Starting phenix.real_space_refine on Sat Feb 7 04:02:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m5e_63642/02_2026/9m5e_63642.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m5e_63642/02_2026/9m5e_63642.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9m5e_63642/02_2026/9m5e_63642.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m5e_63642/02_2026/9m5e_63642.map" model { file = "/net/cci-nas-00/data/ceres_data/9m5e_63642/02_2026/9m5e_63642.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m5e_63642/02_2026/9m5e_63642.cif" } resolution = 3.55 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= 0.020 sd= 0.043 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: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 4 5.21 5 S 197 5.16 5 C 18847 2.51 5 N 5086 2.21 5 O 5525 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29669 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 3244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3244 Classifications: {'peptide': 411} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 26, 'TRANS': 384} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 2, 'ARG:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 2944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2944 Classifications: {'peptide': 373} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 17, 'TRANS': 355} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 2, 'ARG:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 2417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2417 Classifications: {'peptide': 314} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 13, 'TRANS': 300} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 2254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2254 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 272} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1422 Classifications: {'peptide': 178} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 13, 'TRANS': 164} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 1, 'GLN%COO:plan1': 1} Unresolved non-hydrogen planarities: 18 Chain: "F" Number of atoms: 1371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1371 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain: "G" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 850 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain breaks: 1 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 35 Chain: "H" Number of atoms: 3243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3243 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 394} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "I" Number of atoms: 2890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2890 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'HIC:plan-2': 1, 'PHE%COO:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "J" Number of atoms: 2890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2890 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIC:plan-2': 1, 'GLU:plan': 1, 'PHE%COO:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "K" Number of atoms: 2861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2861 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1, 'HIC:plan-2': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "h" Number of atoms: 3144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3144 Classifications: {'peptide': 414} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 20, 'TRANS': 393} Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 6, 'HIS:plan': 2, 'ARG:plan': 4, 'TYR:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 74 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.23, per 1000 atoms: 0.24 Number of scatterers: 29669 At special positions: 0 Unit cell: (145.2, 132, 232.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 197 16.00 P 10 15.00 Mg 4 11.99 O 5525 8.00 N 5086 7.00 C 18847 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: 2.51 Conformation dependent library (CDL) restraints added in 1.4 seconds 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7116 Finding SS restraints... Secondary structure from input PDB file: 187 helices and 41 sheets defined 53.1% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 55 through 59 removed outlier: 3.628A pdb=" N ASP A 59 " --> pdb=" O ASP A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 67 Processing helix chain 'A' and resid 85 through 99 Processing helix chain 'A' and resid 104 through 108 removed outlier: 3.678A pdb=" N HIS A 108 " --> pdb=" O PRO A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 133 removed outlier: 3.549A pdb=" N ARG A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 156 Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.695A pdb=" N ARG A 161 " --> pdb=" O VAL A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 190 Processing helix chain 'A' and resid 196 through 212 removed outlier: 3.780A pdb=" N ARG A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 232 removed outlier: 3.796A pdb=" N SER A 232 " --> pdb=" O LYS A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 248 Processing helix chain 'A' and resid 272 through 276 Processing helix chain 'A' and resid 278 through 282 Processing helix chain 'A' and resid 284 through 288 Processing helix chain 'A' and resid 295 through 307 removed outlier: 4.388A pdb=" N ASP A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 318 Processing helix chain 'A' and resid 323 through 328 removed outlier: 3.705A pdb=" N PHE A 328 " --> pdb=" O SER A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 353 removed outlier: 3.789A pdb=" N ALA A 345 " --> pdb=" O ARG A 341 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 349 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER A 350 " --> pdb=" O ARG A 346 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 374 removed outlier: 4.274A pdb=" N ARG A 374 " --> pdb=" O HIS A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 386 Processing helix chain 'A' and resid 389 through 394 Processing helix chain 'A' and resid 397 through 403 Processing helix chain 'A' and resid 404 through 409 removed outlier: 3.655A pdb=" N ILE A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 64 Processing helix chain 'B' and resid 81 through 93 Processing helix chain 'B' and resid 116 through 130 removed outlier: 3.698A pdb=" N ARG B 120 " --> pdb=" O PRO B 116 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE B 128 " --> pdb=" O VAL B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 150 removed outlier: 3.928A pdb=" N THR B 145 " --> pdb=" O GLN B 141 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 200 removed outlier: 3.568A pdb=" N ARG B 200 " --> pdb=" O LEU B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 221 removed outlier: 4.110A pdb=" N GLU B 211 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THR B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 237 Processing helix chain 'B' and resid 256 through 261 Processing helix chain 'B' and resid 262 through 266 Processing helix chain 'B' and resid 267 through 271 Processing helix chain 'B' and resid 277 through 289 Processing helix chain 'B' and resid 293 through 298 Processing helix chain 'B' and resid 305 through 309 Processing helix chain 'B' and resid 312 through 329 Processing helix chain 'B' and resid 333 through 340 removed outlier: 3.677A pdb=" N SER B 338 " --> pdb=" O GLU B 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 24 Processing helix chain 'D' and resid 37 through 41 Processing helix chain 'D' and resid 47 through 51 Processing helix chain 'D' and resid 63 through 69 Processing helix chain 'D' and resid 71 through 80 removed outlier: 3.630A pdb=" N LEU D 75 " --> pdb=" O GLY D 71 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG D 78 " --> pdb=" O GLU D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 115 Processing helix chain 'D' and resid 117 through 135 removed outlier: 3.548A pdb=" N PHE D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N SER D 123 " --> pdb=" O ASN D 119 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL D 124 " --> pdb=" O CYS D 120 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS D 127 " --> pdb=" O SER D 123 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR D 128 " --> pdb=" O VAL D 124 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU D 133 " --> pdb=" O PHE D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 192 removed outlier: 3.531A pdb=" N ILE D 177 " --> pdb=" O ASP D 173 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL D 180 " --> pdb=" O VAL D 176 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN D 183 " --> pdb=" O LYS D 179 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ARG D 189 " --> pdb=" O PHE D 185 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N ARG D 190 " --> pdb=" O LYS D 186 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 213 removed outlier: 5.131A pdb=" N ASP D 211 " --> pdb=" O GLU D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 233 Processing helix chain 'D' and resid 236 through 245 Processing helix chain 'D' and resid 246 through 278 removed outlier: 3.646A pdb=" N LYS D 259 " --> pdb=" O ILE D 255 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA D 260 " --> pdb=" O LYS D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 281 No H-bonds generated for 'chain 'D' and resid 279 through 281' Processing helix chain 'E' and resid 40 through 53 removed outlier: 4.721A pdb=" N LYS E 50 " --> pdb=" O ILE E 46 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ALA E 51 " --> pdb=" O TYR E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 83 removed outlier: 4.181A pdb=" N TYR E 70 " --> pdb=" O ARG E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 100 removed outlier: 3.968A pdb=" N MET E 95 " --> pdb=" O GLY E 91 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 149 removed outlier: 4.581A pdb=" N VAL E 128 " --> pdb=" O GLN E 124 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN E 135 " --> pdb=" O ALA E 131 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU E 142 " --> pdb=" O GLN E 138 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU E 146 " --> pdb=" O LEU E 142 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LYS E 147 " --> pdb=" O ARG E 143 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE E 149 " --> pdb=" O CYS E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 163 removed outlier: 4.158A pdb=" N PHE E 163 " --> pdb=" O TRP E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 166 No H-bonds generated for 'chain 'E' and resid 164 through 166' Processing helix chain 'E' and resid 167 through 171 Processing helix chain 'F' and resid 4 through 20 removed outlier: 3.652A pdb=" N TYR F 8 " --> pdb=" O THR F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 41 Processing helix chain 'F' and resid 80 through 96 removed outlier: 3.831A pdb=" N ILE F 85 " --> pdb=" O GLU F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 126 Processing helix chain 'F' and resid 127 through 166 removed outlier: 5.054A pdb=" N ASP F 143 " --> pdb=" O MET F 139 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N LYS F 144 " --> pdb=" O GLU F 140 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET F 149 " --> pdb=" O GLU F 145 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU F 162 " --> pdb=" O ARG F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 168 No H-bonds generated for 'chain 'F' and resid 167 through 168' Processing helix chain 'G' and resid 10 through 14 Processing helix chain 'G' and resid 44 through 49 Processing helix chain 'G' and resid 53 through 61 Processing helix chain 'G' and resid 71 through 86 removed outlier: 3.531A pdb=" N GLY G 78 " --> pdb=" O LYS G 74 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER G 79 " --> pdb=" O ASP G 75 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL G 81 " --> pdb=" O ALA G 77 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS G 83 " --> pdb=" O SER G 79 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL G 84 " --> pdb=" O ILE G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 99 removed outlier: 3.666A pdb=" N VAL G 97 " --> pdb=" O ILE G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 116 removed outlier: 3.523A pdb=" N LYS G 110 " --> pdb=" O ASP G 106 