Starting phenix.real_space_refine on Thu Jun 19 00:10:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t5q_25707/06_2025/7t5q_25707.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t5q_25707/06_2025/7t5q_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_25707/06_2025/7t5q_25707.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t5q_25707/06_2025/7t5q_25707.map" model { file = "/net/cci-nas-00/data/ceres_data/7t5q_25707/06_2025/7t5q_25707.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t5q_25707/06_2025/7t5q_25707.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 13.31, per 1000 atoms: 0.61 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: 5.17 Conformation dependent library (CDL) restraints added in 2.9 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: 2.87 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: 7.26 Time building geometry restraints manager: 6.16 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: 3.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.920 Check model and map are aligned: 0.140 Set scattering table: 0.200 Process input model: 49.590 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.900 ------------------------------------------------------------------------------- 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 : 2.02 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.046 0.002 TRP C 131 HIS 0.014 0.001 HIS C 30 PHE 0.031 0.002 PHE B 371 TYR 0.021 0.002 TYR D 146 ARG 0.010 0.001 ARG H 210 Details of bonding type rmsd hydrogen bonds : bond 0.18577 ( 891) hydrogen bonds : angle 6.40201 ( 2460) covalent geometry : bond 0.00517 (22141) covalent geometry : angle 0.86211 (29965) *********************** 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 : 2.334 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: 0.7862 (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: 0.7495 (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: 0.7175 (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: 0.4019 time to fit residues: 352.5149 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 : 2.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 0.6980 chunk 201 optimal weight: 0.0060 chunk 111 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 135 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 208 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 155 optimal weight: 0.8980 chunk 241 optimal weight: 0.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- 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 I 167 ASN I 197 HIS I 205 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.156488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.125700 restraints weight = 34435.577| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.86 r_work: 0.3447 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22141 Z= 0.128 Angle : 0.586 9.400 29965 Z= 0.303 Chirality : 0.044 0.208 3295 Planarity : 0.005 0.062 3845 Dihedral : 6.766 89.329 3008 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.88 % Favored : 95.08 % Rotamer: Outliers : 1.31 % Allowed : 8.88 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.16), residues: 2664 helix: 0.23 (0.17), residues: 932 sheet: 0.18 (0.21), residues: 573 loop : -1.57 (0.18), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 131 HIS 0.004 0.001 HIS D 44 PHE 0.017 0.001 PHE C 169 TYR 0.018 0.001 TYR E 132 ARG 0.006 0.001 ARG J 244 Details of bonding type rmsd hydrogen bonds : bond 0.04658 ( 891) hydrogen bonds : angle 4.60251 ( 2460) covalent geometry : bond 0.00289 (22141) covalent geometry : angle 0.58567 (29965) *********************** 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 626 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 595 time to evaluate : 2.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.7353 (ttmm) cc_final: 0.6988 (ttmm) REVERT: A 79 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.7361 (ttt90) REVERT: A 266 GLU cc_start: 0.7476 (pm20) cc_final: 0.7119 (pm20) REVERT: A 274 GLU cc_start: 0.7334 (pm20) cc_final: 0.7056 (pm20) REVERT: A 302 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7550 (tm-30) REVERT: B 211 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7371 (mm-30) REVERT: B 372 TRP cc_start: 0.8431 (m100) cc_final: 0.8088 (m100) REVERT: C 165 LYS cc_start: 0.8383 (mmtp) cc_final: 0.8181 (mmtp) REVERT: C 257 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7522 (mm-30) REVERT: D 222 TYR cc_start: 0.8636 (m-80) cc_final: 0.8251 (m-80) REVERT: D 237 ARG cc_start: 0.7785 (ttp-110) cc_final: 0.7536 (ttp-110) REVERT: E 9 MET cc_start: 0.6275 (mmm) cc_final: 0.6015 (mmm) REVERT: E 92 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7573 (tm-30) REVERT: E 94 GLU cc_start: 0.8539 (mt-10) cc_final: 0.8274 (mt-10) REVERT: E 95 MET cc_start: 0.7872 (mtm) cc_final: 0.7551 (mtm) REVERT: E 155 LYS cc_start: 0.7742 (mtmm) cc_final: 0.7509 (mtmm) REVERT: F 83 GLU cc_start: 0.7062 (mm-30) cc_final: 0.6664 (mm-30) REVERT: F 146 ILE cc_start: 0.7346 (mt) cc_final: 0.7060 (pt) REVERT: F 163 GLU cc_start: 0.7392 (mm-30) cc_final: 0.7154 (mm-30) REVERT: H 195 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7379 (tm-30) REVERT: H 215 LYS cc_start: 0.8529 (ptpp) cc_final: 0.8171 (ptpp) REVERT: H 286 ASP cc_start: 0.7953 (m-30) cc_final: 0.7291 (m-30) REVERT: H 288 ASP cc_start: 0.7918 (OUTLIER) cc_final: 0.7596 (t0) REVERT: H 325 MET cc_start: 0.7834 (ptp) cc_final: 0.7394 (ptt) REVERT: H 361 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7196 (mt-10) REVERT: I 21 ILE cc_start: 0.8321 (tp) cc_final: 