Starting phenix.real_space_refine on Thu Jan 15 10:48:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cjz_16687/01_2026/8cjz_16687.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cjz_16687/01_2026/8cjz_16687.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8cjz_16687/01_2026/8cjz_16687.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cjz_16687/01_2026/8cjz_16687.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8cjz_16687/01_2026/8cjz_16687.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cjz_16687/01_2026/8cjz_16687.map" } resolution = 3.5 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 134 5.16 5 C 15956 2.51 5 N 4360 2.21 5 O 5110 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25560 Number of models: 1 Model: "" Number of chains: 15 Chain: "Y" Number of atoms: 2632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2632 Classifications: {'peptide': 342} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 331} Chain: "K" Number of atoms: 2632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2632 Classifications: {'peptide': 342} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 331} Chain: "J" Number of atoms: 2632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2632 Classifications: {'peptide': 342} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 331} Chain: "I" Number of atoms: 2632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2632 Classifications: {'peptide': 342} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 331} Chain: "H" Number of atoms: 2632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2632 Classifications: {'peptide': 342} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 331} Chain: "G" Number of atoms: 2632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2632 Classifications: {'peptide': 342} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 331} Chain: "g" Number of atoms: 2544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2544 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 320} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "h" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 630 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 6, 'TRANS': 80} Chain: "B" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 942 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "C" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 942 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "c" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 942 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "F" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 942 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "D" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 942 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "A" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 942 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "E" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 942 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Time building chain proxies: 5.60, per 1000 atoms: 0.22 Number of scatterers: 25560 At special positions: 0 Unit cell: (186.624, 226.368, 145.152, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 134 16.00 O 5110 8.00 N 4360 7.00 C 15956 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.11 Conformation dependent library (CDL) restraints added in 835.6 milliseconds 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6196 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 68 sheets defined 18.8% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'Y' and resid 10 through 17 removed outlier: 3.560A pdb=" N VAL Y 14 " --> pdb=" O THR Y 10 " (cutoff:3.500A) Processing helix chain 'Y' and resid 37 through 42 Processing helix chain 'Y' and resid 98 through 103 Processing helix chain 'Y' and resid 107 through 132 Processing helix chain 'Y' and resid 134 through 138 Processing helix chain 'Y' and resid 162 through 165 removed outlier: 3.870A pdb=" N ASP Y 165 " --> pdb=" O ASP Y 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 162 through 165' Processing helix chain 'Y' and resid 258 through 270 removed outlier: 3.598A pdb=" N LEU Y 262 " --> pdb=" O ASP Y 258 " (cutoff:3.500A) Processing helix chain 'Y' and resid 287 through 297 Processing helix chain 'K' and resid 10 through 16 Processing helix chain 'K' and resid 37 through 42 removed outlier: 3.793A pdb=" N ASP K 41 " --> pdb=" O PRO K 37 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N MET K 42 " --> pdb=" O ILE K 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 37 through 42' Processing helix chain 'K' and resid 98 through 104 removed outlier: 3.889A pdb=" N LYS K 102 " --> pdb=" O GLU K 98 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 130 Processing helix chain 'K' and resid 162 through 165 Processing helix chain 'K' and resid 237 through 239 No H-bonds generated for 'chain 'K' and resid 237 through 239' Processing helix chain 'K' and resid 249 through 254 removed outlier: 3.793A pdb=" N ALA K 254 " --> pdb=" O SER K 250 " (cutoff:3.500A) Processing helix chain 'K' and resid 259 through 270 Processing helix chain 'K' and resid 272 through 276 Processing helix chain 'K' and resid 285 through 297 Processing helix chain 'J' and resid 10 through 17 Processing helix chain 'J' and resid 37 through 42 Processing helix chain 'J' and resid 106 through 132 removed outlier: 3.829A pdb=" N LEU J 110 " --> pdb=" O ASP J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 162 through 165 Processing helix chain 'J' and resid 237 through 241 Processing helix chain 'J' and resid 249 through 253 Processing helix chain 'J' and resid 259 through 270 Processing helix chain 'J' and resid 285 through 297 Processing helix chain 'I' and resid 10 through 16 removed outlier: 3.546A pdb=" N VAL I 14 " --> pdb=" O THR I 10 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 18 No H-bonds generated for 'chain 'I' and resid 17 through 18' Processing helix chain 'I' and resid 19 through 23 removed outlier: 4.059A pdb=" N ASN I 23 " --> pdb=" O GLY I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 36 through 42 removed outlier: 4.168A pdb=" N GLU I 40 " --> pdb=" O ASN I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 104 Processing helix chain 'I' and resid 107 through 131 Processing helix chain 'I' and resid 248 through 253 Processing helix chain 'I' and resid 259 through 271 removed outlier: 4.013A pdb=" N GLU I 271 " --> pdb=" O TYR I 267 " (cutoff:3.500A) Processing helix chain 'I' and resid 272 through 276 Processing helix chain 'I' and resid 285 through 297 Processing helix chain 'H' and resid 10 through 17 removed outlier: 3.669A pdb=" N VAL H 14 " --> pdb=" O THR H 10 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 42 Processing helix chain 'H' and resid 98 through 104 Processing helix chain 'H' and resid 107 through 132 removed outlier: 3.633A pdb=" N MET H 111 " --> pdb=" O LYS H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 166 removed outlier: 3.672A pdb=" N ASP H 165 " --> pdb=" O ASP H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 237 through 239 No H-bonds generated for 'chain 'H' and resid 237 through 239' Processing helix chain 'H' and resid 249 through 255 Processing helix chain 'H' and resid 258 through 269 removed outlier: 3.734A pdb=" N LEU H 262 " --> pdb=" O ASP H 258 " (cutoff:3.500A) Processing helix chain 'H' and resid 285 through 297 removed outlier: 3.597A pdb=" N THR H 289 " --> pdb=" O ASN H 285 " (cutoff:3.500A) Processing helix chain 'H' and resid 310 through 314 removed outlier: 3.812A pdb=" N VAL H 314 " --> pdb=" O PRO H 311 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 17 Processing helix chain 'G' and resid 37 through 42 Processing helix chain 'G' and resid 97 through 104 removed outlier: 3.692A pdb=" N VAL G 101 " --> pdb=" O ASP G 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 133 Processing helix chain 'G' and resid 134 through 139 Processing helix chain 'G' and resid 146 through 150 removed outlier: 3.540A pdb=" N ASN G 150 " --> pdb=" O PRO G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 162 through 165 Processing helix chain 'G' and resid 237 through 241 Processing helix chain 'G' and resid 248 through 255 Processing helix chain 'G' and resid 258 through 266 Processing helix chain 'G' and resid 285 through 297 Processing helix chain 'g' and resid 10 through 18 removed outlier: 3.647A pdb=" N VAL g 14 " --> pdb=" O THR g 10 " (cutoff:3.500A) Processing helix chain 'g' and resid 37 through 42 Processing helix chain 'g' and resid 98 through 104 Processing helix chain 'g' and resid 107 through 132 removed outlier: 3.836A pdb=" N GLU g 114 " --> pdb=" O LEU g 110 " (cutoff:3.500A) Processing helix chain 'g' and resid 146 through 150 removed outlier: 3.823A pdb=" N ASN g 150 " --> pdb=" O PRO g 147 " (cutoff:3.500A) Processing helix chain 'g' and resid 162 through 165 Processing helix chain 'g' and resid 237 through 239 No H-bonds generated for 'chain 'g' and resid 237 through 239' Processing helix chain 'g' and resid 249 through 254 Processing helix chain 'g' and resid 258 through 270 removed outlier: 3.757A pdb=" N LEU g 262 " --> pdb=" O ASP g 258 " (cutoff:3.500A) Processing helix chain 'g' and resid 285 through 292 removed outlier: 3.638A pdb=" N THR g 289 " --> pdb=" O ASN g 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 84 Processing helix chain 'F' and resid 80 through 84 removed outlier: 3.509A pdb=" N ASP F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 8 Processing helix chain 'D' and resid 82 through 84 No H-bonds generated for 'chain 'D' and resid 82 through 84' Processing helix chain 'E' and resid 82 through 84 No H-bonds generated for 'chain 'E' and resid 82 through 84' Processing sheet with id=AA1, first strand: chain 'Y' and resid 44 through 46 removed outlier: 6.277A pdb=" N MET Y 45 " --> pdb=" O TYR Y 194 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N HIS Y 191 " --> pdb=" O THR Y 234 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU Y 225 " --> pdb=" O SER Y 94 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER Y 94 " --> pdb=" O GLU Y 225 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU Y 90 " --> pdb=" O TRP Y 229 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Y' and resid 44 through 46 removed outlier: 6.277A pdb=" N MET Y 45 " --> pdb=" O TYR Y 194 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N HIS Y 191 " --> pdb=" O THR Y 234 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL Y 222 " --> pdb=" O ALA Y 209 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ALA Y 209 " --> pdb=" O VAL Y 222 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ARG Y 224 " --> pdb=" O LEU Y 207 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Y' and resid 53 through 58 removed outlier: 3.561A pdb=" N HIS Y 53 " --> pdb=" O ASP Y 85 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'Y' and resid 152 through 153 removed outlier: 6.809A pdb=" N TYR Y 152 " --> pdb=" O VAL Y 343 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'Y' and resid 167 through 169 removed outlier: 5.930A pdb=" N ILE Y 168 " --> pdb=" O ALA Y 245 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL Y 242 " --> pdb=" O MET Y 182 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'Y' and resid 184 through 185 Processing sheet with id=AA7, first strand: chain 'K' and resid 18 through 20 removed outlier: 7.021A pdb=" N ASN K 23 " --> pdb=" O ASP K 19 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 44 through 46 removed outlier: 3.853A pdb=" N TYR K 194 " --> pdb=" O MET K 45 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU K 90 " --> pdb=" O TRP K 229 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 44 through 46 removed outlier: 3.853A pdb=" N TYR K 194 " --> pdb=" O MET K 45 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL K 222 " --> pdb=" O ALA K 209 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ALA K 209 " --> pdb=" O VAL K 222 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ARG K 224 " --> pdb=" O LEU K 207 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 56 through 58 Processing sheet with id=AB2, first strand: chain 'K' and resid 167 through 169 removed outlier: 6.348A pdb=" N ILE K 168 " --> pdb=" O ALA K 245 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE K 247 " --> pdb=" O ILE K 168 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL K 241 " --> pdb=" O VAL K 184 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N VAL K 184 " --> pdb=" O VAL K 241 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N ARG K 243 " --> pdb=" O MET