVERT: A 147 ASP cc_start: 0.8478 (p0) cc_final: 0.8106 (p0) REVERT: A 176 MET cc_start: 0.7853 (mmt) cc_final: 0.7169 (mmt) REVERT: A 302 MET cc_start: 0.7517 (ptp) cc_final: 0.6171 (ptp) REVERT: A 323 GLN cc_start: 0.9109 (mm110) cc_final: 0.8733 (mm-40) REVERT: A 327 ASP cc_start: 0.8868 (m-30) cc_final: 0.8539 (m-30) REVERT: E 240 ASN cc_start: 0.8296 (t0) cc_final: 0.7974 (t0) REVERT: E 249 GLN cc_start: 0.7909 (tt0) cc_final: 0.7580 (tt0) REVERT: E 271 MET cc_start: 0.8350 (mmm) cc_final: 0.8143 (mmt) REVERT: F 1 MET cc_start: 0.7632 (pmm) cc_final: 0.7201 (pmm) REVERT: F 20 TRP cc_start: 0.8385 (t60) cc_final: 0.7926 (t60) REVERT: F 40 PRO cc_start: 0.9123 (Cg_exo) cc_final: 0.8915 (Cg_endo) REVERT: F 65 ASP cc_start: 0.8381 (p0) cc_final: 0.7315 (t0) REVERT: F 176 MET cc_start: 0.8177 (mmt) cc_final: 0.7102 (mmt) REVERT: F 284 SER cc_start: 0.9305 (p) cc_final: 0.8782 (m) REVERT: F 302 MET cc_start: 0.7416 (ptp) cc_final: 0.5789 (ptp) REVERT: F 323 GLN cc_start: 0.8878 (mm110) cc_final: 0.8571 (mm-40) REVERT: F 327 ASP cc_start: 0.8662 (m-30) cc_final: 0.8352 (m-30) REVERT: I 142 TYR cc_start: 0.7613 (OUTLIER) cc_final: 0.7119 (p90) REVERT: I 284 SER cc_start: 0.9085 (p) cc_final: 0.8735 (m) REVERT: I 295 ILE cc_start: 0.9405 (OUTLIER) cc_final: 0.9139 (mm) REVERT: I 321 TYR cc_start: 0.9112 (t80) cc_final: 0.8893 (t80) REVERT: K 20 TRP cc_start: 0.8281 (t60) cc_final: 0.8035 (t60) REVERT: K 49 TYR cc_start: 0.8867 (m-80) cc_final: 0.8620 (m-10) REVERT: K 65 ASP cc_start: 0.8290 (p0) cc_final: 0.7352 (t0) REVERT: K 174 GLN cc_start: 0.8475 (mm-40) cc_final: 0.7624 (mm-40) REVERT: K 176 MET cc_start: 0.7638 (mmt) cc_final: 0.6892 (mmt) REVERT: K 284 SER cc_start: 0.9389 (OUTLIER) cc_final: 0.8856 (m) REVERT: K 302 MET cc_start: 0.7145 (ptp) cc_final: 0.5960 (ptp) REVERT: N 240 ASN cc_start: 0.8136 (t0) cc_final: 0.7850 (t0) REVERT: N 295 ILE cc_start: 0.9471 (mp) cc_final: 0.9073 (mt) REVERT: N 302 MET cc_start: 0.8222 (ptp) cc_final: 0.7910 (ptp) REVERT: O 20 TRP cc_start: 0.8274 (t60) cc_final: 0.7606 (t60) REVERT: O 65 ASP cc_start: 0.8453 (p0) cc_final: 0.7514 (t0) REVERT: O 176 MET cc_start: 0.7534 (mmt) cc_final: 0.6817 (mmt) REVERT: O 323 GLN cc_start: 0.8964 (mm110) cc_final: 0.8635 (mm-40) REVERT: O 327 ASP cc_start: 0.8876 (m-30) cc_final: 0.8525 (m-30) REVERT: J 46 HIS cc_start: 0.7847 (m170) cc_final: 0.7580 (m170) REVERT: J 241 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8551 (tp) REVERT: B 67 ASN cc_start: 0.8622 (m110) cc_final: 0.8095 (p0) REVERT: G 70 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8509 (tt) REVERT: G 127 PHE cc_start: 0.8112 (t80) cc_final: 0.7579 (t80) REVERT: G 193 GLU cc_start: 0.8335 (tm-30) cc_final: 0.8043 (tm-30) REVERT: G 309 GLN cc_start: 0.9066 (mt0) cc_final: 0.8474 (mt0) REVERT: L 279 ASN cc_start: 0.8612 (OUTLIER) cc_final: 0.8412 (t0) REVERT: C 28 GLN cc_start: 0.9154 (mp-120) cc_final: 0.8825 (mp10) REVERT: C 54 LYS cc_start: 0.7743 (pmmt) cc_final: 0.6599 (tptp) REVERT: C 63 ASP cc_start: 0.7918 (p0) cc_final: 0.7640 (p0) REVERT: H 1 MET cc_start: 0.7191 (ttm) cc_final: 0.6982 (ttt) REVERT: H 28 GLN cc_start: 0.8839 (mp-120) cc_final: 0.8511 (mt0) REVERT: H 52 ASP cc_start: 0.7943 (m-30) cc_final: 0.7705 (p0) REVERT: H 63 ASP cc_start: 0.7335 (p0) cc_final: 0.7026 (p0) REVERT: M 1 MET cc_start: 0.8445 (tpp) cc_final: 0.8067 (tmm) REVERT: M 12 ARG cc_start: 0.8701 (ttt180) cc_final: 0.8489 (ttt180) REVERT: M 28 GLN cc_start: 0.8815 (mp-120) cc_final: 0.8032 (tm-30) REVERT: M 42 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8438 (mm-30) REVERT: M 46 GLN cc_start: 0.8366 (tp40) cc_final: 0.7992 (pt0) REVERT: M 47 ARG cc_start: 0.8782 (mmm160) cc_final: 0.8186 (mmm160) REVERT: M 50 GLN cc_start: 0.8838 (tm-30) cc_final: 0.8485 (tm-30) REVERT: M 54 LYS cc_start: 0.7752 (pmmt) cc_final: 0.7136 (tptp) REVERT: M 66 ASP cc_start: 0.7848 (t0) cc_final: 0.7524 (t0) outliers start: 131 outliers final: 95 residues processed: 655 average time/residue: 0.1672 time to fit residues: 186.9302 Evaluate side-chains 582 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 481 time to evaluate : 1.067 ------------------------------------------------------------------------------- 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 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 228 LYS Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 142 TYR Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 228 LYS Chi-restraints excluded: chain I residue 245 ASP Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 295 ILE Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain I residue 325 VAL Chi-restraints excluded: chain K residue 85 ASN Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain K residue 259 VAL Chi-restraints excluded: chain K residue 284 SER Chi-restraints excluded: chain K residue 290 HIS Chi-restraints excluded: chain N residue 4 VAL Chi-restraints excluded: chain N residue 155 THR Chi-restraints excluded: chain N residue 166 LEU Chi-restraints excluded: chain N residue 208 VAL Chi-restraints excluded: chain N residue 245 ASP Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain O residue 85 ASN Chi-restraints excluded: chain O residue 193 SER Chi-restraints excluded: chain O residue 244 VAL Chi-restraints excluded: chain O residue 245 ASP Chi-restraints excluded: chain O residue 284 SER Chi-restraints excluded: chain O residue 290 HIS Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 69 ASP Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 204 MET Chi-restraints excluded: chain J residue 225 ILE Chi-restraints excluded: chain J residue 241 ILE Chi-restraints excluded: chain J residue 257 VAL Chi-restraints excluded: chain J residue 279 ASN Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 289 THR 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 69 ASP Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 134 SER Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 224 THR Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 279 ASN Chi-restraints excluded: chain G residue 289 THR Chi-restraints excluded: chain G residue 292 LEU Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 69 ASP Chi-restraints excluded: chain L residue 109 VAL 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 279 ASN Chi-restraints excluded: chain L residue 292 LEU Chi-restraints excluded: chain H residue 8 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 126 optimal weight: 0.9980 chunk 407 optimal weight: 1.9990 chunk 182 optimal weight: 10.0000 chunk 348 optimal weight: 9.9990 chunk 219 optimal weight: 9.9990 chunk 381 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 220 optimal weight: 3.9990 chunk 356 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 285 optimal weight: 6.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 16 HIS P 59 GLN D 240 ASN ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 ASN ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 7 ASN K 15 ASN K 261 GLN ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 290 HIS J 279 ASN J 309 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 HIS ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 106 HIS ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 279 ASN ** M 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.104992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.081558 restraints weight = 85990.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.084157 restraints weight = 45311.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.085784 restraints weight = 30423.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.086783 restraints weight = 23949.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.087415 restraints weight = 20761.211| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 34104 Z= 0.152 Angle : 0.620 10.714 46344 Z= 0.321 Chirality : 0.048 0.246 5220 Planarity : 0.005 0.056 5980 Dihedral : 6.841 59.446 5084 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.56 % Allowed : 15.66 % Favored : 80.78 % 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 aren not related in a simple way. whole: -1.39 (0.13), residues: 4240 helix: -0.08 (0.14), residues: 1460 sheet: -1.41 (0.16), residues: 892 loop : -1.22 (0.14), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 47 TYR 0.020 0.002 TYR F 321 PHE 0.023 0.002 PHE J 127 TRP 0.018 0.001 TRP E 20 HIS 0.013 0.001 HIS K 290 Details of bonding type rmsd covalent geometry : bond 0.00339 (34096) covalent geometry : angle 0.61957 (46328) SS BOND : bond 0.00872 ( 8) SS BOND : angle 1.87452 ( 16) hydrogen bonds : bond 0.03234 ( 1404) hydrogen bonds : angle 5.17812 ( 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 679 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 553 time to evaluate : 1.120 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 54 LYS cc_start: 0.7786 (pmmt) cc_final: 0.7097 (tptp) REVERT: P 63 ASP cc_start: 0.7879 (p0) cc_final: 0.7608 (p0) REVERT: D 142 TYR cc_start: 0.7654 (p90) cc_final: 0.7185 (p90) REVERT: D 240 ASN cc_start: 0.7959 (OUTLIER) cc_final: 0.7711 (t0) REVERT: D 295 ILE cc_start: 0.9447 (mp) cc_final: 0.9026 (mt) REVERT: D 332 MET cc_start: 0.8300 (mmp) cc_final: 0.7850 (mmt) REVERT: A 20 TRP cc_start: 0.8117 (t60) cc_final: 0.7605 (t60) REVERT: A 49 TYR cc_start: 0.8675 (m-80) cc_final: 0.8114 (m-10) REVERT: A 65 ASP cc_start: 