0.8111 (tp) REVERT: I 56 GLN cc_start: 0.7417 (tp-100) cc_final: 0.6753 (tp-100) REVERT: I 138 ASN cc_start: 0.7224 (t0) cc_final: 0.6846 (t0) REVERT: I 234 ASN cc_start: 0.7058 (t0) cc_final: 0.6118 (t0) REVERT: I 238 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7298 (mm-30) REVERT: I 318 LYS cc_start: 0.8217 (mmpt) cc_final: 0.7875 (mmtt) REVERT: I 321 LYS cc_start: 0.8504 (tttm) cc_final: 0.8221 (tttm) REVERT: J 22 GLU cc_start: 0.8197 (pm20) cc_final: 0.7989 (pm20) REVERT: J 31 LEU cc_start: 0.8408 (mm) cc_final: 0.8023 (tt) REVERT: J 76 SER cc_start: 0.7791 (t) cc_final: 0.7584 (t) REVERT: J 151 ILE cc_start: 0.8720 (mt) cc_final: 0.8493 (mm) REVERT: J 220 MET cc_start: 0.7551 (tpp) cc_final: 0.7286 (mpp) outliers start: 31 outliers final: 13 residues processed: 601 average time/residue: 0.3857 time to fit residues: 337.8361 Evaluate side-chains 585 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 570 time to evaluate : 2.227 ------------------------------------------------------------------------------- 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 133 SER Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain D residue 107 ASP 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 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 264 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 243 optimal weight: 10.0000 chunk 53 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 182 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 241 optimal weight: 6.9990 chunk 92 optimal weight: 0.9990 chunk 164 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 HIS A 205 GLN ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 HIS D 193 HIS H 161 HIS H 371 HIS ** I 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 101 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.152975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.121131 restraints weight = 34169.623| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.94 r_work: 0.3391 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 22141 Z= 0.202 Angle : 0.610 8.848 29965 Z= 0.320 Chirality : 0.046 0.173 3295 Planarity : 0.005 0.058 3845 Dihedral : 6.303 90.764 3008 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.97 % Favored : 93.99 % Rotamer: Outliers : 2.03 % Allowed : 13.06 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.16), residues: 2664 helix: 0.30 (0.17), residues: 935 sheet: 0.19 (0.21), residues: 589 loop : -1.57 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 131 HIS 0.007 0.001 HIS D 44 PHE 0.025 0.002 PHE C 169 TYR 0.023 0.002 TYR D 250 ARG 0.006 0.001 ARG I 15 Details of bonding type rmsd hydrogen bonds : bond 0.05175 ( 891) hydrogen bonds : angle 4.49922 ( 2460) covalent geometry : bond 0.00474 (22141) covalent geometry : angle 0.61020 (29965) *********************** 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 640 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 592 time to evaluate : 2.332 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 79 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7450 (ttt90) REVERT: A 161 ARG cc_start: 0.7916 (mmt90) cc_final: 0.7438 (mmt180) REVERT: A 266 GLU cc_start: 0.7469 (pm20) cc_final: 0.7126 (pm20) REVERT: A 302 GLU cc_start: 0.7927 (tm-30) cc_final: 0.7516 (tm-30) REVERT: B 170 TYR cc_start: 0.7705 (t80) cc_final: 0.7227 (t80) REVERT: B 211 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7494 (mm-30) REVERT: B 230 GLU cc_start: 0.7263 (mm-30) cc_final: 0.6771 (mm-30) REVERT: B 242 GLU cc_start: 0.7271 (mm-30) cc_final: 0.6978 (mm-30) REVERT: B 372 TRP cc_start: 0.8495 (m100) cc_final: 0.8069 (m100) REVERT: C 28 ASN cc_start: 0.7711 (t0) cc_final: 0.7394 (t0) REVERT: C 101 PHE cc_start: 0.7906 (t80) cc_final: 0.7665 (t80) REVERT: C 257 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7544 (mm-30) REVERT: C 352 MET cc_start: 0.7473 (tmm) cc_final: 0.6840 (tmm) REVERT: D 222 TYR cc_start: 0.8698 (m-80) cc_final: 0.7939 (m-80) REVERT: E 92 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7605 (tm-30) REVERT: E 94 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8281 (mt-10) REVERT: E 95 MET cc_start: 0.7919 (mtm) cc_final: 0.7564 (mtm) REVERT: E 155 LYS cc_start: 0.7758 (mtmm) cc_final: 0.7492 (mtmm) REVERT: F 163 GLU cc_start: 0.7457 (mm-30) cc_final: 0.7188 (mm-30) REVERT: G 111 TYR cc_start: 0.7719 (m-80) cc_final: 0.7227 (m-80) REVERT: H 122 ILE cc_start: 0.8074 (tt) cc_final: 0.7832 (tt) REVERT: H 195 GLU cc_start: 0.7855 (tm-30) cc_final: 0.7473 (tm-30) REVERT: H 214 GLU cc_start: 0.7141 (mt-10) cc_final: 0.6605 (mp0) REVERT: H 215 LYS cc_start: 0.8541 (ptpp) cc_final: 0.8175 (ptpp) REVERT: H 238 LYS cc_start: 0.8249 (mmtm) cc_final: 0.8008 (tppt) REVERT: H 286 ASP cc_start: 0.8064 (m-30) cc_final: 0.7562 (m-30) REVERT: H 288 ASP cc_start: 0.8083 (OUTLIER) cc_final: 0.7732 (t0) REVERT: H 294 TYR cc_start: 0.7431 (OUTLIER) cc_final: 0.6959 (m-10) REVERT: I 21 ILE cc_start: 0.8413 (tp) cc_final: 0.8184 (tp) REVERT: I 56 GLN cc_start: 0.7504 (tp-100) cc_final: 0.6802 (tp-100) REVERT: I 138 ASN cc_start: 0.7290 (t0) cc_final: 0.6953 (t0) REVERT: I 167 ASN cc_start: 0.7952 (t160) cc_final: 0.7298 (t0) REVERT: I 238 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7451 (mm-30) REVERT: I 247 TYR cc_start: 0.7282 (t80) cc_final: 0.6889 (t80) REVERT: I 318 LYS cc_start: 0.8289 (mmpt) cc_final: 0.7866 (mmpt) REVERT: I 321 LYS cc_start: 0.8528 (tttm) cc_final: 0.8194 (tttm) REVERT: J 22 GLU cc_start: 0.8169 (pm20) cc_final: 0.7903 (pm20) REVERT: J 31 LEU cc_start: 0.8481 (mm) cc_final: 0.8101 (tt) REVERT: J 63 ASP cc_start: 0.8449 (t70) cc_final: 0.8242 (t0) REVERT: J 151 ILE cc_start: 0.8814 (mt) cc_final: 0.8583 (mm) REVERT: J 219 ASP cc_start: 0.8396 (OUTLIER) cc_final: 0.7710 (t70) outliers start: 48 outliers final: 36 residues processed: 608 average time/residue: 0.3995 time to fit residues: 353.2721 Evaluate side-chains 618 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 578 time to evaluate : 2.345 ------------------------------------------------------------------------------- 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 185 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 364 ASP 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 366 LYS Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 271 LEU 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 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 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 63 THR Chi-restraints excluded: chain I residue 207 VAL Chi-restraints excluded: chain I residue 269 ILE Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain J residue 192 SER Chi-restraints excluded: chain J residue 196 GLN Chi-restraints excluded: chain J residue 210 ILE Chi-restraints excluded: chain J residue 219 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 226 optimal weight: 8.9990 chunk 88 optimal weight: 0.7980 chunk 173 optimal weight: 0.9990 chunk 158 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 112 optimal weight: 0.8980 chunk 240 optimal weight: 1.9990 chunk 211 optimal weight: 0.0020 chunk 169 optimal weight: 0.0980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN A 205 GLN ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 HIS C 75 ASN H 12 ASN ** 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 = 0.4005 r_free = 0.4005 target = 0.155466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.124714 restraints weight = 34569.605| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.86 r_work: 0.3435 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22141 Z= 0.113 Angle : 0.546 8.653 29965 Z= 0.283 Chirality : 0.043 0.141 3295 Planarity : 0.004 0.057 3845 Dihedral : 5.913 82.072 3008 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.58 % Favored : 95.38 % Rotamer: Outliers : 2.45 % Allowed : 15.55 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.16), residues: 2664 helix: 0.52 (0.17), residues: 942 sheet: 0.37 (0.22), residues: 578 loop : -1.49 (0.18), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 131 HIS 0.003 0.001 HIS D 44 PHE 0.018 0.001 PHE C 111 TYR 0.014 0.001 TYR D 146 ARG 0.004 0.000 ARG J 244 Details of bonding type rmsd hydrogen bonds : bond 0.03920 ( 891) hydrogen bonds : angle 4.21328 ( 2460) covalent geometry : bond 0.00258 (22141) covalent geometry : angle 0.54611 (29965) *********************** 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 643 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 585 time to evaluate : 3.086 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: 0.8310 (mt) cc_final: 0.8051 (mt) REVERT: A 26 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7124 (mm-30) REVERT: A 79 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7401 (ttt90) REVERT: A 94 GLU cc_start: 0.7342 (tt0) cc_final: 0.7115 (tt0) REVERT: A 161 ARG cc_start: 0.7912 (mmt90) cc_final: 0.7388 (mmt180) REVERT: A 302 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7500 (tm-30) REVERT: B 63 GLU cc_start: 0.7295 (pm20) cc_final: 0.6908 (pm20) REVERT: B 211 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7424 (mm-30) REVERT: B 230 GLU cc_start: 0.7241 (mm-30) cc_final: 0.6752 (mm-30) REVERT: B 372 TRP cc_start: 0.8470 (m100) cc_final: 0.7986 (m100) REVERT: C 28 ASN cc_start: 0.7665 (t0) cc_final: 0.7396 (t0) REVERT: C 257 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7528 (mm-30) REVERT: C 352 MET cc_start: 0.7403 (tmm) cc_final: 0.6729 (tmm) REVERT: D 171 ASP cc_start: 0.7299 (t0) cc_final: 0.6996 (t0) REVERT: D 222 TYR cc_start: 0.8617 (m-80) cc_final: 0.7900 (m-80) REVERT: E 92 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7688 (tm-30) REVERT: E 94 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8259 (mt-10) REVERT: E 155 LYS cc_start: 0.7685 (mtmm) cc_final: 0.7484 (mtmm) REVERT: F 163 GLU cc_start: 0.7465 (mm-30) cc_final: 0.7220 (mm-30) REVERT: G 111 TYR cc_start: 0.7678 (m-80) cc_final: 0.7282 (m-80) REVERT: H 122 ILE cc_start: 0.8069 (tt) cc_final: 0.7842 (tt) REVERT: H 195 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7433 (tm-30) REVERT: H 214 GLU cc_start: 0.7144 (mt-10) cc_final: 0.6617 (mp0) REVERT: H 215 LYS cc_start: 0.8506 (ptpp) cc_final: 0.8163 (ptpp) REVERT: H 286 ASP cc_start: 0.8034 (m-30) cc_final: 0.7575 (m-30) REVERT: H 288 ASP cc_start: 0.8026 (m-30) cc_final: 0.7706 (t0) REVERT: H 361 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7292 (mt-10) REVERT: I 21 ILE cc_start: 0.8300 (tp) cc_final: 0.8069 (tp) REVERT: I 56 GLN cc_start: 0.7404 (tp-100) cc_final: 0.6544 (tp-100) REVERT: I 58 ASN cc_start: 0.8009 (m110) cc_final: 0.7674 (m110) REVERT: I 59 MET cc_start: 0.7593 (mpp) cc_final: 0.6938 (mpp) REVERT: I 111 GLU cc_start: 0.7672 (pp20) cc_final: 0.7451 (pp20) REVERT: I 138 ASN cc_start: 0.7235 (t0) cc_final: 0.6868 (t0) REVERT: I 167 ASN cc_start: 0.7710 (t160) cc_final: 0.6887 (t0) REVERT: I 238 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7410 (mm-30) REVERT: I 318 LYS cc_start: 0.8268 (mmpt) cc_final: 0.7867 (mmtt) REVERT: I 321 LYS cc_start: 0.8580 (tttm) cc_final: 0.8236 (tttm) REVERT: J 22 GLU cc_start: 0.8162 (pm20) cc_final: 0.7922 (pm20) REVERT: J 31 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8087 (tt) REVERT: J 63 ASP cc_start: 0.8376 (t70) cc_final: 0.8154 (t0) REVERT: J 70 SER cc_start: 0.6415 (m) cc_final: 0.5975 (m) REVERT: J 76 SER cc_start: 0.7912 (t) cc_final: 0.7704 (t) REVERT: J 151 ILE cc_start: 0.8749 (mt) cc_final: 0.8494 (mm) REVERT: J 219 ASP cc_start: 0.8529 (t70) cc_final: 0.7525 (t0) REVERT: J 220 MET cc_start: 0.7166 (OUTLIER) cc_final: 0.6844 (mpp) outliers start: 58 outliers final: 36 residues processed: 607 average time/residue: 0.4300 time to fit residues: 382.4753 Evaluate side-chains 616 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 577 time to evaluate : 2.514 ------------------------------------------------------------------------------- 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 204 ILE Chi-restraints excluded: chain A residue 370 HIS 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 C residue 23 ILE Chi-restraints excluded: chain C residue 175 GLU 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 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 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 296 ASN Chi-restraints excluded: chain H residue 300 SER 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 26 SER Chi-restraints excluded: chain J residue 31 LEU 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 220 MET Chi-restraints excluded: chain J residue 226 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 138 optimal weight: 9.9990 chunk 239 optimal weight: 5.9990 chunk 238 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 chunk 112 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 256 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 38 optimal weight: 0.0060 overall best weight: 0.7798 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 HIS ** I 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.154872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.123993 restraints weight = 34495.745| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.88 r_work: 0.3427 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22141 Z= 0.132 Angle : 0.558 11.690 29965 Z= 0.288 Chirality : 0.044 0.161 3295 Planarity : 0.004 0.055 3845 Dihedral : 5.887 83.037 3008 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.18 % Favored : 94.78 % Rotamer: Outliers : 2.32 % Allowed : 16.86 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.17), residues: 2664 helix: 0.68 (0.18), residues: 936 sheet: 0.26 (0.22), residues: 590 loop : -1.42 (0.18), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 131 HIS 0.004 0.001 HIS D 44 PHE 0.019 0.001 PHE C 111 TYR 0.016 0.001 TYR D 250 ARG 0.004 0.000 ARG J 244 Details of bonding type rmsd hydrogen bonds : bond 0.04089 ( 891) hydrogen bonds : angle 4.12086 ( 2460) covalent geometry : bond 0.00307 (22141) covalent geometry : angle 0.55825 (29965) *********************** 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 646 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 591 time to evaluate : 6.425 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: 0.8309 (mt) cc_final: 0.8050 (mt) REVERT: A 26 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7107 (mm-30) REVERT: A 79 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7604 (ttt180) REVERT: A 161 ARG cc_start: 0.7921 (mmt90) cc_final: 0.7363 (mmt180) REVERT: A 317 LYS cc_start: 0.8387 (ttmt) cc_final: 0.8008 (ttmm) REVERT: B 63 GLU cc_start: 0.7259 (pm20) cc_final: 0.6929 (pm20) REVERT: B 170 TYR cc_start: 0.7615 (t80) cc_final: 0.7189 (t80) REVERT: B 211 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7434 (mm-30) REVERT: B 230 GLU cc_start: 0.7276 (mm-30) cc_final: 0.6818 (mm-30) REVERT: B 372 TRP cc_start: 0.8478 (m100) cc_final: 0.8002 (m100) REVERT: C 28 ASN cc_start: 0.7718 (t0) cc_final: 0.7332 (t0) REVERT: C 94 ARG cc_start: 0.8786 (mtm-85) cc_final: 0.8249 (mtm-85) REVERT: C 257 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7564 (mm-30) REVERT: C 352 MET cc_start: 0.7450 (tmm) cc_final: 0.6735 (tmm) REVERT: D 111 HIS cc_start: 0.8027 (t70) cc_final: 0.7781 (t70) REVERT: D 222 TYR cc_start: 0.8627 (m-80) cc_final: 0.7886 (m-80) REVERT: E 92 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7662 (tm-30) REVERT: E 94 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8252 (mt-10) REVERT: F 163 GLU cc_start: 0.7465 (mm-30) cc_final: 0.7204 (mm-30) REVERT: G 111 TYR cc_start: 0.7702 (m-80) cc_final: 0.7303 (m-80) REVERT: H 155 SER cc_start: 0.8383 (m) cc_final: 0.8110 (t) REVERT: H 195 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7476 (tm-30) REVERT: H 214 GLU cc_start: 0.7179 (mt-10) cc_final: 0.6699 (mp0) REVERT: H 215 LYS cc_start: 0.8514 (ptpp) cc_final: 0.8155 (ptpp) REVERT: H 286 ASP cc_start: 0.8016 (m-30) cc_final: 0.7571 (m-30) REVERT: H 288 ASP cc_start: 0.8071 (OUTLIER) cc_final: 0.7746 (t0) REVERT: H 361 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7377 (mt-10) REVERT: I 21 ILE cc_start: 0.8327 (tp) cc_final: 0.8076 (tp) REVERT: I 56 GLN cc_start: 0.7440 (tp-100) cc_final: 0.6794 (tp-100) REVERT: I 58 ASN cc_start: 0.8066 (m110) cc_final: 0.7686 (m110) REVERT: I 59 MET cc_start: 0.7672 (mpp) cc_final: 0.7256 (mpp) REVERT: I 111 GLU cc_start: 0.7554 (pp20) cc_final: 0.7257 (pp20) REVERT: I 138 ASN cc_start: 0.7280 (t0) cc_final: 0.6918 (t0) REVERT: I 167 ASN cc_start: 0.7708 (t160) cc_final: 0.6848 (t0) REVERT: I 238 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7423 (mm-30) REVERT: I 318 LYS cc_start: 0.8235 (mmpt) cc_final: 0.7864 (mmtt) REVERT: I 321 LYS cc_start: 0.8563 (tttm) cc_final: 0.8218 (tttm) REVERT: J 22 GLU cc_start: 0.8065 (pm20) cc_final: 0.7835 (pm20) REVERT: J 31 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8057 (tt) REVERT: J 63 ASP cc_start: 0.8430 (t70) cc_final: 0.8208 (t0) REVERT: J 76 SER cc_start: 0.8006 (t) cc_final: 0.7805 (t) REVERT: J 151 ILE cc_start: 0.8759 (mt) cc_final: 0.8498 (mm) REVERT: J 219 ASP cc_start: 0.8547 (t70) cc_final: 0.7638 (t70) outliers start: 55 outliers final: 46 residues processed: 609 average time/residue: 0.7188 time to fit residues: 649.5608 Evaluate side-chains 628 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 579 time to evaluate : 3.077 ------------------------------------------------------------------------------- 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 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 19 LYS 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 175 GLU 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 33 VAL 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 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 269 MET 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 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 26 SER Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 154 VAL 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 220 MET 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 14 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 chunk 203 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 256 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 181 optimal weight: 0.9990 chunk 263 optimal weight: 10.0000 chunk 89 optimal weight: 0.9990 chunk 141 optimal weight: 0.0060 overall best weight: 0.7802 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 HIS C 75 ASN ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 126 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.154122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.122372 restraints weight = 34130.505| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.91 r_work: 0.3425 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22141 Z= 0.132 Angle : 0.553 10.076 29965 Z= 0.287 Chirality : 0.044 0.167 3295 Planarity : 0.004 0.055 3845 Dihedral : 5.856 83.229 3008 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.92 % Favored : 95.05 % Rotamer: Outliers : 3.04 % Allowed : 17.41 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.17), residues: 2664 helix: 0.81 (0.18), residues: 928 sheet: 0.23 (0.21), residues: 596 loop : -1.40 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 131 HIS 0.004 0.001 HIS D 44 PHE 0.019 0.001 PHE C 111 TYR 0.016 0.001 TYR D 250 ARG 0.005 0.000 ARG J 244 Details of bonding type rmsd hydrogen bonds : bond 0.03970 ( 891) hydrogen bonds : angle 4.09487 ( 2460) covalent geometry : bond 0.00307 (22141) covalent geometry : angle 0.55286 (29965) *********************** 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 658 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 586 time to evaluate : 4.110 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 19 LEU cc_start: 0.8306 (mt) cc_final: 0.8039 (mt) REVERT: A 26 GLU cc_start: 0.7477 (mm-30) cc_final: 0.7018 (mm-30) REVERT: A 59 ASP cc_start: 0.7322 (t70) cc_final: 0.7083 (t0) REVERT: A 79 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7545 (ttt180) REVERT: A 161 ARG cc_start: 0.7915 (mmt90) cc_final: 0.7334 (mmt180) REVERT: B 170 TYR cc_start: 0.7622 (t80) cc_final: 0.7204 (t80) REVERT: B 211 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7458 (mm-30) REVERT: B 227 ILE cc_start: 0.7547 (mm) cc_final: 0.7265 (mm) REVERT: B 230 GLU cc_start: 0.7298 (mm-30) cc_final: 0.6855 (mm-30) REVERT: B 242 GLU cc_start: 0.7334 (mm-30) cc_final: 0.7029 (mm-30) REVERT: B 372 TRP cc_start: 0.8463 (m100) cc_final: 0.7991 (m100) REVERT: C 28 ASN cc_start: 0.7698 (t0) cc_final: 0.7306 (t0) REVERT: C 94 ARG cc_start: 0.8801 (mtm-85) cc_final: 0.8281 (mtm-85) REVERT: C 257 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7589 (mm-30) REVERT: C 342 LYS cc_start: 0.8114 (mtpt) cc_final: 0.7812 (mtmt) REVERT: C 352 MET cc_start: 0.7468 (tmm) cc_final: 0.6737 (tmm) REVERT: D 222 TYR cc_start: 0.8628 (m-80) cc_final: 0.7882 (m-80) REVERT: E 92 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7690 (tm-30) REVERT: E 94 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8281 (mt-10) REVERT: F 163 GLU cc_start: 0.7487 (mm-30) cc_final: 0.7203 (mm-30) REVERT: G 111 TYR cc_start: 0.7708 (m-80) cc_final: 0.7315 (m-80) REVERT: H 82 MET cc_start: 0.5562 (tpt) cc_final: 0.4879 (tpt) REVERT: H 155 SER cc_start: 0.8384 (m) cc_final: 0.8134 (t) REVERT: H 195 GLU cc_start: 0.7833 (tm-30) cc_final: 0.7498 (tm-30) REVERT: H 214 GLU cc_start: 0.7207 (mt-10) cc_final: 0.6716 (mt-10) REVERT: H 215 LYS cc_start: 0.8516 (ptpp) cc_final: 0.8163 (ptpp) REVERT: H 285 CYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8036 (m) REVERT: H 288 ASP cc_start: 0.8065 (m-30) cc_final: 0.7734 (t0) REVERT: H 290 ARG cc_start: 0.6676 (OUTLIER) cc_final: 0.6190 (ttt90) REVERT: I 21 ILE cc_start: 0.8396 (tp) cc_final: 0.8106 (tp) REVERT: I 56 GLN cc_start: 0.7436 (tp-100) cc_final: 0.6827 (tp-100) REVERT: I 58 ASN cc_start: 0.8033 (m110) cc_final: 0.7699 (m110) REVERT: I 59 MET cc_start: 0.7741 (mpp) cc_final: 0.6299 (mmm) REVERT: I 111 GLU cc_start: 0.7567 (pp20) cc_final: 0.7123 (pp20) REVERT: I 138 ASN cc_start: 0.7250 (t0) cc_final: 0.6884 (t0) REVERT: I 167 ASN cc_start: 0.7648 (t160) cc_final: 0.7123 (t0) REVERT: I 238 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7406 (mm-30) REVERT: I 