K 182 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N MET K 182 " --> pdb=" O ARG K 243 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ALA K 245 " --> pdb=" O ILE K 180 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ILE K 180 " --> pdb=" O ALA K 245 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ARG K 328 " --> pdb=" O ALA K 280 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N LEU K 282 " --> pdb=" O ARG K 328 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 44 through 46 removed outlier: 3.923A pdb=" N TYR J 194 " --> pdb=" O MET J 45 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 53 through 58 Processing sheet with id=AB5, first strand: chain 'J' and resid 65 through 66 removed outlier: 3.677A pdb=" N THR J 65 " --> pdb=" O GLU I 91 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU I 91 " --> pdb=" O THR J 65 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLY I 208 " --> pdb=" O ARG I 224 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LYS I 226 " --> pdb=" O TYR I 206 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N TYR I 206 " --> pdb=" O LYS I 226 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N GLU I 228 " --> pdb=" O ARG I 204 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ARG I 204 " --> pdb=" O GLU I 228 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 89 through 96 removed outlier: 4.179A pdb=" N VAL J 223 " --> pdb=" O VAL J 96 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ARG J 224 " --> pdb=" O LEU J 207 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 152 through 153 removed outlier: 5.918A pdb=" N TYR J 152 " --> pdb=" O VAL J 343 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'J' and resid 167 through 169 removed outlier: 4.043A pdb=" N ASN J 246 " --> pdb=" O THR J 178 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N THR J 178 " --> pdb=" O ASN J 246 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ARG J 279 " --> pdb=" O TRP J 185 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ALA J 280 " --> pdb=" O PRO J 326 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ARG J 328 " --> pdb=" O ALA J 280 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N LEU J 282 " --> pdb=" O ARG J 328 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 44 through 46 removed outlier: 3.529A pdb=" N HIS I 191 " --> pdb=" O THR I 234 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 80 through 84 Processing sheet with id=AC2, first strand: chain 'I' and resid 65 through 66 removed outlier: 3.527A pdb=" N THR I 65 " --> pdb=" O GLU H 91 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N MET H 45 " --> pdb=" O TYR H 194 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 65 through 66 removed outlier: 3.527A pdb=" N THR I 65 " --> pdb=" O GLU H 91 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY H 208 " --> pdb=" O ARG H 224 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LYS H 226 " --> pdb=" O TYR H 206 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N TYR H 206 " --> pdb=" O LYS H 226 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLU H 228 " --> pdb=" O ARG H 204 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N ARG H 204 " --> pdb=" O GLU H 228 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 152 through 153 removed outlier: 6.418A pdb=" N TYR I 152 " --> pdb=" O VAL I 343 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'I' and resid 167 through 168 removed outlier: 3.557A pdb=" N ILE I 180 " --> pdb=" O ILE I 244 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 321 through 322 Processing sheet with id=AC7, first strand: chain 'H' and resid 79 through 83 removed outlier: 6.289A pdb=" N THR H 79 " --> pdb=" O THR H 59 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N THR H 56 " --> pdb=" O ILE G 29 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 152 through 153 removed outlier: 6.319A pdb=" N TYR H 152 " --> pdb=" O VAL H 343 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'H' and resid 168 through 169 removed outlier: 5.949A pdb=" N ILE H 168 " --> pdb=" O ALA H 245 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'H' and resid 177 through 178 Processing sheet with id=AD2, first strand: chain 'H' and resid 241 through 242 Processing sheet with id=AD3, first strand: chain 'H' and resid 321 through 322 Processing sheet with id=AD4, first strand: chain 'G' and resid 44 through 46 removed outlier: 3.540A pdb=" N TYR G 194 " --> pdb=" O MET G 45 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 54 through 58 Processing sheet with id=AD6, first strand: chain 'G' and resid 89 through 95 removed outlier: 6.263A pdb=" N ARG G 224 " --> pdb=" O LEU G 207 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 167 through 169 Processing sheet with id=AD8, first strand: chain 'G' and resid 184 through 185 removed outlier: 3.879A pdb=" N ARG G 279 " --> pdb=" O TRP G 185 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 282 through 284 removed outlier: 5.896A pdb=" N LEU G 282 " --> pdb=" O ARG G 328 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'g' and resid 44 through 46 removed outlier: 3.541A pdb=" N TYR g 194 " --> pdb=" O MET g 45 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N HIS g 191 " --> pdb=" O THR g 234 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR g 234 " --> pdb=" O HIS g 191 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'g' and resid 53 through 58 Processing sheet with id=AE3, first strand: chain 'g' and resid 89 through 93 removed outlier: 4.380A pdb=" N ASP g 230 " --> pdb=" O GLY g 201 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLY g 201 " --> pdb=" O ASP g 230 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'g' and resid 96 through 97 Processing sheet with id=AE5, first strand: chain 'g' and resid 167 through 169 removed outlier: 6.707A pdb=" N VAL g 241 " --> pdb=" O VAL g 184 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N VAL g 184 " --> pdb=" O VAL g 241 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ARG g 243 " --> pdb=" O MET g 182 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N MET g 182 " --> pdb=" O ARG g 243 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ALA g 245 " --> pdb=" O ILE g 180 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ILE g 180 " --> pdb=" O ALA g 245 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N CYS g 284 " --> pdb=" O ARG g 328 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N MET g 320 " --> pdb=" O VAL g 327 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'h' and resid 24 through 25 Processing sheet with id=AE7, first strand: chain 'h' and resid 61 through 62 removed outlier: 4.595A pdb=" N SER h 49 " --> pdb=" O ASN h 79 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS h 77 " --> pdb=" O VAL h 51 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AE9, first strand: chain 'B' and resid 41 through 42 Processing sheet with id=AF1, first strand: chain 'B' and resid 45 through 47 removed outlier: 3.614A pdb=" N GLU B 47 " --> pdb=" O ALA B 117 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 55 through 56 Processing sheet with id=AF3, first strand: chain 'C' and resid 8 through 14 removed outlier: 5.352A pdb=" N TYR C 11 " --> pdb=" O ALA C 120 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ALA C 120 " --> pdb=" O TYR C 11 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ALA C 117 " --> pdb=" O VAL C 46 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN C 44 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 19 through 20 Processing sheet with id=AF5, first strand: chain 'C' and resid 25 through 26 removed outlier: 4.046A pdb=" N ALA C 74 " --> pdb=" O LEU C 59 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR C 61 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N THR C 72 " --> pdb=" O THR C 61 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AF7, first strand: chain 'c' and resid 3 through 8 removed outlier: 6.540A pdb=" N ASN c 7 " --> pdb=" O VAL c 122 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'c' and resid 13 through 14 removed outlier: 3.506A pdb=" N VAL c 118 " --> pdb=" O GLN c 13 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'c' and resid 25 through 26 Processing sheet with id=AG1, first strand: chain 'c' and resid 79 through 80 removed outlier: 4.219A pdb=" N VAL c 79 " --> pdb=" O LEU c 55 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 3 through 8 removed outlier: 6.423A pdb=" N ASN F 7 " --> pdb=" O VAL F 122 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 13 through 14 Processing sheet with id=AG4, first strand: chain 'F' and resid 25 through 26 removed outlier: 3.550A pdb=" N LEU F 103 " --> pdb=" O ILE F 25 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'D' and resid 10 through 14 removed outlier: 5.071A pdb=" N TYR D 11 " --> pdb=" O ALA D 120 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ALA D 120 " --> pdb=" O TYR D 11 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ALA D 117 " --> pdb=" O VAL D 46 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'D' and resid 19 through 20 removed outlier: 3.513A pdb=" N ALA D 19 " --> pdb=" O TYR D 107 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR D 108 " --> pdb=" O THR D 56 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER D 54 " --> pdb=" O SER D 110 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N THR D 61 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N THR D 72 " --> pdb=" O THR D 61 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'D' and resid 25 through 26 removed outlier: 3.900A pdb=" N THR D 108 " --> pdb=" O THR D 56 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER D 54 " --> pdb=" O SER D 110 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'A' and resid 10 through 14 removed outlier: 3.877A pdb=" N LYS A 12 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N VAL A 118 " --> pdb=" O LYS A 12 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ALA A 117 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS A 88 " --> pdb=" O VAL A 45 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'A' and resid 19 through 20 removed outlier: 4.032A pdb=" N THR A 108 " --> pdb=" O THR A 56 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ALA A 57 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N THR A 75 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU A 59 " --> pdb=" O LEU A 73 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AH2, first strand: chain 'E' and resid 8 through 14 removed outlier: 6.365A pdb=" N ALA E 120 " --> pdb=" O PHE E 9 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N TYR E 11 " --> pdb=" O VAL E 118 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL E 118 " --> pdb=" O TYR E 11 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ALA E 117 " --> pdb=" O VAL E 46 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN E 44 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LYS E 88 " --> pdb=" O VAL E 45 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'E' and resid 25 through 26 removed outlier: 3.761A pdb=" N ILE E 25 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA E 74 " --> pdb=" O LEU E 59 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N THR E 61 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N THR E 72 " --> pdb=" O THR E 61 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'E' and resid 25 through 26 removed outlier: 3.761A pdb=" N ILE E 25 " --> pdb=" O LEU E 103 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'E' and resid 54 through 55 removed outlier: 3.659A pdb=" N LEU E 55 " --> pdb=" O VAL E 79 " (cutoff:3.500A) 693 hydrogen bonds defined for protein. 1812 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: 4.52 Time building geometry restraints manager: 2.