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR G 111 " --> pdb=" O LEU G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 139 removed outlier: 3.873A pdb=" N GLN G 129 " --> pdb=" O ALA G 125 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS G 133 " --> pdb=" O GLN G 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 148 removed outlier: 3.846A pdb=" N VAL G 146 " --> pdb=" O SER G 142 " (cutoff:3.500A) Processing helix chain 'H' and resid 312 through 325 removed outlier: 3.921A pdb=" N LEU H 316 " --> pdb=" O ILE H 312 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N MET H 317 " --> pdb=" O GLY H 313 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU H 318 " --> pdb=" O ALA H 314 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ASN H 323 " --> pdb=" O LEU H 319 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY H 325 " --> pdb=" O ARG H 321 " (cutoff:3.500A) Processing helix chain 'H' and resid 327 through 346 removed outlier: 3.662A pdb=" N ILE H 342 " --> pdb=" O ILE H 338 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLN H 343 " --> pdb=" O VAL H 339 " (cutoff:3.500A) Processing helix chain 'H' and resid 350 through 355 Processing helix chain 'H' and resid 358 through 362 Processing helix chain 'H' and resid 365 through 370 removed outlier: 3.906A pdb=" N LEU H 370 " --> pdb=" O SER H 367 " (cutoff:3.500A) Processing helix chain 'H' and resid 376 through 395 Processing helix chain 'H' and resid 395 through 401 Processing helix chain 'H' and resid 408 through 424 removed outlier: 5.384A pdb=" N THR H 422 " --> pdb=" O LEU H 418 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP H 423 " --> pdb=" O HIS H 419 " (cutoff:3.500A) Processing helix chain 'H' and resid 425 through 451 removed outlier: 5.893A pdb=" N ASN H 436 " --> pdb=" O MET H 432 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N GLU H 437 " --> pdb=" O CYS H 433 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N SER H 440 " --> pdb=" O ASN H 436 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL H 441 " --> pdb=" O GLU H 437 " (cutoff:3.500A) Processing helix chain 'H' and resid 453 through 471 removed outlier: 4.098A pdb=" N LEU H 459 " --> pdb=" O SER H 455 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER H 469 " --> pdb=" O GLY H 465 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU H 470 " --> pdb=" O ALA H 466 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ASP H 471 " --> pdb=" O MET H 467 " (cutoff:3.500A) Processing helix chain 'H' and resid 471 through 481 Processing helix chain 'H' and resid 482 through 494 removed outlier: 3.522A pdb=" N GLU H 486 " --> pdb=" O VAL H 482 " (cutoff:3.500A) Processing helix chain 'H' and resid 497 through 513 Processing helix chain 'H' and resid 522 through 527 Processing helix chain 'H' and resid 527 through 540 removed outlier: 3.722A pdb=" N PHE H 533 " --> pdb=" O PRO H 529 " (cutoff:3.500A) Processing helix chain 'H' and resid 549 through 562 removed outlier: 3.545A pdb=" N LEU H 553 " --> pdb=" O GLN H 549 " (cutoff:3.500A) Processing helix chain 'H' and resid 563 through 565 No H-bonds generated for 'chain 'H' and resid 563 through 565' Processing helix chain 'H' and resid 571 through 580 Processing helix chain 'H' and resid 583 through 597 removed outlier: 3.892A pdb=" N LEU H 591 " --> pdb=" O SER H 587 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU H 592 " --> pdb=" O GLU H 588 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU H 593 " --> pdb=" O LYS H 589 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG H 596 " --> pdb=" O LEU H 592 " (cutoff:3.500A) Processing helix chain 'H' and resid 612 through 622 Processing helix chain 'H' and resid 624 through 629 removed outlier: 3.775A pdb=" N ALA H 629 " --> pdb=" O PRO H 625 " (cutoff:3.500A) Processing helix chain 'H' and resid 632 through 650 removed outlier: 3.640A pdb=" N ALA H 648 " --> pdb=" O VAL H 644 " (cutoff:3.500A) Processing helix chain 'H' and resid 656 through 671 removed outlier: 3.995A pdb=" N SER H 662 " --> pdb=" O MET H 658 " (cutoff:3.500A) Processing helix chain 'H' and resid 672 through 677 removed outlier: 4.006A pdb=" N HIS H 676 " --> pdb=" O PRO H 672 " (cutoff:3.500A) Processing helix chain 'H' and resid 679 through 693 removed outlier: 4.377A pdb=" N ALA H 685 " --> pdb=" O PRO H 681 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG H 689 " --> pdb=" O ALA H 685 " (cutoff:3.500A) Processing helix chain 'H' and resid 697 through 714 removed outlier: 3.800A pdb=" N PHE H 714 " --> pdb=" O MET H 710 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 61 Processing helix chain 'I' and resid 78 through 92 Processing helix chain 'I' and resid 97 through 101 removed outlier: 3.867A pdb=" N GLU I 100 " --> pdb=" O ALA I 97 " (cutoff:3.500A) Processing helix chain 'I' and resid 112 through 126 removed outlier: 3.752A pdb=" N ARG I 116 " --> pdb=" O PRO I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 137 through 145 removed outlier: 3.627A pdb=" N SER I 145 " --> pdb=" O SER I 141 " (cutoff:3.500A) Processing helix chain 'I' and resid 172 through 175 Processing helix chain 'I' and resid 181 through 193 Processing helix chain 'I' and resid 194 through 197 Processing helix chain 'I' and resid 202 through 217 removed outlier: 3.761A pdb=" N GLU I 207 " --> pdb=" O THR I 203 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE I 208 " --> pdb=" O ALA I 204 " (cutoff:3.500A) Processing helix chain 'I' and resid 222 through 231 Processing helix chain 'I' and resid 233 through 237 removed outlier: 4.352A pdb=" N LEU I 236 " --> pdb=" O SER I 233 " (cutoff:3.500A) Processing helix chain 'I' and resid 252 through 260 removed outlier: 3.848A pdb=" N CYS I 257 " --> pdb=" O GLU I 253 " (cutoff:3.500A) Proline residue: I 258 - end of helix Processing helix chain 'I' and resid 261 through 262 No H-bonds generated for 'chain 'I' and resid 261 through 262' Processing helix chain 'I' and resid 263 through 267 Processing helix chain 'I' and resid 273 through 285 Processing helix chain 'I' and resid 286 through 288 No H-bonds generated for 'chain 'I' and resid 286 through 288' Processing helix chain 'I' and resid 289 through 295 removed outlier: 3.723A pdb=" N ALA I 295 " --> pdb=" O LYS I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 301 through 306 removed outlier: 4.182A pdb=" N TYR I 306 " --> pdb=" O THR I 303 " (cutoff:3.500A) Processing helix chain 'I' and resid 308 through 321 Processing helix chain 'I' and resid 334 through 336 No H-bonds generated for 'chain 'I' and resid 334 through 336' Processing helix chain 'I' and resid 337 through 347 Processing helix chain 'I' and resid 351 through 355 Processing helix chain 'I' and resid 359 through 366 Processing helix chain 'I' and resid 368 through 374 removed outlier: 3.961A pdb=" N ARG I 372 " --> pdb=" O SER I 368 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'J' and resid 78 through 92 removed outlier: 4.156A pdb=" N LYS J 84 " --> pdb=" O ASP J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 97 through 101 Processing helix chain 'J' and resid 112 through 126 removed outlier: 3.741A pdb=" N ARG J 116 " --> pdb=" O PRO J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 137 through 145 removed outlier: 3.591A pdb=" N SER J 141 " --> pdb=" O GLN J 137 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU J 142 " --> pdb=" O ALA J 138 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR J 143 " --> pdb=" O VAL J 139 " (cutoff:3.500A) Processing helix chain 'J' and resid 172 through 175 Processing helix chain 'J' and resid 181 through 193 Processing helix chain 'J' and resid 194 through 196 No H-bonds generated for 'chain 'J' and resid 194 through 196' Processing helix chain 'J' and resid 202 through 217 removed outlier: 3.593A pdb=" N GLU J 207 " --> pdb=" O THR J 203 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ILE J 208 " --> pdb=" O ALA J 204 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS J 215 " --> pdb=" O ASP J 211 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N CYS J 217 " --> pdb=" O LYS J 213 " (cutoff:3.500A) Processing helix chain 'J' and resid 222 through 231 Processing helix chain 'J' and resid 233 through 237 removed outlier: 4.115A pdb=" N LEU J 236 " --> pdb=" O SER J 233 " (cutoff:3.500A) Processing helix chain 'J' and resid 252 through 257 Processing helix chain 'J' and resid 258 through 268 Proline residue: J 264 - end of helix Processing helix chain 'J' and resid 273 through 285 Processing helix chain 'J' and resid 286 through 294 removed outlier: 3.537A pdb=" N ARG J 290 " --> pdb=" O ASP J 286 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LYS J 291 " --> pdb=" O ILE J 287 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ASP J 292 " --> pdb=" O ASP J 288 " (cutoff:3.500A) Processing helix chain 'J' and resid 301 through 305 Processing helix chain 'J' and resid 308 through 321 Processing helix chain 'J' and resid 337 through 347 Processing helix chain 'J' and resid 352 through 356 removed outlier: 3.527A pdb=" N TRP J 356 " --> pdb=" O GLN J 353 " (cutoff:3.500A) Processing helix chain 'J' and resid 359 through 366 Processing helix chain 'J' and resid 369 through 374 Processing helix chain 'K' and resid 55 through 61 Processing helix chain 'K' and resid 78 through 92 removed outlier: 3.500A pdb=" N LYS K 84 " --> pdb=" O ASP K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 126 removed outlier: 3.818A pdb=" N ARG K 116 " --> pdb=" O PRO K 112 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET K 123 " --> pdb=" O MET K 119 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE K 124 " --> pdb=" O THR K 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 137 through 145 removed outlier: 3.525A pdb=" N SER K 141 " --> pdb=" O GLN K 137 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU K 142 " --> pdb=" O ALA K 138 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR K 143 " --> pdb=" O VAL K 139 " (cutoff:3.500A) Processing helix chain 'K' and resid 172 through 175 Processing helix chain 'K' and resid 181 through 194 Processing helix chain 'K' and resid 201 through 217 removed outlier: 4.030A pdb=" N GLU K 205 " --> pdb=" O VAL K 201 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU K 207 " --> pdb=" O THR K 203 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE K 208 " --> pdb=" O ALA K 204 " (cutoff:3.500A) Processing helix chain 'K' and resid 222 through 231 Processing helix chain 'K' and resid 252 through 257 Processing helix chain 'K' and resid 258 through 262 Processing helix chain 'K' and resid 263 through 268 Processing helix chain 'K' and resid 273 through 285 Processing helix chain 'K' and resid 289 through 295 removed outlier: 3.864A pdb=" N ALA K 295 " --> pdb=" O LYS K 291 " (cutoff:3.500A) Processing helix chain 'K' and resid 301 through 306 removed outlier: 3.948A pdb=" N TYR K 306 " --> pdb=" O THR K 303 " (cutoff:3.500A) Processing helix chain 'K' and resid 308 through 321 removed outlier: 3.582A pdb=" N ALA K 319 " --> pdb=" O LYS K 315 " (cutoff:3.500A) Processing helix chain 'K' and resid 334 through 336 No H-bonds generated for 'chain 'K' and resid 334 through 336' Processing helix chain 'K' and resid 337 through 347 Processing helix chain 'K' and resid 359 through 363 Processing helix chain 'K' and resid 364 through 373 Proline residue: K 367 - end of helix Processing helix chain 'h' and resid 311 through 325 removed outlier: 5.730A pdb=" N MET h 317 " --> pdb=" O GLY h 313 " (cutoff:3.500A) Processing helix chain 'h' and resid 327 through 346 removed outlier: 3.571A pdb=" N ILE h 338 " --> pdb=" O ALA h 334 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN h 343 " --> pdb=" O VAL h 339 " (cutoff:3.500A) Processing helix chain 'h' and resid 349 through 362 removed outlier: 3.796A pdb=" N MET h 353 " --> pdb=" O SER h 349 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLN h 355 " --> pdb=" O PRO h 351 " (cutoff:3.500A) Processing helix chain 'h' and resid 376 through 391 removed outlier: 3.633A pdb=" N VAL h 384 " --> pdb=" O GLN h 380 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA h 387 " --> pdb=" O GLU h 383 " (cutoff:3.500A) Processing helix chain 'h' and resid 395 through 401 removed outlier: 3.829A pdb=" N SER h 400 " --> pdb=" O ALA h 396 " (cutoff:3.500A) Processing