318 LYS cc_start: 0.8231 (mmpt) cc_final: 0.7989 (mmtt) REVERT: I 321 LYS cc_start: 0.8583 (tttm) cc_final: 0.8270 (tttm) REVERT: J 5 GLN cc_start: 0.8095 (pm20) cc_final: 0.7807 (pm20) REVERT: J 22 GLU cc_start: 0.8071 (pm20) cc_final: 0.7865 (pm20) REVERT: J 31 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8136 (tt) REVERT: J 108 ARG cc_start: 0.6752 (mtm110) cc_final: 0.6464 (mtm-85) REVERT: J 122 TRP cc_start: 0.7655 (m100) cc_final: 0.7389 (m-10) REVERT: J 151 ILE cc_start: 0.8763 (mt) cc_final: 0.8502 (mm) REVERT: J 244 ARG cc_start: 0.6692 (ttt180) cc_final: 0.6426 (ttt180) outliers start: 72 outliers final: 53 residues processed: 613 average time/residue: 0.5575 time to fit residues: 506.4174 Evaluate side-chains 639 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 582 time to evaluate : 2.203 ------------------------------------------------------------------------------- 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 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 19 LYS Chi-restraints excluded: chain B residue 25 SER 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 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 18 LYS Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain E residue 105 ILE 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 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 250 ILE Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 285 CYS Chi-restraints excluded: chain H residue 287 ILE Chi-restraints excluded: chain H residue 290 ARG 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 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 26 SER Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain J residue 192 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 214 optimal weight: 5.9990 chunk 193 optimal weight: 0.8980 chunk 70 optimal weight: 0.0040 chunk 119 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 253 optimal weight: 10.0000 chunk 172 optimal weight: 3.9990 chunk 254 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 186 optimal weight: 0.9990 overall best weight: 1.1196 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 HIS ** I 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.152838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.121072 restraints weight = 34193.504| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.92 r_work: 0.3394 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.2365 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= 0.169 Angle : 0.580 10.397 29965 Z= 0.301 Chirality : 0.045 0.175 3295 Planarity : 0.004 0.055 3845 Dihedral : 5.983 89.714 3008 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.04 % Favored : 93.92 % Rotamer: Outliers : 3.42 % Allowed : 17.71 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.17), residues: 2664 helix: 0.79 (0.18), residues: 931 sheet: 0.22 (0.21), residues: 602 loop : -1.47 (0.18), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 131 HIS 0.005 0.001 HIS I 135 PHE 0.022 0.002 PHE C 169 TYR 0.018 0.001 TYR D 250 ARG 0.008 0.000 ARG J 108 Details of bonding type rmsd hydrogen bonds : bond 0.04434 ( 891) hydrogen bonds : angle 4.18618 ( 2460) covalent geometry : bond 0.00398 (22141) covalent geometry : angle 0.58018 (29965) *********************** 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 672 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 591 time to evaluate : 2.273 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: 0.7523 (mm-30) cc_final: 0.7059 (mm-30) REVERT: A 59 ASP cc_start: 0.7342 (t70) cc_final: 0.6936 (t0) REVERT: A 79 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7578 (ttt180) REVERT: A 161 ARG cc_start: 0.7942 (mmt90) cc_final: 0.7335 (mmt180) REVERT: A 280 GLU cc_start: 0.8087 (tp30) cc_final: 0.7316 (tp30) REVERT: B 170 TYR cc_start: 0.7747 (t80) cc_final: 0.7260 (t80) REVERT: B 211 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7505 (mm-30) REVERT: B 230 GLU cc_start: 0.7252 (mm-30) cc_final: 0.6870 (mm-30) REVERT: B 242 GLU cc_start: 0.7332 (mm-30) cc_final: 0.7026 (mm-30) REVERT: B 372 TRP cc_start: 0.8492 (m100) cc_final: 0.7987 (m100) REVERT: C 28 ASN cc_start: 0.7719 (t0) cc_final: 0.7406 (t0) REVERT: C 257 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7624 (mm-30) REVERT: C 342 LYS cc_start: 0.8108 (mtpt) cc_final: 0.7904 (ptpt) REVERT: C 352 MET cc_start: 0.7505 (tmm) cc_final: 0.6753 (tmm) REVERT: D 222 TYR cc_start: 0.8635 (m-80) cc_final: 0.7833 (m-80) REVERT: E 92 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7701 (tm-30) REVERT: E 94 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8299 (mt-10) REVERT: E 155 LYS cc_start: 0.7803 (mtmm) cc_final: 0.7528 (mtmm) REVERT: F 163 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7214 (mm-30) REVERT: G 111 TYR cc_start: 0.7721 (m-80) cc_final: 0.7285 (m-80) REVERT: H 82 MET cc_start: 0.5594 (tpt) cc_final: 0.4901 (tpt) REVERT: H 155 SER cc_start: 0.8429 (m) cc_final: 0.8146 (t) REVERT: H 195 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7555 (tm-30) REVERT: H 214 GLU cc_start: 0.7223 (mt-10) cc_final: 0.6733 (mt-10) REVERT: H 215 LYS cc_start: 0.8522 (ptpp) cc_final: 0.8178 (ptpp) REVERT: H 285 CYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8276 (m) REVERT: H 288 ASP cc_start: 0.8080 (OUTLIER) cc_final: 0.7739 (t0) REVERT: I 21 ILE cc_start: 0.8432 (tp) cc_final: 0.8141 (tp) REVERT: I 56 GLN cc_start: 0.7486 (tp-100) cc_final: 0.6830 (tp-100) REVERT: I 58 ASN cc_start: 0.8068 (m110) cc_final: 0.7720 (m110) REVERT: I 59 MET cc_start: 0.7745 (mpp) cc_final: 0.7391 (mpp) REVERT: I 138 ASN cc_start: 0.7297 (t0) cc_final: 0.6961 (t0) REVERT: I 167 ASN cc_start: 0.7806 (t160) cc_final: 0.7232 (t0) REVERT: I 238 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7420 (mm-30) REVERT: I 318 LYS cc_start: 0.8227 (mmpt) cc_final: 0.7970 (mmtt) REVERT: I 321 LYS cc_start: 0.8588 (tttm) cc_final: 0.8282 (tttm) REVERT: J 5 GLN cc_start: 0.8113 (pm20) cc_final: 0.7831 (pm20) REVERT: J 31 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8136 (tt) REVERT: J 122 TRP cc_start: 0.7736 (m100) cc_final: 0.7483 (m-10) REVERT: J 151 ILE cc_start: 0.8743 (mt) cc_final: 0.8471 (mm) REVERT: J 215 ARG cc_start: 0.7011 (ttt180) cc_final: 0.6749 (ttt180) REVERT: J 220 MET cc_start: 0.7485 (tpp) cc_final: 0.7269 (mpp) outliers start: 81 outliers final: 67 residues processed: 624 average time/residue: 0.4131 time to fit residues: 378.5458 Evaluate side-chains 653 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 582 time to evaluate : 2.184 ------------------------------------------------------------------------------- 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 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 19 LYS Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 100 ILE 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 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 175 GLU Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain E residue 105 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 G residue 138 VAL 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 186 THR 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 269 MET 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 300 SER Chi-restraints excluded: chain H residue 318 THR Chi-restraints excluded: chain I residue 32 VAL 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 23 LYS Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain J residue 187 MET Chi-restraints excluded: chain J residue 192 SER Chi-restraints excluded: chain J residue 196 GLN Chi-restraints excluded: chain J residue 210 ILE Chi-restraints excluded: chain J residue 226 SER 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 256 optimal weight: 1.9990 chunk 179 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 chunk 238 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 17 optimal weight: 0.0370 chunk 185 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 8 optimal weight: 0.4980 chunk 217 optimal weight: 4.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 HIS C 75 ASN ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 HIS I 167 ASN ** 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 = 0.3993 r_free = 0.3993 target = 0.153717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.123090 restraints weight = 34539.331| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.84 r_work: 0.3425 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22141 Z= 0.119 Angle : 0.563 11.821 29965 Z= 0.289 Chirality : 0.044 0.279 3295 Planarity : 0.004 0.059 3845 Dihedral : 5.821 83.916 3008 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.11 % Favored : 94.86 % Rotamer: Outliers : 2.87 % Allowed : 19.02 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.17), residues: 2664 helix: 0.91 (0.18), residues: 929 sheet: 0.22 (0.21), residues: 602 loop : -1.42 (0.18), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 131 HIS 0.003 0.001 HIS D 44 PHE 0.019 0.001 PHE C 111 TYR 0.020 0.001 TYR B 298 ARG 0.006 0.000 ARG J 244 Details of bonding type rmsd hydrogen bonds : bond 0.03805 ( 891) hydrogen bonds : angle 4.09326 ( 2460) covalent geometry : bond 0.00276 (22141) covalent geometry : angle 0.56349 (29965) *********************** 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 643 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 575 time to evaluate : 3.583 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 19 LEU cc_start: 0.8300 (mt) cc_final: 0.7995 (mt) REVERT: A 26 GLU cc_start: 0.7470 (mm-30) cc_final: 0.7026 (mm-30) REVERT: A 59 ASP cc_start: 0.7340 (t70) cc_final: 0.6931 (t0) REVERT: A 79 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7593 (ttt180) REVERT: A 89 MET cc_start: 0.7765 (tpp) cc_final: 0.6866 (tpp) REVERT: A 161 ARG cc_start: 0.7967 (mmt90) cc_final: 0.7379 (mmt180) REVERT: A 302 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7678 (tm-30) REVERT: B 170 TYR cc_start: 0.7678 (t80) cc_final: 0.7205 (t80) REVERT: B 211 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7445 (mm-30) REVERT: B 230 GLU cc_start: 0.7275 (mm-30) cc_final: 0.6896 (mm-30) REVERT: B 242 GLU cc_start: 0.7316 (mm-30) cc_final: 0.7018 (mm-30) REVERT: B 372 TRP cc_start: 0.8486 (m100) cc_final: 0.7935 (m100) REVERT: C 28 ASN cc_start: 0.7653 (t0) cc_final: 0.7308 (t0) REVERT: C 94 ARG cc_start: 0.8766 (mtm-85) cc_final: 0.8256 (mtm-85) REVERT: C 161 SER cc_start: 0.8103 (OUTLIER) cc_final: 0.7874 (p) REVERT: C 257 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7629 (mm-30) REVERT: C 342 LYS cc_start: 0.8102 (mtpt) cc_final: 0.7687 (mtpt) REVERT: C 352 MET cc_start: 0.7454 (tmm) cc_final: 0.6729 (tmm) REVERT: D 222 TYR cc_start: 0.8577 (m-80) cc_final: 0.7818 (m-80) REVERT: E 92 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7676 (tm-30) REVERT: E 94 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8260 (mt-10) REVERT: E 155 LYS cc_start: 0.7824 (mtmm) cc_final: 0.7582 (mtmm) REVERT: F 83 GLU cc_start: 0.7030 (mm-30) cc_final: 0.6631 (mm-30) REVERT: F 163 GLU cc_start: 0.7519 (mm-30) cc_final: 0.7232 (mm-30) REVERT: G 111 TYR cc_start: 0.7693 (m-80) cc_final: 