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8421 1.34 - 1.46: 3945 1.46 - 1.58: 13320 1.58 - 1.70: 0 1.70 - 1.82: 247 Bond restraints: 25933 Sorted by residual: bond pdb=" C ARG J 273 " pdb=" N VAL J 274 " ideal model delta sigma weight residual 1.332 1.445 -0.113 1.36e-02 5.41e+03 6.91e+01 bond pdb=" C MET c 3 " pdb=" N ASP c 4 " ideal model delta sigma weight residual 1.327 1.428 -0.100 1.47e-02 4.63e+03 4.67e+01 bond pdb=" C ASP G 230 " pdb=" N LEU G 231 " ideal model delta sigma weight residual 1.330 1.248 0.082 1.22e-02 6.72e+03 4.52e+01 bond pdb=" C TRP G 229 " pdb=" N ASP G 230 " ideal model delta sigma weight residual 1.331 1.242 0.089 1.43e-02 4.89e+03 3.88e+01 bond pdb=" C ARG H 67 " pdb=" N ARG H 68 " ideal model delta sigma weight residual 1.331 1.406 -0.075 1.33e-02 5.65e+03 3.18e+01 ... (remaining 25928 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 34022 1.90 - 3.80: 1074 3.80 - 5.69: 129 5.69 - 7.59: 20 7.59 - 9.49: 9 Bond angle restraints: 35254 Sorted by residual: angle pdb=" C LEU I 158 " pdb=" CA LEU I 158 " pdb=" CB LEU I 158 " ideal model delta sigma weight residual 116.54 109.66 6.88 1.15e+00 7.56e-01 3.57e+01 angle pdb=" O TRP G 229 " pdb=" C TRP G 229 " pdb=" N ASP G 230 " ideal model delta sigma weight residual 123.42 118.04 5.38 1.14e+00 7.69e-01 2.23e+01 angle pdb=" C ARG H 67 " pdb=" N ARG H 68 " pdb=" CA ARG H 68 " ideal model delta sigma weight residual 121.05 114.56 6.49 1.43e+00 4.89e-01 2.06e+01 angle pdb=" CA PRO J 311 " pdb=" N PRO J 311 " pdb=" CD PRO J 311 " ideal model delta sigma weight residual 112.00 105.83 6.17 1.40e+00 5.10e-01 1.94e+01 angle pdb=" C MET G 320 " pdb=" CA MET G 320 " pdb=" CB MET G 320 " ideal model delta sigma weight residual 115.89 110.12 5.77 1.32e+00 5.74e-01 1.91e+01 ... (remaining 35249 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 13413 18.00 - 36.00: 1651 36.00 - 53.99: 415 53.99 - 71.99: 75 71.99 - 89.99: 50 Dihedral angle restraints: 15604 sinusoidal: 5926 harmonic: 9678 Sorted by residual: dihedral pdb=" CA ASP F 26 " pdb=" C ASP F 26 " pdb=" N LEU F 27 " pdb=" CA LEU F 27 " ideal model delta harmonic sigma weight residual 180.00 154.38 25.62 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA ASP B 32 " pdb=" C ASP B 32 " pdb=" N ILE B 33 " pdb=" CA ILE B 33 " ideal model delta harmonic sigma weight residual -180.00 -156.32 -23.68 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA TYR G 268 " pdb=" C TYR G 268 " pdb=" N ARG G 269 " pdb=" CA ARG G 269 " ideal model delta harmonic sigma weight residual 180.00 158.77 21.23 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 15601 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2988 0.044 - 0.087: 866 0.087 - 0.131: 307 0.131 - 0.174: 33 0.174 - 0.218: 14 Chirality restraints: 4208 Sorted by residual: chirality pdb=" CG LEU F 27 " pdb=" CB LEU F 27 " pdb=" CD1 LEU F 27 " pdb=" CD2 LEU F 27 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA ILE H 275 " pdb=" N ILE H 275 " pdb=" C ILE H 275 " pdb=" CB ILE H 275 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA MET K 126 " pdb=" N MET K 126 " pdb=" C MET K 126 " pdb=" CB MET K 126 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 4205 not shown) Planarity restraints: 4544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP K 229 " -0.033 2.00e-02 2.50e+03 3.28e-02 2.69e+01 pdb=" CG TRP K 229 " 0.086 2.00e-02 2.50e+03 pdb=" CD1 TRP K 229 " -0.046 2.00e-02 2.50e+03 pdb=" CD2 TRP K 229 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP K 229 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP K 229 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP K 229 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP K 229 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP K 229 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP K 229 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP c 4 " 0.013 2.00e-02 2.50e+03 2.73e-02 7.43e+00 pdb=" C ASP c 4 " -0.047 2.00e-02 2.50e+03 pdb=" O ASP c 4 " 0.018 2.00e-02 2.50e+03 pdb=" N LYS c 5 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP H 66 " -0.013 2.00e-02 2.50e+03 2.44e-02 5.97e+00 pdb=" C TRP H 66 " 0.042 2.00e-02 2.50e+03 pdb=" O TRP H 66 " -0.015 2.00e-02 2.50e+03 pdb=" N ARG H 67 " -0.015 2.00e-02 2.50e+03 ... (remaining 4541 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 1563 2.71 - 3.26: 26919 3.26 - 3.81: 42104 3.81 - 4.35: 50480 4.35 - 4.90: 85485 Nonbonded interactions: 206551 Sorted by model distance: nonbonded pdb=" OD1 ASP E 48 " pdb=" N PHE E 49 " model vdw 2.168 3.120 nonbonded pdb=" OD2 ASP J 138 " pdb=" N LYS J 141 " model vdw 2.197 3.120 nonbonded pdb=" O ASP G 165 " pdb=" OD1 ASP G 165 " model vdw 2.198 3.040 nonbonded pdb=" OG1 THR I 80 " pdb=" OD1 ASP H 13 " model vdw 2.202 3.040 nonbonded pdb=" CG2 VAL E 20 " pdb=" CD ARG E 104 " model vdw 2.204 3.860 ... (remaining 206546 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'c' } ncs_group { reference = (chain 'G' and (resid 3 through 295 or (resid 308 and (name N or name CA or name \ C or name O or name CB )) or resid 309 through 344)) selection = (chain 'H' and (resid 3 through 295 or (resid 308 and (name N or name CA or name \ C or name O or name CB )) or resid 309 through 344)) selection = (chain 'I' and (resid 3 through 295 or (resid 308 and (name N or name CA or name \ C or name O or name CB )) or resid 309 through 344)) selection = (chain 'J' and (resid 3 through 295 or (resid 308 and (name N or name CA or name \ C or name O or name CB )) or resid 309 through 344)) selection = (chain 'K' and (resid 3 through 295 or (resid 308 and (name N or name CA or name \ C or name O or name CB )) or resid 309 through 344)) selection = (chain 'Y' and (resid 3 through 295 or (resid 308 and (name N or name CA or name \ C or name O or name CB )) or resid 309 through 344)) selection = chain 'g' } 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=0.00 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: 47.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 21.700 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.113 25933 Z= 0.280 Angle : 0.772 9.488 35254 Z= 0.450 Chirality : 0.047 0.218 4208 Planarity : 0.004 0.048 4544 Dihedral : 17.561 89.990 9408 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.53 % Favored : 88.44 % Rotamer: Outliers : 0.88 % Allowed : 27.07 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.84 (0.14), residues: 3340 helix: -0.21 (0.23), residues: 543 sheet: -1.72 (0.20), residues: 640 loop : -2.54 (0.12), residues: 2157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 31 TYR 0.034 0.002 TYR H 240 PHE 0.030 0.002 PHE h 73 TRP 0.086 0.002 TRP K 229 HIS 0.005 0.001 HIS H 53 Details of bonding type rmsd covalent geometry : bond 0.00512 (25933) covalent geometry : angle 0.77182 (35254) hydrogen bonds : bond 0.22723 ( 663) hydrogen bonds : angle 8.57488 ( 1812) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 343 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 118 PHE cc_start: 0.8484 (m-10) cc_final: 0.8197 (m-80) REVERT: Y 120 GLU cc_start: 0.7949 (tp30) cc_final: 0.7655 (tp30) REVERT: Y 181 TRP cc_start: 0.7495 (m100) cc_final: 0.6329 (m100) REVERT: Y 321 MET cc_start: 0.7807 (mtp) cc_final: 0.7423 (mtp) REVERT: K 242 VAL cc_start: 0.8685 (p) cc_final: 0.8293 (t) REVERT: K 292 MET cc_start: 0.7774 (ptm) cc_final: 0.7273 (ttp) REVERT: K 321 MET cc_start: 0.7611 (mtt) cc_final: 0.7353 (mtp) REVERT: J 118 PHE cc_start: 0.7981 (m-80) cc_final: 0.7380 (m-80) REVERT: J 214 LEU cc_start: 0.6939 (tt) cc_final: 0.6529 (tp) REVERT: J 229 TRP cc_start: 0.8670 (t60) cc_final: 0.8167 (t60) REVERT: I 120 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7301 (tp30) REVERT: I 182 MET cc_start: 0.8187 (mtp) cc_final: 0.7622 (ttm) REVERT: I 231 LEU cc_start: 0.9602 (OUTLIER) cc_final: 0.9367 (pp) REVERT: I 321 MET cc_start: 0.7661 (mtm) cc_final: 0.7369 (mtp) REVERT: H 99 LYS cc_start: 0.7973 (tptm) cc_final: 0.7052 (pttt) REVERT: H 122 MET cc_start: 0.7964 (mmm) cc_final: 0.7499 (mmm) REVERT: H 126 MET cc_start: 0.7375 (tpp) cc_final: 0.7168 (mmt) REVERT: H 143 MET cc_start: 0.7360 (tpt) cc_final: 0.6246 (mtt) REVERT: H 292 MET cc_start: 0.8124 (mtp) cc_final: 0.7920 (mtm) REVERT: G 199 SER cc_start: 0.7289 (OUTLIER) cc_final: 0.7072 (p) REVERT: G 229 TRP cc_start: 0.7572 (t60) cc_final: 0.7223 (t60) REVERT: g 111 MET cc_start: 0.8111 (mmp) cc_final: 0.7862 (mmm) REVERT: g 122 MET cc_start: 0.8568 (mmm) cc_final: 0.8277 (mtp) REVERT: g 143 MET cc_start: 0.6940 (OUTLIER) cc_final: 0.6688 (ttp) REVERT: g 233 LEU cc_start: 0.8580 (tp) cc_final: 0.8379 (tp) REVERT: g 312 MET cc_start: 0.7048 (tpt) cc_final: 0.6793 (tpt) REVERT: C 2 ILE cc_start: 0.8938 (mp) cc_final: 0.8554 (mt) REVERT: C 7 ASN cc_start: 0.7753 (t0) cc_final: 0.7498 (m-40) REVERT: C 43 ILE cc_start: 0.8565 (mp) cc_final: 0.8228 (tt) REVERT: c 3 MET cc_start: 0.6483 (ttm) cc_final: 0.6182 (ttt) REVERT: c 35 LYS cc_start: 0.7526 (mttp) cc_final: 0.6450 (tmtt) REVERT: F 6 GLU cc_start: 0.4555 (mm-30) cc_final: 0.3790 (tp30) REVERT: D 3 MET cc_start: 0.7052 (tpp) cc_final: 0.6703 (tpp) REVERT: D 59 LEU cc_start: 0.7873 (tp) cc_final: 0.7622 (tp) REVERT: E 3 MET cc_start: 0.7482 (ttt) cc_final: 0.7281 (ttt) outliers start: 24 outliers final: 4 residues processed: 357 average time/residue: 0.1692 time to fit residues: 95.1142 Evaluate side-chains 264 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 257 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 231 LEU Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain g residue 143 MET Chi-restraints excluded: chain C residue 31 ARG Chi-restraints excluded: chain D residue 1 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 ASN G 191 HIS B 60 GLN C 60 GLN D 7 ASN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.092243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.085236 restraints weight = 80397.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.087061 restraints weight = 41802.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.088281 restraints weight = 25485.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.089117 restraints weight = 17236.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.089669 restraints weight = 12463.949| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 25933 Z= 0.140 Angle : 0.638 12.397 35254 Z= 0.334 Chirality : 0.045 0.204 4208 Planarity : 0.004 0.046 4544 Dihedral : 5.490 64.871 3675 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.40 % Favored : 90.57 % Rotamer: Outliers : 3.98 % Allowed : 25.72 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.53 (0.14), residues: 3340 helix: 0.17 (0.23), residues: 560 sheet: -1.37 (0.20), residues: 675 loop : -2.45 (0.13), residues: 2105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG Y 156 TYR 0.019 0.002 TYR C 94 PHE 0.033 0.002 PHE h 73 TRP 0.043 0.002 TRP K 229 HIS 0.005 0.001 HIS J 191 Details of bonding type rmsd covalent geometry : bond 0.00312 (25933) covalent geometry : angle 0.63808 (35254) hydrogen bonds : bond 0.04495 ( 663) hydrogen bonds : angle 5.93571 ( 1812) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 310 time to evaluate : 0.990 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: Y 118 PHE cc_start: 0.8436 (m-10) cc_final: 0.8229 (m-80) REVERT: Y 120 GLU cc_start: 0.7897 (tp30) cc_final: 0.7624 (tp30) REVERT: Y 181 TRP cc_start: 0.7681 (m100) cc_final: 0.6284 (m100) REVERT: Y 321 MET cc_start: 0.7570 (mtp) cc_final: 0.7107 (mtp) REVERT: K 98 GLU cc_start: 0.7632 (tp30) cc_final: 0.6914 (tm-30) REVERT: K 292 MET cc_start: 0.7649 (ptm) cc_final: 0.7134 (ttp) REVERT: K 321 MET cc_start: 0.7615 (mtt) cc_final: 0.7361 (mtp) REVERT: J 118 PHE cc_start: 0.7905 (m-80) cc_final: 0.7408 (m-80) REVERT: J 122 MET cc_start: 0.8050 (mtp) cc_final: 0.7721 (mtp) REVERT: J 214 LEU cc_start: 0.6469 (tt) cc_final: 0.6234 (tp) REVERT: I 74 GLN cc_start: 0.6008 (OUTLIER) cc_final: 0.5492 (mt0) REVERT: I 120 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7195 (tp30) REVERT: I 182 MET cc_start: 0.8383 (mtp) cc_final: 0.7822 (ttm) REVERT: I 321 MET cc_start: 0.7624 (mtm) cc_final: 0.7386 (mtp) REVERT: H 38 ILE cc_start: 0.8673 (OUTLIER) cc_final: 0.8281 (pt) REVERT: H 45 MET cc_start: 0.7771 (ptt) cc_final: 0.7469 (ptp) REVERT: H 99 LYS cc_start: 0.7956 (tptm) cc_final: 0.6986 (pttt) REVERT: H 143 MET cc_start: 0.6936 (tpt) cc_final: 0.5637 (mtt) REVERT: H 193 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8754 (mt) REVERT: H 292 MET cc_start: 0.8233 (mtp) cc_final: 0.8017 (mtm) REVERT: G 42 MET cc_start: 0.6894 (OUTLIER) cc_final: 0.6256 (ptm) REVERT: G 213 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7778 (mm-30) REVERT: G 229 TRP cc_start: 0.7356 (t60) cc_final: 0.6606 (t60) REVERT: G 271 GLU cc_start: 0.5236 (OUTLIER) cc_final: 0.5030 (tt0) REVERT: g 111 MET cc_start: 0.8167 (mmp) cc_final: 0.7872 (mmm) REVERT: C 1 MET cc_start: 0.7971 (mmt) cc_final: 0.7601 (mmm) REVERT: C 2 ILE cc_start: 0.8972 (mp) cc_final: 0.8652 (mt) REVERT: C 3 MET cc_start: 0.7450 (mmm) cc_final: 0.7232 (ttt) REVERT: C 43 ILE cc_start: 0.8664 (mp) cc_final: 0.8359 (tt) REVERT: c 15 ILE cc_start: 0.8447 (OUTLIER) cc_final: 0.8139 (mt) REVERT: c 35 LYS cc_start: 0.7644 (mttp) cc_final: 0.6457 (tmtt) REVERT: c 58 THR cc_start: 0.7230 (OUTLIER) cc_final: 0.7026 (m) REVERT: F 3 MET cc_start: 0.6894 (ttm) cc_final: 0.6649 (ttm) REVERT: F 6 GLU cc_start: 0.4249 (mm-30) cc_final: 0.3770 (tp30) REVERT: D 109 VAL cc_start: 0.8783 (t) cc_final: 0.8577 (t) REVERT: E 31 ARG cc_start: 0.5358 (ptt180) cc_final: 0.4904 (ptt180) REVERT: E 59 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7743 (tp) REVERT: E 94 TYR cc_start: 0.7837 (m-80) cc_final: 0.7390 (m-80) outliers start: 109 outliers final: 39 residues processed: 392 average time/residue: 0.1429 time to fit residues: 93.3022 Evaluate side-chains 320 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 272 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Y residue 310 THR Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 77 LYS Chi-restraints excluded: chain K residue 284 CYS Chi-restraints excluded: chain K residue 314 VAL Chi-restraints excluded: chain J residue 55 THR Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 211 THR Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 273 ARG Chi-restraints excluded: chain J residue 307 VAL Chi-restraints excluded: chain J residue 331 ASP Chi-restraints excluded: chain I residue 74 GLN Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 47 CYS Chi-restraints excluded: chain H residue 53 HIS Chi-restraints excluded: chain H residue 176 ASP Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain H residue 325 ILE Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 42 MET Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 213 GLU Chi-restraints excluded: chain G residue 271 GLU Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 292 MET Chi-restraints excluded: chain g residue 282 LEU Chi-restraints excluded: chain g residue 334 LEU Chi-restraints excluded: chain h residue 8 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain C residue 31 ARG Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain c residue 15 ILE Chi-restraints excluded: chain c residue 41 ILE Chi-restraints excluded: chain c residue 58 THR Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 84 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 123 optimal weight: 1.9990 chunk 198 optimal weight: 6.9990 chunk 155 optimal weight: 9.9990 chunk 125 optimal weight: 10.0000 chunk 247 optimal weight: 9.9990 chunk 165 optimal weight: 5.9990 chunk 179 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 chunk 154 optimal weight: 10.0000 chunk 297 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 124 GLN H 113 ASN D 7 ASN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 126 HIS ** 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 = 0.3627 r_free = 0.3627 target = 0.088946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.082164 restraints weight = 82473.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.083871 restraints weight = 44015.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.085038 restraints weight = 27368.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.085835 restraints weight = 18780.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.086397 restraints weight = 13762.899| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 25933 Z= 0.242 Angle : 0.702 16.237 35254 Z= 0.368 Chirality : 0.047 0.176 4208 Planarity : 0.004 0.053 4544 Dihedral : 5.586 62.091 3664 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.14 % Favored : 88.83 % Rotamer: Outliers : 5.33 % Allowed : 26.16 % Favored : 68.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.67 (0.14), residues: 3340 helix: -0.10 (0.22), residues: 555 sheet: -1.41 (0.20), residues: 650 loop : -2.50 (0.12), residues: 2135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 31 TYR 0.027 0.002 TYR J 306 PHE 0.030 0.002 PHE h 73 TRP 0.030 0.002 TRP K 229 HIS 0.007 0.002 HIS Y 191 Details of bonding type rmsd covalent geometry : bond 0.00552 (25933) covalent geometry : angle 0.70211 (35254) hydrogen bonds : bond 0.04720 ( 663) hydrogen bonds : angle 5.82994 ( 1812) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 277 time to evaluate : 0.952 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: Y 30 GLU cc_start: 0.7308 (mp0) cc_final: 0.7077 (mp0) REVERT: Y 82 GLN cc_start: 0.7146 (OUTLIER) cc_final: 0.6667 (tp40) REVERT: Y 118 PHE cc_start: 0.8553 (m-10) cc_final: 0.8169 (m-80) REVERT: Y 120 GLU cc_start: 0.7976 (tp30) cc_final: 0.7643 (tp30) REVERT: Y 182 MET cc_start: 0.7264 (mtm) cc_final: 0.6962 (mtp) REVERT: Y 321 MET cc_start: 0.7324 (mtp) cc_final: 0.6800 (mtp) REVERT: K 292 MET cc_start: 0.7743 (ptm) cc_final: 0.7430 (ttp) REVERT: K 321 MET cc_start: 0.7718 (mtt) cc_final: 0.7461 (mtp) REVERT: J 118 PHE cc_start: 0.8079 (m-80) cc_final: 0.7712 (m-80) REVERT: J 210 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7504 (mt-10) REVERT: J 233 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8962 (pp) REVERT: I 31 MET cc_start: 0.6999 (ttp) cc_final: 0.6305 (ttp) REVERT: I 44 VAL cc_start: 0.8204 (OUTLIER) cc_final: 0.7941 (m) REVERT: I 74 GLN cc_start: 0.6492 (OUTLIER) cc_final: 0.5912 (mt0) REVERT: I 120 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7328 (tp30) REVERT: H 99 LYS cc_start: 0.8080 (tptm) cc_final: 0.7225 (pttt) REVERT: H 122 MET cc_start: 0.7962 (mmm) cc_final: 0.7709 (mmm) REVERT: H 143 MET cc_start: 0.7558 (tpt) cc_final: 0.6412 (mtt) REVERT: H 193 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8601 (mt) REVERT: H 292 MET cc_start: 0.8139 (mtp) cc_final: 0.7912 (mtm) REVERT: G 36 ASN cc_start: 0.7449 (m-40) cc_final: 0.7161 (m-40) REVERT: G 213 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7759 (mm-30) REVERT: G 229 TRP cc_start: 0.7467 (t60) cc_final: 0.6846 (t60) REVERT: g 126 MET cc_start: 0.8121 (tpp) cc_final: 0.7819 (tpp) REVERT: h 10 VAL cc_start: 0.9254 (OUTLIER) cc_final: 0.9012 (m) REVERT: F 6 GLU cc_start: 0.4990 (mm-30) cc_final: 0.4079 (tp30) REVERT: D 109 VAL cc_start: 0.8892 (OUTLIER) cc_final: 0.8690 (t) REVERT: E 59 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8055 (tp) REVERT: E 93 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7589 (mp10) outliers start: 146 outliers final: 90 residues processed: 398 average time/residue: 0.1409 time to fit residues: 93.3025 Evaluate side-chains 351 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 251 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 14 VAL Chi-restraints excluded: chain Y residue 45 MET Chi-restraints excluded: chain Y residue 61 LEU Chi-restraints excluded: chain Y residue 74 GLN Chi-restraints excluded: chain Y residue 82 GLN Chi-restraints excluded: chain Y residue 90 LEU Chi-restraints excluded: chain Y residue 211 THR Chi-restraints excluded: chain Y residue 237 ASP Chi-restraints excluded: chain Y residue 274 VAL Chi-restraints excluded: chain Y residue 310 THR Chi-restraints excluded: chain Y residue 333 ILE Chi-restraints excluded: chain Y residue 336 THR Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 77 LYS Chi-restraints excluded: chain K residue 233 LEU Chi-restraints excluded: chain K residue 246 ASN Chi-restraints excluded: chain K residue 284 CYS Chi-restraints excluded: chain K residue 314 VAL Chi-restraints excluded: chain J residue 55 THR Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 138 ASP Chi-restraints excluded: chain J residue 211 THR Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain J residue 256 THR Chi-restraints excluded: chain J residue 273 ARG Chi-restraints excluded: chain J residue 301 SER Chi-restraints excluded: chain J residue 307 VAL Chi-restraints excluded: chain J residue 331 ASP Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 74 GLN Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain I residue 176 ASP Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain H residue 47 CYS Chi-restraints excluded: chain H residue 53 HIS Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 158 LEU Chi-restraints excluded: chain H residue 176 ASP Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain H residue 222 VAL Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 325 ILE Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 176 ASP Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 213 GLU Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 292 MET Chi-restraints excluded: chain G residue 309 LEU Chi-restraints excluded: chain G residue 343 VAL Chi-restraints excluded: chain g residue 44 VAL Chi-restraints excluded: chain g residue 45 MET Chi-restraints excluded: chain g residue 65 THR Chi-restraints excluded: chain g residue 79 THR Chi-restraints excluded: chain g residue 242 VAL Chi-restraints excluded: chain g residue 334 LEU Chi-restraints excluded: chain h residue 8 THR Chi-restraints excluded: chain h residue 10 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 31 ARG Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain c residue 33 ILE Chi-restraints excluded: chain c residue 41 ILE Chi-restraints excluded: chain c residue 93 GLN Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 93 GLN Chi-restraints excluded: chain E residue 123 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 296 optimal weight: 20.0000 chunk 28 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 4 optimal weight: 8.9990 chunk 281 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 19 optimal weight: 0.0070 chunk 299 optimal weight: 2.9990 chunk 203 optimal weight: 8.9990 chunk 286 optimal weight: 20.0000 overall best weight: 3.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 166 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.090341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.083505 restraints weight = 81273.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.085229 restraints weight = 43535.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.086387 restraints weight = 27162.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.087193 restraints weight = 18715.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.087768 restraints weight = 13735.613| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 25933 Z= 0.175 Angle : 0.639 14.430 35254 Z= 0.333 Chirality : 0.045 0.204 4208 Planarity : 0.004 0.053 4544 Dihedral : 5.415 62.668 3664 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.27 % Favored : 89.73 % Rotamer: Outliers : 5.22 % Allowed : 26.38 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.54 (0.14), residues: 3340 helix: 0.11 (0.23), residues: 541 sheet: -1.32 (0.20), residues: 649 loop : -2.44 (0.13), residues: 2150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 188 TYR 0.018 0.002 TYR g 70 PHE 0.030 0.002 PHE h 73 TRP 0.027 0.002 TRP K 229 HIS 0.005 0.001 HIS Y 191 Details of bonding type rmsd covalent geometry : bond 0.00400 (25933) covalent geometry : angle 0.63934 (35254) hydrogen bonds : bond 0.04142 ( 663) hydrogen bonds : angle 5.54112 ( 1812) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 273 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 42 MET cc_start: 0.7711 (ttm) cc_final: 0.6925 (mtp) REVERT: Y 82 GLN cc_start: 0.7244 (OUTLIER) cc_final: 0.6901 (tp40) REVERT: Y 118 PHE cc_start: 0.8504 (m-10) cc_final: 0.8162 (m-80) REVERT: Y 120 GLU cc_start: 0.7959 (tp30) cc_final: 0.7620 (tp30) REVERT: Y 182 MET cc_start: 0.7170 (mtm) cc_final: 0.6950 (mtp) REVERT: Y 321 MET cc_start: 0.7221 (mtp) cc_final: 0.6703 (mtp) REVERT: K 292 MET cc_start: 0.7733 (ptm) cc_final: 0.7414 (ttp) REVERT: K 321 MET cc_start: 0.7633 (mtt) cc_final: 0.7375 (mtp) REVERT: K 337 GLU cc_start: 0.5664 (OUTLIER) cc_final: 0.5152 (pm20) REVERT: J 118 PHE cc_start: 0.8068 (m-80) cc_final: 0.7758 (m-80) REVERT: J 233 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8918 (pp) REVERT: I 31 MET cc_start: 0.6969 (ttp) cc_final: 0.6244 (ttp) REVERT: I 74 GLN cc_start: 0.7384 (OUTLIER) cc_final: 0.6732 (mt0) REVERT: I 120 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7161 (tp30) REVERT: I 182 MET cc_start: 0.8354 (mtp) cc_final: 0.7676 (ttm) REVERT: H 99 LYS cc_start: 0.7951 (tptm) cc_final: 0.7080 (pttt) REVERT: H 122 MET cc_start: 0.7950 (mmm) cc_final: 0.7744 (mmm) REVERT: H 143 MET cc_start: 0.7363 (tpt) cc_final: 0.6234 (mtt) REVERT: H 193 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8355 (mt) REVERT: H 292 MET cc_start: 0.8056 (mtp) cc_final: 0.7807 (mtm) REVERT: G 213 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7731 (mm-30) REVERT: G 229 TRP cc_start: 0.7362 (t60) cc_final: 0.6786 (t60) REVERT: G 271 GLU cc_start: 0.5562 (OUTLIER) cc_final: 0.5345 (tt0) REVERT: g 120 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7452 (tp30) REVERT: C 1 MET cc_start: 0.8032 (mmt) cc_final: 0.7644 (mmm) REVERT: c 6 GLU cc_start: 0.4601 (mp0) cc_final: 0.3079 (tp30) REVERT: D 79 VAL cc_start: 0.8277 (OUTLIER) cc_final: 0.8064 (p) REVERT: A 1 MET cc_start: 0.6022 (ptp) cc_final: 0.5101 (mmt) REVERT: A 66 ASN cc_start: 0.8352 (OUTLIER) cc_final: 0.8038 (p0) REVERT: E 59 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7890 (tp) REVERT: E 93 GLN cc_start: 0.7971 (OUTLIER) cc_final: 0.7050 (mp10) REVERT: E 94 TYR cc_start: 0.7830 (m-80) cc_final: 0.7391 (m-80) outliers start: 143 outliers final: 96 residues processed: 388 average time/residue: 0.1389 time to fit residues: 90.4664 Evaluate side-chains 363 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 256 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 14 VAL Chi-restraints excluded: chain Y residue 82 GLN Chi-restraints excluded: chain Y residue 90 LEU Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Y residue 175 SER Chi-restraints excluded: chain Y residue 237 ASP Chi-restraints excluded: chain Y residue 274 VAL Chi-restraints excluded: chain Y residue 310 THR Chi-restraints excluded: chain Y residue 333 ILE Chi-restraints excluded: chain Y residue 336 THR Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 219 VAL Chi-restraints excluded: chain K residue 233 LEU Chi-restraints excluded: chain K residue 246 ASN Chi-restraints excluded: chain K residue 284 CYS Chi-restraints excluded: chain K residue 314 VAL Chi-restraints excluded: chain K residue 337 GLU Chi-restraints excluded: chain J residue 31 MET Chi-restraints excluded: chain J residue 45 MET Chi-restraints excluded: chain J residue 55 THR Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 138 ASP Chi-restraints excluded: chain J residue 211 THR Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain J residue 256 THR Chi-restraints excluded: chain J residue 273 ARG Chi-restraints excluded: chain J residue 301 SER Chi-restraints excluded: chain J residue 307 VAL Chi-restraints excluded: chain J residue 331 ASP Chi-restraints excluded: chain I residue 74 GLN Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain I residue 176 ASP Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain I residue 234 THR Chi-restraints excluded: chain I residue 310 THR Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 47 CYS Chi-restraints excluded: chain H residue 53 HIS Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 158 LEU Chi-restraints excluded: chain H residue 176 ASP Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain H residue 222 VAL Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 309 LEU Chi-restraints excluded: chain H residue 325 ILE Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 213 GLU Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain G residue 271 GLU Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 292 MET Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 343 VAL Chi-restraints excluded: chain g residue 42 MET Chi-restraints excluded: chain g residue 65 THR Chi-restraints excluded: chain g residue 79 THR Chi-restraints excluded: chain g residue 242 VAL Chi-restraints excluded: chain g residue 334 LEU Chi-restraints excluded: chain h residue 8 THR Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain C residue 31 ARG Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain c residue 33 ILE Chi-restraints excluded: chain c residue 41 ILE Chi-restraints excluded: chain c residue 92 VAL Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 93 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 136 optimal weight: 4.9990 chunk 147 optimal weight: 9.9990 chunk 88 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 chunk 319 optimal weight: 6.9990 chunk 201 optimal weight: 0.0570 chunk 142 optimal weight: 0.0670 chunk 229 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 255 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 overall best weight: 2.8242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.090429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.083662 restraints weight = 80814.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.085379 restraints weight = 43178.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.086539 restraints weight = 26866.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.087335 restraints weight = 18404.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.087881 restraints weight = 13498.759| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 25933 Z= 0.169 Angle : 0.629 13.892 35254 Z= 0.328 Chirality : 0.045 0.185 4208 Planarity : 0.004 0.053 4544 Dihedral : 5.365 62.699 3664 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.78 % Favored : 89.22 % Rotamer: Outliers : 5.76 % Allowed : 26.49 % Favored : 67.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.51 (0.14), residues: 3340 helix: 0.09 (0.23), residues: 547 sheet: -1.28 (0.20), residues: 657 loop : -2.41 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 31 TYR 0.017 0.002 TYR J 306 PHE 0.029 0.002 PHE h 73 TRP 0.039 0.002 TRP K 229 HIS 0.004 0.001 HIS A 126 Details of bonding type rmsd covalent geometry : bond 0.00383 (25933) covalent geometry : angle 0.62882 (35254) hydrogen bonds : bond 0.04028 ( 663) hydrogen bonds : angle 5.48337 ( 1812) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 269 time to evaluate : 0.943 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: Y 82 GLN cc_start: 0.7226 (OUTLIER) cc_final: 0.6882 (tp40) REVERT: Y 118 PHE cc_start: 0.8512 (m-10) cc_final: 0.8166 (m-80) REVERT: Y 120 GLU cc_start: 0.7924 (tp30) cc_final: 0.7582 (tp30) REVERT: Y 321 MET cc_start: 0.7207 (mtp) cc_final: 0.6738 (mtp) REVERT: K 126 MET cc_start: 0.8047 (mtp) cc_final: 0.7836 (mtp) REVERT: K 292 MET cc_start: 0.7643 (ptm) cc_final: 0.7342 (ttp) REVERT: K 321 MET cc_start: 0.7611 (mtt) cc_final: 0.7138 (mtp) REVERT: K 337 GLU cc_start: 0.5634 (OUTLIER) cc_final: 0.5385 (pm20) REVERT: J 233 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8929 (pp) REVERT: I 31 MET cc_start: 0.6965 (ttp) cc_final: 0.6243 (ttp) REVERT: I 74 GLN cc_start: 0.7373 (OUTLIER) cc_final: 0.6709 (mt0) REVERT: I 120 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7000 (tp30) REVERT: I 182 MET cc_start: 0.8409 (mtp) cc_final: 0.7817 (ttm) REVERT: I 312 MET cc_start: 0.7346 (ptp) cc_final: 0.7055 (ttp) REVERT: H 99 LYS cc_start: 0.8024 (tptm) cc_final: 0.7092 (pttt) REVERT: H 143 MET cc_start: 0.7385 (tpt) cc_final: 0.6333 (mtt) REVERT: H 193 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8370 (mt) REVERT: H 292 MET cc_start: 0.8154 (mtp) cc_final: 0.7901 (mtm) REVERT: G 213 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7696 (mm-30) REVERT: G 229 TRP cc_start: 0.7346 (t60) cc_final: 0.6758 (t60) REVERT: g 120 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7358 (tp30) REVERT: h 10 VAL cc_start: 0.9210 (OUTLIER) cc_final: 0.8955 (m) REVERT: C 43 ILE cc_start: 0.8777 (mp) cc_final: 0.8438 (tt) REVERT: C 127 GLN cc_start: 0.6683 (OUTLIER) cc_final: 0.6402 (tm-30) REVERT: c 6 GLU cc_start: 0.4441 (mp0) cc_final: 0.3256 (tp30) REVERT: c 119 THR cc_start: 0.8197 (OUTLIER) cc_final: 0.7837 (m) REVERT: D 79 VAL cc_start: 0.8333 (OUTLIER) cc_final: 0.8125 (p) REVERT: A 1 MET cc_start: 0.6181 (ptp) cc_final: 0.5008 (mmp) REVERT: A 66 ASN cc_start: 0.8316 (OUTLIER) cc_final: 0.8013 (p0) REVERT: E 59 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8106 (tp) REVERT: E 93 GLN cc_start: 0.7952 (OUTLIER) cc_final: 0.7023 (mp10) outliers start: 158 outliers final: 113 residues processed: 398 average time/residue: 0.1391 time to fit residues: 92.9977 Evaluate side-chains 378 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 252 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 14 VAL Chi-restraints excluded: chain Y residue 25 THR Chi-restraints excluded: chain Y residue 27 GLU Chi-restraints excluded: chain Y residue 45 MET Chi-restraints excluded: chain Y residue 61 LEU Chi-restraints excluded: chain Y residue 74 GLN Chi-restraints excluded: chain Y residue 82 GLN Chi-restraints excluded: chain Y residue 90 LEU Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Y residue 237 ASP Chi-restraints excluded: chain Y residue 274 VAL Chi-restraints excluded: chain Y residue 310 THR Chi-restraints excluded: chain Y residue 333 ILE Chi-restraints excluded: chain Y residue 336 THR Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 219 VAL Chi-restraints excluded: chain K residue 246 ASN Chi-restraints excluded: chain K residue 284 CYS Chi-restraints excluded: chain K residue 309 LEU Chi-restraints excluded: chain K residue 314 VAL Chi-restraints excluded: chain K residue 337 GLU Chi-restraints excluded: chain J residue 31 MET Chi-restraints excluded: chain J residue 45 MET Chi-restraints excluded: chain J residue 55 THR Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 138 ASP Chi-restraints excluded: chain J residue 211 THR Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain J residue 256 THR Chi-restraints excluded: chain J residue 259 ILE Chi-restraints excluded: chain J residue 273 ARG Chi-restraints excluded: chain J residue 301 SER Chi-restraints excluded: chain J residue 307 VAL Chi-restraints excluded: chain J residue 331 ASP Chi-restraints excluded: chain J residue 336 THR Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 74 GLN Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain I residue 176 ASP Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain I residue 234 THR Chi-restraints excluded: chain I residue 310 THR Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 47 CYS Chi-restraints excluded: chain H residue 53 HIS Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 158 LEU Chi-restraints excluded: chain H residue 176 ASP Chi-restraints excluded: chain H residue 179 SER Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain H residue 222 VAL Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain H residue 309 LEU Chi-restraints excluded: chain H residue 325 ILE Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 95 GLU Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 213 GLU Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 292 MET Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 309 LEU Chi-restraints excluded: chain G residue 343 VAL Chi-restraints excluded: chain g residue 45 MET Chi-restraints excluded: chain g residue 65 THR Chi-restraints excluded: chain g residue 79 THR Chi-restraints excluded: chain g residue 122 MET Chi-restraints excluded: chain g residue 242 VAL Chi-restraints excluded: chain g residue 282 LEU Chi-restraints excluded: chain g residue 334 LEU Chi-restraints excluded: chain h residue 8 THR Chi-restraints excluded: chain h residue 10 VAL Chi-restraints excluded: chain h residue 39 SER Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 127 GLN Chi-restraints excluded: chain c residue 1 MET Chi-restraints excluded: chain c residue 33 ILE Chi-restraints excluded: chain c residue 41 ILE Chi-restraints excluded: chain c residue 92 VAL Chi-restraints excluded: chain c residue 93 GLN Chi-restraints excluded: chain c residue 119 THR Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 93 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 106 optimal weight: 8.9990 chunk 14 optimal weight: 0.8980 chunk 261 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 117 optimal weight: 7.9990 chunk 78 optimal weight: 0.0370 chunk 197 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 37 optimal weight: 0.0770 chunk 278 optimal weight: 5.9990 chunk 143 optimal weight: 10.0000 overall best weight: 1.1818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 GLN B 127 GLN c 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.092669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.085883 restraints weight = 80612.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.087638 restraints weight = 42656.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.088818 restraints weight = 26348.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.089632 restraints weight = 17935.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.090206 restraints weight = 12994.491| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 25933 Z= 0.115 Angle : 0.588 12.447 35254 Z= 0.304 Chirality : 0.043 0.196 4208 Planarity : 0.003 0.050 4544 Dihedral : 5.019 64.777 3660 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 4.85 % Allowed : 27.58 % Favored : 67.