helix chain 'h' and resid 406 through 424 removed outlier: 4.192A pdb=" N CYS h 412 " --> pdb=" O GLY h 408 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR h 422 " --> pdb=" O LEU h 418 " (cutoff:3.500A) Processing helix chain 'h' and resid 425 through 434 removed outlier: 3.502A pdb=" N CYS h 429 " --> pdb=" O ASP h 425 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS h 431 " --> pdb=" O GLU h 427 " (cutoff:3.500A) Processing helix chain 'h' and resid 438 through 451 Processing helix chain 'h' and resid 453 through 471 removed outlier: 3.699A pdb=" N LEU h 458 " --> pdb=" O ALA h 454 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N LEU h 459 " --> pdb=" O SER h 455 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASP h 471 " --> pdb=" O MET h 467 " (cutoff:3.500A) Processing helix chain 'h' and resid 471 through 480 removed outlier: 3.857A pdb=" N SER h 480 " --> pdb=" O SER h 476 " (cutoff:3.500A) Processing helix chain 'h' and resid 482 through 494 Processing helix chain 'h' and resid 497 through 513 removed outlier: 3.712A pdb=" N TYR h 503 " --> pdb=" O GLN h 499 " (cutoff:3.500A) Processing helix chain 'h' and resid 519 through 521 No H-bonds generated for 'chain 'h' and resid 519 through 521' Processing helix chain 'h' and resid 522 through 527 Processing helix chain 'h' and resid 527 through 541 removed outlier: 3.592A pdb=" N ILE h 537 " --> pdb=" O PHE h 533 " (cutoff:3.500A) Processing helix chain 'h' and resid 549 through 564 removed outlier: 4.467A pdb=" N HIS h 564 " --> pdb=" O ALA h 560 " (cutoff:3.500A) Processing helix chain 'h' and resid 571 through 580 removed outlier: 3.500A pdb=" N HIS h 580 " --> pdb=" O ALA h 576 " (cutoff:3.500A) Processing helix chain 'h' and resid 584 through 597 removed outlier: 4.092A pdb=" N LEU h 591 " --> pdb=" O SER h 587 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU h 592 " --> pdb=" O GLU h 588 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU h 593 " --> pdb=" O LYS h 589 " (cutoff:3.500A) Processing helix chain 'h' and resid 612 through 622 Processing helix chain 'h' and resid 624 through 629 Processing helix chain 'h' and resid 632 through 650 Processing helix chain 'h' and resid 654 through 671 removed outlier: 4.169A pdb=" N MET h 658 " --> pdb=" O ASP h 654 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU h 659 " --> pdb=" O LYS h 655 " (cutoff:3.500A) Processing helix chain 'h' and resid 679 through 692 Processing helix chain 'h' and resid 697 through 714 Processing helix chain 'h' and resid 715 through 718 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 4.043A pdb=" N THR A 113 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N CYS A 12 " --> pdb=" O THR A 113 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 62 removed outlier: 3.600A pdb=" N PHE A 61 " --> pdb=" O ALA A 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 78 through 79 Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 185 Processing sheet with id=AA5, first strand: chain 'A' and resid 184 through 185 removed outlier: 3.889A pdb=" N HIS A 176 " --> pdb=" O ASP A 169 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N THR A 166 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N SER A 322 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ILE A 168 " --> pdb=" O SER A 322 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE A 319 " --> pdb=" O ILE A 368 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 254 through 259 Processing sheet with id=AA7, first strand: chain 'B' and resid 30 through 33 removed outlier: 3.520A pdb=" N GLY B 21 " --> pdb=" O VAL B 10 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR B 110 " --> pdb=" O CYS B 11 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 56 through 57 Processing sheet with id=AA9, first strand: chain 'B' and resid 56 through 57 Processing sheet with id=AB1, first strand: chain 'B' and resid 74 through 75 Processing sheet with id=AB2, first strand: chain 'B' and resid 173 through 174 Processing sheet with id=AB3, first strand: chain 'B' and resid 173 through 174 removed outlier: 3.795A pdb=" N HIS B 165 " --> pdb=" O ASP B 158 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE B 301 " --> pdb=" O GLU B 345 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 242 through 245 Processing sheet with id=AB5, first strand: chain 'C' and resid 2 through 4 removed outlier: 6.714A pdb=" N GLN C 344 " --> pdb=" O LEU C 335 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR C 348 " --> pdb=" O GLN C 331 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 14 through 16 removed outlier: 6.780A pdb=" N VAL C 32 " --> pdb=" O GLU C 47 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N GLU C 47 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ILE C 34 " --> pdb=" O VAL C 45 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 55 through 61 removed outlier: 6.590A pdb=" N CYS C 70 " --> pdb=" O THR C 56 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ILE C 58 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL C 68 " --> pdb=" O ILE C 58 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N TRP C 60 " --> pdb=" O ARG C 66 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N ARG C 66 " --> pdb=" O TRP C 60 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 91 through 92 removed outlier: 4.228A pdb=" N CYS C 134 " --> pdb=" O ILE C 92 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N TRP C 131 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ALA C 112 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N VAL C 102 " --> pdb=" O ALA C 112 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLY C 114 " --> pdb=" O ARG C 100 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 145 through 150 removed outlier: 3.518A pdb=" N SER C 147 " --> pdb=" O GLY C 160 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N CYS C 166 " --> pdb=" O GLU C 197 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU C 197 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE C 168 " --> pdb=" O MET C 195 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 205 through 210 removed outlier: 3.545A pdb=" N VAL C 226 " --> pdb=" O LEU C 240 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 247 through 254 removed outlier: 6.529A pdb=" N SER C 257 " --> pdb=" O ILE C 253 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 33 through 35 removed outlier: 4.406A pdb=" N SER D 94 " --> pdb=" O VAL D 85 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 142 through 144 removed outlier: 3.672A pdb=" N TYR D 222 " --> pdb=" O SER D 201 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN D 197 " --> pdb=" O VAL D 226 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 51 through 54 removed outlier: 3.522A pdb=" N LYS F 60 " --> pdb=" O ALA F 75 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE F 114 " --> pdb=" O ILE F 74 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 29 through 32 removed outlier: 6.657A pdb=" N LEU I 8 " --> pdb=" O LEU I 104 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N THR I 106 " --> pdb=" O LEU I 8 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N CYS I 10 " --> pdb=" O THR I 106 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 53 through 54 removed outlier: 3.929A pdb=" N ARG I 37 " --> pdb=" O THR I 66 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 71 through 72 Processing sheet with id=AC9, first strand: chain 'I' and resid 169 through 170 Processing sheet with id=AD1, first strand: chain 'I' and resid 169 through 170 removed outlier: 6.260A pdb=" N ILE I 151 " --> pdb=" O VAL I 298 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N SER I 300 " --> pdb=" O ILE I 151 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU I 153 " --> pdb=" O SER I 300 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ASN I 297 " --> pdb=" O ILE I 330 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 238 through 241 Processing sheet with id=AD3, first strand: chain 'J' and resid 29 through 32 removed outlier: 6.682A pdb=" N LEU J 8 " --> pdb=" O LEU J 104 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N THR J 106 " --> pdb=" O LEU J 8 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N CYS J 10 " --> pdb=" O THR J 106 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 53 through 54 removed outlier: 3.919A pdb=" N ARG J 37 " --> pdb=" O THR J 66 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 71 through 72 Processing sheet with id=AD6, first strand: chain 'J' and resid 169 through 170 Processing sheet with id=AD7, first strand: chain 'J' and resid 169 through 170 Processing sheet with id=AD8, first strand: chain 'J' and resid 238 through 241 Processing sheet with id=AD9, first strand: chain 'K' and resid 29 through 32 removed outlier: 6.903A pdb=" N LEU K 8 " --> pdb=" O LEU K 104 " (cutoff:3.500A) removed outlier: 8.767A pdb=" N THR K 106 " --> pdb=" O LEU K 8 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N CYS K 10 " --> pdb=" O THR K 106 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 53 through 54 Processing sheet with id=AE2, first strand: chain 'K' and resid 71 through 72 Processing sheet with id=AE3, first strand: chain 'K' and resid 169 through 170 Processing sheet with id=AE4, first strand: chain 'K' and resid 169 through 170 Processing sheet with id=AE5, first strand: chain 'K' and resid 238 through 241 1485 hydrogen bonds defined for protein. 4002 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.57 Time building geometry restraints manager: 3.32 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: 9575 1.34 - 1.45: 4429 1.45 - 1.57: 15962 1.57 - 1.69: 15 1.69 - 1.81: 321 Bond restraints: 30302 Sorted by residual: bond pdb=" N PHE B 371 " pdb=" CA PHE B 371 " ideal model delta sigma weight residual 1.457 1.502 -0.044 1.29e-02 6.01e+03 1.17e+01 bond pdb=" N LYS B 368 " pdb=" CA LYS B 368 " ideal model delta sigma weight residual 1.459 1.494 -0.036 1.24e-02 6.50e+03 8.29e+00 bond pdb=" N VAL h 583 " pdb=" CA VAL h 583 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.25e-02 6.40e+03 5.77e+00 bond pdb=" CB VAL C 220 " pdb=" CG2 VAL C 220 " ideal model delta sigma weight residual 1.521 1.445 0.076 3.30e-02 9.18e+02 5.34e+00 bond pdb=" N ASN B 370 " pdb=" CA ASN B 370 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.23e-02 6.61e+03 5.08e+00 ... (remaining 30297 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.84: 40912 3.84 - 7.68: 186 7.68 - 11.52: 8 11.52 - 15.36: 0 15.36 - 19.20: 1 Bond angle restraints: 41107 Sorted by residual: angle pdb=" O HIC K 73 " pdb=" C HIC K 73 " pdb=" N GLY K 74 " ideal model delta sigma weight residual 123.00 103.80 19.20 1.60e+00 3.91e-01 1.44e+02 angle pdb=" N ALA h 581 " pdb=" CA ALA h 581 " pdb=" C ALA h 581 " ideal model delta sigma weight residual 113.17 104.14 9.03 1.26e+00 6.30e-01 5.14e+01 angle pdb=" C ASP B 369 " pdb=" CA ASP B 369 " pdb=" CB ASP B 369 " ideal model delta sigma weight residual 109.70 116.42 -6.72 1.61e+00 3.86e-01 1.74e+01 angle pdb=" C1' ADP I 402 " pdb=" C2' ADP I 402 " pdb=" C3' ADP I 402 " ideal model delta sigma weight residual 111.00 100.09 10.91 3.00e+00 1.11e-01 1.32e+01 angle pdb=" N PHE B 371 " pdb=" CA PHE B 371 " pdb=" CB PHE B 371 " ideal model delta sigma weight residual 110.49 116.62 -6.13 1.69e+00 3.50e-01 1.32e+01 ... (remaining 41102 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.44: 17931 31.44 - 62.89: 321 62.89 - 94.33: 46 94.33 - 125.78: 3 125.78 - 157.22: 6 Dihedral angle restraints: 18307 sinusoidal: 7286 harmonic: 11021 Sorted by residual: dihedral pdb=" O1B ADP J 402 " pdb=" O3A ADP J 402 " pdb=" PB ADP J 402 " pdb=" PA ADP J 402 " ideal model delta sinusoidal sigma weight residual 300.00 142.77 157.22 1 2.00e+01 2.50e-03 4.61e+01 dihedral pdb=" O2A ADP I 402 " pdb=" O3A ADP I 402 " pdb=" PA ADP I 402 " pdb=" PB ADP I 402 " ideal model delta sinusoidal sigma weight residual -60.00 89.86 -149.86 1 2.00e+01 2.50e-03 4.48e+01 dihedral pdb=" C5' ADP K 401 " pdb=" O5' ADP K 401 " pdb=" PA ADP K 401 " pdb=" O2A ADP K 401 " ideal model delta sinusoidal sigma weight residual 300.00 153.08 146.92 1 2.00e+01 2.50e-03 4.41e+01 ... (remaining 18304 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2862 0.048 - 0.095: 1370 0.095 - 0.142: 345 0.142 - 0.190: 55 0.190 - 0.237: 9 Chirality