Starting phenix.real_space_refine on Thu Mar 5 11:16:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t5q_25707/03_2026/7t5q_25707.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t5q_25707/03_2026/7t5q_25707.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t5q_25707/03_2026/7t5q_25707.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t5q_25707/03_2026/7t5q_25707.map" model { file = "/net/cci-nas-00/data/ceres_data/7t5q_25707/03_2026/7t5q_25707.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t5q_25707/03_2026/7t5q_25707.cif" } resolution = 3.4 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= 0.002 sd= 0.029 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 8 5.49 5 Mg 3 5.21 5 S 108 5.16 5 C 13760 2.51 5 N 3705 2.21 5 O 4087 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21671 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3080 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 24, 'TRANS': 359} Chain breaks: 1 Chain: "B" Number of atoms: 2972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2972 Classifications: {'peptide': 372} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 354} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2578 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 12, 'TRANS': 315} Chain breaks: 1 Chain: "D" Number of atoms: 2287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2287 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 9, 'TRANS': 273} Chain: "E" Number of atoms: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1414 Classifications: {'peptide': 174} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 11, 'TRANS': 162} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1364 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 161} Chain: "G" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 482 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain breaks: 1 Chain: "H" Number of atoms: 2812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2812 Classifications: {'peptide': 359} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 339} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2295 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 10, 'TRANS': 272} Chain breaks: 1 Chain: "J" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2295 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 11, 'TRANS': 279} Chain breaks: 2 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" 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} Time building chain proxies: 4.76, per 1000 atoms: 0.22 Number of scatterers: 21671 At special positions: 0 Unit cell: (162.54, 141.04, 166.84, 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 108 16.00 P 8 15.00 Mg 3 11.99 O 4087 8.00 N 3705 7.00 C 13760 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: 1.58 Conformation dependent library (CDL) restraints added in 1.3 seconds 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5074 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 32 sheets defined 42.0% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 55 through 59 removed outlier: 3.700A pdb=" N LEU A 58 " --> pdb=" O VAL A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 67 removed outlier: 3.846A pdb=" N ILE A 67 " --> pdb=" O ASP A 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 64 through 67' Processing helix chain 'A' and resid 85 through 99 removed outlier: 3.754A pdb=" N MET A 89 " --> pdb=" O ASP A 85 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG A 91 " --> pdb=" O ASP A 87 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS A 99 " --> pdb=" O GLN A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 107 Processing helix chain 'A' and resid 119 through 135 removed outlier: 3.608A pdb=" N THR A 126 " --> pdb=" O ASN A 122 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA A 127 " --> pdb=" O ARG A 123 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER A 133 " --> pdb=" O ILE A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 151 removed outlier: 3.901A pdb=" N LEU A 147 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA A 151 " --> pdb=" O LEU A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 156 removed outlier: 3.680A pdb=" N SER A 155 " --> pdb=" O SER A 152 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG A 156 " --> pdb=" O TRP A 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 152 through 156' Processing helix chain 'A' and resid 196 through 209 Processing helix chain 'A' and resid 219 through 231 Processing helix chain 'A' and resid 237 through 248 removed outlier: 3.885A pdb=" N GLU A 241 " --> pdb=" O ASP A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 253 removed outlier: 4.170A pdb=" N TRP A 252 " --> pdb=" O ASP A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 283 removed outlier: 3.836A pdb=" N ILE A 281 " --> pdb=" O GLY A 278 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE A 282 " --> pdb=" O PRO A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 288 Processing helix chain 'A' and resid 295 through 305 removed outlier: 3.545A pdb=" N VAL A 300 " --> pdb=" O ILE A 296 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASP A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 307 No H-bonds generated for 'chain 'A' and resid 306 through 307' Processing helix chain 'A' and resid 308 through 310 No H-bonds generated for 'chain 'A' and resid 308 through 310' Processing helix chain 'A' and resid 311 through 318 removed outlier: 3.873A pdb=" N LEU A 315 " --> pdb=" O VAL A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 327 removed outlier: 3.652A pdb=" N THR A 326 " --> pdb=" O GLY A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 354 removed outlier: 3.785A pdb=" N ARG A 334 " --> pdb=" O ASP A 330 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU A 335 " --> pdb=" O PHE A 331 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 345 " --> pdb=" O ARG A 341 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG A 346 " --> pdb=" O THR A 342 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER A 354 " --> pdb=" O SER A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 386 Processing helix chain 'A' and resid 387 through 393 removed outlier: 3.850A pdb=" N TYR A 391 " --> pdb=" O PRO A 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 64 removed outlier: 4.184A pdb=" N GLU B 63 " --> pdb=" O ASP B 59 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU B 64 " --> pdb=" O GLU B 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 59 through 64' Processing helix chain 'B' and resid 84 through 93 Processing helix chain 'B' and resid 116 through 131 removed outlier: 3.596A pdb=" N VAL B 124 " --> pdb=" O ARG B 120 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE B 128 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU B 129 " --> pdb=" O GLU B 125 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR B 131 " --> pdb=" O MET B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 148 removed outlier: 3.573A pdb=" N LEU B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 179 removed outlier: 3.583A pdb=" N THR B 179 " --> pdb=" O PRO B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 199 removed outlier: 3.573A pdb=" N ILE B 194 " --> pdb=" O THR B 190 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU B 199 " --> pdb=" O LYS B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 220 removed outlier: 3.514A pdb=" N VAL B 213 " --> pdb=" O ASP B 209 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N MET B 215 " --> pdb=" O GLU B 211 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE B 216 " --> pdb=" O THR B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 237 Processing helix chain 'B' and resid 255 through 265 removed outlier: 3.788A pdb=" N PHE B 259 " --> pdb=" O GLY B 256 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU B 260 " --> pdb=" O GLU B 257 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ALA B 261 " --> pdb=" O ARG B 258 " (cutoff:3.500A) Proline residue: B 262 - end of helix removed outlier: 3.556A pdb=" N LEU B 265 " --> pdb=" O PRO B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 272 removed outlier: 3.735A pdb=" N LEU B 270 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE B 271 " --> pdb=" O PRO B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 287 removed outlier: 4.263A pdb=" N GLU B 280 " --> pdb=" O VAL B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 289 No H-bonds generated for 'chain 'B' and resid 288 through 289' Processing helix chain 'B' and resid 290 through 292 No H-bonds generated for 'chain 'B' and resid 290 through 292' Processing helix chain 'B' and resid 293 through 299 removed outlier: 3.563A pdb=" N LYS B 299 " --> pdb=" O SER B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 309 removed outlier: 3.672A pdb=" N THR B 308 " --> pdb=" O GLY B 305 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET B 309 " --> pdb=" O GLY B 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 305 through 309' Processing helix chain 'B' and resid 312 through 325 removed outlier: 3.665A pdb=" N LEU B 317 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU B 318 " --> pdb=" O PRO B 314 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ARG B 319 " --> pdb=" O SER B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 365 removed outlier: 3.534A pdb=" N ALA B 362 " --> pdb=" O GLY B 358 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASP B 363 " --> pdb=" O ALA B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 381 removed outlier: 3.511A pdb=" N GLN B 379 " --> pdb=" O ARG B 375 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU B 380 " --> pdb=" O GLN B 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 339 removed outlier: 4.387A pdb=" N GLN C 338 " --> pdb=" O VAL C 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 25 removed outlier: 3.612A pdb=" N GLU D 12 " --> pdb=" O ASN D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 41 removed outlier: 3.848A pdb=" N GLY D 40 " --> pdb=" O ASP D 37 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL D 41 " --> pdb=" O PHE D 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 37 through 41' Processing helix chain 'D' and resid 63 through 70 removed outlier: 4.304A pdb=" N LEU D 67 " --> pdb=" O PHE D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 81 removed outlier: 4.489A pdb=" N LEU D 75 " --> pdb=" O GLY D 71 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY D 81 " --> pdb=" O LYS D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 84 No H-bonds generated for 'chain 'D' and resid 82 through 84' Processing helix chain 'D' and resid 106 through 114 removed outlier: 3.660A pdb=" N VAL D 110 " --> pdb=" O LYS D 106 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY D 114 " --> pdb=" O VAL D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 135 removed outlier: 4.368A pdb=" N SER D 123 " --> pdb=" O ASN D 119 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N VAL D 124 " --> pdb=" O CYS D 120 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N PHE D 125 " --> pdb=" O PHE D 121 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE D 131 " --> pdb=" O LYS D 127 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLN D 132 " --> pdb=" O TYR D 