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.14), residues: 3340 helix: 0.40 (0.23), residues: 547 sheet: -1.10 (0.21), residues: 652 loop : -2.29 (0.13), residues: 2141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 31 TYR 0.022 0.001 TYR E 94 PHE 0.027 0.001 PHE h 73 TRP 0.035 0.001 TRP K 229 HIS 0.004 0.001 HIS J 191 Details of bonding type rmsd covalent geometry : bond 0.00256 (25933) covalent geometry : angle 0.58785 (35254) hydrogen bonds : bond 0.03524 ( 663) hydrogen bonds : angle 5.19334 ( 1812) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 280 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 42 MET cc_start: 0.7580 (ttm) cc_final: 0.6785 (mtp) REVERT: Y 118 PHE cc_start: 0.8483 (m-10) cc_final: 0.8165 (m-80) REVERT: Y 120 GLU cc_start: 0.7939 (tp30) cc_final: 0.7670 (tp30) REVERT: Y 181 TRP cc_start: 0.7436 (m100) cc_final: 0.6256 (m100) REVERT: Y 321 MET cc_start: 0.7592 (mtp) cc_final: 0.7062 (mtp) REVERT: K 292 MET cc_start: 0.7574 (ptm) cc_final: 0.7182 (ttp) REVERT: K 321 MET cc_start: 0.7527 (mtt) cc_final: 0.7129 (mtp) REVERT: K 337 GLU cc_start: 0.5963 (OUTLIER) cc_final: 0.5342 (pm20) REVERT: J 189 THR cc_start: 0.8478 (p) cc_final: 0.7767 (t) REVERT: J 233 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8956 (pp) REVERT: I 31 MET cc_start: 0.6944 (ttp) cc_final: 0.6244 (ttp) REVERT: I 74 GLN cc_start: 0.7190 (OUTLIER) cc_final: 0.6525 (mt0) REVERT: I 98 GLU cc_start: 0.7873 (tt0) cc_final: 0.7604 (tp30) REVERT: I 120 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7000 (tp30) REVERT: I 312 MET cc_start: 0.7326 (ptp) cc_final: 0.7032 (ttp) REVERT: H 99 LYS cc_start: 0.7976 (tptm) cc_final: 0.7054 (pttt) REVERT: H 122 MET cc_start: 0.7885 (mmm) cc_final: 0.7491 (mmm) REVERT: H 143 MET cc_start: 0.7230 (tpt) cc_final: 0.6211 (mtt) REVERT: H 193 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8341 (mt) REVERT: H 292 MET cc_start: 0.8129 (mtp) cc_final: 0.7890 (mtm) REVERT: G 31 MET cc_start: 0.4825 (ptm) cc_final: 0.4620 (ptp) REVERT: G 213 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7634 (mm-30) REVERT: G 229 TRP cc_start: 0.7201 (t60) cc_final: 0.6681 (t60) REVERT: g 120 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7185 (tp30) REVERT: h 39 SER cc_start: 0.9026 (p) cc_final: 0.8584 (p) REVERT: C 1 MET cc_start: 0.7932 (mmt) cc_final: 0.7334 (mmm) REVERT: C 43 ILE cc_start: 0.8722 (mp) cc_final: 0.8438 (tt) REVERT: c 6 GLU cc_start: 0.4898 (mp0) cc_final: 0.3601 (tp30) REVERT: c 58 THR cc_start: 0.7248 (OUTLIER) cc_final: 0.7012 (m) REVERT: c 119 THR cc_start: 0.8067 (OUTLIER) cc_final: 0.7636 (m) REVERT: c 124 MET cc_start: 0.8046 (tpp) cc_final: 0.7625 (tpp) REVERT: F 63 GLU cc_start: 0.5365 (pm20) cc_final: 0.5060 (pm20) REVERT: A 1 MET cc_start: 0.6008 (ptp) cc_final: 0.5103 (mmp) REVERT: A 4 ASP cc_start: 0.7329 (t0) cc_final: 0.6889 (t0) REVERT: E 59 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8036 (tp) REVERT: E 84 LEU cc_start: 0.7093 (OUTLIER) cc_final: 0.6611 (mp) REVERT: E 93 GLN cc_start: 0.7784 (OUTLIER) cc_final: 0.6990 (mp10) outliers start: 133 outliers final: 90 residues processed: 391 average time/residue: 0.1368 time to fit residues: 90.5461 Evaluate side-chains 359 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 259 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 14 VAL Chi-restraints excluded: chain Y residue 27 GLU Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain Y residue 61 LEU Chi-restraints excluded: chain Y residue 90 LEU Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Y residue 175 SER Chi-restraints excluded: chain Y residue 211 THR Chi-restraints excluded: chain Y residue 237 ASP Chi-restraints excluded: chain Y residue 333 ILE Chi-restraints excluded: chain Y residue 336 THR Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 193 LEU Chi-restraints excluded: chain K residue 233 LEU Chi-restraints excluded: chain K residue 309 LEU Chi-restraints excluded: chain K residue 314 VAL Chi-restraints excluded: chain K residue 337 GLU Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 31 MET Chi-restraints excluded: chain J residue 45 MET Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 138 ASP Chi-restraints excluded: chain J residue 211 THR Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain J residue 259 ILE Chi-restraints excluded: chain J residue 273 ARG Chi-restraints excluded: chain J residue 307 VAL Chi-restraints excluded: chain J residue 331 ASP Chi-restraints excluded: chain J residue 336 THR Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 74 GLN Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain I residue 234 THR Chi-restraints excluded: chain I residue 310 THR Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 53 HIS Chi-restraints excluded: chain H residue 158 LEU Chi-restraints excluded: chain H residue 176 ASP Chi-restraints excluded: chain H residue 179 SER Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain H residue 309 LEU Chi-restraints excluded: chain H residue 325 ILE Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 213 GLU Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain g residue 44 VAL Chi-restraints excluded: chain g residue 65 THR Chi-restraints excluded: chain g residue 79 THR Chi-restraints excluded: chain g residue 122 MET Chi-restraints excluded: chain g residue 242 VAL Chi-restraints excluded: chain g residue 334 LEU Chi-restraints excluded: chain h residue 8 THR Chi-restraints excluded: chain h residue 10 VAL Chi-restraints excluded: chain h residue 31 SER Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain c residue 1 MET Chi-restraints excluded: chain c residue 58 THR Chi-restraints excluded: chain c residue 92 VAL Chi-restraints excluded: chain c residue 93 GLN Chi-restraints excluded: chain c residue 119 THR Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 93 GLN Chi-restraints excluded: chain E residue 114 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 140 optimal weight: 0.9980 chunk 321 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 chunk 74 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 36 optimal weight: 0.3980 chunk 102 optimal weight: 4.9990 chunk 5 optimal weight: 8.9990 chunk 171 optimal weight: 7.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 191 HIS ** D 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 44 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.092827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.086087 restraints weight = 80512.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.087828 restraints weight = 42503.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.089007 restraints weight = 26202.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.089765 restraints weight = 17830.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.090344 restraints weight = 13141.712| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25933 Z= 0.118 Angle : 0.589 12.019 35254 Z= 0.305 Chirality : 0.044 0.235 4208 Planarity : 0.004 0.050 4544 Dihedral : 4.954 65.401 3660 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.34 % Favored : 90.66 % Rotamer: Outliers : 4.56 % Allowed : 27.98 % Favored : 67.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.14), residues: 3340 helix: 0.45 (0.23), residues: 550 sheet: -1.03 (0.20), residues: 665 loop : -2.24 (0.13), residues: 2125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 101 TYR 0.021 0.001 TYR C 94 PHE 0.027 0.001 PHE h 73 TRP 0.031 0.001 TRP K 229 HIS 0.004 0.001 HIS J 191 Details of bonding type rmsd covalent geometry : bond 0.00266 (25933) covalent geometry : angle 0.58868 (35254) hydrogen bonds : bond 0.03474 ( 663) hydrogen bonds : angle 5.15252 ( 1812) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 279 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 118 PHE cc_start: 0.8477 (m-10) cc_final: 0.8113 (m-80) REVERT: Y 120 GLU cc_start: 0.7955 (tp30) cc_final: 0.7666 (tp30) REVERT: Y 181 TRP cc_start: 0.7505 (m100) cc_final: 0.6187 (m100) REVERT: Y 321 MET cc_start: 0.7341 (mtp) cc_final: 0.6841 (mtp) REVERT: K 292 MET cc_start: 0.7563 (ptm) cc_final: 0.7148 (ttp) REVERT: K 321 MET cc_start: 0.7497 (mtt) cc_final: 0.7138 (mtp) REVERT: K 337 GLU cc_start: 0.5938 (OUTLIER) cc_final: 0.5331 (pm20) REVERT: J 189 THR cc_start: 0.8489 (p) cc_final: 0.7768 (t) REVERT: I 31 MET cc_start: 0.6932 (ttp) cc_final: 0.6241 (ttp) REVERT: I 74 GLN cc_start: 0.7218 (OUTLIER) cc_final: 0.6514 (mt0) REVERT: I 120 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7017 (tp30) REVERT: I 182 MET cc_start: 0.8058 (mtp) cc_final: 0.7850 (mtp) REVERT: I 312 MET cc_start: 0.7335 (ptp) cc_final: 0.7047 (ttp) REVERT: H 57 ILE cc_start: 0.7534 (mm) cc_final: 0.7322 (tp) REVERT: H 99 LYS cc_start: 0.7975 (tptm) cc_final: 0.7135 (pttt) REVERT: H 122 MET cc_start: 0.7782 (mmm) cc_final: 0.7377 (mmm) REVERT: H 143 MET cc_start: 0.7158 (tpt) cc_final: 0.6239 (mtt) REVERT: H 193 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8347 (mt) REVERT: H 292 MET cc_start: 0.8137 (mtp) cc_final: 0.7904 (mtm) REVERT: G 95 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7207 (pt0) REVERT: G 229 TRP cc_start: 0.7192 (t60) cc_final: 0.6694 (t60) REVERT: g 120 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7172 (tp30) REVERT: h 6 ILE cc_start: 0.8557 (OUTLIER) cc_final: 0.8295 (mm) REVERT: h 39 SER cc_start: 0.9127 (p) cc_final: 0.8704 (p) REVERT: C 1 MET cc_start: 0.7895 (mmt) cc_final: 0.7430 (mmm) REVERT: C 43 ILE cc_start: 0.8766 (mp) cc_final: 0.8426 (tt) REVERT: C 127 GLN cc_start: 0.6651 (OUTLIER) cc_final: 0.6366 (tm-30) REVERT: c 6 GLU cc_start: 0.4804 (mp0) cc_final: 0.3626 (tp30) REVERT: c 58 THR cc_start: 0.7279 (OUTLIER) cc_final: 0.7042 (m) REVERT: c 119 THR cc_start: 0.8049 (OUTLIER) cc_final: 0.7609 (m) REVERT: c 124 MET cc_start: 0.8050 (tpp) cc_final: 0.7643 (tpp) REVERT: D 1 MET cc_start: 0.5723 (mtm) cc_final: 0.5304 (mtm) REVERT: A 1 MET cc_start: 0.6045 (ptp) cc_final: 0.5078 (mmp) REVERT: E 59 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.7970 (tp) REVERT: E 84 LEU cc_start: 0.7081 (OUTLIER) cc_final: 0.6637 (mp) REVERT: E 93 GLN cc_start: 0.7947 (OUTLIER) cc_final: 0.7255 (mp10) outliers start: 125 outliers final: 97 residues processed: 380 average time/residue: 0.1383 time to fit residues: 88.8924 Evaluate side-chains 372 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 264 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 14 VAL Chi-restraints excluded: chain Y residue 27 GLU Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain Y residue 61 LEU Chi-restraints excluded: chain Y residue 74 GLN Chi-restraints excluded: chain Y residue 90 LEU Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Y residue 175 SER Chi-restraints excluded: chain Y residue 211 THR Chi-restraints excluded: chain Y residue 237 ASP Chi-restraints excluded: chain Y residue 333 ILE Chi-restraints excluded: chain Y residue 336 THR Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 193 LEU Chi-restraints excluded: chain K residue 219 VAL Chi-restraints excluded: chain K residue 233 LEU Chi-restraints excluded: chain K residue 309 LEU Chi-restraints excluded: chain K residue 314 VAL Chi-restraints excluded: chain K residue 337 GLU Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 45 MET Chi-restraints excluded: chain J residue 55 THR Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 138 ASP Chi-restraints excluded: chain J residue 211 THR Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 273 ARG Chi-restraints excluded: chain J residue 307 VAL Chi-restraints excluded: chain J residue 331 ASP Chi-restraints excluded: chain J residue 336 THR Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 74 GLN Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain I residue 234 THR Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 310 THR Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 53 HIS Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 158 LEU Chi-restraints excluded: chain H residue 176 ASP Chi-restraints excluded: chain H residue 179 SER Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 273 ARG Chi-restraints excluded: chain H residue 309 LEU Chi-restraints excluded: chain H residue 325 ILE Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 95 GLU Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain g residue 44 VAL Chi-restraints excluded: chain g residue 65 THR Chi-restraints excluded: chain g residue 79 THR Chi-restraints excluded: chain g residue 122 MET Chi-restraints excluded: chain g residue 242 VAL Chi-restraints excluded: chain g residue 282 LEU Chi-restraints excluded: chain g residue 334 LEU Chi-restraints excluded: chain h residue 6 ILE Chi-restraints excluded: chain h residue 8 THR Chi-restraints excluded: chain h residue 10 VAL Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 127 GLN Chi-restraints excluded: chain c residue 1 MET Chi-restraints excluded: chain c residue 58 THR Chi-restraints excluded: chain c residue 93 GLN Chi-restraints excluded: chain c residue 119 THR Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 93 GLN Chi-restraints excluded: chain E residue 114 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 316 optimal weight: 10.0000 chunk 302 optimal weight: 6.9990 chunk 172 optimal weight: 10.0000 chunk 227 optimal weight: 0.0030 chunk 230 optimal weight: 0.2980 chunk 293 optimal weight: 7.9990 chunk 118 optimal weight: 3.9990 chunk 312 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 overall best weight: 3.