restraints: 4641 Sorted by residual: chirality pdb=" CA ARG G 145 " pdb=" N ARG G 145 " pdb=" C ARG G 145 " pdb=" CB ARG G 145 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" C3' ADP A 502 " pdb=" C2' ADP A 502 " pdb=" C4' ADP A 502 " pdb=" O3' ADP A 502 " both_signs ideal model delta sigma weight residual False -2.51 -2.75 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CB ILE B 251 " pdb=" CA ILE B 251 " pdb=" CG1 ILE B 251 " pdb=" CG2 ILE B 251 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 4638 not shown) Planarity restraints: 5270 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIC K 73 " 0.091 2.00e-02 2.50e+03 1.64e-01 2.69e+02 pdb=" C HIC K 73 " -0.284 2.00e-02 2.50e+03 pdb=" O HIC K 73 " 0.100 2.00e-02 2.50e+03 pdb=" N GLY K 74 " 0.093 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 334 " -0.295 9.50e-02 1.11e+02 1.33e-01 1.20e+01 pdb=" NE ARG A 334 " 0.024 2.00e-02 2.50e+03 pdb=" CZ ARG A 334 " -0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG A 334 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG A 334 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 147 " 0.253 9.50e-02 1.11e+02 1.14e-01 9.05e+00 pdb=" NE ARG I 147 " -0.021 2.00e-02 2.50e+03 pdb=" CZ ARG I 147 " 0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG I 147 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG I 147 " 0.003 2.00e-02 2.50e+03 ... (remaining 5267 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 24 2.40 - 3.03: 18599 3.03 - 3.65: 42395 3.65 - 4.28: 66244 4.28 - 4.90: 109927 Nonbonded interactions: 237189 Sorted by model distance: nonbonded pdb="MG MG A 501 " pdb=" O3B ADP A 502 " model vdw 1.776 2.170 nonbonded pdb=" NE2 GLN J 137 " pdb="MG MG J 401 " model vdw 1.895 2.250 nonbonded pdb="MG MG B 401 " pdb=" O1B ADP B 402 " model vdw 1.907 2.170 nonbonded pdb=" OD2 ASP I 154 " pdb="MG MG I 401 " model vdw 1.968 2.170 nonbonded pdb=" OD2 ASP J 11 " pdb="MG MG J 401 " model vdw 2.036 2.170 ... (remaining 237184 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 'H' and (resid 307 through 366 or (resid 367 through 369 and (name N or n \ ame CA or name C or name O or name CB )) or resid 370 through 371 or (resid 372 \ and (name N or name CA or name C or name O or name CB )) or resid 373 through 49 \ 6 or (resid 497 through 498 and (name N or name CA or name C or name O or name C \ B )) or resid 499 through 543 or (resid 544 through 545 and (name N or name CA o \ r name C or name O or name CB )) or resid 546 through 595 or (resid 596 and (nam \ e N or name CA or name C or name O or name CB )) or resid 597 or (resid 598 and \ (name N or name CA or name C or name O or name CB )) or resid 599 through 601 or \ (resid 602 and (name N or name CA or name C or name O or name CB )) or resid 60 \ 3 through 626 or (resid 627 through 629 and (name N or name CA or name C or name \ O or name CB )) or resid 630 through 631 or (resid 632 and (name N or name CA o \ r name C or name O or name CB )) or resid 633 through 634 or (resid 635 through \ 636 and (name N or name CA or name C or name O or name CB )) or resid 637 throug \ h 638 or (resid 639 and (name N or name CA or name C or name O or name CB )) or \ resid 640 through 646 or (resid 647 through 649 and (name N or name CA or name C \ or name O or name CB )) or resid 650 or (resid 651 and (name N or name CA or na \ me C or name O or name CB )) or resid 652 through 658 or (resid 659 and (name N \ or name CA or name C or name O or name CB )) or resid 660 through 669 or (resid \ 670 through 671 and (name N or name CA or name C or name O or name CB )) or resi \ d 672 through 677 or (resid 678 and (name N or name CA or name C or name O or na \ me CB )) or resid 679 through 682 or (resid 683 and (name N or name CA or name C \ or name O or name CB )) or resid 684 through 691 or (resid 692 through 694 and \ (name N or name CA or name C or name O or name CB )) or resid 695 through 703 or \ (resid 704 and (name N or name CA or name C or name O or name CB )) or resid 70 \ 5 through 707 or (resid 708 and (name N or name CA or name C or name O or name C \ B )) or resid 709 through 715 or (resid 716 through 717 and (name N or name CA o \ r name C or name O or name CB )) or resid 718 through 720)) selection = (chain 'h' and (resid 307 through 367 or (resid 368 through 369 and (name N or n \ ame CA or name C or name O or name CB )) or resid 370 through 373 or (resid 374 \ and (name N or name CA or name C or name O or name CB )) or resid 375 through 71 \ 1 or (resid 712 through 713 and (name N or name CA or name C or name O or name C \ B )) or resid 714 through 720)) } ncs_group { reference = (chain 'I' and ((resid 5 and (name N or name CA or name C or name O or name CB ) \ ) or resid 6 through 11 or (resid 12 and (name N or name CA or name C or name O \ or name CB )) or resid 13 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 99 or (resid 100 and (name N or n \ ame CA or name C or name O or name CB )) or resid 101 through 166 or (resid 167 \ and (name N or name CA or name C or name O or name CB )) or resid 168 through 32 \ 2 or (resid 323 and (name N or name CA or name C or name O or name CB )) or resi \ d 324 through 371 or (resid 372 through 373 and (name N or name CA or name C or \ name O or name CB )) or resid 374 or resid 402)) selection = (chain 'J' and ((resid 5 and (name N or name CA or name C or name O or name CB ) \ ) or resid 6 through 11 or (resid 12 and (name N or name CA or name C or name O \ or name CB )) or resid 13 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 71 or (resid 72 and (name N or na \ me CA or name C or name O or name CB )) or resid 73 through 99 or (resid 100 and \ (name N or name CA or name C or name O or name CB )) or resid 101 through 322 o \ r (resid 323 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 24 through 371 or (resid 372 through 373 and (name N or name CA or name C or nam \ e O or name CB )) or resid 374 or resid 402)) selection = (chain 'K' and (resid 5 through 71 or (resid 72 and (name N or name CA or name C \ or name O or name CB )) or resid 73 through 401)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 27.810 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 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 : 0.008 0.076 30302 Z= 0.359 Angle : 0.811 19.197 41107 Z= 0.437 Chirality : 0.056 0.237 4641 Planarity : 0.009 0.164 5270 Dihedral : 13.582 157.222 11191 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % 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: -1.88 (0.13), residues: 3749 helix: -1.81 (0.10), residues: 1648 sheet: -0.53 (0.21), residues: 558 loop : -0.59 (0.16), residues: 1543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.003 ARG I 183 TYR 0.025 0.004 TYR B 310 PHE 0.035 0.003 PHE C 111 TRP 0.044 0.003 TRP J 356 HIS 0.011 0.002 HIS I 101 Details of bonding type rmsd covalent geometry : bond 0.00830 (30302) covalent geometry : angle 0.81095 (41107) hydrogen bonds : bond 0.21737 ( 1473) hydrogen bonds : angle 8.29136 ( 4002) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 476 time to evaluate : 1.047 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: B 1 MET cc_start: 0.6584 (mmt) cc_final: 0.6316 (mmt) REVERT: E 95 MET cc_start: 0.7312 (tpp) cc_final: 0.7033 (tpp) REVERT: E 116 ILE cc_start: 0.7904 (mt) cc_final: 0.7675 (mt) REVERT: E 172 SER cc_start: 0.8395 (m) cc_final: 0.7885 (p) REVERT: F 49 GLN cc_start: 0.8124 (tp40) cc_final: 0.7887 (tt0) REVERT: F 67 ILE cc_start: 0.8908 (tt) cc_final: 0.8680 (tp) REVERT: F 149 MET cc_start: 0.8258 (mmm) cc_final: 0.7989 (mmm) REVERT: G 13 LYS cc_start: 0.8038 (tttt) cc_final: 0.7778 (mttm) REVERT: H 317 MET cc_start: 0.7315 (mmm) cc_final: 0.6925 (tpp) REVERT: H 431 LYS cc_start: 0.8498 (ttpp) cc_final: 0.7312 (mmtm) REVERT: H 448 TYR cc_start: 0.8531 (t80) cc_final: 0.8316 (t80) REVERT: H 500 LYS cc_start: 0.8921 (ttpt) cc_final: 0.8514 (tmtt) REVERT: I 81 ASP cc_start: 0.7178 (m-30) cc_final: 0.6872 (m-30) REVERT: I 132 MET cc_start: 0.8434 (ppp) cc_final: 0.8040 (ppp) REVERT: J 132 MET cc_start: 0.8178 (ptm) cc_final: 0.7970 (ptm) REVERT: J 227 MET cc_start: 0.8198 (mmm) cc_final: 0.7966 (mmm) REVERT: J 291 LYS cc_start: 0.8055 (tttm) cc_final: 0.7797 (mmtt) REVERT: J 305 MET cc_start: 0.8914 (mmm) cc_final: 0.8603 (mmp) REVERT: J 320 LEU cc_start: 0.8031 (mt) cc_final: 0.7776 (mt) REVERT: K 8 LEU cc_start: 0.9137 (tt) cc_final: 0.8906 (mp) REVERT: K 49 GLN cc_start: 0.6559 (mt0) cc_final: 0.6089 (mt0) REVERT: K 59 GLN cc_start: 0.9154 (tp40) cc_final: 0.8817 (tp40) REVERT: K 111 ASN cc_start: 0.8315 (m-40) cc_final: 0.8037 (m-40) REVERT: K 217 CYS cc_start: 0.7417 (m) cc_final: 0.7181 (m) REVERT: K 290 ARG cc_start: 0.7996 (mtt180) cc_final: 0.7625 (mtt-85) REVERT: K 328 LYS cc_start: 0.8459 (ptpt) cc_final: 0.8071 (tmtt) REVERT: K 351 THR cc_start: 0.8577 (p) cc_final: 0.8286 (t) REVERT: h 353 MET cc_start: 0.8258 (mmp) cc_final: 0.7988 (mmm) REVERT: h 391 ARG cc_start: 0.8174 (ttp80) cc_final: 0.7820 (ttm110) REVERT: h 554 CYS cc_start: 0.8441 (m) cc_final: 0.7664 (t) REVERT: h 590 LEU cc_start: 0.8899 (tp) cc_final: 0.8380 (pp) REVERT: h 615 LEU cc_start: 0.8953 (mt) cc_final: 0.8702 (mp) REVERT: h 657 ARG cc_start: 0.8160 (ttp-170) cc_final: 0.7878 (ttt180) REVERT: h 664 MET cc_start: 0.8935 (tpt) cc_final: 0.8562 (tpp) outliers start: 0 outliers final: 0 residues processed: 476 average time/residue: 0.2070 time to fit residues: 150.9096 Evaluate side-chains 303 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 9.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN ** A 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 HIS C 52 ASN C 129 ASN D 101 ASN D 119 ASN D 252 HIS E 114 ASN ** F 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 HIS H 328 HIS H 380 GLN H 525 HIS H 532 GLN H 556 ASN ** H 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 280 ASN K 49 GLN K 88 HIS K 128 ASN h 522 HIS h 562 ASN h 676 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.077945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.066386 restraints weight = 109300.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.068209 restraints weight = 53077.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.069395 restraints weight = 32000.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.070167 restraints weight = 22345.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.070649 restraints weight = 17346.159| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30302 Z= 0.136 Angle : 0.658 11.821 41107 Z= 0.339 Chirality : 0.045 0.247 4641 Planarity : 0.004 0.053 5270 Dihedral : 8.492 143.768 4163 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.79 % Allowed : 5.16 % Favored : 94.05 % 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: -0.33 (0.14), residues: 3749 helix: -0.15 (0.12), residues: 1716 sheet: -0.20 (0.21), residues: 558 loop : -0.06 (0.17), residues: 1475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 161 TYR 0.029 0.001 TYR A 400 PHE 0.026 0.002 PHE B 355 TRP 0.027 0.002 TRP G 130 HIS 0.007 0.001 HIS J 101 Details of bonding type rmsd covalent geometry : bond 0.00287 (30302) covalent geometry : angle 0.65776 (41107) hydrogen bonds : bond 0.04823 ( 1473) hydrogen bonds : angle 5.27164 ( 4002) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 347 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 TRP cc_start: 0.7086 (t60) cc_final: 0.6513 (t60) REVERT: A 372 MET cc_start: 0.8294 (mmt) cc_final: 0.8029 (mmt) REVERT: B 1 MET cc_start: 0.6696 (mmt) cc_final: 0.6200 (tpp) REVERT: B 361 LEU cc_start: 0.8040 (tp) cc_final: 0.7687 (mm) REVERT: D 207 LEU cc_start: 0.8732 (pt) cc_final: 0.8497 (tp) REVERT: E 95 MET cc_start: 0.7197 (tpp) cc_final: 0.6593 (tpp) REVERT: E 102 ASN cc_start: 0.6304 (p0) cc_final: 0.6076 (p0) REVERT: E 170 ASN cc_start: 0.8705 (t0) cc_final: 0.8347 (t0) REVERT: F 49 GLN cc_start: 0.7900 (tp40) cc_final: 0.7589 (tt0) REVERT: F 80 ASP cc_start: 0.7836 (t0) cc_final: 0.7218 (t0) REVERT: F 149 MET cc_start: 0.7688 (mmm) cc_final: 0.7422 (mtm) REVERT: G 93 ILE cc_start: 0.8026 (tt) cc_final: 0.7673 (mp) REVERT: H 317 MET cc_start: 0.7005 (mmm) cc_final: 0.6796 (tmm) REVERT: H 431 LYS cc_start: 0.8388 (ttpp) cc_final: 0.7479 (mmtp) REVERT: H 436 ASN cc_start: 0.7281 (t0) cc_final: 0.7022 (t0) REVERT: H 500 LYS cc_start: 0.8964 (ttpt) cc_final: 0.8577 (tmtt) REVERT: H 579 LYS cc_start: 0.8860 (mttt) cc_final: 0.8277 (mtmm) REVERT: I 44 MET cc_start: 0.4446 (tmm) cc_final: 0.4046 (tmm) REVERT: I 80 ASP cc_start: 0.7923 (OUTLIER) cc_final: 0.7548 (m-30) REVERT: I 81 ASP cc_start: 0.7223 (m-30) cc_final: 0.6915 (m-30) REVERT: J 82 MET cc_start: 0.7551 (tpt) cc_final: 0.7054 (tpp) REVERT: J 132 MET cc_start: 0.8141 (ptm) cc_final: 0.7923 (ptm) REVERT: J 285 CYS cc_start: 0.8160 (m) cc_final: 0.7647 (m) REVERT: J 291 LYS cc_start: 0.8082 (tttm) cc_final: 0.7691 (mmtt) REVERT: J 305 MET cc_start: 0.9057 (mmm) cc_final: 0.8784 (mmp) REVERT: J 320 LEU cc_start: 0.7949 (mt) cc_final: 0.7583 (mt) REVERT: K 113 LYS cc_start: 0.8531 (mtpt) cc_final: 0.8304 (ttmt) REVERT: K 132 MET cc_start: 0.8273 (tmm) cc_final: 0.8036 (tmm) REVERT: K 161 HIS cc_start: 0.7675 (p-80) cc_final: 0.7464 (p-80) REVERT: K 217 CYS cc_start: 0.7695 (m) cc_final: 0.7429 (m) REVERT: K 280 ASN cc_start: 0.8770 (m-40) cc_final: 0.8527 (m110) REVERT: K 283 MET cc_start: 0.8936 (mmm) cc_final: 0.8684 (mmm) REVERT: K 290 ARG cc_start: 0.7776 (mtt180) cc_final: 0.7248 (mtt-85) REVERT: K 299 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8372 (mtp) REVERT: K 340 TRP cc_start: 0.8531 (t60) cc_final: 0.7321 (t60) REVERT: K 357 ILE cc_start: 0.8429 (mm) cc_final: 0.7968 (mm) REVERT: h 353 MET cc_start: 0.8169 (mmp) cc_final: 0.7773 (mmp) REVERT: h 391 ARG cc_start: 0.8239 (ttp80) cc_final: 0.7789 (ttm110) REVERT: h 467 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.7721 (mtp) REVERT: h 491 MET cc_start: 0.8160 (ttm) cc_final: 0.7875 (mtp) REVERT: h 562 ASN cc_start: 0.8690 (t0) cc_final: 0.8438 (t0) REVERT: h 590 LEU cc_start: 0.8702 (tp) cc_final: 0.8196 (pp) REVERT: h 661 LEU cc_start: 0.9253 (tp) cc_final: 0.8971 (mt) REVERT: h 664 MET cc_start: 0.8941 (tpt) cc_final: 0.8351 (tmm) REVERT: h 705 MET cc_start: 0.8621 (mtt) cc_final: 0.8334 (ptp) outliers start: 25 outliers final: 9 residues processed: 357 average time/residue: 0.1899 time to fit residues: 107.0026 Evaluate side-chains 296 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 284 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 352 HIS Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain K residue 299 MET Chi-restraints excluded: chain K residue 311 ASP Chi-restraints excluded: chain h residue 467 MET Chi-restraints excluded: chain h residue 552 ASP Chi-restraints excluded: chain h residue 574 MET Chi-restraints excluded: chain h residue 593 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 361 optimal weight: 20.0000 chunk 102 optimal weight: 0.0870 chunk 188 optimal weight: 0.4980 chunk 132 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 358 optimal weight: 8.9990 chunk 237 optimal weight: 9.9990 chunk 334 optimal weight: 9.9990 chunk 82 optimal weight: 1.9990 chunk 119 optimal weight: 10.0000 chunk 225 optimal weight: 4.9990 overall best weight: 2.9164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 HIS B 206 HIS ** B 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 HIS H 328 HIS ** H 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 101 HIS K 162 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.076890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.065560 restraints weight = 111024.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.067275 restraints weight = 55980.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.068363 restraints weight = 34630.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.069094 restraints weight = 24754.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.069560 restraints weight = 19523.981| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 30302 Z= 0.188 Angle : 0.633 8.907 41107 Z= 0.324 Chirality : 0.046 0.219 4641 Planarity : 0.004 0.046 5270 Dihedral : 8.083 146.562 4163 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.01 % Allowed : 7.69 % Favored : 91.30 % 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: 0.01 (0.14), residues: 3749 helix: 0.30 (0.13), residues: 1708 sheet: -0.16 (0.21), residues: 566 loop : -0.04 (0.17), residues: 1475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 372 TYR 0.015 0.001 TYR B 131 PHE 0.023 0.002 PHE A 131 TRP 0.016 0.002 TRP J 356 HIS 0.007 0.001 HIS F 88 Details of bonding type rmsd covalent geometry : bond 0.00426 (30302) covalent geometry : angle 0.63266 (41107) hydrogen bonds : bond 0.04526 ( 1473) hydrogen bonds : angle 4.98193 ( 4002) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 294 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 TRP cc_start: 0.7152 (t60) cc_final: 0.6639 (t60) REVERT: A 372 MET cc_start: 0.8462 (mmt) cc_final: 0.8141 (mmt) REVERT: E 95 MET cc_start: 0.7316 (tpp) cc_final: 0.6784 (tpp) REVERT: E 102 ASN cc_start: 0.6314 (p0) cc_final: 0.6004 (p0) REVERT: E 170 ASN cc_start: 0.8553 (t0) cc_final: 0.8344 (t0) REVERT: F 149 MET cc_start: 0.7705 (mmm) cc_final: 0.7343 (mtm) REVERT: G 93 ILE cc_start: 0.7952 (tt) cc_final: 0.7644 (mp) REVERT: G 94 GLU cc_start: 0.7977 (tp30) cc_final: 0.7772 (tp30) REVERT: H 431 LYS cc_start: 0.8455 (ttpp) cc_final: 0.7562 (mmtp) REVERT: H 436 ASN cc_start: 0.7245 (t0) cc_final: 0.6995 (t0) REVERT: H 579 LYS cc_start: 0.8802 (mttt) cc_final: 0.8323 (mtmm) REVERT: H 658 MET cc_start: 0.7665 (tmm) cc_final: 0.7337 (ptp) REVERT: H 664 MET cc_start: 0.8678 (mmm) cc_final: 0.8371 (tpt) REVERT: I 44 MET cc_start: 0.4348 (tmm) cc_final: 0.4059 (tmm) REVERT: I 80 ASP cc_start: 0.7724 (OUTLIER) cc_final: 0.7329 (m-30) REVERT: I 81 ASP cc_start: 0.7041 (m-30) cc_final: 0.6764 (m-30) REVERT: I 269 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7765 (ttm) REVERT: J 82 MET cc_start: 0.7427 (tpt) cc_final: 0.6999 (tpp) REVERT: J 132 MET cc_start: 0.8109 (ptm) cc_final: 0.7892 (ptm) REVERT: J 283 MET cc_start: 0.8522 (mmt) cc_final: 0.8176 (mmm) REVERT: J 285 CYS cc_start: 0.8347 (m) cc_final: 0.7924 (m) REVERT: J 291 LYS cc_start: 0.8098 (tttm) cc_final: 0.7786 (mmtt) REVERT: J 305 MET cc_start: 0.9001 (mmm) cc_final: 0.8699 (mmp) REVERT: K 72 GLU cc_start: 0.7473 (mm-30) cc_final: 0.7221 (mm-30) REVERT: K 161 HIS cc_start: 0.7717 (p-80) cc_final: 0.7457 (p-80) REVERT: K 227 MET cc_start: 0.8715 (mmm) cc_final: 0.8442 (mmm) REVERT: K 290 ARG cc_start: 0.7845 (mtt180) cc_final: 0.7354 (mtt-85) REVERT: K 340 TRP cc_start: 0.8516 (t60) cc_final: 0.7349 (t60) REVERT: K 357 ILE cc_start: 0.8529 (mm) cc_final: 0.8105 (mm) REVERT: h 353 MET cc_start: 0.8069 (mmp) cc_final: 0.7818 (mmp) REVERT: h 382 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8260 (mt) REVERT: h 391 ARG cc_start: 0.8234 (ttp80) cc_final: 0.7860 (ttm110) REVERT: h 467 MET cc_start: 0.7897 (OUTLIER) cc_final: 0.7455 (mpp) REVERT: h 491 MET cc_start: 0.7989 (ttm) cc_final: 0.7717 (mtp) REVERT: h 562 ASN cc_start: 0.8752 (t0) cc_final: 0.8512 (t0) REVERT: h 590 LEU cc_start: 0.8688 (tp) cc_final: 0.8149 (pp) REVERT: h 661 LEU cc_start: 0.9276 (tp) cc_final: 0.8992 (mt) REVERT: h 664 MET cc_start: 0.8925 (tpt) cc_final: 0.8365 (tmm) REVERT: h 702 MET cc_start: 0.7829 (mmm) cc_final: 0.7552 (mmm) REVERT: h 705 MET cc_start: 0.8571 (mtt) cc_final: 0.8282 (ptp) outliers start: 32 outliers final: 18 residues processed: 314 average time/residue: 0.1696 time to fit residues: 85.6119 Evaluate side-chains 296 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 274 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 352 HIS Chi-restraints excluded: chain B residue 372 TRP Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain E residue 83 GLN Chi-restraints excluded: chain F residue 129 HIS Chi-restraints excluded: chain H residue 418 LEU Chi-restraints excluded: chain H residue 542 LEU Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain J residue 287 ILE Chi-restraints excluded: chain K residue 274 ILE Chi-restraints excluded: chain K residue 311 ASP Chi-restraints excluded: chain h residue 382 LEU Chi-restraints excluded: chain h residue 467 MET Chi-restraints excluded: chain h residue 552 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 122 optimal weight: 8.9990 chunk 54 optimal weight: 8.9990 chunk 154 optimal weight: 4.9990 chunk 310 optimal weight: 8.9990 chunk 249 optimal weight: 7.9990 chunk 267 optimal weight: 5.9990 chunk 120 optimal weight: 0.7980 chunk 105 optimal weight: 5.9990 chunk 272 optimal weight: 6.9990 chunk 82 optimal weight: 10.0000 chunk 358 optimal weight: 10.0000 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 HIS B 323 GLN C 30 HIS E 57 ASN ** F 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 676 HIS K 92 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.075604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.064314 restraints weight = 111388.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.065974 restraints weight = 56891.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.067048 restraints weight = 35570.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.067732 restraints weight = 25557.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.068191 restraints weight = 20410.643| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 30302 Z= 0.281 Angle : 0.687 8.456 41107 Z= 0.352 Chirality : 0.048 0.173 4641 Planarity : 0.005 0.044 5270 Dihedral : 7.992 146.924 4163 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.46 % Allowed : 9.62 % Favored : 88.93 % 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: -0.15 (0.14), residues: 3749 helix: 0.26 (0.13), residues: 1723 sheet: -0.20 (0.22), residues: 560 loop : -0.28 (0.16), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 166 TYR 0.030 0.002 TYR A 400 PHE 0.032 0.002 PHE C 111 TRP 0.015 0.002 TRP J 356 HIS 0.020 0.002 HIS F 129 Details of bonding type rmsd covalent geometry : bond 0.00642 (30302) covalent geometry : angle 0.68710 (41107) hydrogen bonds : bond 0.04674 ( 1473) hydrogen bonds : angle 5.02200 ( 4002) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 279 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 TRP cc_start: 0.7147 (t60) cc_final: 0.6761 (t60) REVERT: A 222 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6957 (pt0) REVERT: A 372 MET cc_start: 0.8502 (mmt) cc_final: 0.8072 (mmt) REVERT: D 266 MET cc_start: 0.7563 (tpp) cc_final: 0.7116 (mmt) REVERT: E 102 ASN cc_start: 0.6456 (p0) cc_final: 0.6147 (p0) REVERT: G 93 ILE cc_start: 0.8105 (tt) cc_final: 0.7893 (mm) REVERT: H 431 LYS cc_start: 0.8506 (ttpp) cc_final: 0.7600 (mmtp) REVERT: H 436 ASN cc_start: 0.7403 (t0) cc_final: 0.7129 (t0) REVERT: I 80 ASP cc_start: 0.7819 (OUTLIER) cc_final: 0.7365 (m-30) REVERT: I 81 ASP cc_start: 0.7044 (m-30) cc_final: 0.6740 (m-30) REVERT: I 269 MET cc_start: 0.8014 (OUTLIER) cc_final: 0.7802 (ttm) REVERT: J 47 MET cc_start: 0.7958 (ttp) cc_final: 0.7750 (ptp) REVERT: J 82 MET cc_start: 0.7480 (tpt) cc_final: 0.6916 (tpp) REVERT: J 123 MET cc_start: 0.8714 (mmm) cc_final: 0.8399 (tpp) REVERT: J 283 MET cc_start: 0.8525 (mmt) cc_final: 0.8066 (mmm) REVERT: J 285 CYS cc_start: 0.8466 (m) cc_final: 0.7980 (m) REVERT: J 291 LYS cc_start: 0.8147 (tttm) cc_final: 0.7799 (mmtt) REVERT: J 305 MET cc_start: 0.8978 (mmm) cc_final: 0.8655 (mmp) REVERT: K 132 MET cc_start: 0.7982 (tmm) cc_final: 0.7465 (tmm) REVERT: K 161 HIS cc_start: 0.7788 (p-80) cc_final: 0.7544 (p-80) REVERT: K 280 ASN cc_start: 0.8795 (m-40) cc_final: 0.8572 (m110) REVERT: K 290 ARG cc_start: 0.7883 (mtt180) cc_final: 0.7497 (mtt180) REVERT: K 296 ASN cc_start: 0.7852 (m-40) cc_final: 0.7258 (m110) REVERT: K 357 ILE cc_start: 0.8501 (mm) cc_final: 0.8127 (mm) REVERT: h 353 MET cc_start: 0.8144 (mmp) cc_final: 0.7889 (mmp) REVERT: h 358 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.8073 (tm) REVERT: h 391 ARG cc_start: 0.8413 (ttp80) cc_final: 0.8021 (ttm110) REVERT: h 467 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.7561 (mpp) REVERT: h 491 MET cc_start: 0.8077 (ttm) cc_final: 0.7738 (mtp) REVERT: h 562 ASN cc_start: 0.8859 (t0) cc_final: 0.8623 (t0) REVERT: h 590 LEU cc_start: 0.8761 (tp) cc_final: 0.8320 (pp) REVERT: h 615 LEU cc_start: 0.8916 (mp) cc_final: 0.8510 (pp) REVERT: h 637 MET cc_start: 0.7799 (mmm) cc_final: 0.7459 (mmp) REVERT: h 661 LEU cc_start: 0.9260 (tp) cc_final: 0.9022 (mt) REVERT: h 664 MET cc_start: 0.8921 (tpt) cc_final: 0.8338 (tmm) REVERT: h 702 MET cc_start: 0.7804 (mmm) cc_final: 0.7583 (mmm) REVERT: h 705 MET cc_start: 0.8712 (mtt) cc_final: 0.8488 (ptp) outliers start: 46 outliers final: 29 residues processed: 309 average time/residue: 0.1774 time to fit residues: 88.7543 Evaluate side-chains 300 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 266 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 352 HIS Chi-restraints excluded: chain B residue 372 TRP Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain E residue 18 ASN Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain G residue 53 MET Chi-restraints excluded: chain H residue 338 ILE Chi-restraints excluded: chain H residue 418 LEU Chi-restraints excluded: chain H residue 542 LEU Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain J residue 269 MET Chi-restraints excluded: chain J residue 287 ILE Chi-restraints excluded: chain K residue 274 ILE Chi-restraints excluded: chain K residue 311 ASP Chi-restraints excluded: chain K residue 320 LEU Chi-restraints excluded: chain h residue 358 LEU Chi-restraints excluded: chain h residue 467 MET Chi-restraints excluded: chain h residue 552 ASP Chi-restraints excluded: chain h residue 574 MET Chi-restraints excluded: chain h residue 593 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 141 optimal weight: 4.9990 chunk 128 optimal weight: 0.8980 chunk 229 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 342 optimal weight: 0.8980 chunk 325 optimal weight: 9.9990 chunk 162 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 238 optimal weight: 5.9990 chunk 351 optimal weight: 6.9990 chunk 155 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 ASN E 57 ASN F 28 GLN F 129 HIS ** H 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.077219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.065936 restraints weight = 110690.