128 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU D 133 " --> pdb=" O PHE D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 183 removed outlier: 3.545A pdb=" N VAL D 175 " --> pdb=" O ASP D 171 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL D 176 " --> pdb=" O ASP D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 192 removed outlier: 4.109A pdb=" N ARG D 189 " --> pdb=" O PHE D 185 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ARG D 190 " --> pdb=" O LYS D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 211 removed outlier: 3.753A pdb=" N ASP D 211 " --> pdb=" O LEU D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 245 removed outlier: 3.804A pdb=" N THR D 240 " --> pdb=" O ALA D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 279 removed outlier: 3.683A pdb=" N LYS D 259 " --> pdb=" O ILE D 255 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA D 260 " --> pdb=" O LYS D 256 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR D 264 " --> pdb=" O ALA D 260 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG D 265 " --> pdb=" O TYR D 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 48 Processing helix chain 'E' and resid 48 through 53 removed outlier: 3.583A pdb=" N ASN E 52 " --> pdb=" O TYR E 48 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL E 53 " --> pdb=" O PHE E 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 48 through 53' Processing helix chain 'E' and resid 64 through 82 removed outlier: 3.643A pdb=" N LEU E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TYR E 70 " --> pdb=" O ARG E 66 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU E 73 " --> pdb=" O ILE E 69 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER E 76 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU E 77 " --> pdb=" O LEU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 99 Processing helix chain 'E' and resid 113 through 117 removed outlier: 3.889A pdb=" N ILE E 116 " --> pdb=" O LEU E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 149 removed outlier: 3.880A pdb=" N VAL E 128 " --> pdb=" O GLN E 124 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLY E 141 " --> pdb=" O ARG E 137 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LEU E 142 " --> pdb=" O GLN E 138 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ARG E 143 " --> pdb=" O GLU E 139 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLU E 146 " --> pdb=" O LEU E 142 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LYS E 147 " --> pdb=" O ARG E 143 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE E 149 " --> pdb=" O CYS E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 171 Processing helix chain 'F' and resid 4 through 18 removed outlier: 3.834A pdb=" N TYR F 8 " --> pdb=" O THR F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 47 Processing helix chain 'F' and resid 80 through 97 removed outlier: 3.675A pdb=" N ARG F 97 " --> pdb=" O PHE F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 125 Processing helix chain 'F' and resid 128 through 168 removed outlier: 3.691A pdb=" N VAL F 132 " --> pdb=" O LYS F 128 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU F 140 " --> pdb=" O ILE F 136 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE F 142 " --> pdb=" O PHE F 138 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ASP F 143 " --> pdb=" O MET F 139 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU F 151 " --> pdb=" O SER F 147 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA F 157 " --> pdb=" O VAL F 153 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ARG F 158 " --> pdb=" O ASN F 154 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ILE F 159 " --> pdb=" O ALA F 155 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL F 160 " --> pdb=" O ARG F 156 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASN F 167 " --> pdb=" O GLU F 163 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N PHE F 168 " --> pdb=" O PHE F 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 86 Processing helix chain 'G' and resid 101 through 114 removed outlier: 3.884A pdb=" N LEU G 105 " --> pdb=" O ASN G 101 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE G 114 " --> pdb=" O ILE G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 137 removed outlier: 3.886A pdb=" N VAL G 124 " --> pdb=" O ASN G 120 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU G 130 " --> pdb=" O LEU G 126 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS G 131 " --> pdb=" O GLN G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 146 removed outlier: 4.250A pdb=" N ILE G 141 " --> pdb=" O GLY G 137 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL G 142 " --> pdb=" O VAL G 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 61 Processing helix chain 'H' and resid 78 through 92 removed outlier: 3.825A pdb=" N MET H 82 " --> pdb=" O ASN H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 125 removed outlier: 3.740A pdb=" N ARG H 116 " --> pdb=" O PRO H 112 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLU H 117 " --> pdb=" O LYS H 113 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N MET H 119 " --> pdb=" O ASN H 115 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR H 120 " --> pdb=" O ARG H 116 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE H 122 " --> pdb=" O LYS H 118 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 146 removed outlier: 3.999A pdb=" N SER H 141 " --> pdb=" O GLN H 137 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU H 142 " --> pdb=" O ALA H 138 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N TYR H 143 " --> pdb=" O VAL H 139 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 197 removed outlier: 3.735A pdb=" N GLU H 195 " --> pdb=" O LYS H 191 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG H 196 " --> pdb=" O ILE H 192 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY H 197 " --> pdb=" O LEU H 193 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 204 No H-bonds generated for 'chain 'H' and resid 202 through 204' Processing helix chain 'H' and resid 205 through 216 removed outlier: 3.657A pdb=" N VAL H 209 " --> pdb=" O GLU H 205 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP H 211 " --> pdb=" O GLU H 207 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS H 213 " --> pdb=" O VAL H 209 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS H 215 " --> pdb=" O ASP H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 233 Processing helix chain 'H' and resid 251 through 255 removed outlier: 3.713A pdb=" N ARG H 254 " --> pdb=" O GLY H 251 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N PHE H 255 " --> pdb=" O ASN H 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 251 through 255' Processing helix chain 'H' and resid 257 through 262 Processing helix chain 'H' and resid 276 through 284 removed outlier: 3.938A pdb=" N ILE H 282 " --> pdb=" O THR H 278 " (cutoff:3.500A) Processing helix chain 'H' and resid 289 through 295 removed outlier: 3.998A pdb=" N ALA H 295 " --> pdb=" O LYS H 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 308 through 319 removed outlier: 3.555A pdb=" N ARG H 312 " --> pdb=" O GLY H 308 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET H 313 " --> pdb=" O ILE H 309 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR H 318 " --> pdb=" O GLN H 314 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA H 319 " --> pdb=" O LYS H 315 " (cutoff:3.500A) Processing helix chain 'H' and resid 334 through 336 No H-bonds generated for 'chain 'H' and resid 334 through 336' Processing helix chain 'H' and resid 337 through 348 removed outlier: 3.519A pdb=" N LEU H 346 " --> pdb=" O GLY H 342 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER H 348 " --> pdb=" O SER H 344 " (cutoff:3.500A) Processing helix chain 'H' and resid 349 through 354 removed outlier: 3.930A pdb=" N GLN H 353 " --> pdb=" O SER H 350 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLN H 354 " --> pdb=" O THR H 351 " (cutoff:3.500A) Processing helix chain 'H' and resid 359 through 366 Processing helix chain 'H' and resid 368 through 372 removed outlier: 3.557A pdb=" N HIS H 371 " --> pdb=" O SER H 368 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 23 Processing helix chain 'I' and resid 29 through 40 Processing helix chain 'I' and resid 42 through 50 removed outlier: 4.096A pdb=" N GLU I 48 " --> pdb=" O ASN I 44 " (cutoff:3.500A) Processing helix chain 'I' and resid 50 through 62 removed outlier: 3.828A pdb=" N PHE I 62 " --> pdb=" O ASN I 58 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 134 removed outlier: 3.553A pdb=" N ALA I 130 " --> pdb=" O SER I 126 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR I 131 " --> pdb=" O ALA I 127 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP I 134 " --> pdb=" O ALA I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 220 through 249 removed outlier: 4.476A pdb=" N ALA I 225 " --> pdb=" O GLU I 221 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LYS I 226 " --> pdb=" O ALA I 222 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU I 227 " --> pdb=" O GLN I 223 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N PHE I 228 " --> pdb=" O THR I 224 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ILE I 229 " --> pdb=" O ALA I 225 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR I 249 " --> pdb=" O GLU I 245 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 276 Processing helix chain 'I' and resid 312 through 324 removed outlier: 3.693A pdb=" N GLN I 317 " --> pdb=" O MET I 313 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LYS I 318 " --> pdb=" O GLU I 314 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG I 319 " --> pdb=" O VAL I 315 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 16 removed outlier: 3.679A pdb=" N ASP J 7 " --> pdb=" O ASP J 3 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG J 15 " --> pdb=" O ASP J 11 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU J 16 " --> pdb=" O LEU J 12 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 19 No H-bonds generated for 'chain 'J' and resid 17 through 19' Processing helix chain 'J' and resid 20 through 32 removed outlier: 3.640A pdb=" N VAL J 32 " --> pdb=" O LEU J 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 35 through 43 removed outlier: 3.618A pdb=" N LEU J 39 " --> pdb=" O LEU J 35 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU J 40 " --> pdb=" O CYS J 36 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER J 41 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER J 42 " --> pdb=" O ASP J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 90 through 112 removed outlier: 4.095A pdb=" N LYS J 95 " --> pdb=" O ALA J 91 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LEU J 96 " --> pdb=" O ARG J 92 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA J 100 " --> pdb=" O LEU J 96 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASP J 105 " --> pdb=" O ASN J 101 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU J 110 " --> pdb=" O GLN J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 208 through 231 removed outlier: 3.601A pdb=" N ASN J 212 " --> pdb=" O PRO J 208 " (cutoff:3.500A) Processing helix chain 'J' and