0.8397 (p0) cc_final: 0.7557 (t0) REVERT: A 147 ASP cc_start: 0.8400 (p0) cc_final: 0.8033 (p0) REVERT: A 176 MET cc_start: 0.7752 (mmt) cc_final: 0.7147 (mmt) REVERT: A 284 SER cc_start: 0.9234 (OUTLIER) cc_final: 0.8729 (m) REVERT: A 302 MET cc_start: 0.7693 (ptp) cc_final: 0.6384 (ptp) REVERT: A 323 GLN cc_start: 0.9108 (mm110) cc_final: 0.8790 (tt0) REVERT: E 240 ASN cc_start: 0.8168 (OUTLIER) cc_final: 0.7899 (t0) REVERT: F 20 TRP cc_start: 0.8347 (t60) cc_final: 0.7920 (t60) REVERT: F 40 PRO cc_start: 0.9112 (Cg_exo) cc_final: 0.8846 (Cg_endo) REVERT: F 65 ASP cc_start: 0.8319 (p0) cc_final: 0.7376 (t0) REVERT: F 176 MET cc_start: 0.8231 (mmt) cc_final: 0.7277 (mmt) REVERT: F 284 SER cc_start: 0.9327 (p) cc_final: 0.9064 (p) REVERT: F 302 MET cc_start: 0.7466 (ptp) cc_final: 0.5975 (ptp) REVERT: F 323 GLN cc_start: 0.8855 (mm110) cc_final: 0.8529 (mm-40) REVERT: F 327 ASP cc_start: 0.8655 (m-30) cc_final: 0.8305 (m-30) REVERT: I 142 TYR cc_start: 0.7512 (OUTLIER) cc_final: 0.6953 (p90) REVERT: I 295 ILE cc_start: 0.9408 (OUTLIER) cc_final: 0.9092 (mm) REVERT: I 302 MET cc_start: 0.8169 (ptp) cc_final: 0.7909 (ptp) REVERT: I 314 TRP cc_start: 0.9439 (m100) cc_final: 0.9063 (m100) REVERT: I 321 TYR cc_start: 0.9048 (t80) cc_final: 0.8843 (t80) REVERT: K 20 TRP cc_start: 0.8259 (t60) cc_final: 0.8037 (t60) REVERT: K 65 ASP cc_start: 0.8152 (p0) cc_final: 0.7439 (t0) REVERT: K 174 GLN cc_start: 0.8390 (mm-40) cc_final: 0.7653 (mm-40) REVERT: K 271 MET cc_start: 0.7775 (mmt) cc_final: 0.7525 (mmp) REVERT: K 284 SER cc_start: 0.9299 (OUTLIER) cc_final: 0.8799 (m) REVERT: K 302 MET cc_start: 0.7103 (ptp) cc_final: 0.5859 (ptp) REVERT: K 323 GLN cc_start: 0.8839 (mm-40) cc_final: 0.8635 (mt0) REVERT: N 295 ILE cc_start: 0.9457 (mp) cc_final: 0.9097 (mt) REVERT: O 17 MET cc_start: 0.8459 (tpt) cc_final: 0.7858 (tpt) REVERT: O 20 TRP cc_start: 0.8249 (t60) cc_final: 0.7476 (t60) REVERT: O 65 ASP cc_start: 0.8381 (p0) cc_final: 0.7586 (t0) REVERT: O 176 MET cc_start: 0.7434 (mmt) cc_final: 0.6798 (mmt) REVERT: O 323 GLN cc_start: 0.8868 (mm110) cc_final: 0.8503 (mm-40) REVERT: O 327 ASP cc_start: 0.8859 (m-30) cc_final: 0.8479 (m-30) REVERT: J 46 HIS cc_start: 0.7674 (m170) cc_final: 0.7333 (m170) REVERT: J 113 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8460 (tp) REVERT: J 127 PHE cc_start: 0.7707 (t80) cc_final: 0.5917 (t80) REVERT: J 241 ILE cc_start: 0.8677 (OUTLIER) cc_final: 0.8443 (tp) REVERT: J 279 ASN cc_start: 0.8593 (OUTLIER) cc_final: 0.8358 (t0) REVERT: B 67 ASN cc_start: 0.8680 (m110) cc_final: 0.8155 (p0) REVERT: G 70 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8414 (tt) REVERT: G 127 PHE cc_start: 0.8157 (t80) cc_final: 0.7600 (t80) REVERT: G 193 GLU cc_start: 0.8381 (tm-30) cc_final: 0.8085 (tm-30) REVERT: G 309 GLN cc_start: 0.9030 (mt0) cc_final: 0.8382 (mt0) REVERT: L 131 LEU cc_start: 0.9418 (tt) cc_final: 0.9001 (mp) REVERT: L 180 ASP cc_start: 0.8202 (m-30) cc_final: 0.7852 (m-30) REVERT: L 241 ILE cc_start: 0.8827 (OUTLIER) cc_final: 0.8524 (tp) REVERT: L 309 GLN cc_start: 0.8915 (mt0) cc_final: 0.8150 (mp10) REVERT: C 28 GLN cc_start: 0.9063 (mp-120) cc_final: 0.8762 (mp10) REVERT: C 63 ASP cc_start: 0.7818 (p0) cc_final: 0.7509 (p0) REVERT: C 69 GLU cc_start: 0.7938 (mp0) cc_final: 0.7651 (mp0) REVERT: H 1 MET cc_start: 0.6995 (ttm) cc_final: 0.6263 (tpp) REVERT: H 28 GLN cc_start: 0.8860 (mp-120) cc_final: 0.8472 (mt0) REVERT: H 63 ASP cc_start: 0.7450 (p0) cc_final: 0.7074 (p0) REVERT: M 12 ARG cc_start: 0.8691 (ttt180) cc_final: 0.8473 (ttt180) REVERT: M 28 GLN cc_start: 0.8800 (mp-120) cc_final: 0.7995 (tm-30) REVERT: M 46 GLN cc_start: 0.8348 (tp40) cc_final: 0.7979 (pt0) REVERT: M 47 ARG cc_start: 0.8843 (mmm160) cc_final: 0.8178 (mmm160) REVERT: M 50 GLN cc_start: 0.8826 (tm-30) cc_final: 0.8459 (tm-30) REVERT: M 54 LYS cc_start: 0.7820 (pmmt) cc_final: 0.7223 (tptp) REVERT: M 66 ASP cc_start: 0.7990 (t0) cc_final: 0.7732 (t0) outliers start: 126 outliers final: 80 residues processed: 641 average time/residue: 0.1761 time to fit residues: 190.5090 Evaluate side-chains 582 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 491 time to evaluate : 1.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 240 ASN Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain 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 245 ASP Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 251 GLU Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain I residue 295 ILE Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain I residue 325 VAL Chi-restraints excluded: chain K residue 85 ASN Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain K residue 259 VAL Chi-restraints excluded: chain K residue 284 SER Chi-restraints excluded: chain K residue 290 HIS Chi-restraints excluded: chain N residue 4 VAL Chi-restraints excluded: chain N residue 155 THR Chi-restraints excluded: chain N residue 208 VAL Chi-restraints excluded: chain N residue 218 VAL Chi-restraints excluded: chain N residue 245 ASP Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain O residue 85 ASN Chi-restraints excluded: chain O residue 193 SER Chi-restraints excluded: chain O residue 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 113 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 241 ILE Chi-restraints excluded: chain J residue 279 ASN Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 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 289 THR Chi-restraints excluded: chain G residue 292 LEU Chi-restraints excluded: chain G residue 301 SER Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 182 VAL Chi-restraints excluded: chain L residue 225 ILE Chi-restraints excluded: chain L residue 241 ILE Chi-restraints excluded: chain L residue 257 VAL Chi-restraints excluded: chain L residue 292 LEU Chi-restraints excluded: chain C residue 8 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 27 optimal weight: 0.9980 chunk 397 optimal weight: 6.9990 chunk 386 optimal weight: 4.9990 chunk 393 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 173 optimal weight: 5.9990 chunk 169 optimal weight: 1.9990 chunk 28 optimal weight: 0.2980 chunk 369 optimal weight: 0.9980 chunk 278 optimal weight: 3.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 16 HIS P 59 GLN ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 174 GLN ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 ASN ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 290 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 O 323 GLN ** J 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 HIS ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 HIS L 106 HIS ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.105278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.081114 restraints weight = 87239.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.083678 restraints weight = 46880.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.085335 restraints weight = 32101.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.086325 restraints weight = 25495.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.086923 restraints weight = 22262.817| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 34104 Z= 0.155 Angle : 0.627 13.023 46344 Z= 0.322 Chirality : 0.047 0.250 5220 Planarity : 0.004 0.054 5980 Dihedral : 6.757 59.855 5084 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.75 % Allowed : 16.45 % Favored : 79.80 % 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 aren not related in a simple way. whole: -1.17 (0.13), residues: 4240 helix: 0.10 (0.14), residues: 1460 sheet: -1.25 (0.16), residues: 900 loop : -1.11 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 47 TYR 0.018 0.002 TYR G 217 PHE 0.021 0.001 PHE B 127 TRP 0.014 0.001 TRP E 20 HIS 0.009 0.001 HIS B 46 Details of bonding type rmsd covalent geometry : bond 0.00347 (34096) covalent geometry : angle 0.62592 (46328) SS BOND : bond 0.00834 ( 8) SS BOND : angle 2.23324 ( 16) hydrogen bonds : bond 0.03215 ( 1404) hydrogen bonds : angle 5.10270 ( 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 667 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 534 time to evaluate : 1.262 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 54 LYS cc_start: 0.7708 (pmmt) cc_final: 0.7036 (tptp) REVERT: P 63 ASP cc_start: 0.7881 (p0) cc_final: 0.7604 (p0) REVERT: D 142 TYR cc_start: 0.7596 (OUTLIER) cc_final: 0.6995 (p90) REVERT: D 295 ILE cc_start: 0.9459 (mp) cc_final: 0.9068 (mt) REVERT: D 332 MET cc_start: 0.8338 (mmp) cc_final: 0.7866 (mmt) REVERT: A 20 TRP cc_start: 0.8153 (t60) cc_final: 0.7612 (t60) REVERT: A 65 ASP cc_start: 0.8349 (p0) cc_final: 0.7641 (t0) REVERT: A 147 ASP cc_start: 0.8409 (p0) cc_final: 0.8097 (p0) REVERT: A 176 MET cc_start: 0.7705 (mmt) cc_final: 0.7204 (mmt) REVERT: A 302 MET cc_start: 0.7674 (ptp) cc_final: 0.6247 (ptp) REVERT: A 323 GLN cc_start: 0.9089 (mm110) cc_final: 0.8805 (tt0) REVERT: E 240 ASN cc_start: 0.8373 (t0) cc_final: 0.8007 (t0) REVERT: E 246 PHE cc_start: 0.8644 (t80) cc_final: 0.8281 (t80) REVERT: E 332 MET cc_start: 0.8230 (mmp) cc_final: 0.7819 (mmm) REVERT: F 20 TRP cc_start: 0.8384 (t60) cc_final: 0.7932 (t60) REVERT: F 40 PRO cc_start: 0.9101 (Cg_exo) cc_final: 0.8839 (Cg_endo) REVERT: F 65 ASP cc_start: 0.8330 (p0) cc_final: 0.7367 (t0) REVERT: F 176 MET cc_start: 0.8135 (mmt) cc_final: 0.7293 (mmt) REVERT: F 284 SER cc_start: 0.9305 (p) cc_final: 0.9074 (p) REVERT: F 302 MET cc_start: 0.7434 (ptp) cc_final: 0.5964 (ptp) REVERT: F 323 GLN cc_start: 0.8817 (mm110) cc_final: 0.8510 (mm-40) REVERT: F 327 ASP cc_start: 0.8621 (m-30) cc_final: 0.8261 (m-30) REVERT: I 142 TYR cc_start: 0.7640 (OUTLIER) cc_final: 0.6988 (p90) REVERT: I 246 PHE cc_start: 0.8663 (t80) cc_final: 0.8378 (t80) REVERT: I 295 ILE cc_start: 0.9392 (OUTLIER) cc_final: 0.9069 (mm) REVERT: I 314 TRP cc_start: 0.9371 (m100) cc_final: 0.9044 (m100) REVERT: I 321 TYR cc_start: 0.9071 (t80) cc_final: 0.8860 (t80) REVERT: K 17 MET cc_start: 0.8634 (tpt) cc_final: 0.8428 (tpt) REVERT: K 20 TRP cc_start: 0.8355 (t60) cc_final: 0.8044 (t60) REVERT: K 65 ASP cc_start: 0.8176 (p0) cc_final: 0.7564 (t0) REVERT: K 174 GLN cc_start: 0.8443 (mm-40) cc_final: 0.7698 (mm-40) REVERT: K 176 MET cc_start: 0.7594 (mmt) cc_final: 0.6779 (mmt) REVERT: K 271 MET cc_start: 0.7829 (mmt) cc_final: 0.7568 (mmp) REVERT: K 284 SER cc_start: 0.9296 (OUTLIER) cc_final: 0.8906 (m) REVERT: K 302 MET cc_start: 0.7117 (ptp) cc_final: 0.5850 (ptp) REVERT: N 295 ILE cc_start: 0.9454 (mp) cc_final: 0.9091 (mt) REVERT: O 20 TRP cc_start: 0.8301 (t60) cc_final: 0.7473 (t60) REVERT: O 65 ASP cc_start: 0.8391 (p0) cc_final: 0.7668 (t0) REVERT: O 176 MET cc_start: 0.7367 (mmt) cc_final: 0.6768 (mmt) REVERT: O 207 ILE cc_start: 0.9495 (mp) cc_final: 0.9295 (mp) REVERT: O 323 GLN cc_start: 0.8906 (mm-40) cc_final: 0.8511 (mm-40) REVERT: O 327 ASP cc_start: 0.8863 (m-30) cc_final: 0.8506 (m-30) REVERT: J 46 HIS cc_start: 0.7713 (m170) cc_final: 0.7274 (m-70) REVERT: J 241 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8380 (tp) REVERT: B 67 ASN cc_start: 0.8816 (m110) cc_final: 0.8117 (p0) REVERT: B 131 LEU cc_start: 0.9439 (tt) cc_final: 0.9083 (mm) REVERT: G 46 HIS cc_start: 0.7903 (m-70) cc_final: 0.7361 (m-70) REVERT: G 67 ASN cc_start: 0.8249 (p0) cc_final: 0.8006 (p0) REVERT: G 70 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8348 (tt) REVERT: G 80 ASN cc_start: 0.7238 (m110) cc_final: 0.6332 (t0) REVERT: G 127 PHE cc_start: 0.8165 (t80) cc_final: 0.7615 (t80) REVERT: G 131 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9201 (mp) REVERT: G 193 GLU cc_start: 0.8444 (tm-30) cc_final: 0.8180 (tm-30) REVERT: L 78 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8428 (mm) REVERT: L 131 LEU cc_start: 0.9412 (tt) cc_final: 0.9027 (mp) REVERT: L 180 ASP cc_start: 0.8251 (m-30) cc_final: 0.7897 (m-30) REVERT: L 241 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8540 (tp) REVERT: C 28 GLN cc_start: 0.9012 (mp-120) cc_final: 0.8662 (mp10) REVERT: C 63 ASP cc_start: 0.7856 (p0) cc_final: 0.7558 (p0) REVERT: H 1 MET cc_start: 0.7232 (ttm) cc_final: 0.6448 (tpp) REVERT: H 4 LEU cc_start: 0.8738 (tp) cc_final: 0.8468 (tp) REVERT: H 28 GLN cc_start: 0.8825 (mp-120) cc_final: 0.8384 (mt0) REVERT: H 63 ASP cc_start: 0.7425 (p0) cc_final: 0.6991 (p0) REVERT: M 1 MET cc_start: 0.8748 (tpp) cc_final: 0.8526 (tmm) REVERT: M 12 ARG cc_start: 0.8720 (ttt180) cc_final: 0.8475 (ttt180) REVERT: M 42 GLU cc_start: 0.8927 (mm-30) cc_final: 0.8607 (mm-30) REVERT: M 46 GLN cc_start: 0.8350 (tp40) cc_final: 0.7953 (pt0) REVERT: M 47 ARG cc_start: 0.8871 (mmm160) cc_final: 0.8095 (mmm160) REVERT: M 49 GLU cc_start: 0.8419 (mm-30) cc_final: 0.7971 (mm-30) REVERT: M 50 GLN cc_start: 0.8846 (tm-30) cc_final: 0.8505 (tm-30) REVERT: M 52 ASP cc_start: 0.8062 (m-30) cc_final: 0.7846 (p0) REVERT: M 54 LYS cc_start: 0.7940 (pmmt) cc_final: 0.7332 (tptp) REVERT: M 66 ASP cc_start: 0.8080 (t0) cc_final: 0.7837 (t0) outliers start: 133 outliers final: 96 residues processed: 634 average time/residue: 0.1616 time to fit residues: 174.8426 Evaluate side-chains 599 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 494 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 284 SER Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 142 TYR Chi-restraints excluded: chain I residue 166 LEU Chi-restraints excluded: chain I residue 168 GLU Chi-restraints excluded: chain I residue 205 MET Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 228 LYS Chi-restraints excluded: chain I residue 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 I residue 325 VAL Chi-restraints excluded: chain K residue 85 ASN Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain K residue 259 VAL Chi-restraints excluded: chain K residue 284 SER Chi-restraints excluded: chain K residue 290 HIS Chi-restraints excluded: chain N residue 4 VAL Chi-restraints excluded: chain N residue 155 THR Chi-restraints excluded: chain N residue 208 VAL Chi-restraints excluded: chain N residue 218 VAL Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain O residue 85 ASN Chi-restraints excluded: chain O residue 193 SER Chi-restraints excluded: chain O residue 244 VAL Chi-restraints excluded: chain O residue 245 ASP Chi-restraints excluded: chain O residue 284 SER Chi-restraints excluded: chain 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 257 VAL 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 257 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 134 SER Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 224 THR Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 289 THR Chi-restraints excluded: chain G residue 292 LEU Chi-restraints excluded: chain G residue 301 SER Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 69 ASP Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 182 VAL Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 225 ILE Chi-restraints excluded: chain L residue 236 CYS Chi-restraints excluded: chain L residue 241 ILE Chi-restraints excluded: chain L residue 257 VAL Chi-restraints excluded: chain L residue 292 LEU Chi-restraints excluded: chain C residue 8 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 149 optimal weight: 0.0270 chunk 188 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 376 optimal weight: 0.6980 chunk 267 optimal weight: 10.0000 chunk 309 optimal weight: 0.9980 overall best weight: 0.8840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 59 GLN ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 7 ASN ** 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 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 187 GLN J 279 ASN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 46 HIS ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 GLN H 28 GLN ** M 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.106552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.083360 restraints weight = 85809.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.086028 restraints weight = 44855.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.087670 restraints weight = 29896.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.088694 restraints weight = 23464.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.089247 restraints weight = 20268.351| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 34104 Z= 0.118 Angle : 0.607 12.186 46344 Z= 0.310 Chirality : 0.047 0.274 5220 Planarity : 0.004 0.052 5980 Dihedral : 6.496 58.049 5084 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.75 % Allowed : 16.70 % Favored : 79.54 % 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 aren not related in a simple way. whole: -0.90 (0.13), residues: 4240 helix: 0.28 (0.14), residues: 1468 sheet: -1.02 (0.16), residues: 880 loop : -0.98 (0.15), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 120 TYR 0.018 0.001 TYR N 142 PHE 0.026 0.001 PHE J 68 TRP 0.012 0.001 TRP E 20 HIS 0.012 0.001 HIS K 290 Details of bonding type rmsd covalent geometry : bond 0.00262 (34096) covalent geometry : angle 0.60594 (46328) SS BOND : bond 0.00742 ( 8) SS BOND : angle 1.79459 ( 16) hydrogen bonds : bond 0.03040 ( 1404) hydrogen bonds : angle 4.95029 ( 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 705 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 572 time to evaluate : 1.084 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 37 GLU cc_start: 0.8769 (tp30) cc_final: 0.8459 (tp30) REVERT: P 54 LYS cc_start: 0.7849 (pmmt) cc_final: 0.7169 (tptp) REVERT: P 63 ASP cc_start: 0.7798 (p0) cc_final: 0.7550 (p0) REVERT: D 142 TYR cc_start: 0.7504 (OUTLIER) cc_final: 0.6826 (p90) REVERT: D 246 PHE cc_start: 0.8821 (t80) cc_final: 0.8527 (t80) REVERT: D 295 ILE cc_start: 0.9436 (mp) cc_final: 0.9072 (mt) REVERT: D 332 MET cc_start: 0.8217 (mmp) cc_final: 0.7825 (mmt) REVERT: A 20 TRP cc_start: 0.8109 (t60) cc_final: 0.7546 (t60) REVERT: A 65 ASP cc_start: 0.8244 (p0) cc_final: 0.7701 (t0) REVERT: A 147 ASP cc_start: 0.8264 (p0) cc_final: 0.7903 (p0) REVERT: A 176 MET cc_start: 0.7596 (mmt) cc_final: 0.7266 (mmt) REVERT: A 302 MET cc_start: 0.7654 (ptp) cc_final: 0.6301 (ptp) REVERT: A 323 GLN cc_start: 0.9064 (mm110) cc_final: 0.8452 (tt0) REVERT: A 327 ASP cc_start: 0.8914 (m-30) cc_final: 0.8507 (m-30) REVERT: E 177 MET cc_start: 0.7549 (ttp) cc_final: 0.7294 (ttp) REVERT: E 240 ASN cc_start: 0.8238 (t0) cc_final: 0.7977 (t0) REVERT: E 246 PHE cc_start: 0.8744 (t80) cc_final: 0.8378 (t80) REVERT: E 295 ILE cc_start: 0.9264 (mm) cc_final: 0.9012 (mm) REVERT: E 332 MET cc_start: 0.8166 (mmp) cc_final: 0.7704 (mmt) REVERT: F 20 TRP cc_start: 0.8331 (t60) cc_final: 0.7981 (t60) REVERT: F 40 PRO cc_start: 0.9069 (Cg_exo) cc_final: 0.8840 (Cg_endo) REVERT: F 65 ASP cc_start: 