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.067653 restraints weight = 55306.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.068754 restraints weight = 34097.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.069403 restraints weight = 24315.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.069926 restraints weight = 19428.285| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30302 Z= 0.126 Angle : 0.579 13.209 41107 Z= 0.292 Chirality : 0.043 0.166 4641 Planarity : 0.004 0.047 5270 Dihedral : 7.454 151.698 4163 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.33 % Allowed : 10.60 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.14), residues: 3749 helix: 0.64 (0.13), residues: 1722 sheet: -0.07 (0.22), residues: 559 loop : -0.12 (0.17), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 166 TYR 0.018 0.001 TYR A 400 PHE 0.028 0.001 PHE E 168 TRP 0.015 0.001 TRP K 79 HIS 0.010 0.001 HIS F 129 Details of bonding type rmsd covalent geometry : bond 0.00282 (30302) covalent geometry : angle 0.57869 (41107) hydrogen bonds : bond 0.03755 ( 1473) hydrogen bonds : angle 4.63617 ( 4002) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 292 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 TRP cc_start: 0.7069 (t60) cc_final: 0.6631 (t60) REVERT: A 372 MET cc_start: 0.8389 (mmt) cc_final: 0.7992 (mmt) REVERT: B 1 MET cc_start: 0.5538 (mmt) cc_final: 0.5218 (tpt) REVERT: B 346 ASP cc_start: 0.7440 (p0) cc_final: 0.7196 (p0) REVERT: D 1 MET cc_start: 0.7168 (mtm) cc_final: 0.6785 (ttp) REVERT: D 266 MET cc_start: 0.7418 (tpp) cc_final: 0.6956 (mmt) REVERT: E 95 MET cc_start: 0.6963 (tpp) cc_final: 0.6483 (tpp) REVERT: E 102 ASN cc_start: 0.6436 (p0) cc_final: 0.6103 (p0) REVERT: E 167 GLN cc_start: 0.7494 (tt0) cc_final: 0.6951 (tt0) REVERT: F 129 HIS cc_start: 0.6300 (OUTLIER) cc_final: 0.6079 (p-80) REVERT: F 149 MET cc_start: 0.7723 (OUTLIER) cc_final: 0.7229 (mpp) REVERT: G 93 ILE cc_start: 0.7894 (tt) cc_final: 0.7632 (mm) REVERT: H 357 LEU cc_start: 0.8142 (mt) cc_final: 0.7891 (tp) REVERT: H 413 TYR cc_start: 0.7834 (m-80) cc_final: 0.6807 (t80) REVERT: H 432 MET cc_start: 0.7197 (mmm) cc_final: 0.6647 (mmm) REVERT: H 436 ASN cc_start: 0.7546 (t0) cc_final: 0.7221 (t0) REVERT: H 658 MET cc_start: 0.7633 (tmm) cc_final: 0.7082 (ptp) REVERT: I 80 ASP cc_start: 0.7735 (OUTLIER) cc_final: 0.7371 (m-30) REVERT: I 81 ASP cc_start: 0.7013 (m-30) cc_final: 0.6685 (m-30) REVERT: I 269 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.7786 (ttm) REVERT: J 82 MET cc_start: 0.7401 (tpt) cc_final: 0.6802 (tpp) REVERT: J 283 MET cc_start: 0.8524 (mmt) cc_final: 0.8098 (mmm) REVERT: J 285 CYS cc_start: 0.8319 (m) cc_final: 0.7822 (m) REVERT: J 291 LYS cc_start: 0.8172 (tttm) cc_final: 0.7856 (mmtt) REVERT: J 305 MET cc_start: 0.8962 (mmm) cc_final: 0.8632 (mmp) REVERT: K 82 MET cc_start: 0.8093 (tpp) cc_final: 0.7813 (tpp) REVERT: K 132 MET cc_start: 0.7961 (tmm) cc_final: 0.7367 (tmm) REVERT: K 290 ARG cc_start: 0.7827 (mtt180) cc_final: 0.7527 (mtt180) REVERT: K 296 ASN cc_start: 0.7649 (m-40) cc_final: 0.7074 (m110) REVERT: K 327 ILE cc_start: 0.7740 (OUTLIER) cc_final: 0.7516 (tp) REVERT: K 357 ILE cc_start: 0.8439 (mm) cc_final: 0.7999 (mm) REVERT: h 353 MET cc_start: 0.8051 (mmp) cc_final: 0.7788 (mmp) REVERT: h 358 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7888 (tm) REVERT: h 391 ARG cc_start: 0.8210 (ttp80) cc_final: 0.7808 (ttm110) REVERT: h 467 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.7398 (mpp) REVERT: h 491 MET cc_start: 0.7994 (ttm) cc_final: 0.7575 (mtp) REVERT: h 510 MET cc_start: 0.8196 (OUTLIER) cc_final: 0.7977 (ttp) REVERT: h 562 ASN cc_start: 0.8814 (t0) cc_final: 0.8577 (t0) REVERT: h 590 LEU cc_start: 0.8647 (tp) cc_final: 0.8149 (pp) REVERT: h 615 LEU cc_start: 0.8878 (mp) cc_final: 0.8464 (pp) REVERT: h 637 MET cc_start: 0.7690 (mmm) cc_final: 0.7429 (mmp) REVERT: h 661 LEU cc_start: 0.9220 (tp) cc_final: 0.9003 (mt) REVERT: h 664 MET cc_start: 0.8918 (tpt) cc_final: 0.8368 (tmm) REVERT: h 705 MET cc_start: 0.8618 (mtt) cc_final: 0.8407 (ptp) outliers start: 42 outliers final: 21 residues processed: 316 average time/residue: 0.1811 time to fit residues: 93.6160 Evaluate side-chains 301 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 272 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 352 HIS Chi-restraints excluded: chain B residue 372 TRP Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain E residue 18 ASN Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 129 HIS Chi-restraints excluded: chain F residue 149 MET Chi-restraints excluded: chain G residue 53 MET Chi-restraints excluded: chain H residue 409 VAL Chi-restraints excluded: chain H residue 418 LEU Chi-restraints excluded: chain H residue 542 LEU Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain K residue 274 ILE Chi-restraints excluded: chain K residue 311 ASP Chi-restraints excluded: chain K residue 320 LEU Chi-restraints excluded: chain K residue 327 ILE Chi-restraints excluded: chain h residue 358 LEU Chi-restraints excluded: chain h residue 467 MET Chi-restraints excluded: chain h residue 510 MET Chi-restraints excluded: chain h residue 552 ASP Chi-restraints excluded: chain h residue 571 ASN Chi-restraints excluded: chain h residue 658 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 261 optimal weight: 10.0000 chunk 270 optimal weight: 7.9990 chunk 281 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 218 optimal weight: 0.8980 chunk 33 optimal weight: 7.9990 chunk 225 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 157 optimal weight: 0.3980 chunk 356 optimal weight: 10.0000 chunk 118 optimal weight: 6.9990 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 HIS ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 HIS H 323 ASN ** H 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 87 HIS K 162 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.076082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.064707 restraints weight = 112938.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.066476 restraints weight = 57065.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.067637 restraints weight = 35225.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.068377 restraints weight = 25028.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.068887 restraints weight = 19714.752| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 30302 Z= 0.207 Angle : 0.625 15.997 41107 Z= 0.316 Chirality : 0.045 0.184 4641 Planarity : 0.004 0.046 5270 Dihedral : 7.527 170.873 4163 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.55 % Allowed : 10.95 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.14), residues: 3749 helix: 0.67 (0.13), residues: 1711 sheet: -0.10 (0.22), residues: 567 loop : -0.24 (0.16), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 166 TYR 0.017 0.001 TYR A 400 PHE 0.033 0.002 PHE E 168 TRP 0.029 0.002 TRP G 130 HIS 0.022 0.001 HIS F 129 Details of bonding type rmsd covalent geometry : bond 0.00475 (30302) covalent geometry : angle 0.62542 (41107) hydrogen bonds : bond 0.04048 ( 1473) hydrogen bonds : angle 4.69500 ( 4002) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 271 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 TRP cc_start: 0.6976 (t60) cc_final: 0.6544 (t60) REVERT: A 372 MET cc_start: 0.8440 (mmt) cc_final: 0.7960 (mmt) REVERT: B 158 ASP cc_start: 0.7245 (t0) cc_final: 0.6917 (t0) REVERT: D 1 MET cc_start: 0.7225 (mtm) cc_final: 0.6823 (ttp) REVERT: D 266 MET cc_start: 0.7428 (tpp) cc_final: 0.7059 (mmt) REVERT: E 95 MET cc_start: 0.7015 (tpp) cc_final: 0.6577 (tpp) REVERT: E 102 ASN cc_start: 0.6488 (p0) cc_final: 0.6152 (p0) REVERT: E 167 GLN cc_start: 0.7228 (tt0) cc_final: 0.6666 (tt0) REVERT: H 357 LEU cc_start: 0.8135 (mt) cc_final: 0.7893 (tp) REVERT: H 413 TYR cc_start: 0.7882 (m-80) cc_final: 0.6876 (t80) REVERT: H 432 MET cc_start: 0.7273 (mmm) cc_final: 0.6838 (mmm) REVERT: H 436 ASN cc_start: 0.7597 (t0) cc_final: 0.7264 (t0) REVERT: H 637 MET cc_start: 0.7749 (tpp) cc_final: 0.6870 (mpp) REVERT: I 80 ASP cc_start: 0.7799 (OUTLIER) cc_final: 0.7329 (m-30) REVERT: I 81 ASP cc_start: 0.6996 (m-30) cc_final: 0.6661 (m-30) REVERT: I 269 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7839 (ttm) REVERT: J 82 MET cc_start: 0.7434 (tpt) cc_final: 0.6849 (tpp) REVERT: J 283 MET cc_start: 0.8530 (mmt) cc_final: 0.8066 (mmm) REVERT: J 285 CYS cc_start: 0.8478 (m) cc_final: 0.7918 (m) REVERT: J 291 LYS cc_start: 0.8193 (tttm) cc_final: 0.7863 (mmtt) REVERT: J 305 MET cc_start: 0.8977 (mmm) cc_final: 0.8671 (mmp) REVERT: K 82 MET cc_start: 0.8011 (tpp) cc_final: 0.7756 (tpp) REVERT: K 132 MET cc_start: 0.7999 (tmm) cc_final: 0.7415 (tmm) REVERT: K 290 ARG cc_start: 0.7884 (mtt180) cc_final: 0.7611 (mtt180) REVERT: K 296 ASN cc_start: 0.7626 (m-40) cc_final: 0.7109 (m110) REVERT: K 357 ILE cc_start: 0.8533 (mm) cc_final: 0.8126 (mm) REVERT: h 353 MET cc_start: 0.8037 (mmp) cc_final: 0.7784 (mmp) REVERT: h 358 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7962 (tm) REVERT: h 391 ARG cc_start: 0.8252 (ttp80) cc_final: 0.7871 (ttm110) REVERT: h 467 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.7528 (mpp) REVERT: h 491 MET cc_start: 0.8025 (ttm) cc_final: 0.7706 (mtp) REVERT: h 562 ASN cc_start: 0.8784 (t0) cc_final: 0.8567 (t0) REVERT: h 590 LEU cc_start: 0.8704 (tp) cc_final: 0.8231 (pp) REVERT: h 615 LEU cc_start: 0.8769 (mp) cc_final: 0.8445 (pp) REVERT: h 664 MET cc_start: 0.8850 (tpt) cc_final: 0.8323 (tmm) REVERT: h 702 MET cc_start: 0.7923 (mmm) cc_final: 0.7623 (mmm) REVERT: h 705 MET cc_start: 0.8661 (mtt) cc_final: 0.8449 (ptp) outliers start: 49 outliers final: 31 residues processed: 300 average time/residue: 0.1826 time to fit residues: 89.8127 Evaluate side-chains 289 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 254 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 352 HIS Chi-restraints excluded: chain B residue 372 TRP Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain C residue 30 HIS Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 129 HIS Chi-restraints excluded: chain G residue 53 MET Chi-restraints excluded: chain H residue 409 VAL Chi-restraints excluded: chain H residue 418 LEU Chi-restraints excluded: chain H residue 542 LEU Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain K residue 87 HIS Chi-restraints excluded: chain K residue 179 ASP Chi-restraints excluded: chain K residue 311 ASP Chi-restraints excluded: chain K residue 320 LEU Chi-restraints excluded: chain h residue 358 LEU Chi-restraints excluded: chain h residue 368 MET Chi-restraints excluded: chain h residue 467 MET Chi-restraints excluded: chain h residue 552 ASP Chi-restraints excluded: chain h residue 571 ASN Chi-restraints excluded: chain h residue 574 MET Chi-restraints excluded: chain h residue 655 LYS Chi-restraints excluded: chain h residue 658 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 325 optimal weight: 7.9990 chunk 290 optimal weight: 3.9990 chunk 98 optimal weight: 8.9990 chunk 300 optimal weight: 10.0000 chunk 253 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 149 optimal weight: 8.9990 chunk 150 optimal weight: 7.9990 chunk 52 optimal weight: 0.3980 chunk 56 optimal weight: 9.9990 chunk 335 optimal weight: 9.