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.090504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.083704 restraints weight = 81728.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.085403 restraints weight = 43805.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.086562 restraints weight = 27396.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.087366 restraints weight = 18839.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.087931 restraints weight = 13853.029| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 25933 Z= 0.202 Angle : 0.660 13.274 35254 Z= 0.342 Chirality : 0.045 0.229 4208 Planarity : 0.004 0.051 4544 Dihedral : 5.270 63.466 3660 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.32 % Favored : 88.68 % Rotamer: Outliers : 5.29 % Allowed : 27.36 % Favored : 67.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.14), residues: 3340 helix: 0.18 (0.23), residues: 549 sheet: -1.19 (0.21), residues: 633 loop : -2.30 (0.13), residues: 2158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 31 TYR 0.029 0.002 TYR C 94 PHE 0.028 0.002 PHE h 73 TRP 0.077 0.003 TRP H 181 HIS 0.005 0.001 HIS A 126 Details of bonding type rmsd covalent geometry : bond 0.00461 (25933) covalent geometry : angle 0.66021 (35254) hydrogen bonds : bond 0.04062 ( 663) hydrogen bonds : angle 5.39191 ( 1812) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 267 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 27 GLU cc_start: 0.6780 (OUTLIER) cc_final: 0.6374 (pm20) REVERT: Y 118 PHE cc_start: 0.8595 (m-10) cc_final: 0.8234 (m-80) REVERT: Y 120 GLU cc_start: 0.7997 (tp30) cc_final: 0.7611 (tp30) REVERT: Y 321 MET cc_start: 0.7544 (mtp) cc_final: 0.7093 (mtp) REVERT: K 292 MET cc_start: 0.7630 (ptm) cc_final: 0.7373 (ttp) REVERT: K 321 MET cc_start: 0.7656 (mtt) cc_final: 0.7234 (mtp) REVERT: K 337 GLU cc_start: 0.5678 (OUTLIER) cc_final: 0.5071 (pm20) REVERT: J 210 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7714 (pt0) REVERT: J 233 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8917 (pp) REVERT: I 31 MET cc_start: 0.7027 (ttp) cc_final: 0.6354 (ttp) REVERT: I 74 GLN cc_start: 0.6185 (OUTLIER) cc_final: 0.5565 (mt0) REVERT: I 98 GLU cc_start: 0.7964 (tt0) cc_final: 0.7732 (tp30) REVERT: I 120 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7010 (tp30) REVERT: H 99 LYS cc_start: 0.8108 (tptm) cc_final: 0.7199 (pttt) REVERT: H 122 MET cc_start: 0.7841 (mmm) cc_final: 0.7455 (mmm) REVERT: H 143 MET cc_start: 0.6787 (tpt) cc_final: 0.6176 (mtt) REVERT: H 193 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8342 (mt) REVERT: H 292 MET cc_start: 0.8227 (mtp) cc_final: 0.7982 (mtm) REVERT: G 31 MET cc_start: 0.5271 (ptm) cc_final: 0.4980 (ptp) REVERT: G 95 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7427 (pt0) REVERT: g 120 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7343 (tp30) REVERT: h 6 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.8402 (mm) REVERT: h 10 VAL cc_start: 0.9313 (OUTLIER) cc_final: 0.9100 (m) REVERT: h 39 SER cc_start: 0.9045 (OUTLIER) cc_final: 0.8628 (p) REVERT: C 1 MET cc_start: 0.8016 (mmt) cc_final: 0.7461 (mmm) REVERT: C 13 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7786 (tt0) REVERT: c 6 GLU cc_start: 0.4615 (mp0) cc_final: 0.3281 (tp30) REVERT: c 58 THR cc_start: 0.7465 (OUTLIER) cc_final: 0.7261 (m) REVERT: c 119 THR cc_start: 0.8221 (OUTLIER) cc_final: 0.7847 (m) REVERT: c 124 MET cc_start: 0.8060 (tpp) cc_final: 0.7650 (tpp) REVERT: D 79 VAL cc_start: 0.8500 (OUTLIER) cc_final: 0.8273 (p) REVERT: A 1 MET cc_start: 0.6363 (ptp) cc_final: 0.4976 (mmt) REVERT: E 59 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7965 (tp) REVERT: E 93 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7348 (mp10) REVERT: E 124 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.7841 (ttm) outliers start: 145 outliers final: 109 residues processed: 387 average time/residue: 0.1384 time to fit residues: 90.9270 Evaluate side-chains 378 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 253 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 14 VAL Chi-restraints excluded: chain Y residue 27 GLU Chi-restraints excluded: chain Y residue 45 MET Chi-restraints excluded: chain Y residue 74 GLN Chi-restraints excluded: chain Y residue 90 LEU Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Y residue 175 SER Chi-restraints excluded: chain Y residue 211 THR Chi-restraints excluded: chain Y residue 231 LEU Chi-restraints excluded: chain Y residue 237 ASP Chi-restraints excluded: chain Y residue 310 THR Chi-restraints excluded: chain Y residue 333 ILE Chi-restraints excluded: chain Y residue 336 THR Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 158 LEU Chi-restraints excluded: chain K residue 219 VAL Chi-restraints excluded: chain K residue 233 LEU Chi-restraints excluded: chain K residue 309 LEU Chi-restraints excluded: chain K residue 314 VAL Chi-restraints excluded: chain K residue 337 GLU Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 45 MET Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 138 ASP Chi-restraints excluded: chain J residue 211 THR Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain J residue 242 VAL Chi-restraints excluded: chain J residue 273 ARG Chi-restraints excluded: chain J residue 301 SER Chi-restraints excluded: chain J residue 307 VAL Chi-restraints excluded: chain J residue 331 ASP Chi-restraints excluded: chain J residue 336 THR Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 74 GLN Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain I residue 176 ASP Chi-restraints excluded: chain I residue 234 THR Chi-restraints excluded: chain I residue 310 THR Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 47 CYS Chi-restraints excluded: chain H residue 53 HIS Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 176 ASP Chi-restraints excluded: chain H residue 179 SER Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 273 ARG Chi-restraints excluded: chain H residue 309 LEU Chi-restraints excluded: chain H residue 325 ILE Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 95 GLU Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 176 ASP Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 343 VAL Chi-restraints excluded: chain g residue 42 MET Chi-restraints excluded: chain g residue 44 VAL Chi-restraints excluded: chain g residue 45 MET Chi-restraints excluded: chain g residue 65 THR Chi-restraints excluded: chain g residue 79 THR Chi-restraints excluded: chain g residue 122 MET Chi-restraints excluded: chain g residue 177 LEU Chi-restraints excluded: chain g residue 242 VAL Chi-restraints excluded: chain g residue 282 LEU Chi-restraints excluded: chain g residue 334 LEU Chi-restraints excluded: chain h residue 6 ILE Chi-restraints excluded: chain h residue 8 THR Chi-restraints excluded: chain h residue 10 VAL Chi-restraints excluded: chain h residue 39 SER Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain c residue 58 THR Chi-restraints excluded: chain c residue 92 VAL Chi-restraints excluded: chain c residue 93 GLN Chi-restraints excluded: chain c residue 112 THR Chi-restraints excluded: chain c residue 119 THR Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 93 GLN Chi-restraints excluded: chain E residue 124 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 61 optimal weight: 20.0000 chunk 103 optimal weight: 5.9990 chunk 119 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 273 optimal weight: 3.9990 chunk 282 optimal weight: 10.0000 chunk 125 optimal weight: 0.8980 chunk 179 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 59 optimal weight: 0.9990 chunk 323 optimal weight: 10.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 93 GLN ** D 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.091970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.085208 restraints weight = 81329.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.086942 restraints weight = 43162.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.088107 restraints weight = 26750.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.088872 restraints weight = 18277.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.089453 restraints weight = 13520.901| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25933 Z= 0.137 Angle : 0.617 12.554 35254 Z= 0.319 Chirality : 0.044 0.197 4208 Planarity : 0.004 0.052 4544 Dihedral : 5.121 64.726 3660 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.58 % Favored : 90.42 % Rotamer: Outliers : 4.60 % Allowed : 27.95 % Favored : 67.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.14), residues: 3340 helix: 0.33 (0.23), residues: 549 sheet: -1.12 (0.20), residues: 642 loop : -2.24 (0.13), residues: 2149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 273 TYR 0.020 0.001 TYR C 94 PHE 0.026 0.001 PHE h 73 TRP 0.061 0.002 TRP H 181 HIS 0.004 0.001 HIS A 126 Details of bonding type rmsd covalent geometry : bond 0.00312 (25933) covalent geometry : angle 0.61674 (35254) hydrogen bonds : bond 0.03672 ( 663) hydrogen bonds : angle 5.26260 ( 1812) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 262 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 27 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.6691 (pm20) REVERT: Y 118 PHE cc_start: 0.8532 (m-10) cc_final: 0.8187 (m-80) REVERT: Y 120 GLU cc_start: 0.7981 (tp30) cc_final: 0.7661 (tp30) REVERT: Y 321 MET cc_start: 0.7440 (mtp) cc_final: 0.6991 (mtp) REVERT: K 292 MET cc_start: 0.7590 (ptm) cc_final: 0.7254 (ttp) REVERT: K 321 MET cc_start: 0.7562 (mtt) cc_final: 0.7197 (mtp) REVERT: K 337 GLU cc_start: 0.5566 (OUTLIER) cc_final: 0.5018 (pm20) REVERT: J 189 THR cc_start: 0.8428 (p) cc_final: 0.7806 (t) REVERT: J 233 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8950 (pp) REVERT: I 31 MET cc_start: 0.6870 (ttp) cc_final: 0.6176 (ttp) REVERT: I 74 GLN cc_start: 0.7238 (OUTLIER) cc_final: 0.6523 (mt0) REVERT: I 98 GLU cc_start: 0.7849 (tt0) cc_final: 0.7624 (tp30) REVERT: I 120 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7010 (tp30) REVERT: H 57 ILE cc_start: 0.7434 (mm) cc_final: 0.7184 (tp) REVERT: H 99 LYS cc_start: 0.8082 (tptm) cc_final: 0.7174 (pttt) REVERT: H 122 MET cc_start: 0.7822 (mmm) cc_final: 0.7429 (mmm) REVERT: H 143 MET cc_start: 0.6677 (tpt) cc_final: 0.6104 (mtt) REVERT: H 193 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8327 (mt) REVERT: H 292 MET cc_start: 0.8230 (mtp) cc_final: 0.8004 (mtm) REVERT: G 36 ASN cc_start: 0.7141 (m-40) cc_final: 0.6850 (m-40) REVERT: G 95 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7587 (pt0) REVERT: G 229 TRP cc_start: 0.7393 (t60) cc_final: 0.6695 (t60) REVERT: g 120 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7192 (tp30) REVERT: h 6 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8388 (mm) REVERT: h 39 SER cc_start: 0.9072 (OUTLIER) cc_final: 0.8589 (p) REVERT: C 1 MET cc_start: 0.7850 (mmt) cc_final: 0.7370 (mmm) REVERT: C 43 ILE cc_start: 0.8776 (mp) cc_final: 0.8494 (tt) REVERT: c 6 GLU cc_start: 0.4924 (mp0) cc_final: 0.3722 (tp30) REVERT: c 58 THR cc_start: 0.7321 (OUTLIER) cc_final: 0.7087 (m) REVERT: c 119 THR cc_start: 0.8181 (OUTLIER) cc_final: 0.7779 (m) REVERT: c 124 MET cc_start: 0.7978 (tpp) cc_final: 0.7575 (tpp) REVERT: A 1 MET cc_start: 0.6175 (ptp) cc_final: 0.5054 (mmp) REVERT: A 4 ASP cc_start: 0.7442 (t0) cc_final: 0.6930 (t0) REVERT: E 59 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7902 (tp) REVERT: E 84 LEU cc_start: 0.6942 (OUTLIER) cc_final: 0.6584 (mp) REVERT: E 93 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.7275 (mp10) outliers start: 126 outliers final: 103 residues processed: 368 average time/residue: 0.1356 time to fit residues: 85.2088 Evaluate side-chains 372 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 256 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 14 VAL Chi-restraints excluded: chain Y residue 27 GLU Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain Y residue 61 LEU Chi-restraints excluded: chain Y residue 74 GLN Chi-restraints excluded: chain Y residue 90 LEU Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Y residue 175 SER Chi-restraints excluded: chain Y