0.8296 (p0) cc_final: 0.7452 (t0) REVERT: F 176 MET cc_start: 0.8207 (mmt) cc_final: 0.7262 (mmt) REVERT: F 284 SER cc_start: 0.9263 (p) cc_final: 0.9034 (p) REVERT: F 302 MET cc_start: 0.7369 (ptp) cc_final: 0.6665 (ptp) REVERT: F 323 GLN cc_start: 0.8786 (mm110) cc_final: 0.8433 (mm-40) REVERT: F 327 ASP cc_start: 0.8584 (m-30) cc_final: 0.8252 (m-30) REVERT: I 142 TYR cc_start: 0.7616 (OUTLIER) cc_final: 0.6747 (p90) REVERT: I 246 PHE cc_start: 0.8749 (t80) cc_final: 0.8526 (t80) REVERT: I 295 ILE cc_start: 0.9361 (OUTLIER) cc_final: 0.9042 (mm) REVERT: I 321 TYR cc_start: 0.9024 (t80) cc_final: 0.8801 (t80) REVERT: K 65 ASP cc_start: 0.8114 (p0) cc_final: 0.7577 (t0) REVERT: K 174 GLN cc_start: 0.8430 (mm-40) cc_final: 0.7723 (mm-40) REVERT: K 176 MET cc_start: 0.7637 (mmt) cc_final: 0.6917 (mmt) REVERT: K 271 MET cc_start: 0.7810 (mmt) cc_final: 0.7580 (mmp) REVERT: K 284 SER cc_start: 0.9263 (OUTLIER) cc_final: 0.8899 (m) REVERT: K 302 MET cc_start: 0.7295 (ptp) cc_final: 0.6066 (ptp) REVERT: N 226 GLN cc_start: 0.7821 (tm-30) cc_final: 0.7469 (tm-30) REVERT: N 240 ASN cc_start: 0.8227 (t0) cc_final: 0.7972 (t0) REVERT: N 295 ILE cc_start: 0.9429 (mp) cc_final: 0.9060 (mt) REVERT: N 314 TRP cc_start: 0.9290 (m100) cc_final: 0.8776 (m100) REVERT: O 17 MET cc_start: 0.8487 (tpt) cc_final: 0.8048 (tpt) REVERT: O 20 TRP cc_start: 0.8281 (t60) cc_final: 0.7326 (t60) REVERT: O 65 ASP cc_start: 0.8306 (p0) cc_final: 0.7559 (t0) REVERT: O 176 MET cc_start: 0.7227 (mmt) cc_final: 0.6721 (mmt) REVERT: O 265 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7717 (tp30) REVERT: O 323 GLN cc_start: 0.8877 (mm-40) cc_final: 0.8552 (mm-40) REVERT: O 327 ASP cc_start: 0.8887 (m-30) cc_final: 0.8469 (m-30) REVERT: J 46 HIS cc_start: 0.7616 (m170) cc_final: 0.7029 (m-70) REVERT: J 69 ASP cc_start: 0.7524 (m-30) cc_final: 0.6225 (t0) REVERT: J 131 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.8988 (mp) REVERT: B 67 ASN cc_start: 0.8693 (m110) cc_final: 0.8108 (p0) REVERT: B 131 LEU cc_start: 0.9411 (tt) cc_final: 0.9072 (mm) REVERT: B 204 MET cc_start: 0.8914 (ptm) cc_final: 0.8197 (ppp) REVERT: G 46 HIS cc_start: 0.7698 (m170) cc_final: 0.7308 (m-70) REVERT: G 70 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8306 (tt) REVERT: G 80 ASN cc_start: 0.7204 (m110) cc_final: 0.6276 (t0) REVERT: G 127 PHE cc_start: 0.8123 (t80) cc_final: 0.7572 (t80) REVERT: G 193 GLU cc_start: 0.8393 (tm-30) cc_final: 0.8153 (tm-30) REVERT: L 69 ASP cc_start: 0.7800 (m-30) cc_final: 0.6780 (t70) REVERT: L 131 LEU cc_start: 0.9407 (tt) cc_final: 0.9035 (mp) REVERT: L 180 ASP cc_start: 0.8147 (m-30) cc_final: 0.7838 (m-30) REVERT: L 241 ILE cc_start: 0.8790 (OUTLIER) cc_final: 0.8498 (tp) REVERT: L 316 MET cc_start: 0.9162 (mmm) cc_final: 0.8951 (mmt) REVERT: C 28 GLN cc_start: 0.9049 (mp10) cc_final: 0.8664 (mp10) REVERT: C 63 ASP cc_start: 0.7739 (p0) cc_final: 0.7444 (p0) REVERT: C 69 GLU cc_start: 0.7915 (mp0) cc_final: 0.7534 (mp0) REVERT: H 1 MET cc_start: 0.7006 (ttm) cc_final: 0.6424 (tpp) REVERT: H 12 ARG cc_start: 0.8462 (ttt180) cc_final: 0.8132 (ttt180) REVERT: H 63 ASP cc_start: 0.7300 (p0) cc_final: 0.6854 (p0) REVERT: M 1 MET cc_start: 0.8768 (tpp) cc_final: 0.8563 (tmm) REVERT: M 12 ARG cc_start: 0.8704 (ttt180) cc_final: 0.8496 (ttt180) REVERT: M 28 GLN cc_start: 0.8796 (mp-120) cc_final: 0.7926 (tm-30) REVERT: M 39 LEU cc_start: 0.9016 (mp) cc_final: 0.8408 (tp) REVERT: M 46 GLN cc_start: 0.8394 (tp40) cc_final: 0.7992 (pt0) REVERT: M 47 ARG cc_start: 0.8908 (mmm160) cc_final: 0.8107 (mmm160) REVERT: M 50 GLN cc_start: 0.8843 (tm-30) cc_final: 0.8504 (tm-30) REVERT: M 54 LYS cc_start: 0.7938 (pmmt) cc_final: 0.7357 (tptp) REVERT: M 66 ASP cc_start: 0.8073 (t0) cc_final: 0.7797 (t0) REVERT: M 69 GLU cc_start: 0.7838 (mp0) cc_final: 0.7599 (mp0) outliers start: 133 outliers final: 95 residues processed: 660 average time/residue: 0.1592 time to fit residues: 177.6372 Evaluate side-chains 623 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 520 time to evaluate : 1.010 ------------------------------------------------------------------------------- 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 245 ASP Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 205 MET 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 197 LEU Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain I residue 142 TYR Chi-restraints excluded: chain I residue 166 LEU Chi-restraints excluded: chain I residue 182 SER Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 228 LYS Chi-restraints excluded: chain I residue 244 VAL Chi-restraints excluded: chain I residue 245 ASP Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 251 GLU Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain I residue 295 ILE Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain K residue 17 MET Chi-restraints excluded: chain K residue 85 ASN Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain K residue 259 VAL Chi-restraints excluded: chain K residue 284 SER Chi-restraints excluded: chain N residue 4 VAL Chi-restraints excluded: chain N residue 155 THR Chi-restraints excluded: chain N residue 208 VAL Chi-restraints excluded: chain N residue 218 VAL Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain O residue 34 ILE Chi-restraints excluded: chain O residue 85 ASN Chi-restraints excluded: chain O residue 193 SER Chi-restraints excluded: chain O residue 244 VAL Chi-restraints excluded: chain O residue 245 ASP Chi-restraints excluded: chain O residue 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 28 LEU Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 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 B residue 97 ASP Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 314 LEU 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 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 289 THR Chi-restraints excluded: chain G residue 301 SER Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 182 VAL Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 225 ILE Chi-restraints excluded: chain L residue 241 ILE Chi-restraints excluded: chain L residue 257 VAL Chi-restraints excluded: chain L residue 292 LEU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain M residue 2 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 380 optimal weight: 1.9990 chunk 401 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 367 optimal weight: 5.9990 chunk 352 optimal weight: 6.9990 chunk 171 optimal weight: 0.8980 chunk 176 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 345 optimal weight: 4.9990 chunk 327 optimal weight: 6.9990 chunk 228 optimal weight: 0.6980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 331 HIS A 15 ASN A 323 GLN ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 45 HIS ** N 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 157 ASN ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 ASN L 206 GLN 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 = 0.3712 r_free = 0.3712 target = 0.105932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.082682 restraints weight = 86453.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.085317 restraints weight = 45217.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.086967 restraints weight = 30213.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.087977 restraints weight = 23728.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.088521 restraints weight = 20546.879| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 34104 Z= 0.137 Angle : 0.625 13.180 46344 Z= 0.319 Chirality : 0.048 0.303 5220 Planarity : 0.004 0.052 5980 Dihedral : 6.471 58.458 5084 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.89 % Allowed : 17.33 % Favored : 78.78 % 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 aren not related in a simple way. whole: -0.77 (0.13), residues: 4240 helix: 0.32 (0.14), residues: 1476 sheet: -0.99 (0.17), residues: 856 loop : -0.83 (0.15), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 47 TYR 0.018 0.001 TYR N 142 PHE 0.023 0.001 PHE B 127 TRP 0.020 0.001 TRP K 20 HIS 0.008 0.001 HIS P 16 Details of bonding type rmsd covalent geometry : bond 0.00310 (34096) covalent geometry : angle 0.62355 (46328) SS BOND : bond 0.00351 ( 8) SS BOND : angle 2.38172 ( 16) hydrogen bonds : bond 0.03110 ( 1404) hydrogen bonds : angle 4.97090 ( 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 676 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 538 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 37 GLU cc_start: 0.8802 (tp30) cc_final: 0.8473 (tp30) REVERT: P 54 LYS cc_start: 0.7865 (pmmt) cc_final: 0.7119 (tptp) REVERT: P 63 ASP cc_start: 0.7739 (p0) cc_final: 0.7520 (p0) REVERT: D 142 TYR cc_start: 0.7451 (OUTLIER) cc_final: 0.6505 (p90) REVERT: D 295 ILE cc_start: 0.9443 (mp) cc_final: 0.9071 (mt) REVERT: A 20 TRP cc_start: 0.8155 (t60) cc_final: 0.7562 (t60) REVERT: A 65 ASP cc_start: 0.8227 (p0) cc_final: 0.7713 (t0) REVERT: A 147 ASP cc_start: 0.8364 (p0) cc_final: 0.8021 (p0) REVERT: A 176 MET cc_start: 0.7658 (mmt) cc_final: 0.7291 (mmt) REVERT: A 302 MET cc_start: 0.7638 (ptp) cc_final: 0.6295 (ptp) REVERT: A 323 GLN cc_start: 0.9086 (mm-40) cc_final: 0.8526 (mm-40) REVERT: A 327 ASP cc_start: 0.8943 (m-30) cc_final: 0.8493 (m-30) REVERT: E 240 ASN cc_start: 0.8267 (t0) cc_final: 0.8013 (t0) REVERT: E 246 PHE cc_start: 