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 HIS ** H 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 87 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.076175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.064887 restraints weight = 110542.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.066549 restraints weight = 55506.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.067641 restraints weight = 34437.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.068353 restraints weight = 24626.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.068805 restraints weight = 19480.323| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 30302 Z= 0.197 Angle : 0.627 14.970 41107 Z= 0.315 Chirality : 0.045 0.314 4641 Planarity : 0.004 0.046 5270 Dihedral : 7.467 170.431 4163 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.65 % Allowed : 11.67 % Favored : 86.68 % 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: 0.21 (0.14), residues: 3749 helix: 0.72 (0.13), residues: 1710 sheet: -0.13 (0.22), residues: 568 loop : -0.28 (0.16), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 166 TYR 0.017 0.001 TYR A 400 PHE 0.027 0.002 PHE B 355 TRP 0.021 0.002 TRP K 79 HIS 0.022 0.001 HIS F 129 Details of bonding type rmsd covalent geometry : bond 0.00452 (30302) covalent geometry : angle 0.62679 (41107) hydrogen bonds : bond 0.04011 ( 1473) hydrogen bonds : angle 4.66834 ( 4002) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 267 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 ASP cc_start: 0.7807 (OUTLIER) cc_final: 0.7593 (t0) REVERT: A 153 TRP cc_start: 0.6978 (t60) cc_final: 0.6581 (t60) REVERT: A 372 MET cc_start: 0.8449 (mmt) cc_final: 0.7957 (mmm) REVERT: B 158 ASP cc_start: 0.7239 (t0) cc_final: 0.6917 (t0) REVERT: B 246 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7744 (mp) REVERT: D 1 MET cc_start: 0.7203 (mtm) cc_final: 0.6845 (ttp) REVERT: D 266 MET cc_start: 0.7415 (tpp) cc_final: 0.6992 (mmt) REVERT: E 95 MET cc_start: 0.6995 (tpp) cc_final: 0.6561 (tpp) REVERT: E 102 ASN cc_start: 0.6512 (p0) cc_final: 0.6161 (p0) REVERT: E 167 GLN cc_start: 0.7136 (tt0) cc_final: 0.6663 (tt0) REVERT: H 357 LEU cc_start: 0.8206 (mt) cc_final: 0.7937 (tp) REVERT: H 413 TYR cc_start: 0.7884 (m-80) cc_final: 0.6875 (t80) REVERT: H 432 MET cc_start: 0.7184 (mmm) cc_final: 0.6778 (mmm) REVERT: H 436 ASN cc_start: 0.7588 (t0) cc_final: 0.7259 (t0) REVERT: H 637 MET cc_start: 0.7701 (tpp) cc_final: 0.6891 (mpp) REVERT: I 80 ASP cc_start: 0.7695 (OUTLIER) cc_final: 0.7216 (m-30) REVERT: I 81 ASP cc_start: 0.6953 (m-30) cc_final: 0.6613 (m-30) REVERT: I 269 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.7824 (ttm) REVERT: J 82 MET cc_start: 0.7392 (tpt) cc_final: 0.6836 (tpp) REVERT: J 283 MET cc_start: 0.8497 (mmt) cc_final: 0.8036 (mmm) REVERT: J 285 CYS cc_start: 0.8446 (m) cc_final: 0.7888 (m) REVERT: J 291 LYS cc_start: 0.8177 (tttm) cc_final: 0.7856 (mmtt) REVERT: J 305 MET cc_start: 0.8940 (mmm) cc_final: 0.8605 (mmp) REVERT: K 82 MET cc_start: 0.8151 (tpp) cc_final: 0.7890 (tpp) REVERT: K 120 THR cc_start: 0.9207 (m) cc_final: 0.9004 (p) REVERT: K 132 MET cc_start: 0.8036 (tmm) cc_final: 0.7406 (tmm) REVERT: K 290 ARG cc_start: 0.7834 (mtt180) cc_final: 0.7555 (mtt180) REVERT: K 357 ILE cc_start: 0.8413 (mm) cc_final: 0.7972 (mm) REVERT: h 353 MET cc_start: 0.8093 (mmp) cc_final: 0.7830 (mmp) REVERT: h 358 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7970 (tm) REVERT: h 391 ARG cc_start: 0.8294 (ttp80) cc_final: 0.7884 (ttm110) REVERT: h 467 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7513 (mpp) REVERT: h 491 MET cc_start: 0.8059 (ttm) cc_final: 0.7718 (mtp) REVERT: h 562 ASN cc_start: 0.8790 (t0) cc_final: 0.8552 (t0) REVERT: h 590 LEU cc_start: 0.8661 (tp) cc_final: 0.8184 (pp) REVERT: h 664 MET cc_start: 0.8958 (tpt) cc_final: 0.8442 (tmm) REVERT: h 702 MET cc_start: 0.7841 (mmm) cc_final: 0.7561 (mmm) REVERT: h 705 MET cc_start: 0.8705 (mtt) cc_final: 0.8473 (ptp) outliers start: 52 outliers final: 39 residues processed: 300 average time/residue: 0.1915 time to fit residues: 93.6065 Evaluate side-chains 305 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 260 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 352 HIS Chi-restraints excluded: chain B residue 372 TRP Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 30 HIS Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain E residue 18 ASN Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 129 HIS Chi-restraints excluded: chain G residue 53 MET Chi-restraints excluded: chain H residue 409 VAL Chi-restraints excluded: chain H residue 418 LEU Chi-restraints excluded: chain H residue 542 LEU Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain J residue 287 ILE Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 282 ILE Chi-restraints excluded: chain K residue 311 ASP Chi-restraints excluded: chain K residue 320 LEU Chi-restraints excluded: chain h residue 358 LEU Chi-restraints excluded: chain h residue 368 MET Chi-restraints excluded: chain h residue 467 MET Chi-restraints excluded: chain h residue 552 ASP Chi-restraints excluded: chain h residue 571 ASN Chi-restraints excluded: chain h residue 574 MET Chi-restraints excluded: chain h residue 658 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 287 optimal weight: 8.9990 chunk 178 optimal weight: 6.9990 chunk 161 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 183 optimal weight: 10.0000 chunk 342 optimal weight: 0.7980 chunk 179 optimal weight: 3.9990 chunk 166 optimal weight: 6.9990 chunk 339 optimal weight: 9.9990 chunk 309 optimal weight: 9.9990 chunk 175 optimal weight: 6.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 HIS H 436 ASN K 87 HIS K 162 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.075275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.064020 restraints weight = 111484.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.065692 restraints weight = 56807.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.066750 restraints weight = 35405.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.067448 restraints weight = 25475.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.067889 restraints weight = 20249.879| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 30302 Z= 0.283 Angle : 0.689 14.276 41107 Z= 0.348 Chirality : 0.048 0.262 4641 Planarity : 0.005 0.045 5270 Dihedral : 7.566 168.187 4163 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.87 % Allowed : 11.99 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.14), residues: 3749 helix: 0.64 (0.13), residues: 1701 sheet: -0.24 (0.22), residues: 570 loop : -0.38 (0.16), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 166 TYR 0.015 0.002 TYR K 53 PHE 0.031 0.002 PHE B 355 TRP 0.024 0.002 TRP G 130 HIS 0.016 0.001 HIS F 129 Details of bonding type rmsd covalent geometry : bond 0.00646 (30302) covalent geometry : angle 0.68879 (41107) hydrogen bonds : bond 0.04408 ( 1473) hydrogen bonds : angle 4.81880 ( 4002) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 264 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 ASP cc_start: 0.7822 (OUTLIER) cc_final: 0.7581 (t0) REVERT: A 153 TRP cc_start: 0.7002 (t60) cc_final: 0.6626 (t60) REVERT: A 372 MET cc_start: 0.8431 (mmt) cc_final: 0.7911 (mmt) REVERT: B 158 ASP cc_start: 0.7259 (t0) cc_final: 0.6927 (t0) REVERT: B 246 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7791 (mp) REVERT: D 266 MET cc_start: 0.7489 (tpp) cc_final: 0.7085 (mmt) REVERT: E 95 MET cc_start: 0.7034 (tpp) cc_final: 0.6604 (tpp) REVERT: E 102 ASN cc_start: 0.6538 (p0) cc_final: 0.6195 (p0) REVERT: E 143 ARG cc_start: 0.6446 (mmp80) cc_final: 0.6050 (mmp80) REVERT: E 167 GLN cc_start: 0.7136 (tt0) cc_final: 0.6800 (tt0) REVERT: H 357 LEU cc_start: 0.8256 (mt) cc_final: 0.7982 (tp) REVERT: H 413 TYR cc_start: 0.7962 (m-80) cc_final: 0.6962 (t80) REVERT: H 432 MET cc_start: 0.7229 (mmm) cc_final: 0.6855 (mmm) REVERT: H 436 ASN cc_start: 0.7461 (t0) cc_final: 0.7121 (t0) REVERT: H 637 MET cc_start: 0.7654 (tpp) cc_final: 0.7024 (mpp) REVERT: H 658 MET cc_start: 0.7770 (tmm) cc_final: 0.7563 (tpp) REVERT: I 80 ASP cc_start: 0.7738 (OUTLIER) cc_final: 0.7236 (m-30) REVERT: I 81 ASP cc_start: 0.6923 (m-30) cc_final: 0.6589 (m-30) REVERT: J 82 MET cc_start: 0.7414 (tpt) cc_final: 0.6889 (tpp) REVERT: J 283 MET cc_start: 0.8528 (mmt) cc_final: 0.8051 (mmm) REVERT: J 285 CYS cc_start: 0.8487 (m) cc_final: 0.7939 (m) REVERT: J 291 LYS cc_start: 0.8180 (tttm) cc_final: 0.7899 (mmtt) REVERT: J 305 MET cc_start: 0.8939 (mmm) cc_final: 0.8651 (mmp) REVERT: K 82 MET cc_start: 0.8123 (tpp) cc_final: 0.7818 (tpp) REVERT: K 120 THR cc_start: 0.9201 (m) cc_final: 0.8991 (p) REVERT: K 296 ASN cc_start: 0.7762 (m-40) cc_final: 0.7197 (m110) REVERT: K 357 ILE cc_start: 0.8480 (mm) cc_final: 0.8163 (mm) REVERT: h 353 MET cc_start: 0.8137 (mmp) cc_final: 0.7916 (mmt) REVERT: h 358 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7989 (tm) REVERT: h 391 ARG cc_start: 0.8374 (ttp80) cc_final: 0.7959 (ttm110) REVERT: h 467 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7553 (mpp) REVERT: h 491 MET cc_start: 0.8113 (ttm) cc_final: 0.7681 (mtp) REVERT: h 562 ASN cc_start: 0.8845 (t0) cc_final: 0.8602 (t0) REVERT: h 590 LEU cc_start: 0.8686 (tp) cc_final: 0.8229 (pp) REVERT: h 615 LEU cc_start: 0.8882 (mp) cc_final: 0.8454 (pp) REVERT: h 637 MET cc_start: 0.7767 (mmm) cc_final: 0.7413 (mmp) REVERT: h 664 MET cc_start: 0.8943 (tpt) cc_final: 0.8442 (tmm) REVERT: h 705 MET cc_start: 0.8758 (mtt) cc_final: 0.8555 (mtt) outliers start: 59 outliers final: 45 residues processed: 300 average time/residue: 0.1966 time to fit residues: 96.2402 Evaluate side-chains 308 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 258 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 352 HIS Chi-restraints excluded: chain B residue 372 TRP Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 30 HIS Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain E residue 18 ASN Chi-restraints excluded: chain E residue 83 GLN Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 129 HIS Chi-restraints excluded: chain G residue 53 MET Chi-restraints excluded: chain H residue 409 VAL Chi-restraints excluded: chain H residue 418 LEU Chi-restraints excluded: chain H residue 542 LEU Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 85 ILE Chi-restraints excluded: chain J residue 287 ILE Chi-restraints excluded: chain K residue 87 HIS Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain K residue 282 ILE Chi-restraints excluded: chain K residue 311 ASP Chi-restraints excluded: chain h residue 358 LEU Chi-restraints excluded: chain h residue 467 MET Chi-restraints excluded: chain h residue 552 ASP Chi-restraints excluded: chain h residue 571 ASN Chi-restraints excluded: chain h residue 574 MET Chi-restraints excluded: chain h residue 658 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 311 optimal weight: 8.9990 chunk 144 optimal weight: 6.9990 chunk 217 optimal weight: 0.8980 chunk 40 optimal weight: 20.0000 chunk 277 optimal weight: 0.5980 chunk 359 optimal weight: 10.0000 chunk 157 optimal weight: 5.9990 chunk 176 optimal weight: 9.9990 chunk 94 optimal weight: 1.9990 chunk 169 optimal weight: 3.9990 chunk 276 optimal weight: 1.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 GLN F 129 HIS K 87 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.076574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.065279 restraints weight = 110414.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.066993 restraints weight = 55342.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.068092 restraints weight = 34097.