resid 235 through 244 removed outlier: 3.724A pdb=" N ARG J 244 " --> pdb=" O VAL J 240 " (cutoff:3.500A) Processing helix chain 'J' and resid 250 through 274 removed outlier: 3.659A pdb=" N PHE J 255 " --> pdb=" O ASP J 251 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLN J 257 " --> pdb=" O GLN J 253 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N LEU J 258 " --> pdb=" O LYS J 254 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE J 271 " --> pdb=" O THR J 267 " (cutoff:3.500A) Processing helix chain 'J' and resid 292 through 302 removed outlier: 4.512A pdb=" N MET J 300 " --> pdb=" O VAL J 296 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU J 301 " --> pdb=" O GLY J 297 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.704A pdb=" N VAL A 10 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR A 113 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N CYS A 12 " --> pdb=" O THR A 113 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A 142 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 139 " --> pdb=" O HIS A 395 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 62 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 removed outlier: 3.653A pdb=" N TYR A 184 " --> pdb=" O ALA A 181 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 184 through 185 removed outlier: 3.653A pdb=" N TYR A 184 " --> pdb=" O ALA A 181 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER A 322 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 6.731A 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 removed outlier: 3.669A pdb=" N LYS A 254 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 30 through 33 removed outlier: 3.546A pdb=" N CYS B 11 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR B 110 " --> pdb=" O CYS B 11 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL B 136 " --> pdb=" O MET B 373 " (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 74 through 75 Processing sheet with id=AB1, first strand: chain 'B' and resid 180 through 182 removed outlier: 6.472A pdb=" N VAL B 155 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N SER B 304 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL B 157 " --> pdb=" O SER B 304 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE B 301 " --> pdb=" O GLU B 345 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 242 through 245 Processing sheet with id=AB3, first strand: chain 'C' and resid 3 through 5 removed outlier: 4.760A pdb=" N ALA C 351 " --> pdb=" O GLY C 347 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLY C 347 " --> pdb=" O ALA C 351 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 14 through 16 removed outlier: 6.746A pdb=" N VAL C 32 " --> pdb=" O GLU C 47 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLU C 47 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE C 34 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 55 through 61 Processing sheet with id=AB6, first strand: chain 'C' and resid 99 through 104 removed outlier: 6.428A pdb=" N GLY C 114 " --> pdb=" O THR C 100 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N VAL C 102 " --> pdb=" O ALA C 112 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ALA C 112 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N TRP C 104 " --> pdb=" O LYS C 110 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N LYS C 110 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER C 115 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LEU C 119 " --> pdb=" O SER C 115 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 145 through 150 removed outlier: 6.759A pdb=" N GLY C 160 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LEU C 148 " --> pdb=" O ALA C 158 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ALA C 158 " --> pdb=" O LEU C 148 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N TRP C 150 " --> pdb=" O LEU C 156 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N LEU C 156 " --> pdb=" O TRP C 150 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N SER C 170 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU C 194 " --> pdb=" O SER C 170 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 207 through 212 removed outlier: 3.937A pdb=" N GLY C 209 " --> pdb=" O VAL C 222 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N THR C 227 " --> pdb=" O SER C 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 249 through 254 removed outlier: 3.602A pdb=" N SER C 284 " --> pdb=" O LEU C 271 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ASN C 273 " --> pdb=" O PHE C 282 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N PHE C 282 " --> pdb=" O ASN C 273 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 33 through 34 removed outlier: 3.682A pdb=" N VAL D 93 " --> pdb=" O ILE D 59 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 142 through 144 removed outlier: 3.512A pdb=" N VAL D 154 " --> pdb=" O ALA D 142 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N TYR D 222 " --> pdb=" O SER D 201 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER D 201 " --> pdb=" O TYR D 222 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 51 through 56 removed outlier: 7.228A pdb=" N GLU F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 29 through 32 removed outlier: 6.513A pdb=" N LEU H 8 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N THR H 106 " --> pdb=" O LEU H 8 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N CYS H 10 " --> pdb=" O THR H 106 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 35 through 36 removed outlier: 4.738A pdb=" N TYR H 53 " --> pdb=" O GLY H 36 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 71 through 72 removed outlier: 3.518A pdb=" N GLU H 72 " --> pdb=" O ILE H 75 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 131 through 132 Processing sheet with id=AC8, first strand: chain 'H' and resid 169 through 170 Processing sheet with id=AC9, first strand: chain 'H' and resid 169 through 170 removed outlier: 6.071A pdb=" N ILE H 151 " --> pdb=" O VAL H 298 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ASN H 297 " --> pdb=" O ILE H 330 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 238 through 241 Processing sheet with id=AD2, first strand: chain 'I' and resid 64 through 66 Processing sheet with id=AD3, first strand: chain 'I' and resid 86 through 87 removed outlier: 4.254A pdb=" N GLN I 109 " --> pdb=" O SER I 95 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N LYS I 97 " --> pdb=" O ASP I 107 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ASP I 107 " --> pdb=" O LYS I 97 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 140 through 148 removed outlier: 3.501A pdb=" N VAL I 189 " --> pdb=" O LYS I 178 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN I 205 " --> pdb=" O GLY J 190 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL I 207 " --> pdb=" O ASN J 188 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 49 through 51 894 hydrogen bonds defined for protein. 2460 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.31 Time building geometry restraints manager: 2.21 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: 6808 1.34 - 1.46: 3738 1.46 - 1.58: 11409 1.58 - 1.70: 13 1.70 - 1.82: 173 Bond restraints: 22141 Sorted by residual: bond pdb=" C ILE A 193 " pdb=" N PRO A 194 " ideal model delta sigma weight residual 1.334 1.370 -0.037 8.40e-03 1.42e+04 1.93e+01 bond pdb=" CA GLU I 68 " pdb=" C GLU I 68 " ideal model delta sigma weight residual 1.523 1.569 -0.045 1.34e-02 5.57e+03 1.14e+01 bond pdb=" C GLY E 30 " pdb=" N PRO E 31 " ideal model delta sigma weight residual 1.335 1.362 -0.027 8.70e-03 1.32e+04 9.60e+00 bond pdb=" CE1 HIC H 73 " pdb=" NE2 HIC H 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.49e+00 bond pdb=" CG HIC H 73 " pdb=" CD2 HIC H 73 " ideal model delta sigma weight residual 1.369 1.409 -0.040 2.00e-02 2.50e+03 4.07e+00 ... (remaining 22136 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 28982 2.09 - 4.18: 794 4.18 - 6.27: 172 6.27 - 8.36: 16 8.36 - 10.44: 1 Bond angle restraints: 29965 Sorted by residual: angle pdb=" C ASP B 346 " pdb=" N PRO B 347 " pdb=" CA PRO B 347 " ideal model delta sigma weight residual 119.66 122.79 -3.13 7.20e-01 1.93e+00 1.89e+01 angle pdb=" CA GLN E 124 " pdb=" CB GLN E 124 " pdb=" CG GLN E 124 " ideal model delta sigma weight residual 114.10 121.77 -7.67 2.00e+00 2.50e-01 1.47e+01 angle pdb=" O PRO B 347 " pdb=" C PRO B 347 " pdb=" N PRO B 348 " ideal model delta sigma weight residual 121.15 122.91 -1.76 4.70e-01 4.53e+00 1.40e+01 angle pdb=" CA MET D 182 " pdb=" CB MET D 182 " pdb=" CG MET D 182 " ideal model delta sigma weight residual 114.10 121.17 -7.07 2.00e+00 2.50e-01 1.25e+01 angle pdb=" CA GLU I 68 " pdb=" C GLU I 68 " pdb=" O GLU I 68 " ideal model delta sigma weight residual 120.51 115.70 4.81 1.43e+00 4.89e-01 1.13e+01 ... (remaining 29960 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 12065 17.79 - 35.57: 1060 35.57 - 53.36: 207 53.36 - 71.15: 26 71.15 - 88.94: 14 Dihedral angle restraints: 13372 sinusoidal: 5512 harmonic: 7860 Sorted by residual: dihedral pdb=" O1B ADP H 401 " pdb=" O3A ADP H 401 " pdb=" PB ADP H 401 " pdb=" PA ADP H 401 " ideal model delta sinusoidal sigma weight residual -60.00 -143.42 83.42 1 2.00e+01 2.50e-03 2.12e+01 dihedral pdb=" CA ILE J 249 " pdb=" C ILE J 249 " pdb=" N PRO J 250 " pdb=" CA PRO J 250 " ideal model delta harmonic sigma weight residual 180.00 157.02 22.98 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CA PRO I 26 " pdb=" C PRO I 26 " pdb=" N GLY I 27 " pdb=" CA GLY I 27 " ideal model delta harmonic sigma weight residual 180.00 157.28 22.72 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 13369 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2739 0.061 - 0.123: 479 0.123 - 0.184: 71 0.184 - 0.246: 2 0.246 - 0.307: 4 Chirality restraints: 3295 Sorted by residual: chirality pdb=" C2' ATP B 502 " pdb=" C1' ATP B 502 " pdb=" C3' ATP B 502 " pdb=" O2' ATP B 502 " both_signs ideal model delta sigma weight residual False -2.68 -2.99 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" C2' ATP A 502 " pdb=" C1' ATP A 502 " pdb=" C3' ATP A 502 " pdb=" O2' ATP A 502 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" C3' ATP A 502 " pdb=" C2' ATP A 502 " pdb=" C4' ATP A 502 " pdb=" O3' ATP A 502 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 3292 not shown) Planarity restraints: 3845 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 183 " -0.052 5.00e-02 4.00e+02 7.87e-02 9.92e+00 pdb=" N PRO C 184 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO C 184 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 184 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO I 183 " 0.051 5.00e-02 4.00e+02 7.65e-02 9.37e+00 pdb=" N PRO I 184 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO I 184 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO I 184 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE J 249 " -0.048 5.00e-02 4.00e+02 7.33e-02 8.59e+00 pdb=" N PRO J 250 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO J 250 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO J 250 " -0.041 5.00e-02 4.00e+02 ... (remaining 3842 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 99 2.57 - 3.15: 16273 3.15 - 