0.8733 (t80) cc_final: 0.8322 (t80) REVERT: E 295 ILE cc_start: 0.9278 (mm) cc_final: 0.9016 (mm) REVERT: F 20 TRP cc_start: 0.8348 (t60) cc_final: 0.8046 (t60) REVERT: F 40 PRO cc_start: 0.9093 (Cg_exo) cc_final: 0.8862 (Cg_endo) REVERT: F 65 ASP cc_start: 0.8245 (p0) cc_final: 0.7459 (t0) REVERT: F 176 MET cc_start: 0.8119 (mmt) cc_final: 0.7359 (mmt) REVERT: F 284 SER cc_start: 0.9282 (p) cc_final: 0.9048 (p) REVERT: F 302 MET cc_start: 0.7439 (ptp) cc_final: 0.6751 (ptp) REVERT: F 323 GLN cc_start: 0.8780 (mm110) cc_final: 0.8415 (mm-40) REVERT: F 327 ASP cc_start: 0.8598 (m-30) cc_final: 0.8248 (m-30) REVERT: I 142 TYR cc_start: 0.7567 (OUTLIER) cc_final: 0.6536 (p90) REVERT: I 246 PHE cc_start: 0.8718 (t80) cc_final: 0.8435 (t80) REVERT: I 295 ILE cc_start: 0.9356 (OUTLIER) cc_final: 0.9030 (mm) REVERT: I 321 TYR cc_start: 0.9062 (t80) cc_final: 0.8839 (t80) REVERT: K 65 ASP cc_start: 0.8113 (p0) cc_final: 0.7597 (t0) REVERT: K 176 MET cc_start: 0.7709 (mmt) cc_final: 0.6897 (mmt) REVERT: K 284 SER cc_start: 0.9227 (OUTLIER) cc_final: 0.8847 (m) REVERT: K 302 MET cc_start: 0.7335 (ptp) cc_final: 0.6059 (ptp) REVERT: N 295 ILE cc_start: 0.9437 (mp) cc_final: 0.9030 (mt) REVERT: O 20 TRP cc_start: 0.8299 (t60) cc_final: 0.7419 (t60) REVERT: O 48 LYS cc_start: 0.8860 (tttt) cc_final: 0.8595 (tttm) REVERT: O 65 ASP cc_start: 0.8202 (p0) cc_final: 0.7753 (t0) REVERT: O 176 MET cc_start: 0.7512 (mmt) cc_final: 0.6865 (mmt) REVERT: O 177 MET cc_start: 0.7593 (tmm) cc_final: 0.7366 (tmm) REVERT: O 265 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7729 (tp30) REVERT: O 323 GLN cc_start: 0.8856 (mm-40) cc_final: 0.8407 (mt0) REVERT: O 327 ASP cc_start: 0.8901 (m-30) cc_final: 0.8517 (m-30) REVERT: J 46 HIS cc_start: 0.7569 (m170) cc_final: 0.7238 (m170) REVERT: J 131 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.8999 (mp) REVERT: B 67 ASN cc_start: 0.8687 (m110) cc_final: 0.8103 (p0) REVERT: B 131 LEU cc_start: 0.9396 (tt) cc_final: 0.9072 (mm) REVERT: G 46 HIS cc_start: 0.7734 (m170) cc_final: 0.7386 (m-70) REVERT: G 70 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8387 (tt) REVERT: G 80 ASN cc_start: 0.7260 (m110) cc_final: 0.6476 (t0) REVERT: G 127 PHE cc_start: 0.8137 (t80) cc_final: 0.7749 (t80) REVERT: G 193 GLU cc_start: 0.8390 (tm-30) cc_final: 0.8148 (tm-30) REVERT: L 69 ASP cc_start: 0.7821 (m-30) cc_final: 0.6741 (t70) REVERT: L 131 LEU cc_start: 0.9408 (tt) cc_final: 0.9054 (mp) REVERT: L 180 ASP cc_start: 0.8238 (m-30) cc_final: 0.7904 (m-30) REVERT: L 241 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8452 (tp) REVERT: C 1 MET cc_start: 0.8637 (tpp) cc_final: 0.8213 (tmm) REVERT: C 28 GLN cc_start: 0.9057 (mp10) cc_final: 0.8681 (mp10) REVERT: C 39 LEU cc_start: 0.8834 (mp) cc_final: 0.8335 (tp) REVERT: C 63 ASP cc_start: 0.7792 (p0) cc_final: 0.7504 (p0) REVERT: C 69 GLU cc_start: 0.8034 (mp0) cc_final: 0.7763 (mp0) REVERT: H 1 MET cc_start: 0.7131 (ttm) cc_final: 0.6538 (tpp) REVERT: H 12 ARG cc_start: 0.8391 (ttt180) cc_final: 0.8174 (ttt180) REVERT: H 63 ASP cc_start: 0.7333 (p0) cc_final: 0.6921 (p0) REVERT: M 1 MET cc_start: 0.8296 (tpp) cc_final: 0.7215 (tmm) REVERT: M 12 ARG cc_start: 0.8716 (ttt180) cc_final: 0.8476 (ttt180) REVERT: M 28 GLN cc_start: 0.8778 (mp-120) cc_final: 0.7892 (tm-30) REVERT: M 39 LEU cc_start: 0.8948 (mp) cc_final: 0.8392 (tp) REVERT: M 42 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8573 (mm-30) REVERT: M 46 GLN cc_start: 0.8398 (tp40) cc_final: 0.7993 (pt0) REVERT: M 47 ARG cc_start: 0.8886 (mmm160) cc_final: 0.8021 (mmm160) REVERT: M 50 GLN cc_start: 0.8810 (tm-30) cc_final: 0.8499 (tm-30) REVERT: M 54 LYS cc_start: 0.8061 (pmmt) cc_final: 0.7390 (tptp) REVERT: M 66 ASP cc_start: 0.8111 (t0) cc_final: 0.7840 (t0) outliers start: 138 outliers final: 106 residues processed: 636 average time/residue: 0.1491 time to fit residues: 162.8924 Evaluate side-chains 619 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 505 time to evaluate : 1.055 ------------------------------------------------------------------------------- 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 205 MET Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 228 LYS Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 142 TYR Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain 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 301 THR Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 17 MET Chi-restraints excluded: chain K residue 85 ASN Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain K residue 259 VAL Chi-restraints excluded: chain K residue 278 SER Chi-restraints excluded: chain K residue 284 SER Chi-restraints excluded: chain N residue 4 VAL Chi-restraints excluded: chain N residue 137 VAL Chi-restraints excluded: chain N residue 155 THR Chi-restraints excluded: chain N residue 208 VAL Chi-restraints excluded: chain N residue 218 VAL Chi-restraints excluded: chain N residue 243 VAL Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain N residue 302 MET Chi-restraints excluded: chain O residue 22 GLN Chi-restraints excluded: chain O residue 34 ILE Chi-restraints excluded: chain O residue 85 ASN Chi-restraints excluded: chain O residue 193 SER Chi-restraints excluded: chain O residue 244 VAL Chi-restraints excluded: chain O residue 245 ASP Chi-restraints excluded: chain O residue 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 28 LEU Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 204 MET Chi-restraints excluded: chain J residue 225 ILE Chi-restraints excluded: chain J residue 257 VAL 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 289 THR Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 134 SER Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 224 THR Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 289 THR Chi-restraints excluded: chain G residue 301 SER Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 182 VAL Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 206 GLN Chi-restraints excluded: chain L residue 225 ILE Chi-restraints excluded: chain L residue 236 CYS Chi-restraints excluded: chain L residue 241 ILE Chi-restraints excluded: chain L residue 257 VAL Chi-restraints excluded: chain M residue 59 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 3 optimal weight: 3.9990 chunk 250 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 363 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 169 optimal weight: 0.4980 chunk 174 optimal weight: 0.0070 chunk 374 optimal weight: 3.9990 chunk 344 optimal weight: 7.9990 chunk 396 optimal weight: 4.9990 chunk 246 optimal weight: 0.9990 overall best weight: 0.8402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 GLN ** 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 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 290 HIS ** J 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 279 ASN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.107291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.084141 restraints weight = 86512.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.086797 restraints weight = 45030.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.088462 restraints weight = 30073.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.089512 restraints weight = 23567.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.090160 restraints weight = 20313.850| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.4581 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= 0.119 Angle : 0.633 13.082 46344 Z= 0.319 Chirality : 0.048 0.325 5220 Planarity : 0.004 0.051 5980 Dihedral : 6.326 57.962 5084 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.64 % Allowed : 18.17 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.13), residues: 4240 helix: 0.30 (0.13), residues: 1504 sheet: -0.87 (0.17), residues: 856 loop : -0.81 (0.15), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 207 TYR 0.030 0.001 TYR B 89 PHE 0.030 0.001 PHE G 68 TRP 0.041 0.001 TRP K 20 HIS 0.009 0.001 HIS P 16 Details of bonding type rmsd covalent geometry : bond 0.00267 (34096) covalent geometry : angle 0.63167 (46328) SS BOND : bond 0.00234 ( 8) SS BOND : angle 1.97154 ( 16) hydrogen bonds : bond 0.03083 ( 1404) hydrogen bonds : angle 4.89067 ( 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 704 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 575 time to evaluate : 0.779 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: 0.8681 (ttt180) cc_final: 0.8363 (ttt180) REVERT: P 37 GLU cc_start: 0.8779 (tp30) cc_final: 0.8470 (tp30) REVERT: P 54 LYS cc_start: 0.7890 (OUTLIER) cc_final: 0.7192 (tptp) REVERT: P 63 ASP cc_start: 0.7523 (p0) cc_final: 0.7275 (p0) REVERT: P 66 ASP cc_start: 0.8138 (t0) cc_final: 0.7935 (t0) REVERT: D 142 TYR cc_start: 0.7335 (OUTLIER) cc_final: 0.6974 (p90) REVERT: D 240 ASN cc_start: 0.7851 (t0) cc_final: 0.7371 (t0) REVERT: D 295 ILE cc_start: 0.9434 (mp) cc_final: 0.9085 (mt) REVERT: A 20 TRP cc_start: 0.8100 (t60) cc_final: 0.7501 (t60) REVERT: A 65 ASP cc_start: 0.8168 (p0) cc_final: 0.7704 (t0) REVERT: A 147 ASP cc_start: 0.8328 (p0) cc_final: 0.8028 (p0) REVERT: A 176 MET cc_start: 0.7629 (mmt) cc_final: 0.7334 (mmt) REVERT: A 302 MET cc_start: 0.7603 (ptp) cc_final: 0.6261 (ptp) REVERT: A 323 GLN cc_start: 0.9083 (mm-40) cc_final: 0.8504 (mt0) REVERT: A 327 ASP cc_start: 0.8869 (m-30) cc_final: 0.8456 (m-30) REVERT: E 240 ASN cc_start: 0.8215 (t0) cc_final: 0.7937 (t0) REVERT: E 246 PHE cc_start: 0.8718 (t80) cc_final: 0.8266 (t80) REVERT: E 295 ILE cc_start: 0.9266 (mm) cc_final: 0.9004 (mm) REVERT: F 20 TRP cc_start: 0.8313 (t60) cc_final: 0.8009 (t60) REVERT: F 40 PRO cc_start: 0.9058 (Cg_exo) cc_final: 0.8833 (Cg_endo) REVERT: F 65 ASP cc_start: 0.8212 (p0) cc_final: 0.7682 (t0) REVERT: F 93 ILE cc_start: 0.7616 (mp) cc_final: 0.7212 (mm) REVERT: F 176 MET cc_start: 0.8232 (mmt) cc_final: 0.7286 (mmt) REVERT: F 284 SER cc_start: 0.9258 (p) cc_final: 0.9042 (p) REVERT: F 302 MET cc_start: 0.7398 (ptp) cc_final: 0.6690 (ptp) REVERT: F 323 GLN cc_start: 0.8783 (mm110) cc_final: 0.8378 (mm-40) REVERT: F 327 ASP cc_start: 0.8609 (m-30) cc_final: 0.8270 (m-30) REVERT: I 142 TYR cc_start: 0.7507 (OUTLIER) cc_final: 0.6158 (p90) REVERT: I 295 ILE cc_start: 0.9341 (OUTLIER) cc_final: 0.9008 (mm) REVERT: I 321 TYR cc_start: 0.9036 (t80) cc_final: 0.8810 (t80) REVERT: K 65 ASP cc_start: 0.8002 (p0) cc_final: 0.7602 (t0) REVERT: K 176 MET cc_start: 0.7705 (mmt) cc_final: 0.6888 (mmt) REVERT: K 284 SER cc_start: 0.9260 (OUTLIER) cc_final: 0.8893 (m) REVERT: K 302 MET cc_start: 0.7370 (ptp) cc_final: 0.6081 (ptp) REVERT: N 226 GLN cc_start: 0.7890 (tm-30) cc_final: 0.7597 (tm-30) REVERT: N 295 ILE cc_start: 0.9397 (mp) cc_final: 0.9021 (mt) REVERT: N 314 TRP cc_start: 0.9288 (m100) cc_final: 0.8736 (m100) REVERT: O 20 TRP cc_start: 0.8290 (t60) cc_final: 0.7402 (t60) REVERT: O 65 ASP cc_start: 0.8173 (p0) cc_final: 0.7706 (t0) REVERT: O 176 MET cc_start: 0.7458 (mmt) cc_final: 0.6874 (mmt) REVERT: O 265 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7755 (tp30) REVERT: O 323 GLN cc_start: 0.8856 (mm-40) cc_final: 0.8408 (mt0) REVERT: O 327 ASP cc_start: 0.8915 (m-30) cc_final: 0.8499 (m-30) REVERT: J 46 HIS cc_start: 0.7453 (m170) cc_final: 0.7168 (m90) REVERT: J 131 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9074 (mp) REVERT: B 42 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.7839 (mt) REVERT: B 67 ASN cc_start: 0.8730 (m110) cc_final: 0.8191 (p0) REVERT: B 131 LEU cc_start: 0.9391 (tt) cc_final: 0.9076 (mm) REVERT: B 241 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8415 (tp) REVERT: G 46 HIS cc_start: 0.7687 (m170) cc_final: 0.7448 (m-70) REVERT: G 70 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8311 (tt) REVERT: G 80 ASN cc_start: 0.7180 (m110) cc_final: 0.6609 (t0) REVERT: G 127 PHE cc_start: 0.8173 (t80) cc_final: 0.7613 (t80) REVERT: G 193 GLU cc_start: 0.8364 (tm-30) cc_final: 0.8146 (tm-30) REVERT: G 241 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8417 (tp) REVERT: L 69 ASP cc_start: 0.7897 (OUTLIER) cc_final: 0.7105 (t70) REVERT: L 131 LEU cc_start: 0.9386 (tt) cc_final: 0.9039 (mp) REVERT: L 241 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8476 (tp) REVERT: C 1 MET cc_start: 0.8745 (tpp) cc_final: 0.7724 (tmm) REVERT: C 4 LEU cc_start: 0.8698 (pp) cc_final: 0.8260 (tp) REVERT: C 28 GLN cc_start: 0.9050 (mp10) cc_final: 0.8695 (mp10) REVERT: C 40 GLN cc_start: 0.9238 (mm-40) cc_final: 0.8884 (mm-40) REVERT: C 63 ASP cc_start: 0.7666 (p0) cc_final: 0.7418 (p0) REVERT: H 1 MET cc_start: 0.7106 (ttm) cc_final: 0.6602 (tpp) REVERT: H 63 ASP cc_start: 0.7323 (p0) cc_final: 0.6904 (p0) REVERT: M 12 ARG cc_start: 0.8741 (ttt180) cc_final: 0.8375 (ttt180) REVERT: M 39 LEU cc_start: 0.8965 (mp) cc_final: 0.8411 (mp) REVERT: M 42 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8545 (mm-30) REVERT: M 46 GLN cc_start: 0.8386 (tp40) cc_final: 0.7996 (pt0) REVERT: M 47 ARG cc_start: 0.8855 (mmm160) cc_final: 0.8004 (mmm160) REVERT: M 50 GLN cc_start: 0.8787 (tm-30) cc_final: 0.8566 (tm-30) REVERT: M 66 ASP cc_start: 0.8039 (t0) cc_final: 0.7795 (t0) REVERT: M 69 GLU cc_start: 0.7926 (mp0) cc_final: 0.7675 (mp0) outliers start: 129 outliers final: 98 residues processed: 662 average time/residue: 0.1518 time to fit residues: 173.0852 Evaluate side-chains 639 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 528 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain P residue 54 LYS Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 142 TYR Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 228 LYS Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 325 VAL 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 F residue 137 VAL Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain 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 245 ASP 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 K residue 4 VAL Chi-restraints excluded: chain K residue 17 MET Chi-restraints excluded: chain K residue 85 ASN Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain K residue 259 VAL Chi-restraints excluded: chain K residue 278 SER Chi-restraints excluded: chain K residue 284 SER Chi-restraints excluded: chain N residue 137 VAL Chi-restraints excluded: chain N residue 208 VAL Chi-restraints excluded: chain N residue 218 VAL Chi-restraints excluded: chain N residue 241 VAL Chi-restraints excluded: chain N residue 243 VAL Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain O residue 34 ILE Chi-restraints excluded: chain O residue 85 ASN Chi-restraints excluded: chain O residue 193 SER Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 244 VAL Chi-restraints excluded: chain O residue 245 ASP Chi-restraints excluded: chain O residue 265 GLU Chi-restraints excluded: chain O residue 284 SER Chi-restraints excluded: chain O residue 290 HIS Chi-restraints excluded: chain O residue 326 LEU 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 42 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 289 THR Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 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 42 LEU Chi-restraints excluded: chain L residue 69 ASP Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 182 VAL Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 225 ILE Chi-restraints excluded: chain L residue 241 ILE Chi-restraints excluded: chain L residue 257 VAL Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain M residue 4 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 90 optimal weight: 0.4980 chunk 219 optimal weight: 0.5980 chunk 384 optimal weight: 2.9990 chunk 86 optimal weight: 0.0020 chunk 293 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 214 optimal weight: 10.0000 chunk 337 optimal weight: 5.9990 chunk 139 optimal weight: 7.9990 chunk 256 optimal weight: 7.9990 chunk 333 optimal weight: 8.9990 overall best weight: 1.0192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 15 ASN A 240 ASN E 57 GLN ** E 174 GLN ** 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 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 206 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 HIS ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 206 GLN ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 HIS ** H 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 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 = 0.3731 r_free = 0.3731 target = 0.107148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.083948 restraints weight = 86384.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.086595 restraints weight = 45232.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.088246 restraints weight = 30242.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.089275 restraints weight = 23754.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.089909 restraints weight = 20581.168| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.4720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 34104 Z= 0.128 Angle : 0.654 14.940 46344 Z= 0.332 Chirality : 0.048 0.326 5220 Planarity : 0.004 0.050 5980 Dihedral : 6.307 57.716 5084 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.67 % Allowed : 18.59 % Favored : 77.74 % 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 aren not related in a simple way. whole: -0.66 (0.13), residues: 4240 helix: 0.31 (0.14), residues: 1500 sheet: -0.85 (0.17), residues: 864 loop : -0.72 (0.15), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 47 TYR 0.026 0.001 TYR B 89 PHE 0.030 0.001 PHE J 68 TRP 0.056 0.001 TRP K 20 HIS 0.011 0.001 HIS P 16 Details of bonding type rmsd covalent geometry : bond 0.00290 (34096) covalent geometry : angle 0.65243 (46328) SS BOND : bond 0.00339 ( 8) SS BOND : angle 2.75456 ( 16) hydrogen bonds : bond 0.03153 ( 1404) hydrogen bonds : angle 4.88366 ( 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 681 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 551 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 37 GLU cc_start: 0.8729 (tp30) cc_final: 0.8442 (tp30) REVERT: P 39 LEU cc_start: 0.8902 (mp) cc_final: 0.8359 (tp) REVERT: P 54 LYS cc_start: 0.7942 (pmmt) cc_final: 0.7241 (tptp) REVERT: P 63 ASP cc_start: 0.7584 (p0) cc_final: 0.7329 (p0) REVERT: P 66 ASP cc_start: 0.8199 (t0) cc_final: 0.7945 (t0) REVERT: D 142 TYR cc_start: 0.7156 (OUTLIER) cc_final: 0.6898 (p90) REVERT: D 177 MET cc_start: 0.6794 (tmm) cc_final: 0.6589 (tmm) REVERT: D 295 ILE cc_start: 0.9439 (mp) cc_final: 0.9083 (mt) REVERT: A 20 TRP cc_start: 0.8116 (t60) cc_final: 0.7489 (t60) REVERT: A 65 ASP cc_start: 0.8145 (p0) cc_final: 0.7745 (t0) REVERT: A 147 ASP cc_start: 0.8325 (p0) cc_final: 0.8024 (p0) REVERT: A 176 MET cc_start: 0.7592 (mmt) cc_final: 0.7327 (mmt) REVERT: A 240 ASN cc_start: 0.8354 (OUTLIER) cc_final: 0.7846 (t0) REVERT: A 302 MET cc_start: 0.7580 (ptp) cc_final: 0.6254 (ptp) REVERT: A 323 GLN cc_start: 0.9090 (mm-40) cc_final: 0.8500 (mt0) REVERT: A 327 ASP cc_start: 0.8908 (m-30) cc_final: 0.8452 (m-30) REVERT: E 240 ASN cc_start: 0.8270 (t0) cc_final: 0.8024 (t0) REVERT: E 246 PHE cc_start: 0.8660 (t80) cc_final: 0.8214 (t80) REVERT: F 20 TRP cc_start: 0.8334 (t60) cc_final: 0.7986 (t60) REVERT: F 40 PRO cc_start: 0.9076 (Cg_exo) cc_final: 0.8849 (Cg_endo) REVERT: F 65 ASP cc_start: 0.8179 (p0) cc_final: 0.7741 (t0) REVERT: F 93 ILE cc_start: 0.7575 (mp) cc_final: 0.7181 (mm) REVERT: F 129 ASN cc_start: 0.6616 (p0) cc_final: 0.6344 (p0) REVERT: F 176 MET cc_start: 0.8157 (mmt) cc_final: 0.7555 (mmt) REVERT: F 245 ASP cc_start: 0.7828 (OUTLIER) cc_final: 0.7614 (p0) REVERT: F 284 SER cc_start: 0.9265 (p) cc_final: 0.9043 (p) REVERT: F 302 MET cc_start: 0.7396 (ptp) cc_final: 0.6728 (ptp) REVERT: F 323 GLN cc_start: 0.8745 (mm110) cc_final: 0.8326 (mm-40) REVERT: F 327 ASP cc_start: 0.8629 (m-30) cc_final: 0.8282 (m-30) REVERT: I 142 TYR cc_start: 0.7439 (OUTLIER) cc_final: 0.6258 (p90) REVERT: I 295 ILE cc_start: 0.9340 (OUTLIER) cc_final: 0.8990 (mm) REVERT: I 321 TYR cc_start: 0.9067 (t80) cc_final: 0.8833 (t80) REVERT: K 65 ASP cc_start: 0.7978 (p0) cc_final: 0.7611 (t0) REVERT: K 176 MET cc_start: 0.7739 (mmt) cc_final: 0.6891 (mmt) REVERT: K 284 SER cc_start: 0.9236 (OUTLIER) cc_final: 0.8867 (m) REVERT: K 302 MET cc_start: 0.7331 (ptp) cc_final: 0.5905 (ptp) REVERT: N 226 GLN cc_start: 0.7966 (tm-30) cc_final: 0.7677 (tm-30) REVERT: N 269 THR cc_start: 0.8250 (p) cc_final: 0.8023 (p) REVERT: N 295 ILE cc_start: 0.9378 (mp) cc_final: 0.8907 (mt) REVERT: N 314 TRP cc_start: 0.9289 (m100) cc_final: 0.8728 (m100) REVERT: O 17 MET cc_start: 0.8558 (tpt) cc_final: 0.8241 (tpt) REVERT: O 20 TRP cc_start: 0.8288 (t60) cc_final: 0.7281 (t60) REVERT: O 65 ASP cc_start: 0.8118 (p0) cc_final: 0.7801 (t0) REVERT: O 176 MET cc_start: 0.7477 (mmt) cc_final: 0.6923 (mmt) REVERT: O 323 GLN cc_start: 0.8840 (mm-40) cc_final: 0.8405 (mt0) REVERT: O 327 ASP cc_start: 0.8844 (m-30) cc_final: 0.8473 (m-30) REVERT: J 37 MET cc_start: 0.8456 (tmm) cc_final: 0.8227 (tpp) REVERT: J 46 HIS cc_start: 0.7405 (m170) cc_final: 0.7074 (m90) REVERT: J 85 MET cc_start: 0.8210 (tpt) cc_final: 0.7828 (tpt) REVERT: J 131 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.8969 (mp) REVERT: B 67 ASN cc_start: 0.8730 (m110) cc_final: 0.8223 (p0) REVERT: B 131 LEU cc_start: 0.9387 (tt) cc_final: 0.9082 (mm) REVERT: B 241 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8465 (tp) REVERT: G 46 HIS cc_start: 0.7700 (m170) cc_final: 0.7445 (m-70) REVERT: G 70 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8288 (tt) REVERT: G 80 ASN cc_start: 0.7168 (m110) cc_final: 0.6563 (t0) REVERT: G 85 MET cc_start: 0.8336 (tpt) cc_final: 0.8012 (tpt) REVERT: G 127 PHE cc_start: 0.8179 (t80) cc_final: 0.7767 (t80) REVERT: G 193 GLU cc_start: 0.8344 (tm-30) cc_final: 0.8129 (tm-30) REVERT: G 241 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8455 (tp) REVERT: L 69 ASP cc_start: 0.7583 (m-30) cc_final: 0.7239 (t70) REVERT: L 78 LEU cc_start: 0.8701 (mm) cc_final: 0.8486 (mm) REVERT: L 84 ILE cc_start: 0.8173 (OUTLIER) cc_final: 0.7973 (tp) REVERT: L 131 LEU cc_start: 0.9383 (tt) cc_final: 0.9034 (mp) REVERT: L 241 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8521 (tp) REVERT: C 1 MET cc_start: 0.8757 (tpp) cc_final: 0.5496 (mmt) REVERT: C 4 LEU cc_start: 0.8617 (pp) cc_final: 0.7751 (tp) REVERT: C 28 GLN cc_start: 0.9039 (mp10) cc_final: 0.8696 (mp10) REVERT: C 40 GLN cc_start: 0.9231 (mm-40) cc_final: 0.8875 (mm-40) REVERT: C 47 ARG cc_start: 0.8874 (tpp80) cc_final: 0.8267 (tpp80) REVERT: C 63 ASP cc_start: 0.7685 (p0) cc_final: 0.7431 (p0) REVERT: C 69 GLU cc_start: 0.7828 (mp0) cc_final: 0.7278 (mp0) REVERT: H 1 MET cc_start: 0.7138 (ttm) cc_final: 0.6644 (tpp) REVERT: H 28 GLN cc_start: 0.8850 (mp10) cc_final: 0.8624 (mp10) REVERT: H 54 LYS cc_start: 0.8458 (pttm) cc_final: 0.8163 (pttm) REVERT: H 63 ASP cc_start: 0.7285 (p0) cc_final: 0.7008 (p0) REVERT: M 12 ARG cc_start: 0.8684 (ttt180) cc_final: 0.8482 (ttt180) REVERT: M 46 GLN cc_start: 0.8369 (tp40) cc_final: 0.8002 (pt0) REVERT: M 47 ARG cc_start: 0.8893 (mmm160) cc_final: 0.7999 (mmm160) REVERT: M 50 GLN cc_start: 0.8836 (tm-30) cc_final: 0.8548 (tm-30) REVERT: M 66 ASP cc_start: 0.7959 (t0) cc_final: 0.7677 (t0) REVERT: M 69 GLU cc_start: 0.7852 (mp0) cc_final: 0.7597 (mp0) outliers start: 130 outliers final: 100 residues processed: 643 average time/residue: 0.1602 time to fit residues: 176.0456 Evaluate side-chains 641 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 529 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 228 LYS Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 240 ASN 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 243 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 142 TYR Chi-restraints excluded: chain I residue 166 LEU Chi-restraints excluded: chain I residue 182 SER Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 228 LYS Chi-restraints excluded: chain I residue 244 VAL Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 251 GLU Chi-restraints excluded: chain I residue 295 ILE Chi-restraints excluded: chain I residue 301 THR Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 17 MET Chi-restraints excluded: chain K residue 85 ASN Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain K residue 259 VAL Chi-restraints excluded: chain K residue 278 SER Chi-restraints excluded: chain K residue 284 SER Chi-restraints excluded: chain N residue 4 VAL Chi-restraints excluded: chain N residue 137 VAL Chi-restraints excluded: chain N residue 205 MET Chi-restraints excluded: chain N residue 208 VAL Chi-restraints excluded: chain N residue 218 VAL Chi-restraints excluded: chain N residue 241 VAL Chi-restraints excluded: chain N residue 243 VAL Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain O residue 34 ILE Chi-restraints excluded: chain O residue 85 ASN Chi-restraints excluded: chain O residue 149 VAL Chi-restraints excluded: chain O residue 193 SER Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 244 VAL Chi-restraints excluded: chain O residue 245 ASP Chi-restraints excluded: chain O residue 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 289 THR Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 181 VAL 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 301 SER Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 84 ILE 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 206 GLN Chi-restraints excluded: chain L residue 225 ILE Chi-restraints excluded: chain L residue 241 ILE Chi-restraints excluded: chain L residue 257 VAL Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain M residue 4 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 72 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 172 optimal weight: 8.9990 chunk 179 optimal weight: 6.9990 chunk 413 optimal weight: 1.9990 chunk 195 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 296 optimal weight: 2.9990 chunk 323 optimal weight: 0.9990 chunk 264 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 GLN ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 15 ASN O 290 HIS ** J 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 HIS ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 206 GLN ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 16 HIS ** 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 = 0.3747 r_free = 0.3747 target = 0.108071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.085076 restraints weight = 86587.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.087744 restraints weight = 45181.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.089467 restraints weight = 30146.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.090510 restraints weight = 23429.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.091067 restraints weight = 20200.153| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.4874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 34104 Z= 0.124 Angle : 0.683 15.080 46344 Z= 0.342 Chirality : 0.048 0.329 5220 Planarity : 0.004 0.051 5980 Dihedral : 6.268 57.409 5084 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.30 % Allowed : 19.27 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.13), residues: 4240 helix: 0.34 (0.14), residues: 1496 sheet: -0.79 (0.17), residues: 864 loop : -0.68 (0.15), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 47 TYR 0.026 0.001 TYR B 89 PHE 0.032 0.001 PHE J 68 TRP 0.080 0.001 TRP K 20 HIS 0.011 0.001 HIS B 284 Details of bonding type rmsd covalent geometry : bond 0.00279 (34096) covalent geometry : angle 0.67994 (46328) SS BOND : bond 0.00332 ( 8) SS BOND : angle 3.79017 ( 16) hydrogen bonds : bond 0.03159 ( 1404) hydrogen bonds : angle 4.84410 ( 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 695 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 578 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 37 GLU cc_start: 0.8730 (tp30) cc_final: 0.8441 (tp30) REVERT: P 39 LEU cc_start: 0.8898 (mp) cc_final: 0.8392 (tp) REVERT: P 54 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7480 (tptp) REVERT: P 63 ASP cc_start: 0.7489 (p0) cc_final: 0.7225 (p0) REVERT: D 295 ILE cc_start: 0.9443 (mp) cc_final: 0.9078 (mt) REVERT: D 332 MET cc_start: 0.7802 (mmp) cc_final: 0.7540 (mmp) REVERT: A 20 TRP cc_start: 0.8084 (t60) cc_final: 0.7440 (t60) REVERT: A 65 ASP cc_start: 0.8073 (p0) cc_final: 0.7761 (t0) REVERT: A 147 ASP cc_start: 0.8348 (p0) cc_final: 0.8052 (p0) REVERT: A 302 MET cc_start: 0.7483 (ptp) cc_final: 0.6171 (ptp) REVERT: A 323 GLN cc_start: 0.9056 (mm-40) cc_final: 0.8542 (mt0) REVERT: A 327 ASP cc_start: 0.8898 (m-30) cc_final: 0.8462 (m-30) REVERT: E 240 ASN cc_start: 0.8251 (t0) cc_final: 0.7984 (t0) REVERT: E 246 PHE cc_start: 0.8723 (t80) cc_final: 0.8296 (t80) REVERT: E 304 LEU cc_start: 0.8748 (mt) cc_final: 0.8525 (tp) REVERT: F 20 TRP cc_start: 0.8336 (t60) cc_final: 0.8039 (t60) REVERT: F 40 PRO cc_start: 0.9055 (Cg_exo) cc_final: 0.8821 (Cg_endo) REVERT: F 65 ASP cc_start: 0.8157 (p0) cc_final: 0.7685 (t0) REVERT: F 93 ILE cc_start: 0.7586 (mp) cc_final: 0.7207 (mm) REVERT: F 129 ASN cc_start: 0.6551 (p0) cc_final: 0.6265 (p0) REVERT: F 176 MET cc_start: 0.8176 (mmt) cc_final: 0.7198 (mmt) REVERT: F 284 SER cc_start: 0.9247 (p) cc_final: 0.9023 (p) REVERT: F 302 MET cc_start: 0.7381 (ptp) cc_final: 0.6694 (ptp) REVERT: F 323 GLN cc_start: 0.8750 (mm110) cc_final: 0.8335 (mm-40) REVERT: F 327 ASP cc_start: 0.8621 (m-30) cc_final: 0.8271 (m-30) REVERT: I 142 TYR cc_start: 0.7331 (OUTLIER) cc_final: 0.6116 (p90) REVERT: I 228 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8508 (mtmm) REVERT: I 295 ILE cc_start: 0.9348 (OUTLIER) cc_final: 0.8975 (mm) REVERT: I 321 TYR cc_start: 0.9039 (t80) cc_final: 0.8824 (t80) REVERT: K 65 ASP cc_start: 0.7928 (p0) cc_final: 0.7627 (t0) REVERT: K 176 MET cc_start: 0.7720 (mmt) cc_final: 0.6869 (mmt) REVERT: K 284 SER cc_start: 0.9197 (OUTLIER) cc_final: 0.8841 (m) REVERT: K 302 MET cc_start: 0.7312 (ptp) cc_final: 0.5877 (ptp) REVERT: N 226 GLN cc_start: 0.7950 (tm-30) cc_final: 0.7660 (tm-30) REVERT: N 295 ILE cc_start: 0.9390 (mp) cc_final: 0.8967 (mt) REVERT: N 314 TRP cc_start: 0.9220 (m100) cc_final: 0.8757 (m100) REVERT: O 20 TRP cc_start: 0.8253 (t60) cc_final: 0.7246 (t60) REVERT: O 65 ASP cc_start: 0.8095 (p0) cc_final: 0.7758 (t0) REVERT: O 176 MET cc_start: 0.7459 (mmt) cc_final: 0.6915 (mmt) REVERT: O 323 GLN cc_start: 0.8858 (mm-40) cc_final: 0.8423 (mt0) REVERT: O 327 ASP cc_start: 0.8888 (m-30) cc_final: 0.8485 (m-30) REVERT: J 37 MET cc_start: 0.8430 (tmm) cc_final: 0.8217 (tpp) REVERT: J 46 HIS cc_start: 0.7329 (m170) cc_final: 0.6979 (m90) REVERT: J 85 MET cc_start: 0.8210 (tpt) cc_final: 0.7847 (tpt) REVERT: J 131 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.8981 (mp) REVERT: B 42 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.7844 (mt) REVERT: B 56 MET cc_start: 0.6177 (ptp) cc_final: 0.5962 (ptp) REVERT: B 67 ASN cc_start: 0.8820 (m110) cc_final: 0.8177 (p0) REVERT: B 131 LEU cc_start: 0.9382 (tt) cc_final: 0.9075 (mm) REVERT: B 241 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8476 (tp) REVERT: G 46 HIS cc_start: 0.7642 (m170) cc_final: 0.7384 (m-70) REVERT: G 80 ASN cc_start: 0.6982 (m110) cc_final: 0.6571 (t0) REVERT: G 85 MET cc_start: 0.8196 (tpt) cc_final: 0.7921 (tpt) REVERT: G 127 PHE cc_start: 0.8178 (t80) cc_final: 0.7688 (t80) REVERT: G 193 GLU cc_start: 0.8380 (tm-30) cc_final: 0.8173 (tm-30) REVERT: G 241 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8414 (tp) REVERT: L 42 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8200 (mt) REVERT: L 69 ASP cc_start: 0.7659 (m-30) cc_final: 0.7135 (t70) REVERT: L 84 ILE cc_start: 0.8123 (OUTLIER) cc_final: 0.7912 (tp) REVERT: L 131 LEU cc_start: 0.9386 (tt) cc_final: 0.9032 (mp) REVERT: C 1 MET cc_start: 0.8716 (tpp) cc_final: 0.5528 (mmt) REVERT: C 4 LEU cc_start: 0.8611 (pp) cc_final: 0.7766 (tp) REVERT: C 28 GLN cc_start: 0.9095 (mp10) cc_final: 0.8739 (mp10) REVERT: C 40 GLN cc_start: 0.9216 (mm-40) cc_final: 0.8958 (mm-40) REVERT: C 47 ARG cc_start: 0.8880 (tpp80) cc_final: 0.8237 (tpp80) REVERT: C 50 GLN cc_start: 0.8150 (mm110) cc_final: 0.7930 (mm110) REVERT: C 63 ASP cc_start: 0.7742 (p0) cc_final: 0.7488 (p0) REVERT: C 69 GLU cc_start: 0.7837 (mp0) cc_final: 0.7267 (mp0) REVERT: H 1 MET cc_start: 0.7225 (ttm) cc_final: 0.6745 (tpp) REVERT: H 63 ASP cc_start: 0.7104 (p0) cc_final: 0.6708 (p0) REVERT: M 12 ARG cc_start: 0.8740 (ttt180) cc_final: 0.8376 (ttt180) REVERT: M 38 GLU cc_start: 0.8864 (mm-30) cc_final: 0.8524 (tt0) REVERT: M 46 GLN cc_start: 0.8383 (tp40) cc_final: 0.8038 (pt0) REVERT: M 47 ARG cc_start: 0.8883 (mmm160) cc_final: 0.7970 (mmm160) REVERT: M 50 GLN cc_start: 0.8818 (tm-30) cc_final: 0.8506 (tm-30) REVERT: M 66 ASP cc_start: 0.7929 (t0) cc_final: 0.7585 (t0) REVERT: M 69 GLU cc_start: 0.7856 (mp0) cc_final: 0.7601 (mp0) outliers start: 117 outliers final: 95 residues processed: 654 average time/residue: 0.1541 time to fit residues: 172.8308 Evaluate side-chains 642 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 536 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain P residue 54 LYS Chi-restraints excluded: chain P residue 61 CYS Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 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 243 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain 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 F residue 137 VAL Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain 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 295 ILE Chi-restraints excluded: chain I residue 301 THR Chi-restraints excluded: chain I residue 302 MET Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 17 MET Chi-restraints excluded: chain K residue 85 ASN Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain K residue 259 VAL Chi-restraints excluded: chain K residue 278 SER Chi-restraints excluded: chain K residue 284 SER Chi-restraints excluded: chain N residue 4 VAL Chi-restraints excluded: chain N residue 137 VAL Chi-restraints excluded: chain N residue 205 MET Chi-restraints excluded: chain N residue 208 VAL Chi-restraints excluded: chain N residue 218 VAL Chi-restraints excluded: chain N residue 243 VAL Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain O residue 34 ILE Chi-restraints excluded: chain O residue 85 ASN Chi-restraints excluded: chain O residue 137 VAL Chi-restraints excluded: chain O residue 193 SER Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 244 VAL Chi-restraints excluded: chain O residue 245 ASP Chi-restraints excluded: chain O residue 290 HIS Chi-restraints excluded: chain J residue 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 42 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 257 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 181 VAL 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 301 SER Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 84 ILE 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 206 GLN Chi-restraints excluded: chain L residue 225 ILE Chi-restraints excluded: chain L residue 257 VAL Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain H residue 61 CYS Chi-restraints excluded: chain M residue 4 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: 3.9990 chunk 309 optimal weight: 6.9990 chunk 258 optimal weight: 0.6980 chunk 179 optimal weight: 6.9990 chunk 331 optimal weight: 0.2980 chunk 278 optimal weight: 0.2980 chunk 288 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 367 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 GLN ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 ASN ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 290 HIS ** J 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 HIS ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 206 GLN ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 HIS H 59 GLN M 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 = 0.3749 r_free = 0.3749 target = 0.108120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.085099 restraints weight = 86237.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.087784 restraints weight = 45044.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.089445 restraints weight = 30023.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.090493 restraints weight = 23555.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.091159 restraints weight = 20308.784| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.5003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34104 Z= 0.123 Angle : 0.681 15.326 46344 Z= 0.341 Chirality : 0.048 0.353 5220 Planarity : 0.004 0.050 5980 Dihedral : 6.208 57.335 5084 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.22 % Allowed : 19.78 % Favored : 77.00 % 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 aren not related in a simple way. whole: -0.52 (0.13), residues: 4240 helix: 0.40 (0.14), residues: 1488 sheet: -0.67 (0.17), residues: 856 loop : -0.66 (0.15), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 47 TYR 0.028 0.001 TYR F 49 PHE 0.031 0.002 PHE J 68 TRP 0.116 0.001 TRP K 20 HIS 0.011 0.001 HIS M 16 Details of bonding type rmsd covalent geometry : bond 0.00278 (34096) covalent geometry : angle 0.67798 (46328) SS BOND : bond 0.00405 ( 8) SS BOND : angle 3.29529 ( 16) hydrogen bonds : bond 0.03150 ( 1404) hydrogen bonds : angle 4.85072 ( 4500) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5573.39 seconds wall clock time: 97 minutes 33.15 seconds (5853.15 seconds total)