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.068799 restraints weight = 24315.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.069205 restraints weight = 19249.224| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 30302 Z= 0.141 Angle : 0.605 14.188 41107 Z= 0.304 Chirality : 0.044 0.237 4641 Planarity : 0.004 0.046 5270 Dihedral : 7.364 169.699 4163 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.49 % Allowed : 12.46 % Favored : 86.05 % 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: 0.29 (0.14), residues: 3749 helix: 0.83 (0.13), residues: 1706 sheet: -0.13 (0.22), residues: 572 loop : -0.28 (0.17), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 166 TYR 0.015 0.001 TYR A 400 PHE 0.025 0.001 PHE B 355 TRP 0.039 0.002 TRP G 130 HIS 0.041 0.001 HIS K 87 Details of bonding type rmsd covalent geometry : bond 0.00321 (30302) covalent geometry : angle 0.60494 (41107) hydrogen bonds : bond 0.03797 ( 1473) hydrogen bonds : angle 4.58026 ( 4002) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 266 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 TRP cc_start: 0.6893 (t60) cc_final: 0.6464 (t60) REVERT: A 372 MET cc_start: 0.8426 (mmt) cc_final: 0.7875 (mmm) REVERT: B 158 ASP cc_start: 0.7198 (t0) cc_final: 0.6905 (t0) REVERT: B 246 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7677 (mp) REVERT: B 346 ASP cc_start: 0.7429 (p0) cc_final: 0.7209 (p0) REVERT: D 1 MET cc_start: 0.7205 (mtm) cc_final: 0.6836 (ttp) REVERT: D 266 MET cc_start: 0.7411 (tpp) cc_final: 0.7192 (mtm) REVERT: E 95 MET cc_start: 0.6937 (tpp) cc_final: 0.6531 (tpp) REVERT: E 102 ASN cc_start: 0.6649 (p0) cc_final: 0.6295 (p0) REVERT: E 167 GLN cc_start: 0.7078 (tt0) cc_final: 0.6624 (tt0) REVERT: F 95 MET cc_start: 0.7990 (OUTLIER) cc_final: 0.7013 (ttm) REVERT: H 357 LEU cc_start: 0.8139 (mt) cc_final: 0.7877 (tp) REVERT: H 413 TYR cc_start: 0.7917 (m-80) cc_final: 0.6990 (t80) REVERT: H 432 MET cc_start: 0.7204 (mmm) cc_final: 0.6823 (mmm) REVERT: H 436 ASN cc_start: 0.7541 (t0) cc_final: 0.7200 (t0) REVERT: H 514 MET cc_start: 0.6770 (tpp) cc_final: 0.6515 (tpp) REVERT: H 637 MET cc_start: 0.7530 (tpp) cc_final: 0.6969 (mpp) REVERT: I 80 ASP cc_start: 0.7671 (OUTLIER) cc_final: 0.7213 (m-30) REVERT: I 81 ASP cc_start: 0.6899 (m-30) cc_final: 0.6552 (m-30) REVERT: I 82 MET cc_start: 0.7877 (tpp) cc_final: 0.7600 (tpt) REVERT: J 82 MET cc_start: 0.7385 (tpt) cc_final: 0.6888 (tpp) REVERT: J 283 MET cc_start: 0.8482 (mmt) cc_final: 0.8043 (mmm) REVERT: J 285 CYS cc_start: 0.8433 (m) cc_final: 0.7873 (m) REVERT: J 291 LYS cc_start: 0.8156 (tttm) cc_final: 0.7901 (mmtt) REVERT: J 305 MET cc_start: 0.8908 (mmm) cc_final: 0.8567 (mmp) REVERT: K 190 MET cc_start: 0.8189 (mtm) cc_final: 0.7945 (mtt) REVERT: K 296 ASN cc_start: 0.7665 (m-40) cc_final: 0.7077 (m110) REVERT: K 357 ILE cc_start: 0.8405 (mm) cc_final: 0.8006 (mm) REVERT: h 353 MET cc_start: 0.8063 (mmp) cc_final: 0.7802 (mmp) REVERT: h 358 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7935 (tm) REVERT: h 391 ARG cc_start: 0.8281 (ttp80) cc_final: 0.7851 (ttm110) REVERT: h 467 MET cc_start: 0.7911 (OUTLIER) cc_final: 0.7489 (mpp) REVERT: h 491 MET cc_start: 0.8063 (ttm) cc_final: 0.7706 (mtp) REVERT: h 514 MET cc_start: 0.8429 (mmm) cc_final: 0.7927 (mmm) REVERT: h 562 ASN cc_start: 0.8754 (t0) cc_final: 0.8518 (t0) REVERT: h 590 LEU cc_start: 0.8607 (tp) cc_final: 0.8124 (pp) REVERT: h 615 LEU cc_start: 0.8867 (mp) cc_final: 0.8427 (pp) REVERT: h 664 MET cc_start: 0.8951 (tpt) cc_final: 0.8427 (tmm) REVERT: h 705 MET cc_start: 0.8646 (mtt) cc_final: 0.8409 (ptp) outliers start: 47 outliers final: 37 residues processed: 293 average time/residue: 0.1930 time to fit residues: 92.6626 Evaluate side-chains 303 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 261 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 372 TRP Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 30 HIS Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain E residue 18 ASN Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 129 HIS Chi-restraints excluded: chain G residue 53 MET Chi-restraints excluded: chain H residue 409 VAL Chi-restraints excluded: chain H residue 418 LEU Chi-restraints excluded: chain H residue 542 LEU Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 123 MET Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain K residue 87 HIS Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain K residue 311 ASP Chi-restraints excluded: chain h residue 358 LEU Chi-restraints excluded: chain h residue 368 MET Chi-restraints excluded: chain h residue 467 MET Chi-restraints excluded: chain h residue 571 ASN Chi-restraints excluded: chain h residue 574 MET Chi-restraints excluded: chain h residue 658 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 212 optimal weight: 10.0000 chunk 264 optimal weight: 10.0000 chunk 320 optimal weight: 5.9990 chunk 196 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 203 optimal weight: 1.9990 chunk 255 optimal weight: 0.0570 chunk 342 optimal weight: 0.8980 chunk 17 optimal weight: 9.9990 chunk 180 optimal weight: 2.9990 chunk 281 optimal weight: 5.9990 overall best weight: 0.9300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 HIS J 297 ASN K 49 GLN K 87 HIS K 92 ASN ** h 582 ASN ** 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 = 0.3552 r_free = 0.3552 target = 0.077489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.066211 restraints weight = 109741.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.067926 restraints weight = 54917.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.069030 restraints weight = 33965.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.069752 restraints weight = 24155.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.070221 restraints weight = 19049.323| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 30302 Z= 0.111 Angle : 0.583 13.922 41107 Z= 0.292 Chirality : 0.043 0.215 4641 Planarity : 0.004 0.047 5270 Dihedral : 7.185 173.968 4163 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.08 % Allowed : 12.88 % Favored : 86.05 % 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: 0.49 (0.14), residues: 3749 helix: 0.97 (0.13), residues: 1711 sheet: 0.01 (0.22), residues: 563 loop : -0.17 (0.17), residues: 1475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 166 TYR 0.010 0.001 TYR F 8 PHE 0.024 0.001 PHE B 355 TRP 0.053 0.002 TRP G 130 HIS 0.038 0.001 HIS K 87 Details of bonding type rmsd covalent geometry : bond 0.00245 (30302) covalent geometry : angle 0.58336 (41107) hydrogen bonds : bond 0.03459 ( 1473) hydrogen bonds : angle 4.44293 ( 4002) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7498 Ramachandran restraints generated. 3749 Oldfield, 0 Emsley, 3749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 275 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 TRP cc_start: 0.6856 (t60) cc_final: 0.6442 (t60) REVERT: A 372 MET cc_start: 0.8332 (mmt) cc_final: 0.7728 (mmm) REVERT: B 158 ASP cc_start: 0.7260 (t0) cc_final: 0.6905 (t0) REVERT: B 346 ASP cc_start: 0.7377 (p0) cc_final: 0.7131 (p0) REVERT: D 1 MET cc_start: 0.7195 (mtm) cc_final: 0.6835 (ttp) REVERT: E 95 MET cc_start: 0.6901 (tpp) cc_final: 0.6520 (tpp) REVERT: E 102 ASN cc_start: 0.6663 (p0) cc_final: 0.6323 (p0) REVERT: E 143 ARG cc_start: 0.6420 (mmp80) cc_final: 0.6016 (mmp80) REVERT: E 167 GLN cc_start: 0.7146 (tt0) cc_final: 0.6693 (tt0) REVERT: G 94 GLU cc_start: 0.7927 (tp30) cc_final: 0.7640 (tp30) REVERT: H 357 LEU cc_start: 0.8082 (mt) cc_final: 0.7858 (tp) REVERT: H 413 TYR cc_start: 0.7916 (m-80) cc_final: 0.7082 (t80) REVERT: H 432 MET cc_start: 0.7183 (mmm) cc_final: 0.6764 (mmm) REVERT: H 436 ASN cc_start: 0.7604 (t0) cc_final: 0.7243 (t0) REVERT: H 637 MET cc_start: 0.7437 (tpp) cc_final: 0.6857 (mpp) REVERT: I 80 ASP cc_start: 0.7673 (OUTLIER) cc_final: 0.7208 (m-30) REVERT: I 81 ASP cc_start: 0.6960 (m-30) cc_final: 0.6590 (m-30) REVERT: I 82 MET cc_start: 0.7872 (tpp) cc_final: 0.7588 (tpt) REVERT: I 313 MET cc_start: 0.8149 (mmm) cc_final: 0.7381 (tpt) REVERT: J 82 MET cc_start: 0.7391 (tpt) cc_final: 0.6858 (tpp) REVERT: J 283 MET cc_start: 0.8473 (mmt) cc_final: 0.8033 (mmm) REVERT: J 285 CYS cc_start: 0.8339 (m) cc_final: 0.7844 (m) REVERT: J 291 LYS cc_start: 0.8137 (tttm) cc_final: 0.7840 (mmtt) REVERT: J 305 MET cc_start: 0.8920 (mmm) cc_final: 0.8577 (mmp) REVERT: K 190 MET cc_start: 0.8178 (mtm) cc_final: 0.7927 (mtt) REVERT: K 227 MET cc_start: 0.8600 (mmm) cc_final: 0.8219 (mmm) REVERT: K 280 ASN cc_start: 0.8722 (m-40) cc_final: 0.8519 (m110) REVERT: K 296 ASN cc_start: 0.7601 (m-40) cc_final: 0.7080 (m110) REVERT: K 357 ILE cc_start: 0.8443 (mm) cc_final: 0.8080 (mm) REVERT: h 353 MET cc_start: 0.8024 (mmp) cc_final: 0.7791 (mmp) REVERT: h 358 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7985 (tm) REVERT: h 391 ARG cc_start: 0.8217 (ttp80) cc_final: 0.7808 (ttm110) REVERT: h 467 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7403 (mpp) REVERT: h 491 MET cc_start: 0.8053 (ttm) cc_final: 0.7709 (mtp) REVERT: h 514 MET cc_start: 0.8463 (mmm) cc_final: 0.8016 (mmm) REVERT: h 562 ASN cc_start: 0.8734 (t0) cc_final: 0.8487 (t0) REVERT: h 590 LEU cc_start: 0.8579 (tp) cc_final: 0.8101 (pp) REVERT: h 615 LEU cc_start: 0.8878 (mp) cc_final: 0.8434 (pp) REVERT: h 664 MET cc_start: 0.8948 (tpt) cc_final: 0.8431 (tmm) REVERT: h 705 MET cc_start: 0.8633 (mtt) cc_final: 0.8373 (ptp) outliers start: 34 outliers final: 22 residues processed: 294 average time/residue: 0.1869 time to fit residues: 90.4373 Evaluate side-chains 290 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 265 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain E residue 18 ASN Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 129 HIS Chi-restraints excluded: chain G residue 53 MET Chi-restraints excluded: chain H residue 418 LEU Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain K residue 87 HIS Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain K residue 311 ASP Chi-restraints excluded: chain h residue 358 LEU Chi-restraints excluded: chain h residue 368 MET Chi-restraints excluded: chain h residue 467 MET Chi-restraints excluded: chain h residue 571 ASN Chi-restraints excluded: chain h residue 574 MET Chi-restraints excluded: chain h residue 658 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 4 optimal weight: 9.9990 chunk 330 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 85 optimal weight: 7.9990 chunk 366 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 chunk 260 optimal weight: 10.0000 chunk 120 optimal weight: 0.9990 chunk 233 optimal weight: 3.9990 chunk 199 optimal weight: 7.9990 chunk 184 optimal weight: 7.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 HIS ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 HIS K 49 GLN K 87 HIS K 92 ASN h 582 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.075744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.064495 restraints weight = 111800.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.066149 restraints weight = 56748.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.067216 restraints weight = 35397.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.067914 restraints weight = 25477.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.068360 restraints weight = 20254.708| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 30302 Z= 0.244 Angle : 0.666 13.603 41107 Z= 0.335 Chirality : 0.046 0.214 4641 Planarity : 0.005 0.047 5270 Dihedral : 7.280 167.147 4163 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.17 % Allowed : 13.13 % Favored : 85.70 % 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: 0.30 (0.14), residues: 3749 helix: 0.84 (0.13), residues: 1705 sheet: -0.16 (0.22), residues: 575 loop : -0.26 (0.17), residues: 1469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 166 TYR 0.014 0.002 TYR K 53 PHE 0.030 0.002 PHE B 355 TRP 0.045 0.002 TRP G 130 HIS 0.042 0.002 HIS K 87 Details of bonding type rmsd covalent geometry : bond 0.00557 (30302) covalent geometry : angle 0.66633 (41107) hydrogen bonds : bond 0.04060 ( 1473) hydrogen bonds : angle 4.64416 ( 4002) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4993.95 seconds wall clock time: 87 minutes 25.76 seconds (5245.76 seconds total)