3.73: 30793 3.73 - 4.32: 41728 4.32 - 4.90: 72220 Nonbonded interactions: 161113 Sorted by model distance: nonbonded pdb="MG MG B 501 " pdb=" O1B ATP B 502 " model vdw 1.984 2.170 nonbonded pdb=" O2B ADP H 401 " pdb="MG MG H 402 " model vdw 1.998 2.170 nonbonded pdb=" O1B ADP H 401 " pdb="MG MG H 402 " model vdw 2.018 2.170 nonbonded pdb=" O ILE A 129 " pdb=" OG SER A 133 " model vdw 2.079 3.040 nonbonded pdb=" O GLU I 200 " pdb=" OH TYR J 232 " model vdw 2.114 3.040 ... (remaining 161108 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.380 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 19.690 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 22141 Z= 0.227 Angle : 0.862 10.444 29965 Z= 0.467 Chirality : 0.049 0.307 3295 Planarity : 0.006 0.079 3845 Dihedral : 13.793 88.937 8298 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.08 % Allowed : 0.17 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.15), residues: 2664 helix: -0.51 (0.16), residues: 915 sheet: -0.20 (0.21), residues: 585 loop : -1.74 (0.17), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 210 TYR 0.021 0.002 TYR D 146 PHE 0.031 0.002 PHE B 371 TRP 0.046 0.002 TRP C 131 HIS 0.014 0.001 HIS C 30 Details of bonding type rmsd covalent geometry : bond 0.00517 (22141) covalent geometry : angle 0.86211 (29965) hydrogen bonds : bond 0.18577 ( 891) hydrogen bonds : angle 6.40201 ( 2460) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 603 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ASP cc_start: 0.7484 (m-30) cc_final: 0.7225 (m-30) REVERT: A 302 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7503 (tm-30) REVERT: B 361 LEU cc_start: 0.8564 (tp) cc_final: 0.8333 (tt) REVERT: B 368 LYS cc_start: 0.8085 (pptt) cc_final: 0.7768 (pptt) REVERT: B 372 TRP cc_start: 0.8508 (m100) cc_final: 0.8132 (m100) REVERT: C 242 LEU cc_start: 0.7487 (tp) cc_final: 0.7238 (tp) REVERT: C 245 GLU cc_start: 0.7903 (pm20) cc_final: 0.7698 (pm20) REVERT: C 257 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7450 (mm-30) REVERT: E 87 SER cc_start: 0.7440 (t) cc_final: 0.7164 (p) REVERT: E 92 GLU cc_start: 0.8055 (tm-30) cc_final: 0.7384 (tm-30) REVERT: E 95 MET cc_start: 0.7818 (mtm) cc_final: 0.7494 (mtm) REVERT: F 83 GLU cc_start: 0.7139 (mm-30) cc_final: 0.6708 (mm-30) REVERT: F 154 ASN cc_start: 0.8177 (t0) cc_final: 0.7944 (t0) REVERT: G 111 TYR cc_start: 0.7388 (m-80) cc_final: 0.7174 (m-80) REVERT: H 61 LYS cc_start: 0.7814 (mttm) cc_final: 0.7597 (mttm) REVERT: H 195 GLU cc_start: 0.7606 (tm-30) cc_final: 0.7191 (tm-30) REVERT: H 215 LYS cc_start: 0.8434 (ptpp) cc_final: 0.8025 (ptpp) REVERT: H 282 ILE cc_start: 0.7727 (tt) cc_final: 0.7459 (tt) REVERT: I 12 GLU cc_start: 0.6708 (mm-30) cc_final: 0.6379 (mm-30) REVERT: I 15 ARG cc_start: 0.7202 (ptt-90) cc_final: 0.6716 (ptt-90) REVERT: I 21 ILE cc_start: 0.8397 (tp) cc_final: 0.8197 (tp) REVERT: I 56 GLN cc_start: 0.7370 (tp-100) cc_final: 0.6780 (tp-100) REVERT: I 234 ASN cc_start: 0.7130 (t0) cc_final: 0.6181 (t0) REVERT: I 238 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7280 (mm-30) REVERT: I 316 MET cc_start: 0.7886 (tpp) cc_final: 0.7542 (tpp) REVERT: I 321 LYS cc_start: 0.8387 (tttm) cc_final: 0.7834 (tttm) REVERT: J 10 LEU cc_start: 0.8537 (mt) cc_final: 0.8011 (mt) REVERT: J 11 ASP cc_start: 0.8005 (m-30) cc_final: 0.7390 (m-30) REVERT: J 63 ASP cc_start: 0.8269 (t70) cc_final: 0.8016 (t70) REVERT: J 151 ILE cc_start: 0.8601 (mt) cc_final: 0.8389 (mm) REVERT: J 220 MET cc_start: 0.7503 (tpp) cc_final: 0.7275 (mpp) outliers start: 2 outliers final: 0 residues processed: 604 average time/residue: 0.1715 time to fit residues: 150.7915 Evaluate side-chains 562 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 562 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 0.3980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN C 28 ASN C 30 HIS H 161 HIS I 167 ASN ** I 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.155107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.124273 restraints weight = 34581.986| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.86 r_work: 0.3422 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22141 Z= 0.168 Angle : 0.613 9.454 29965 Z= 0.319 Chirality : 0.045 0.211 3295 Planarity : 0.005 0.062 3845 Dihedral : 6.901 88.914 3008 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.37 % Favored : 94.59 % Rotamer: Outliers : 1.39 % Allowed : 8.75 % Favored : 89.86 % 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: -0.89 (0.16), residues: 2664 helix: 0.16 (0.17), residues: 933 sheet: 0.17 (0.21), residues: 573 loop : -1.59 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 14 TYR 0.020 0.002 TYR D 250 PHE 0.021 0.002 PHE C 169 TRP 0.031 0.002 TRP C 131 HIS 0.005 0.001 HIS D 44 Details of bonding type rmsd covalent geometry : bond 0.00389 (22141) covalent geometry : angle 0.61338 (29965) hydrogen bonds : bond 0.05038 ( 891) hydrogen bonds : angle 4.69076 ( 2460) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 594 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.7485 (ttt180) REVERT: A 87 ASP cc_start: 0.7427 (m-30) cc_final: 0.7217 (m-30) REVERT: A 161 ARG cc_start: 0.7946 (mmt90) cc_final: 0.7462 (mpt180) REVERT: A 266 GLU cc_start: 0.7485 (pm20) cc_final: 0.7130 (pm20) REVERT: A 274 GLU cc_start: 0.7304 (pm20) cc_final: 0.7023 (pm20) REVERT: A 302 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7534 (tm-30) REVERT: B 211 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7423 (mm-30) REVERT: B 372 TRP cc_start: 0.8443 (m100) cc_final: 0.8124 (m100) REVERT: C 257 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7543 (mm-30) REVERT: D 171 ASP cc_start: 0.7322 (t0) cc_final: 0.6925 (t0) REVERT: D 222 TYR cc_start: 0.8649 (m-80) cc_final: 0.8145 (m-80) REVERT: D 237 ARG cc_start: 0.7795 (ttp-110) cc_final: 0.7549 (ttp-110) REVERT: E 9 MET cc_start: 0.6336 (mmm) cc_final: 0.6040 (mmm) REVERT: E 92 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7588 (tm-30) REVERT: E 94 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8288 (mt-10) REVERT: E 95 MET cc_start: 0.7872 (mtm) cc_final: 0.7568 (mtm) REVERT: E 155 LYS cc_start: 0.7756 (mtmm) cc_final: 0.7527 (mtmm) REVERT: F 83 GLU cc_start: 0.7094 (mm-30) cc_final: 0.6701 (mm-30) REVERT: F 163 GLU cc_start: 0.7395 (mm-30) cc_final: 0.7160 (mm-30) REVERT: G 107 MET cc_start: 0.7204 (tpp) cc_final: 0.6987 (tpp) REVERT: H 195 GLU cc_start: 0.7755 (tm-30) cc_final: 0.7379 (tm-30) REVERT: H 215 LYS cc_start: 0.8546 (ptpp) cc_final: 0.8187 (ptpp) REVERT: H 238 LYS cc_start: 0.8147 (mmtm) cc_final: 0.7909 (tppt) REVERT: H 286 ASP cc_start: 0.7990 (m-30) cc_final: 0.7372 (m-30) REVERT: H 288 ASP cc_start: 0.8006 (OUTLIER) cc_final: 0.7665 (t0) REVERT: H 361 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7205 (mt-10) REVERT: I 21 ILE cc_start: 0.8373 (tp) cc_final: 0.8168 (tp) REVERT: I 56 GLN cc_start: 0.7445 (tp-100) cc_final: 0.6775 (tp-100) REVERT: I 138 ASN cc_start: 0.7241 (t0) cc_final: 0.6898 (t0) REVERT: I 167 ASN cc_start: 0.7821 (t160) cc_final: 0.7107 (t0) REVERT: I 238 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7363 (mm-30) REVERT: I 318 LYS cc_start: 0.8232 (mmpt) cc_final: 0.7802 (mmpt) REVERT: I 321 LYS cc_start: 0.8510 (tttm) cc_final: 0.8167 (tttm) REVERT: J 31 LEU cc_start: 0.8424 (mm) cc_final: 0.8035 (tt) REVERT: J 151 ILE cc_start: 0.8753 (mt) cc_final: 0.8530 (mm) REVERT: J 220 MET cc_start: 0.7526 (tpp) cc_final: 0.7265 (mpp) outliers start: 33 outliers final: 16 residues processed: 601 average time/residue: 0.1673 time to fit residues: 146.1424 Evaluate side-chains 594 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 576 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain H residue 177 ARG Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 190 MET Chi-restraints excluded: chain H residue 285 CYS Chi-restraints excluded: chain H residue 288 ASP Chi-restraints excluded: chain H residue 296 ASN Chi-restraints excluded: chain H residue 318 THR Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain J residue 219 ASP Chi-restraints excluded: chain J residue 240 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 11 optimal weight: 0.7980 chunk 207 optimal weight: 0.2980 chunk 4 optimal weight: 0.8980 chunk 149 optimal weight: 0.0000 chunk 146 optimal weight: 7.9990 chunk 125 optimal weight: 0.0980 chunk 75 optimal weight: 3.9990 chunk 265 optimal weight: 3.9990 chunk 162 optimal weight: 0.6980 chunk 106 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 overall best weight: 0.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN C 28 ASN C 30 HIS C 75 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.156942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.125090 restraints weight = 34533.776| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.94 r_work: 0.3450 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 22141 Z= 0.104 Angle : 0.542 8.176 29965 Z= 0.281 Chirality : 0.043 0.157 3295 Planarity : 0.004 0.057 3845 Dihedral : 6.001 81.603 3008 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.20 % Favored : 95.76 % Rotamer: Outliers : 1.39 % Allowed : 12.72 % Favored : 85.88 % 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: -0.61 (0.16), residues: 2664 helix: 0.52 (0.17), residues: 935 sheet: 0.24 (0.22), residues: 576 loop : -1.50 (0.18), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 120 TYR 0.014 0.001 TYR E 132 PHE 0.016 0.001 PHE C 111 TRP 0.021 0.001 TRP C 131 HIS 0.003 0.001 HIS D 44 Details of bonding type rmsd covalent geometry : bond 0.00229 (22141) covalent geometry : angle 0.54190 (29965) hydrogen bonds : bond 0.03942 ( 891) hydrogen bonds : angle 4.31697 ( 2460) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 581 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8318 (mt) cc_final: 0.8059 (mt) REVERT: A 79 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.7376 (ttt90) REVERT: A 266 GLU cc_start: 0.7421 (pm20) cc_final: 0.7075 (pm20) REVERT: A 274 GLU cc_start: 0.7242 (pm20) cc_final: 0.6976 (pm20) REVERT: A 302 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7493 (tm-30) REVERT: B 211 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7346 (mm-30) REVERT: B 230 GLU cc_start: 0.7230 (mm-30) cc_final: 0.6706 (mm-30) REVERT: B 372 TRP cc_start: 0.8434 (m100) cc_final: 0.8065 (m100) REVERT: C 28 ASN cc_start: 0.7562 (OUTLIER) cc_final: 0.7214 (t0) REVERT: C 257 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7536 (mm-30) REVERT: C 352 MET cc_start: 0.7300 (tmm) cc_final: 0.6750 (tmm) REVERT: D 171 ASP cc_start: 0.7306 (t0) cc_final: 0.6949 (t0) REVERT: D 222 TYR cc_start: 0.8644 (m-80) cc_final: 0.8033 (m-80) REVERT: E 92 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7605 (tm-30) REVERT: E 94 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8265 (mt-10) REVERT: E 95 MET cc_start: 0.7869 (mtm) cc_final: 0.7529 (mtm) REVERT: F 163 GLU cc_start: 0.7431 (mm-30) cc_final: 0.7203 (mm-30) REVERT: G 107 MET cc_start: 0.7176 (tpp) cc_final: 0.6955 (tpp) REVERT: H 159 VAL cc_start: 0.8444 (p) cc_final: 0.8160 (m) REVERT: H 195 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7409 (tm-30) REVERT: H 214 GLU cc_start: 0.7165 (mt-10) cc_final: 0.6601 (mp0) REVERT: H 215 LYS cc_start: 0.8534 (ptpp) cc_final: 0.8188 (ptpp) REVERT: H 288 