residue 211 THR Chi-restraints excluded: chain Y residue 231 LEU Chi-restraints excluded: chain Y residue 237 ASP Chi-restraints excluded: chain Y residue 310 THR Chi-restraints excluded: chain Y residue 312 MET Chi-restraints excluded: chain Y residue 333 ILE Chi-restraints excluded: chain Y residue 336 THR Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 158 LEU Chi-restraints excluded: chain K residue 219 VAL Chi-restraints excluded: chain K residue 233 LEU Chi-restraints excluded: chain K residue 309 LEU Chi-restraints excluded: chain K residue 314 VAL Chi-restraints excluded: chain K residue 337 GLU Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 45 MET Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 138 ASP Chi-restraints excluded: chain J residue 211 THR Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain J residue 242 VAL Chi-restraints excluded: chain J residue 273 ARG Chi-restraints excluded: chain J residue 307 VAL Chi-restraints excluded: chain J residue 331 ASP Chi-restraints excluded: chain J residue 336 THR Chi-restraints excluded: chain J residue 343 VAL Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 74 GLN Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain I residue 234 THR Chi-restraints excluded: chain I residue 310 THR Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 53 HIS Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 176 ASP Chi-restraints excluded: chain H residue 179 SER Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain H residue 222 VAL Chi-restraints excluded: chain H residue 273 ARG Chi-restraints excluded: chain H residue 309 LEU Chi-restraints excluded: chain H residue 325 ILE Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 95 GLU Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 343 VAL Chi-restraints excluded: chain g residue 44 VAL Chi-restraints excluded: chain g residue 65 THR Chi-restraints excluded: chain g residue 79 THR Chi-restraints excluded: chain g residue 122 MET Chi-restraints excluded: chain g residue 242 VAL Chi-restraints excluded: chain g residue 282 LEU Chi-restraints excluded: chain g residue 334 LEU Chi-restraints excluded: chain h residue 6 ILE Chi-restraints excluded: chain h residue 8 THR Chi-restraints excluded: chain h residue 10 VAL Chi-restraints excluded: chain h residue 39 SER Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain c residue 1 MET Chi-restraints excluded: chain c residue 41 ILE Chi-restraints excluded: chain c residue 58 THR Chi-restraints excluded: chain c residue 92 VAL Chi-restraints excluded: chain c residue 93 GLN Chi-restraints excluded: chain c residue 112 THR Chi-restraints excluded: chain c residue 119 THR Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 93 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 304 optimal weight: 20.0000 chunk 321 optimal weight: 5.9990 chunk 188 optimal weight: 9.9990 chunk 246 optimal weight: 0.0070 chunk 253 optimal weight: 8.9990 chunk 166 optimal weight: 2.9990 chunk 316 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 214 optimal weight: 0.8980 chunk 104 optimal weight: 8.9990 chunk 185 optimal weight: 0.9980 overall best weight: 1.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 GLN ** c 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.092430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.085660 restraints weight = 80752.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.087408 restraints weight = 42985.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.088568 restraints weight = 26612.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.089357 restraints weight = 18204.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.089927 restraints weight = 13384.395| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25933 Z= 0.132 Angle : 0.616 12.251 35254 Z= 0.318 Chirality : 0.044 0.195 4208 Planarity : 0.004 0.052 4544 Dihedral : 5.064 65.635 3660 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.91 % Favored : 90.09 % Rotamer: Outliers : 4.67 % Allowed : 28.13 % Favored : 67.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.19 (0.14), residues: 3340 helix: 0.43 (0.23), residues: 549 sheet: -1.07 (0.21), residues: 642 loop : -2.22 (0.13), residues: 2149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 273 TYR 0.017 0.001 TYR c 94 PHE 0.025 0.001 PHE h 73 TRP 0.056 0.002 TRP H 181 HIS 0.004 0.001 HIS J 191 Details of bonding type rmsd covalent geometry : bond 0.00302 (25933) covalent geometry : angle 0.61621 (35254) hydrogen bonds : bond 0.03599 ( 663) hydrogen bonds : angle 5.21336 ( 1812) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 262 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 27 GLU cc_start: 0.6989 (OUTLIER) cc_final: 0.6656 (pm20) REVERT: Y 111 MET cc_start: 0.7572 (mmm) cc_final: 0.7336 (mmt) REVERT: Y 118 PHE cc_start: 0.8533 (m-10) cc_final: 0.8188 (m-80) REVERT: Y 120 GLU cc_start: 0.7976 (tp30) cc_final: 0.7639 (tp30) REVERT: Y 321 MET cc_start: 0.7425 (mtp) cc_final: 0.6981 (mtp) REVERT: K 292 MET cc_start: 0.7570 (ptm) cc_final: 0.7215 (ttp) REVERT: K 321 MET cc_start: 0.7441 (mtt) cc_final: 0.7092 (mtp) REVERT: K 337 GLU cc_start: 0.5529 (OUTLIER) cc_final: 0.5005 (pm20) REVERT: J 189 THR cc_start: 0.8398 (p) cc_final: 0.7784 (t) REVERT: J 233 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8946 (pp) REVERT: I 31 MET cc_start: 0.6819 (ttp) cc_final: 0.6194 (ttp) REVERT: I 74 GLN cc_start: 0.7203 (OUTLIER) cc_final: 0.6499 (mt0) REVERT: I 98 GLU cc_start: 0.7839 (tt0) cc_final: 0.7628 (tp30) REVERT: I 120 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7008 (tp30) REVERT: H 57 ILE cc_start: 0.7737 (mm) cc_final: 0.7433 (tp) REVERT: H 99 LYS cc_start: 0.8129 (tptm) cc_final: 0.7249 (pttt) REVERT: H 122 MET cc_start: 0.7834 (mmm) cc_final: 0.7437 (mmm) REVERT: H 143 MET cc_start: 0.6636 (tpt) cc_final: 0.6092 (mtt) REVERT: H 193 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8336 (mt) REVERT: H 292 MET cc_start: 0.8212 (mtp) cc_final: 0.7980 (mtm) REVERT: G 36 ASN cc_start: 0.7098 (m-40) cc_final: 0.6823 (m-40) REVERT: G 229 TRP cc_start: 0.7429 (t60) cc_final: 0.6711 (t60) REVERT: g 120 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7178 (tp30) REVERT: h 6 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8400 (mm) REVERT: h 39 SER cc_start: 0.9147 (OUTLIER) cc_final: 0.8695 (p) REVERT: C 1 MET cc_start: 0.7831 (mmt) cc_final: 0.7427 (mmm) REVERT: C 43 ILE cc_start: 0.8772 (mp) cc_final: 0.8523 (tt) REVERT: c 6 GLU cc_start: 0.4938 (mp0) cc_final: 0.3754 (tp30) REVERT: c 58 THR cc_start: 0.7314 (OUTLIER) cc_final: 0.7075 (m) REVERT: c 119 THR cc_start: 0.8099 (OUTLIER) cc_final: 0.7692 (m) REVERT: c 124 MET cc_start: 0.7956 (tpp) cc_final: 0.7565 (tpp) REVERT: D 79 VAL cc_start: 0.8507 (OUTLIER) cc_final: 0.8297 (p) REVERT: A 1 MET cc_start: 0.6186 (ptp) cc_final: 0.4938 (mmp) REVERT: A 4 ASP cc_start: 0.7645 (t0) cc_final: 0.7346 (t0) REVERT: E 59 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7894 (tp) REVERT: E 84 LEU cc_start: 0.6915 (OUTLIER) cc_final: 0.6571 (mp) REVERT: E 93 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7301 (mp10) outliers start: 128 outliers final: 108 residues processed: 370 average time/residue: 0.1353 time to fit residues: 85.4828 Evaluate side-chains 380 residues out of total 2742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 259 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 11 LEU Chi-restraints excluded: chain Y residue 14 VAL Chi-restraints excluded: chain Y residue 27 GLU Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain Y residue 61 LEU Chi-restraints excluded: chain Y residue 74 GLN Chi-restraints excluded: chain Y residue 90 LEU Chi-restraints excluded: chain Y residue 122 MET Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Y residue 175 SER Chi-restraints excluded: chain Y residue 211 THR Chi-restraints excluded: chain Y residue 231 LEU Chi-restraints excluded: chain Y residue 237 ASP Chi-restraints excluded: chain Y residue 310 THR Chi-restraints excluded: chain Y residue 312 MET Chi-restraints excluded: chain Y residue 333 ILE Chi-restraints excluded: chain Y residue 336 THR Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 158 LEU Chi-restraints excluded: chain K residue 219 VAL Chi-restraints excluded: chain K residue 233 LEU Chi-restraints excluded: chain K residue 309 LEU Chi-restraints excluded: chain K residue 314 VAL Chi-restraints excluded: chain K residue 337 GLU Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 45 MET Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 138 ASP Chi-restraints excluded: chain J residue 211 THR Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain J residue 242 VAL Chi-restraints excluded: chain J residue 273 ARG Chi-restraints excluded: chain J residue 307 VAL Chi-restraints excluded: chain J residue 331 ASP Chi-restraints excluded: chain J residue 336 THR Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 74 GLN Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 176 ASP Chi-restraints excluded: chain I residue 234 THR Chi-restraints excluded: chain I residue 310 THR Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 47 CYS Chi-restraints excluded: chain H residue 53 HIS Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 176 ASP Chi-restraints excluded: chain H residue 179 SER Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain H residue 222 VAL Chi-restraints excluded: chain H residue 273 ARG Chi-restraints excluded: chain H residue 309 LEU Chi-restraints excluded: chain H residue 325 ILE Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 343 VAL Chi-restraints excluded: chain g residue 44 VAL Chi-restraints excluded: chain g residue 65 THR Chi-restraints excluded: chain g residue 79 THR Chi-restraints excluded: chain g residue 122 MET Chi-restraints excluded: chain g residue 177 LEU Chi-restraints excluded: chain g residue 282 LEU Chi-restraints excluded: chain g residue 334 LEU Chi-restraints excluded: chain h residue 6 ILE Chi-restraints excluded: chain h residue 8 THR Chi-restraints excluded: chain h residue 10 VAL Chi-restraints excluded: chain h residue 39 SER Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 93 GLN Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain c residue 41 ILE Chi-restraints excluded: chain c residue 58 THR Chi-restraints excluded: chain c residue 92 VAL Chi-restraints excluded: chain c residue 93 GLN Chi-restraints excluded: chain c residue 112 THR Chi-restraints excluded: chain c residue 119 THR Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 93 GLN Chi-restraints excluded: chain E residue 114 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 256 optimal weight: 8.9990 chunk 81 optimal weight: 1.9990 chunk 165 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 chunk 186 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 chunk 206 optimal weight: 6.9990 chunk 292 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 211 optimal weight: 4.9990 chunk 98 optimal weight: 0.4980 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 272 ASN ** H 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 93 GLN ** D 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.092394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.085601 restraints weight = 80682.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.087334 restraints weight = 43053.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.088493 restraints weight = 26779.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.089312 restraints weight = 18374.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.089854 restraints weight = 13378.789| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 25933 Z= 0.141 Angle : 0.625 12.373 35254 Z= 0.323 Chirality : 0.044 0.211 4208 Planarity : 0.004 0.058 4544 Dihedral : 5.073 65.831 3660 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.03 % Favored : 89.97 % Rotamer: Outliers : 4.93 % Allowed : 27.91 % Favored : 67.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.14), residues: 3340 helix: 0.41 (0.23), residues: 548 sheet: -1.06 (0.20), residues: 642 loop : -2.21 (0.13), residues: 2150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 273 TYR 0.029 0.001 TYR C 94 PHE 0.026 0.002 PHE K 142 TRP 0.059 0.002 TRP K 229 HIS 0.005 0.001 HIS C 126 Details of bonding type rmsd covalent geometry : bond 0.00326 (25933) covalent geometry : angle 0.62533 (35254) hydrogen bonds : bond 0.03650 ( 663) hydrogen bonds : angle 5.22232 ( 1812) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4846.69 seconds wall clock time: 84 minutes 55.30 seconds (5095.30 seconds total)