ASP cc_start: 0.7992 (m-30) cc_final: 0.7657 (t0) REVERT: H 294 TYR cc_start: 0.7406 (OUTLIER) cc_final: 0.7011 (m-10) REVERT: I 40 LEU cc_start: 0.8184 (tp) cc_final: 0.7864 (tp) REVERT: I 56 GLN cc_start: 0.7437 (tp-100) cc_final: 0.6741 (tp-100) REVERT: I 138 ASN cc_start: 0.7184 (t0) cc_final: 0.6782 (t0) REVERT: I 167 ASN cc_start: 0.7634 (t160) cc_final: 0.7286 (t0) REVERT: I 238 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7356 (mm-30) REVERT: I 318 LYS cc_start: 0.8243 (mmpt) cc_final: 0.7847 (mmtt) REVERT: I 321 LYS cc_start: 0.8518 (tttm) cc_final: 0.8197 (tttm) REVERT: J 12 LEU cc_start: 0.8499 (mt) cc_final: 0.8230 (mt) REVERT: J 22 GLU cc_start: 0.8114 (pm20) cc_final: 0.7900 (pm20) REVERT: J 31 LEU cc_start: 0.8414 (mm) cc_final: 0.8050 (tt) REVERT: J 63 ASP cc_start: 0.8323 (t70) cc_final: 0.8102 (t0) REVERT: J 80 ASP cc_start: 0.7102 (m-30) cc_final: 0.6848 (t0) REVERT: J 151 ILE cc_start: 0.8728 (mt) cc_final: 0.8482 (mm) REVERT: J 219 ASP cc_start: 0.8376 (t70) cc_final: 0.7527 (t0) outliers start: 33 outliers final: 20 residues processed: 590 average time/residue: 0.1643 time to fit residues: 141.6428 Evaluate side-chains 601 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 578 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 28 ASN Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 177 ARG Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 190 MET Chi-restraints excluded: chain H residue 285 CYS Chi-restraints excluded: chain H residue 294 TYR Chi-restraints excluded: chain H residue 296 ASN Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 207 VAL Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain J residue 196 GLN Chi-restraints excluded: chain J residue 210 ILE Chi-restraints excluded: chain J residue 240 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 65 optimal weight: 4.9990 chunk 94 optimal weight: 0.0670 chunk 175 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 188 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 chunk 224 optimal weight: 0.1980 chunk 134 optimal weight: 1.9990 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN A 28 GLN A 108 HIS A 205 GLN C 30 HIS C 75 ASN H 12 ASN J 101 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.155093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.123379 restraints weight = 34549.490| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.94 r_work: 0.3435 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22141 Z= 0.131 Angle : 0.554 9.094 29965 Z= 0.286 Chirality : 0.043 0.145 3295 Planarity : 0.004 0.064 3845 Dihedral : 5.909 84.574 3008 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.99 % Favored : 94.97 % Rotamer: Outliers : 1.99 % Allowed : 14.75 % Favored : 83.26 % 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 (0.16), residues: 2664 helix: 0.63 (0.18), residues: 941 sheet: 0.24 (0.22), residues: 587 loop : -1.42 (0.18), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 108 TYR 0.018 0.001 TYR D 250 PHE 0.018 0.001 PHE C 111 TRP 0.026 0.001 TRP C 131 HIS 0.004 0.001 HIS D 44 Details of bonding type rmsd covalent geometry : bond 0.00304 (22141) covalent geometry : angle 0.55354 (29965) hydrogen bonds : bond 0.04095 ( 891) hydrogen bonds : angle 4.20636 ( 2460) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 603 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8321 (mt) cc_final: 0.8057 (mt) REVERT: A 26 GLU cc_start: 0.7498 (mm-30) cc_final: 0.7134 (mm-30) REVERT: A 79 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.7418 (ttt90) REVERT: A 99 LYS cc_start: 0.8430 (tttt) cc_final: 0.8196 (mttt) REVERT: A 302 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7467 (tm-30) REVERT: B 211 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7395 (mm-30) REVERT: B 230 GLU cc_start: 0.7272 (mm-30) cc_final: 0.6760 (mm-30) REVERT: B 320 GLU cc_start: 0.7451 (mm-30) cc_final: 0.7232 (mt-10) REVERT: B 372 TRP cc_start: 0.8455 (m100) cc_final: 0.8104 (m100) REVERT: C 94 ARG cc_start: 0.8762 (mtm-85) cc_final: 0.8217 (mtm-85) REVERT: C 154 ASN cc_start: 0.8246 (t0) cc_final: 0.7834 (t0) REVERT: C 257 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7546 (mm-30) REVERT: C 352 MET cc_start: 0.7359 (tmm) cc_final: 0.6716 (tmm) REVERT: D 171 ASP cc_start: 0.7305 (t0) cc_final: 0.6976 (t0) REVERT: D 222 TYR cc_start: 0.8646 (m-80) cc_final: 0.7926 (m-80) REVERT: E 92 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7671 (tm-30) REVERT: E 94 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8259 (mt-10) REVERT: E 155 LYS cc_start: 0.7708 (mtmm) cc_final: 0.7505 (mtmm) REVERT: F 78 GLN cc_start: 0.8120 (mp10) cc_final: 0.7899 (mp10) REVERT: F 163 GLU cc_start: 0.7448 (mm-30) cc_final: 0.7208 (mm-30) REVERT: G 107 MET cc_start: 0.7199 (tpp) cc_final: 0.6928 (tpp) REVERT: G 111 TYR cc_start: 0.7577 (m-80) cc_final: 0.7185 (m-80) REVERT: H 195 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7475 (tm-30) REVERT: H 214 GLU cc_start: 0.7179 (mt-10) cc_final: 0.6643 (mp0) REVERT: H 215 LYS cc_start: 0.8540 (ptpp) cc_final: 0.8207 (ptpp) REVERT: H 288 ASP cc_start: 0.8053 (OUTLIER) cc_final: 0.7721 (t0) REVERT: H 361 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7308 (mt-10) REVERT: I 56 GLN cc_start: 0.7384 (tp-100) cc_final: 0.6653 (tp-100) REVERT: I 58 ASN cc_start: 0.7950 (m110) cc_final: 0.7600 (m110) REVERT: I 59 MET cc_start: 0.7594 (mpp) cc_final: 0.7026 (mpp) REVERT: I 111 GLU cc_start: 0.7643 (pp20) cc_final: 0.7439 (pp20) REVERT: I 138 ASN cc_start: 0.7252 (t0) cc_final: 0.6889 (t0) REVERT: I 167 ASN cc_start: 0.7661 (t160) cc_final: 0.7187 (t0) REVERT: I 238 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7401 (mm-30) REVERT: I 316 MET cc_start: 0.7808 (tpp) cc_final: 0.7212 (mpp) REVERT: I 318 LYS cc_start: 0.8262 (mmpt) cc_final: 0.7866 (mmtt) REVERT: I 321 LYS cc_start: 0.8513 (tttm) cc_final: 0.8162 (tttm) REVERT: J 12 LEU cc_start: 0.8560 (mt) cc_final: 0.8314 (mt) REVERT: J 22 GLU cc_start: 0.8019 (pm20) cc_final: 0.7781 (pm20) REVERT: J 27 ASP cc_start: 0.8245 (m-30) cc_final: 0.7983 (m-30) REVERT: J 31 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8053 (tt) REVERT: J 63 ASP cc_start: 0.8389 (t70) cc_final: 0.8168 (t0) REVERT: J 151 ILE cc_start: 0.8750 (mt) cc_final: 0.8503 (mm) REVERT: J 219 ASP cc_start: 0.8334 (t70) cc_final: 0.7611 (t70) outliers start: 47 outliers final: 33 residues processed: 620 average time/residue: 0.1665 time to fit residues: 150.5529 Evaluate side-chains 611 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 575 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 175 ILE Chi-restraints excluded: chain H residue 177 ARG Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 190 MET Chi-restraints excluded: chain H residue 285 CYS Chi-restraints excluded: chain H residue 288 ASP Chi-restraints excluded: chain H residue 296 ASN Chi-restraints excluded: chain H residue 318 THR Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 207 VAL Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 108 ARG Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain J residue 196 GLN Chi-restraints excluded: chain J residue 210 ILE Chi-restraints excluded: chain J residue 240 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 187 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 135 optimal weight: 6.9990 chunk 204 optimal weight: 0.9980 chunk 141 optimal weight: 0.5980 chunk 201 optimal weight: 0.1980 chunk 255 optimal weight: 1.9990 chunk 120 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 207 optimal weight: 9.9990 chunk 262 optimal weight: 10.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN C 28 ASN C 30 HIS D 21 ASN D 193 HIS D 242 ASN H 371 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.152788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.120948 restraints weight = 34309.723| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.96 r_work: 0.3407 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 22141 Z= 0.172 Angle : 0.573 8.876 29965 Z= 0.300 Chirality : 0.044 0.152 3295 Planarity : 0.005 0.057 3845 Dihedral : 5.987 86.185 3008 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.33 % Favored : 94.63 % Rotamer: Outliers : 2.79 % Allowed : 15.68 % Favored : 81.53 % 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: -0.48 (0.17), residues: 2664 helix: 0.66 (0.18), residues: 938 sheet: 0.27 (0.22), residues: 588 loop : -1.45 (0.18), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 260 TYR 0.020 0.001 TYR D 250 PHE 0.022 0.002 PHE C 169 TRP 0.036 0.002 TRP C 131 HIS 0.005 0.001 HIS D 44 Details of bonding type rmsd covalent geometry : bond 0.00405 (22141) covalent geometry : angle 0.57335 (29965) hydrogen bonds : bond 0.04459 ( 891) hydrogen bonds : angle 4.23113 ( 2460) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 590 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.7554 (mm-30) cc_final: 0.7175 (mm-30) REVERT: A 79 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7434 (ttt90) REVERT: A 99 LYS cc_start: 0.8408 (tttt) cc_final: 0.8148 (mttt) REVERT: A 161 ARG cc_start: 0.7935 (mmt90) cc_final: 0.7387 (mmt180) REVERT: A 274 GLU cc_start: 0.7198 (pm20) cc_final: 0.6995 (pm20) REVERT: A 316 TYR cc_start: 0.8360 (m-80) cc_final: 0.8095 (m-80) REVERT: B 63 GLU cc_start: 0.7245 (pm20) cc_final: 0.6944 (pm20) REVERT: B 170 TYR cc_start: 0.7660 (t80) cc_final: 0.7166 (t80) REVERT: B 211 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7457 (mm-30) REVERT: B 230 GLU cc_start: 0.7264 (mm-30) cc_final: 0.6806 (mm-30) REVERT: B 320 GLU cc_start: 0.7405 (mm-30) cc_final: 0.7177 (mt-10) REVERT: B 372 TRP cc_start: 0.8480 (m100) cc_final: 0.8096 (m100) REVERT: C 257 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7541 (mm-30) REVERT: C 352 MET cc_start: 0.7468 (tmm) cc_final: 0.6781 (tmm) REVERT: D 222 TYR cc_start: 0.8646 (m-80) cc_final: 0.7899 (m-80) REVERT: E 92 GLU cc_start: 0.8253 (tm-30) cc_final: 0.7723 (tm-30) REVERT: E 94 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8305 (mt-10) REVERT: E 155 LYS cc_start: 0.7720 (mtmm) cc_final: 0.7499 (mtmm) REVERT: F 78 GLN cc_start: 0.8117 (mp10) cc_final: 0.7910 (mp10) REVERT: F 163 GLU cc_start: 0.7487 (mm-30) cc_final: 0.7220 (mm-30) REVERT: G 107 MET cc_start: 0.7161 (tpp) cc_final: 0.6889 (tpp) REVERT: G 111 TYR cc_start: 0.7714 (m-80) cc_final: 0.7253 (m-80) REVERT: H 187 ASP cc_start: 0.8159 (m-30) cc_final: 0.7827 (t0) REVERT: H 195 GLU cc_start: 0.7842 (tm-30) cc_final: 0.7492 (tm-30) REVERT: H 214 GLU cc_start: 0.7219 (mt-10) cc_final: 0.6708 (mp0) REVERT: H 215 LYS cc_start: 0.8572 (ptpp) cc_final: 0.8195 (ptpp) REVERT: H 285 CYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8151 (m) REVERT: H 288 ASP cc_start: 0.8033 (OUTLIER) cc_final: 0.7700 (t0) REVERT: H 361 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7432 (mt-10) REVERT: I 56 GLN cc_start: 0.7459 (tp-100) cc_final: 0.6817 (tp-100) REVERT: I 58 ASN cc_start: 0.8033 (m110) cc_final: 0.7664 (m110) REVERT: I 59 MET cc_start: 0.7711 (mpp) cc_final: 0.7292 (mpp) REVERT: I 111 GLU cc_start: 0.7691 (pp20) cc_final: 0.7238 (pp20) REVERT: I 138 ASN cc_start: 0.7287 (t0) cc_final: 0.6963 (t0) REVERT: I 167 ASN cc_start: 0.7783 (t160) cc_final: 0.7312 (t0) REVERT: I 238 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7429 (mm-30) REVERT: I 247 TYR cc_start: 0.7250 (t80) cc_final: 0.6828 (t80) REVERT: I 318 LYS cc_start: 0.8263 (mmpt) cc_final: 0.7995 (mmtt) REVERT: I 321 LYS cc_start: 0.8550 (tttm) cc_final: 0.8243 (tttm) REVERT: J 5 GLN cc_start: 0.8092 (pm20) cc_final: 0.7814 (pm20) REVERT: J 14 ARG cc_start: 0.7620 (ptt-90) cc_final: 0.7232 (ptt-90) REVERT: J 22 GLU cc_start: 0.7987 (pm20) cc_final: 0.7719 (pm20) REVERT: J 31 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8122 (mt) REVERT: J 63 ASP cc_start: 0.8437 (t70) cc_final: 0.8226 (t0) REVERT: J 151 ILE cc_start: 0.8772 (mt) cc_final: 0.8535 (mm) REVERT: J 219 ASP cc_start: 0.8281 (t70) cc_final: 0.7450 (t70) outliers start: 66 outliers final: 49 residues processed: 615 average time/residue: 0.1632 time to fit residues: 147.2791 Evaluate side-chains 618 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 565 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain E residue 19 MET Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 175 ILE Chi-restraints excluded: chain H residue 177 ARG Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 190 MET Chi-restraints excluded: chain H residue 198 TYR Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 285 CYS Chi-restraints excluded: chain H residue 288 ASP Chi-restraints excluded: chain H residue 294 TYR Chi-restraints excluded: chain H residue 296 ASN Chi-restraints excluded: chain H residue 300 SER Chi-restraints excluded: chain H residue 318 THR Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 164 GLN Chi-restraints excluded: chain I residue 207 VAL Chi-restraints excluded: chain I residue 269 ILE Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 108 ARG Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain J residue 178 GLN Chi-restraints excluded: chain J residue 196 GLN Chi-restraints excluded: chain J residue 210 ILE Chi-restraints excluded: chain J residue 240 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 180 optimal weight: 3.9990 chunk 204 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 144 optimal weight: 10.0000 chunk 115 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 168 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN C 30 HIS D 278 ASN J 126 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.151290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.119655 restraints weight = 34392.004| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.93 r_work: 0.3383 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 22141 Z= 0.221 Angle : 0.619 9.603 29965 Z= 0.324 Chirality : 0.046 0.188 3295 Planarity : 0.005 0.055 3845 Dihedral : 6.181 94.092 3008 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.23 % Favored : 93.73 % Rotamer: Outliers : 3.30 % Allowed : 16.44 % Favored : 80.26 % 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: -0.60 (0.16), residues: 2664 helix: 0.55 (0.17), residues: 939 sheet: 0.14 (0.21), residues: 600 loop : -1.50 (0.18), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 244 TYR 0.021 0.002 TYR D 250 PHE 0.026 0.002 PHE C 169 TRP 0.042 0.002 TRP C 131 HIS 0.006 0.001 HIS D 44 Details of bonding type rmsd covalent geometry : bond 0.00521 (22141) covalent geometry : angle 0.61858 (29965) hydrogen bonds : bond 0.04997 ( 891) hydrogen bonds : angle 4.37341 ( 2460) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 583 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.7558 (mm-30) cc_final: 0.7103 (mm-30) REVERT: A 79 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7462 (ttt90) REVERT: A 161 ARG cc_start: 0.7941 (mmt90) cc_final: 0.7362 (mmt180) REVERT: B 170 TYR cc_start: 0.7782 (t80) cc_final: 0.7397 (t80) REVERT: B 211 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7562 (mm-30) REVERT: B 227 ILE cc_start: 0.7708 (mm) cc_final: 0.7470 (mm) REVERT: B 230 GLU cc_start: 0.7257 (mm-30) cc_final: 0.6844 (mm-30) REVERT: B 242 GLU cc_start: 0.7310 (mm-30) cc_final: 0.7014 (mm-30) REVERT: B 320 GLU cc_start: 0.7400 (mm-30) cc_final: 0.7180 (mt-10) REVERT: B 372 TRP cc_start: 0.8498 (m100) cc_final: 0.8021 (m100) REVERT: C 257 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7577 (mm-30) REVERT: C 342 LYS cc_start: 0.8126 (mtpt) cc_final: 0.7826 (mtmt) REVERT: C 352 MET cc_start: 0.7507 (tmm) cc_final: 0.6787 (tmm) REVERT: D 35 PHE cc_start: 0.7981 (m-10) cc_final: 0.7681 (m-10) REVERT: D 222 TYR cc_start: 0.8649 (m-80) cc_final: 0.7859 (m-80) REVERT: E 92 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7699 (tm-30) REVERT: E 94 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8281 (mt-10) REVERT: E 155 LYS cc_start: 0.7754 (mtmm) cc_final: 0.7506 (mtmm) REVERT: F 78 GLN cc_start: 0.8142 (mp10) cc_final: 0.7929 (mp10) REVERT: F 163 GLU cc_start: 0.7506 (mm-30) cc_final: 0.7194 (mm-30) REVERT: G 111 TYR cc_start: 0.7794 (m-80) cc_final: 0.7396 (m-80) REVERT: H 82 MET cc_start: 0.5737 (tpt) cc_final: 0.5014 (tpt) REVERT: H 187 ASP cc_start: 0.8203 (m-30) cc_final: 0.7877 (t0) REVERT: H 195 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7497 (tm-30) REVERT: H 214 GLU cc_start: 0.7207 (mt-10) cc_final: 0.6756 (mt-10) REVERT: H 215 LYS cc_start: 0.8556 (ptpp) cc_final: 0.8192 (ptpp) REVERT: H 259 GLU cc_start: 0.8188 (tp30) cc_final: 0.7682 (tp30) REVERT: H 285 CYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8269 (m) REVERT: H 288 ASP cc_start: 0.8052 (OUTLIER) cc_final: 0.7730 (t0) REVERT: H 290 ARG cc_start: 0.6925 (mtt90) cc_final: 0.6266 (ttt90) REVERT: H 316 GLU cc_start: 0.6428 (tm-30) cc_final: 0.5915 (mm-30) REVERT: H 334 GLU cc_start: 0.7230 (pp20) cc_final: 0.6761 (pp20) REVERT: I 56 GLN cc_start: 0.7483 (tp-100) cc_final: 0.6888 (tp-100) REVERT: I 58 ASN cc_start: 0.8089 (m110) cc_final: 0.7733 (m110) REVERT: I 59 MET cc_start: 0.7732 (mpp) cc_final: 0.6218 (mmm) REVERT: I 138 ASN cc_start: 0.7313 (t0) cc_final: 0.7032 (t0) REVERT: I 155 ILE cc_start: 0.2896 (mt) cc_final: 0.2496 (pt) REVERT: I 167 ASN cc_start: 0.7932 (t160) cc_final: 0.7419 (t0) REVERT: I 238 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7461 (mm-30) REVERT: I 318 LYS cc_start: 0.8218 (mmpt) cc_final: 0.7928 (mmtt) REVERT: I 321 LYS cc_start: 0.8507 (tttm) cc_final: 0.8197 (tttm) REVERT: J 5 GLN cc_start: 0.8088 (pm20) cc_final: 0.7804 (pm20) REVERT: J 14 ARG cc_start: 0.7671 (ptt-90) cc_final: 0.7304 (ptt-90) REVERT: J 22 GLU cc_start: 0.7950 (pm20) cc_final: 0.7741 (pm20) REVERT: J 31 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8088 (tt) REVERT: J 63 ASP cc_start: 0.8509 (t70) cc_final: 0.8279 (t0) REVERT: J 151 ILE cc_start: 0.8792 (mt) cc_final: 0.8532 (mm) REVERT: J 199 LYS cc_start: 0.7853 (tmmt) cc_final: 0.7647 (tmmt) REVERT: J 219 ASP cc_start: 0.8295 (OUTLIER) cc_final: 0.7444 (t0) outliers start: 78 outliers final: 60 residues processed: 610 average time/residue: 0.1666 time to fit residues: 149.1852 Evaluate side-chains 640 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 575 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain B residue 105 CYS Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 366 LYS Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 129 ASN Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 157 LYS Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 175 ILE Chi-restraints excluded: chain H residue 177 ARG Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 190 MET Chi-restraints excluded: chain H residue 198 TYR Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 285 CYS Chi-restraints excluded: chain H residue 287 ILE Chi-restraints excluded: chain H residue 288 ASP Chi-restraints excluded: chain H residue 294 TYR Chi-restraints excluded: chain H residue 296 ASN Chi-restraints excluded: chain H residue 318 THR Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 164 GLN Chi-restraints excluded: chain I residue 207 VAL Chi-restraints excluded: chain I residue 256 LYS Chi-restraints excluded: chain I residue 269 ILE Chi-restraints excluded: chain J residue 23 LYS Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 132 ILE Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain J residue 178 GLN Chi-restraints excluded: chain J residue 187 MET Chi-restraints excluded: chain J residue 196 GLN Chi-restraints excluded: chain J residue 210 ILE Chi-restraints excluded: chain J residue 219 ASP Chi-restraints excluded: chain J residue 240 VAL Chi-restraints excluded: chain J residue 264 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 37 optimal weight: 0.8980 chunk 112 optimal weight: 0.0970 chunk 253 optimal weight: 10.0000 chunk 224 optimal weight: 0.8980 chunk 123 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 101 optimal weight: 0.5980 chunk 188 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN B 119 ASN C 30 HIS ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.154411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.122669 restraints weight = 34288.218| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.91 r_work: 0.3423 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22141 Z= 0.118 Angle : 0.564 11.173 29965 Z= 0.290 Chirality : 0.043 0.162 3295 Planarity : 0.004 0.056 3845 Dihedral : 5.860 84.887 3008 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.69 % Favored : 95.27 % Rotamer: Outliers : 2.62 % Allowed : 18.72 % Favored : 78.66 % 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: -0.39 (0.17), residues: 2664 helix: 0.86 (0.18), residues: 926 sheet: 0.18 (0.21), residues: 602 loop : -1.44 (0.18), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 244 TYR 0.015 0.001 TYR E 132 PHE 0.018 0.001 PHE C 111 TRP 0.021 0.001 TRP C 131 HIS 0.003 0.001 HIS D 44 Details of bonding type rmsd covalent geometry : bond 0.00273 (22141) covalent geometry : angle 0.56377 (29965) hydrogen bonds : bond 0.03847 ( 891) hydrogen bonds : angle 4.13016 ( 2460) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 573 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8291 (mt) cc_final: 0.7994 (mt) REVERT: A 26 GLU cc_start: 0.7506 (mm-30) cc_final: 0.7049 (mm-30) REVERT: A 79 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7438 (ttt90) REVERT: A 161 ARG cc_start: 0.7930 (mmt90) cc_final: 0.7321 (mmt180) REVERT: B 85 MET cc_start: 0.7251 (mmm) cc_final: 0.6909 (mmt) REVERT: B 170 TYR cc_start: 0.7658 (t80) cc_final: 0.7178 (t80) REVERT: B 211 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7453 (mm-30) REVERT: B 230 GLU cc_start: 0.7279 (mm-30) cc_final: 0.6884 (mm-30) REVERT: B 320 GLU cc_start: 0.7429 (mm-30) cc_final: 0.7214 (mt-10) REVERT: B 372 TRP cc_start: 0.8484 (m100) cc_final: 0.7965 (m100) REVERT: C 257 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7595 (mm-30) REVERT: C 342 LYS cc_start: 0.8116 (mtpt) cc_final: 0.7818 (mtmt) REVERT: C 352 MET cc_start: 0.7463 (tmm) cc_final: 0.6776 (tmm) REVERT: D 35 PHE cc_start: 0.7860 (m-10) cc_final: 0.7643 (m-10) REVERT: D 222 TYR cc_start: 0.8585 (m-80) cc_final: 0.7813 (m-80) REVERT: E 92 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7685 (tm-30) REVERT: E 94 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8270 (mt-10) REVERT: E 155 LYS cc_start: 0.7693 (mtmm) cc_final: 0.7471 (mtmm) REVERT: F 154 ASN cc_start: 0.8307 (t0) cc_final: 0.8100 (t0) REVERT: F 163 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7233 (mm-30) REVERT: G 111 TYR cc_start: 0.7739 (m-80) cc_final: 0.7328 (m-80) REVERT: H 82 MET cc_start: 0.5489 (tpt) cc_final: 0.4805 (tpt) REVERT: H 155 SER cc_start: 0.8368 (m) cc_final: 0.8115 (t) REVERT: H 187 ASP cc_start: 0.8145 (m-30) cc_final: 0.7822 (t0) REVERT: H 195 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7522 (tm-30) REVERT: H 214 GLU cc_start: 0.7196 (mt-10) cc_final: 0.6708 (mt-10) REVERT: H 215 LYS cc_start: 0.8528 (ptpp) cc_final: 0.8174 (ptpp) REVERT: H 285 CYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8171 (m) REVERT: H 288 ASP cc_start: 0.7999 (m-30) cc_final: 0.7683 (t0) REVERT: H 316 GLU cc_start: 0.6218 (tm-30) cc_final: 0.5802 (mm-30) REVERT: I 56 GLN cc_start: 0.7452 (tp-100) cc_final: 0.6843 (tp-100) REVERT: I 58 ASN cc_start: 0.8033 (m110) cc_final: 0.7681 (m110) REVERT: I 59 MET cc_start: 0.7693 (mpp) cc_final: 0.6232 (mmm) REVERT: I 138 ASN cc_start: 0.7306 (t0) cc_final: 0.6967 (t0) REVERT: I 155 ILE cc_start: 0.2713 (mt) cc_final: 0.2499 (pt) REVERT: I 167 ASN cc_start: 0.7720 (t160) cc_final: 0.7164 (t0) REVERT: I 238 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7409 (mm-30) REVERT: I 316 MET cc_start: 0.7790 (tpp) cc_final: 0.7215 (mpp) REVERT: I 318 LYS cc_start: 0.8195 (mmpt) cc_final: 0.7806 (mmtt) REVERT: I 321 LYS cc_start: 0.8574 (tttm) cc_final: 0.8242 (tttm) REVERT: J 5 GLN cc_start: 0.8098 (pm20) cc_final: 0.7793 (pm20) REVERT: J 14 ARG cc_start: 0.7620 (ptt-90) cc_final: 0.7302 (ptt-90) REVERT: J 22 GLU cc_start: 0.7938 (pm20) cc_final: 0.7647 (pm20) REVERT: J 31 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8177 (tt) REVERT: J 63 ASP cc_start: 0.8442 (t70) cc_final: 0.8240 (t0) REVERT: J 151 ILE cc_start: 0.8734 (mt) cc_final: 0.8487 (mm) REVERT: J 199 LYS cc_start: 0.7884 (tmmt) cc_final: 0.7682 (tmmt) REVERT: J 219 ASP cc_start: 0.8271 (t70) cc_final: 0.7712 (t70) REVERT: J 220 MET cc_start: 0.7561 (tpt) cc_final: 0.7168 (mpp) outliers start: 62 outliers final: 46 residues processed: 597 average time/residue: 0.1651 time to fit residues: 145.0225 Evaluate side-chains 616 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 567 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain B residue 105 CYS Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 175 ILE Chi-restraints excluded: chain H residue 177 ARG Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 190 MET Chi-restraints excluded: chain H residue 198 TYR Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 285 CYS Chi-restraints excluded: chain H residue 294 TYR Chi-restraints excluded: chain H residue 296 ASN Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 164 GLN Chi-restraints excluded: chain I residue 207 VAL Chi-restraints excluded: chain I residue 269 ILE Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 108 ARG Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain J residue 178 GLN Chi-restraints excluded: chain J residue 196 GLN Chi-restraints excluded: chain J residue 210 ILE Chi-restraints excluded: chain J residue 240 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 163 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 263 optimal weight: 0.7980 chunk 51 optimal weight: 0.0770 chunk 33 optimal weight: 0.0070 chunk 79 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN C 30 HIS ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.154993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.123225 restraints weight = 34277.943| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.93 r_work: 0.3432 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22141 Z= 0.110 Angle : 0.560 11.508 29965 Z= 0.288 Chirality : 0.043 0.181 3295 Planarity : 0.004 0.062 3845 Dihedral : 5.682 81.318 3008 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.92 % Favored : 95.05 % Rotamer: Outliers : 2.32 % Allowed : 19.44 % Favored : 78.23 % 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: -0.26 (0.17), residues: 2664 helix: 0.99 (0.18), residues: 928 sheet: 0.20 (0.21), residues: 602 loop : -1.36 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 244 TYR 0.015 0.001 TYR E 132 PHE 0.024 0.001 PHE C 246 TRP 0.018 0.001 TRP C 131 HIS 0.003 0.001 HIS D 44 Details of bonding type rmsd covalent geometry : bond 0.00252 (22141) covalent geometry : angle 0.55961 (29965) hydrogen bonds : bond 0.03599 ( 891) hydrogen bonds : angle 4.03866 ( 2460) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 569 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8284 (mt) cc_final: 0.7991 (mt) REVERT: A 26 GLU cc_start: 0.7480 (mm-30) cc_final: 0.7017 (mm-30) REVERT: A 79 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7427 (ttt90) REVERT: B 10 VAL cc_start: 0.8484 (p) cc_final: 0.8225 (m) REVERT: B 170 TYR cc_start: 0.7593 (t80) cc_final: 0.7113 (t80) REVERT: B 211 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7437 (mm-30) REVERT: B 230 GLU cc_start: 0.7306 (mm-30) cc_final: 0.6956 (mm-30) REVERT: B 320 GLU cc_start: 0.7442 (mm-30) cc_final: 0.7232 (mt-10) REVERT: B 372 TRP cc_start: 0.8487 (m100) cc_final: 0.7995 (m100) REVERT: C 94 ARG cc_start: 0.8765 (mtm-85) cc_final: 0.8262 (mtm-85) REVERT: C 257 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7624 (mm-30) REVERT: C 342 LYS cc_start: 0.8091 (mtpt) cc_final: 0.7681 (mtpt) REVERT: C 352 MET cc_start: 0.7451 (tmm) cc_final: 0.6774 (tmm) REVERT: D 35 PHE cc_start: 0.7874 (m-10) cc_final: 0.7672 (m-10) REVERT: D 222 TYR cc_start: 0.8579 (m-80) cc_final: 0.7813 (m-80) REVERT: E 92 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7704 (tm-30) REVERT: E 94 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8271 (mt-10) REVERT: F 163 GLU cc_start: 0.7515 (mm-30) cc_final: 0.7234 (mm-30) REVERT: G 107 MET cc_start: 0.7102 (tpp) cc_final: 0.6850 (tpp) REVERT: G 111 TYR cc_start: 0.7714 (m-80) cc_final: 0.7312 (m-80) REVERT: H 82 MET cc_start: 0.5447 (tpt) cc_final: 0.4803 (tpt) REVERT: H 155 SER cc_start: 0.8372 (m) cc_final: 0.8122 (t) REVERT: H 187 ASP cc_start: 0.8136 (m-30) cc_final: 0.7806 (t0) REVERT: H 195 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7510 (tm-30) REVERT: H 210 ARG cc_start: 0.8004 (ttm-80) cc_final: 0.6974 (ttp80) REVERT: H 214 GLU cc_start: 0.7203 (mt-10) cc_final: 0.6252 (mt-10) REVERT: H 215 LYS cc_start: 0.8513 (ptpp) cc_final: 0.8160 (ptpp) REVERT: H 285 CYS cc_start: 0.8512 (OUTLIER) cc_final: 0.7982 (m) REVERT: H 288 ASP cc_start: 0.7988 (m-30) cc_final: 0.7672 (t0) REVERT: H 290 ARG cc_start: 0.6682 (mtt90) cc_final: 0.6298 (ttt90) REVERT: H 316 GLU cc_start: 0.6223 (tm-30) cc_final: 0.5776 (mm-30) REVERT: I 56 GLN cc_start: 0.7400 (tp-100) cc_final: 0.6783 (tp-100) REVERT: I 58 ASN cc_start: 0.8058 (m110) cc_final: 0.7692 (m110) REVERT: I 59 MET cc_start: 0.7667 (mpp) cc_final: 0.6190 (mmm) REVERT: I 138 ASN cc_start: 0.7266 (t0) cc_final: 0.6924 (t0) REVERT: I 155 ILE cc_start: 0.2803 (mt) cc_final: 0.2508 (pt) REVERT: I 167 ASN cc_start: 0.7645 (OUTLIER) cc_final: 0.7088 (t0) REVERT: I 176 GLU cc_start: 0.6650 (tt0) cc_final: 0.6426 (tm-30) REVERT: I 238 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7399 (mm-30) REVERT: I 316 MET cc_start: 0.7741 (tpp) cc_final: 0.7199 (mpp) REVERT: I 318 LYS cc_start: 0.8197 (mmpt) cc_final: 0.7932 (mmtt) REVERT: I 321 LYS cc_start: 0.8574 (tttm) cc_final: 0.8264 (tttm) REVERT: J 105 ASP cc_start: 0.7315 (p0) cc_final: 0.7109 (p0) REVERT: J 108 ARG cc_start: 0.6632 (OUTLIER) cc_final: 0.6357 (mtm-85) REVERT: J 117 SER cc_start: 0.7163 (p) cc_final: 0.6525 (p) REVERT: J 151 ILE cc_start: 0.8705 (mt) cc_final: 0.8450 (mm) REVERT: J 220 MET cc_start: 0.7555 (tpt) cc_final: 0.7110 (mpp) outliers start: 55 outliers final: 44 residues processed: 589 average time/residue: 0.1641 time to fit residues: 141.7634 Evaluate side-chains 608 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 560 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 105 CYS Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 157 LYS Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 175 ILE Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 190 MET Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 285 CYS Chi-restraints excluded: chain H residue 294 TYR Chi-restraints excluded: chain H residue 296 ASN Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 164 GLN Chi-restraints excluded: chain I residue 167 ASN Chi-restraints excluded: chain I residue 178 LYS Chi-restraints excluded: chain I residue 207 VAL Chi-restraints excluded: chain I residue 269 ILE Chi-restraints excluded: chain J residue 108 ARG Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain J residue 178 GLN Chi-restraints excluded: chain J residue 196 GLN Chi-restraints excluded: chain J residue 210 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 134 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 156 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 237 optimal weight: 2.9990 chunk 239 optimal weight: 1.9990 chunk 136 optimal weight: 0.0970 chunk 175 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN C 30 HIS ** D 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.153091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.121340 restraints weight = 34451.906| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.93 r_work: 0.3400 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 22141 Z= 0.178 Angle : 0.606 12.032 29965 Z= 0.315 Chirality : 0.045 0.192 3295 Planarity : 0.005 0.059 3845 Dihedral : 5.944 88.858 3008 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.04 % Favored : 93.92 % Rotamer: Outliers : 2.79 % Allowed : 19.57 % Favored : 77.64 % 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: -0.36 (0.17), residues: 2664 helix: 0.88 (0.18), residues: 933 sheet: 0.21 (0.21), residues: 595 loop : -1.43 (0.18), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 244 TYR 0.021 0.001 TYR D 250 PHE 0.024 0.002 PHE C 246 TRP 0.022 0.002 TRP C 131 HIS 0.005 0.001 HIS I 135 Details of bonding type rmsd covalent geometry : bond 0.00422 (22141) covalent geometry : angle 0.60638 (29965) hydrogen bonds : bond 0.04462 ( 891) hydrogen bonds : angle 4.19648 ( 2460) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 572 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8322 (mt) cc_final: 0.8036 (mt) REVERT: A 26 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7034 (mm-30) REVERT: A 79 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7612 (ttt180) REVERT: A 161 ARG cc_start: 0.7952 (mmt90) cc_final: 0.7336 (mmt180) REVERT: B 170 TYR cc_start: 0.7736 (t80) cc_final: 0.7259 (t80) REVERT: B 211 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7522 (mm-30) REVERT: B 230 GLU cc_start: 0.7280 (mm-30) cc_final: 0.6979 (mm-30) REVERT: B 320 GLU cc_start: 0.7463 (mm-30) cc_final: 0.7252 (mt-10) REVERT: B 372 TRP cc_start: 0.8520 (m100) cc_final: 0.8035 (m100) REVERT: C 257 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7638 (mm-30) REVERT: C 342 LYS cc_start: 0.8108 (mtpt) cc_final: 0.7903 (ptpt) REVERT: C 352 MET cc_start: 0.7492 (tmm) cc_final: 0.6788 (tmm) REVERT: D 35 PHE cc_start: 0.7982 (m-10) cc_final: 0.7760 (m-10) REVERT: D 111 HIS cc_start: 0.8028 (t70) cc_final: 0.7783 (t70) REVERT: D 222 TYR cc_start: 0.8649 (m-80) cc_final: 0.7812 (m-80) REVERT: E 92 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7687 (tm-30) REVERT: E 94 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8288 (mt-10) REVERT: E 123 LYS cc_start: 0.8759 (pttm) cc_final: 0.8529 (pttm) REVERT: E 155 LYS cc_start: 0.7923 (mtmm) cc_final: 0.7594 (mtmm) REVERT: F 163 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7260 (mm-30) REVERT: G 111 TYR cc_start: 0.7769 (m-80) cc_final: 0.7367 (m-80) REVERT: H 82 MET cc_start: 0.5604 (tpt) cc_final: 0.4919 (tpt) REVERT: H 155 SER cc_start: 0.8431 (m) cc_final: 0.8145 (t) REVERT: H 177 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.7976 (mtp85) REVERT: H 187 ASP cc_start: 0.8177 (m-30) cc_final: 0.7830 (t0) REVERT: H 195 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7532 (tm-30) REVERT: H 214 GLU cc_start: 0.7229 (mt-10) cc_final: 0.6733 (mt-10) REVERT: H 215 LYS cc_start: 0.8524 (ptpp) cc_final: 0.8167 (ptpp) REVERT: H 256 ARG cc_start: 0.8093 (mtp180) cc_final: 0.7891 (mtp-110) REVERT: H 259 GLU cc_start: 0.8368 (mm-30) cc_final: 0.8094 (mm-30) REVERT: H 285 CYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8279 (m) REVERT: H 288 ASP cc_start: 0.8040 (m-30) cc_final: 0.7723 (t0) REVERT: H 300 SER cc_start: 0.9008 (t) cc_final: 0.8638 (m) REVERT: H 316 GLU cc_start: 0.6371 (tm-30) cc_final: 0.5911 (mm-30) REVERT: I 56 GLN cc_start: 0.7462 (tp-100) cc_final: 0.6848 (tp-100) REVERT: I 58 ASN cc_start: 0.8072 (m110) cc_final: 0.7709 (m110) REVERT: I 59 MET cc_start: 0.7725 (mpp) cc_final: 0.6239 (mmm) REVERT: I 122 GLU cc_start: 0.7448 (mm-30) cc_final: 0.7000 (mm-30) REVERT: I 134 ASP cc_start: 0.6913 (p0) cc_final: 0.6639 (p0) REVERT: I 138 ASN cc_start: 0.7319 (t0) cc_final: 0.6991 (t0) REVERT: I 155 ILE cc_start: 0.2889 (mt) cc_final: 0.2573 (pt) REVERT: I 167 ASN cc_start: 0.7834 (t160) cc_final: 0.7307 (t0) REVERT: I 176 GLU cc_start: 0.6664 (tt0) cc_final: 0.6453 (tm-30) REVERT: I 238 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7446 (mm-30) REVERT: I 318 LYS cc_start: 0.8218 (mmpt) cc_final: 0.7948 (mmtt) REVERT: I 321 LYS cc_start: 0.8571 (tttm) cc_final: 0.8280 (tttm) REVERT: J 14 ARG cc_start: 0.7726 (ptt-90) cc_final: 0.7364 (ptt-90) REVERT: J 31 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8205 (tt) REVERT: J 151 ILE cc_start: 0.8743 (mt) cc_final: 0.8491 (mm) REVERT: J 244 ARG cc_start: 0.6848 (ttt180) cc_final: 0.6563 (ttt180) outliers start: 66 outliers final: 55 residues processed: 600 average time/residue: 0.1710 time to fit residues: 149.5367 Evaluate side-chains 627 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 568 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 105 CYS Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 175 ILE Chi-restraints excluded: chain H residue 177 ARG Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 190 MET Chi-restraints excluded: chain H residue 198 TYR Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 285 CYS Chi-restraints excluded: chain H residue 294 TYR Chi-restraints excluded: chain H residue 296 ASN Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 178 LYS Chi-restraints excluded: chain I residue 207 VAL Chi-restraints excluded: chain I residue 256 LYS Chi-restraints excluded: chain I residue 269 ILE Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 108 ARG Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 132 ILE Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain J residue 178 GLN Chi-restraints excluded: chain J residue 187 MET Chi-restraints excluded: chain J residue 196 GLN Chi-restraints excluded: chain J residue 210 ILE Chi-restraints excluded: chain J residue 264 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 176 optimal weight: 1.9990 chunk 264 optimal weight: 8.9990 chunk 115 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 234 optimal weight: 0.9980 chunk 153 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 252 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN C 30 HIS ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.153109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.121418 restraints weight = 34484.914| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.93 r_work: 0.3405 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22141 Z= 0.154 Angle : 0.605 12.462 29965 Z= 0.311 Chirality : 0.045 0.214 3295 Planarity : 0.004 0.064 3845 Dihedral : 5.917 88.137 3008 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.56 % Favored : 94.41 % Rotamer: Outliers : 2.45 % Allowed : 20.54 % Favored : 77.01 % 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: -0.32 (0.17), residues: 2664 helix: 0.91 (0.18), residues: 930 sheet: 0.21 (0.21), residues: 598 loop : -1.40 (0.18), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 244 TYR 0.017 0.001 TYR D 250 PHE 0.019 0.002 PHE C 111 TRP 0.019 0.001 TRP C 131 HIS 0.004 0.001 HIS D 44 Details of bonding type rmsd covalent geometry : bond 0.00363 (22141) covalent geometry : angle 0.60489 (29965) hydrogen bonds : bond 0.04112 ( 891) hydrogen bonds : angle 4.15863 ( 2460) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 559 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8321 (mt) cc_final: 0.8031 (mt) REVERT: A 26 GLU cc_start: 0.7489 (mm-30) cc_final: 0.7031 (mm-30) REVERT: A 79 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7647 (ttt180) REVERT: A 161 ARG cc_start: 0.7986 (mmt90) cc_final: 0.7398 (mmt180) REVERT: B 170 TYR cc_start: 0.7662 (t80) cc_final: 0.7200 (t80) REVERT: B 211 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7505 (mm-30) REVERT: B 230 GLU cc_start: 0.7324 (mm-30) cc_final: 0.7022 (mm-30) REVERT: B 242 GLU cc_start: 0.7320 (mm-30) cc_final: 0.7015 (mm-30) REVERT: B 320 GLU cc_start: 0.7463 (mm-30) cc_final: 0.7254 (mt-10) REVERT: B 343 ARG cc_start: 0.7381 (ttt90) cc_final: 0.7171 (ttt90) REVERT: B 372 TRP cc_start: 0.8533 (m100) cc_final: 0.8024 (m100) REVERT: C 257 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7660 (mm-30) REVERT: C 342 LYS cc_start: 0.8100 (mtpt) cc_final: 0.7898 (ptpt) REVERT: C 352 MET cc_start: 0.7453 (tmm) cc_final: 0.6756 (tmm) REVERT: D 35 PHE cc_start: 0.7931 (m-10) cc_final: 0.7698 (m-10) REVERT: D 222 TYR cc_start: 0.8604 (m-80) cc_final: 0.7776 (m-80) REVERT: E 92 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7683 (tm-30) REVERT: E 94 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8282 (mt-10) REVERT: E 123 LYS cc_start: 0.8731 (pttm) cc_final: 0.8506 (pttm) REVERT: E 155 LYS cc_start: 0.7865 (mtmm) cc_final: 0.7542 (mtmm) REVERT: F 163 GLU cc_start: 0.7551 (mm-30) cc_final: 0.7268 (mm-30) REVERT: G 111 TYR cc_start: 0.7757 (m-80) cc_final: 0.7320 (m-80) REVERT: H 82 MET cc_start: 0.5511 (tpt) cc_final: 0.4855 (tpt) REVERT: H 155 SER cc_start: 0.8440 (m) cc_final: 0.8137 (t) REVERT: H 177 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7986 (mtp85) REVERT: H 187 ASP cc_start: 0.8169 (m-30) cc_final: 0.7833 (t0) REVERT: H 195 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7521 (tm-30) REVERT: H 210 ARG cc_start: 0.8076 (ttm-80) cc_final: 0.7137 (ttp80) REVERT: H 214 GLU cc_start: 0.7230 (mt-10) cc_final: 0.6543 (mt-10) REVERT: H 215 LYS cc_start: 0.8518 (ptpp) cc_final: 0.8167 (ptpp) REVERT: H 259 GLU cc_start: 0.8355 (mm-30) cc_final: 0.8069 (mm-30) REVERT: H 285 CYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8217 (m) REVERT: H 288 ASP cc_start: 0.8017 (m-30) cc_final: 0.7697 (t0) REVERT: H 300 SER cc_start: 0.9007 (t) cc_final: 0.8596 (m) REVERT: H 316 GLU cc_start: 0.6309 (tm-30) cc_final: 0.5864 (mm-30) REVERT: I 56 GLN cc_start: 0.7391 (tp-100) cc_final: 0.6762 (tp-100) REVERT: I 58 ASN cc_start: 0.8055 (m110) cc_final: 0.7689 (m110) REVERT: I 59 MET cc_start: 0.7674 (mpp) cc_final: 0.6205 (mmm) REVERT: I 122 GLU cc_start: 0.7419 (mm-30) cc_final: 0.6963 (mm-30) REVERT: I 134 ASP cc_start: 0.6977 (p0) cc_final: 0.6706 (p0) REVERT: I 138 ASN cc_start: 0.7319 (t0) cc_final: 0.6991 (t0) REVERT: I 155 ILE cc_start: 0.2862 (mt) cc_final: 0.2563 (pt) REVERT: I 167 ASN cc_start: 0.7794 (t160) cc_final: 0.7253 (t0) REVERT: I 176 GLU cc_start: 0.6671 (tt0) cc_final: 0.6455 (tm-30) REVERT: I 238 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7420 (mm-30) REVERT: I 316 MET cc_start: 0.7766 (tpp) cc_final: 0.7194 (mpp) REVERT: I 318 LYS cc_start: 0.8206 (mmpt) cc_final: 0.7924 (mmtt) REVERT: I 321 LYS cc_start: 0.8565 (tttm) cc_final: 0.8259 (tttm) REVERT: J 14 ARG cc_start: 0.7718 (ptt-90) cc_final: 0.7357 (ptt-90) REVERT: J 44 ASP cc_start: 0.8443 (p0) cc_final: 0.7647 (p0) REVERT: J 151 ILE cc_start: 0.8759 (mt) cc_final: 0.8497 (mm) REVERT: J 219 ASP cc_start: 0.8278 (t70) cc_final: 0.7517 (t70) outliers start: 58 outliers final: 52 residues processed: 583 average time/residue: 0.1736 time to fit residues: 146.9435 Evaluate side-chains 612 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 557 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 105 CYS Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 175 ILE Chi-restraints excluded: chain H residue 177 ARG Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 190 MET Chi-restraints excluded: chain H residue 198 TYR Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 285 CYS Chi-restraints excluded: chain H residue 287 ILE Chi-restraints excluded: chain H residue 294 TYR Chi-restraints excluded: chain H residue 296 ASN Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 164 GLN Chi-restraints excluded: chain I residue 178 LYS Chi-restraints excluded: chain I residue 207 VAL Chi-restraints excluded: chain I residue 269 ILE Chi-restraints excluded: chain J residue 108 ARG Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain J residue 178 GLN Chi-restraints excluded: chain J residue 187 MET Chi-restraints excluded: chain J residue 196 GLN Chi-restraints excluded: chain J residue 210 ILE Chi-restraints excluded: chain J residue 264 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 262 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 0.0980 chunk 83 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 chunk 182 optimal weight: 4.9990 chunk 205 optimal weight: 0.5980 chunk 14 optimal weight: 5.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN C 30 HIS ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 24 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.153811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.122130 restraints weight = 34449.094| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.92 r_work: 0.3413 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22141 Z= 0.154 Angle : 0.614 13.123 29965 Z= 0.315 Chirality : 0.044 0.218 3295 Planarity : 0.005 0.062 3845 Dihedral : 5.921 88.028 3008 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.86 % Favored : 94.11 % Rotamer: Outliers : 2.54 % Allowed : 20.58 % Favored : 76.88 % 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: -0.34 (0.17), residues: 2664 helix: 0.87 (0.18), residues: 932 sheet: 0.18 (0.21), residues: 600 loop : -1.38 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 244 TYR 0.018 0.001 TYR D 250 PHE 0.020 0.002 PHE C 111 TRP 0.018 0.001 TRP C 131 HIS 0.005 0.001 HIS I 135 Details of bonding type rmsd covalent geometry : bond 0.00364 (22141) covalent geometry : angle 0.61388 (29965) hydrogen bonds : bond 0.04161 ( 891) hydrogen bonds : angle 4.18578 ( 2460) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4962.83 seconds wall clock time: 85 minutes 44.03 seconds (5144.03 seconds total)