0.7292 (m-80) REVERT: H 82 MET cc_start: 0.5434 (tpt) cc_final: 0.4797 (tpt) REVERT: H 155 SER cc_start: 0.8375 (m) cc_final: 0.8107 (t) REVERT: H 195 GLU cc_start: 0.7842 (tm-30) cc_final: 0.7525 (tm-30) REVERT: H 210 ARG cc_start: 0.8013 (ttm-80) cc_final: 0.7052 (ttp80) REVERT: H 214 GLU cc_start: 0.7204 (mt-10) cc_final: 0.6544 (mt-10) REVERT: H 215 LYS cc_start: 0.8497 (ptpp) cc_final: 0.8161 (ptpp) REVERT: H 285 CYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8103 (m) REVERT: H 288 ASP cc_start: 0.8069 (m-30) cc_final: 0.7721 (t0) REVERT: I 21 ILE cc_start: 0.8417 (tp) cc_final: 0.8106 (tp) REVERT: I 56 GLN cc_start: 0.7419 (tp-100) cc_final: 0.6801 (tp-100) REVERT: I 58 ASN cc_start: 0.8062 (m110) cc_final: 0.7698 (m110) REVERT: I 59 MET cc_start: 0.7664 (mpp) cc_final: 0.6242 (mmm) REVERT: I 138 ASN cc_start: 0.7287 (t0) cc_final: 0.6946 (t0) REVERT: I 167 ASN cc_start: 0.7670 (t0) cc_final: 0.7191 (t0) REVERT: I 238 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7409 (mm-30) REVERT: I 318 LYS cc_start: 0.8218 (mmpt) cc_final: 0.7944 (mmtt) REVERT: I 321 LYS cc_start: 0.8588 (tttm) cc_final: 0.8276 (tttm) REVERT: J 31 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8147 (tt) REVERT: J 44 ASP cc_start: 0.8283 (p0) cc_final: 0.7856 (p0) REVERT: J 63 ASP cc_start: 0.8407 (t70) cc_final: 0.8201 (t0) REVERT: J 122 TRP cc_start: 0.7689 (m100) cc_final: 0.7416 (m-10) REVERT: J 151 ILE cc_start: 0.8691 (mt) cc_final: 0.8430 (mm) REVERT: J 215 ARG cc_start: 0.6977 (ttt180) cc_final: 0.6708 (ttt180) REVERT: J 219 ASP cc_start: 0.8379 (t70) cc_final: 0.7966 (t70) outliers start: 68 outliers final: 54 residues processed: 602 average time/residue: 0.5407 time to fit residues: 477.1308 Evaluate side-chains 628 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 570 time to evaluate : 2.368 ------------------------------------------------------------------------------- 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 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 19 LYS 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 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 67 ILE Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 175 GLU 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 E residue 105 ILE Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain G residue 138 VAL 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 250 ILE Chi-restraints excluded: chain H residue 269 MET 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 H residue 318 THR Chi-restraints excluded: chain I residue 32 VAL 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 26 SER Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 154 VAL 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 226 SER Chi-restraints excluded: chain J residue 240 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 180 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 195 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 118 optimal weight: 0.5980 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 HIS ** I 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.152041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.120147 restraints weight = 34190.939| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.93 r_work: 0.3378 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 22141 Z= 0.241 Angle : 0.652 12.084 29965 Z= 0.339 Chirality : 0.047 0.241 3295 Planarity : 0.005 0.059 3845 Dihedral : 6.213 95.104 3008 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.64 % Favored : 93.32 % Rotamer: Outliers : 3.04 % Allowed : 18.81 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.16), residues: 2664 helix: 0.61 (0.17), residues: 941 sheet: 0.16 (0.21), residues: 604 loop : -1.49 (0.18), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 131 HIS 0.008 0.001 HIS I 135 PHE 0.027 0.002 PHE C 169 TYR 0.033 0.002 TYR B 298 ARG 0.005 0.001 ARG H 335 Details of bonding type rmsd hydrogen bonds : bond 0.05054 ( 891) hydrogen bonds : angle 4.35152 ( 2460) covalent geometry : bond 0.00568 (22141) covalent geometry : angle 0.65179 (29965) *********************** 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 650 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 578 time to evaluate : 2.519 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: 0.7533 (mm-30) cc_final: 0.7057 (mm-30) REVERT: A 59 ASP cc_start: 0.7388 (t70) cc_final: 0.6970 (t0) REVERT: A 79 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7625 (ttt180) REVERT: A 161 ARG cc_start: 0.7939 (mmt90) cc_final: 0.7305 (mmt180) REVERT: A 302 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7665 (tm-30) REVERT: B 85 MET cc_start: 0.7363 (mmm) cc_final: 0.6986 (mmt) REVERT: B 96 GLU cc_start: 0.7197 (tm-30) cc_final: 0.6910 (tm-30) REVERT: B 170 TYR cc_start: 0.7842 (t80) cc_final: 0.7371 (t80) REVERT: B 173 PHE cc_start: 0.7732 (m-80) cc_final: 0.7500 (m-80) REVERT: B 211 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7584 (mm-30) REVERT: B 227 ILE cc_start: 0.7725 (mm) cc_final: 0.7441 (mm) REVERT: B 230 GLU cc_start: 0.7264 (mm-30) cc_final: 0.6926 (mm-30) REVERT: B 372 TRP cc_start: 0.8543 (m100) cc_final: 0.8047 (m100) REVERT: C 161 SER cc_start: 0.8201 (OUTLIER) cc_final: 0.7987 (p) REVERT: C 257 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7627 (mm-30) REVERT: C 352 MET cc_start: 0.7480 (tmm) cc_final: 0.6697 (tmm) REVERT: D 111 HIS cc_start: 0.8087 (t70) cc_final: 0.7857 (t70) REVERT: D 222 TYR cc_start: 0.8663 (m-80) cc_final: 0.7819 (m-80) REVERT: E 9 MET cc_start: 0.5614 (ttm) cc_final: 0.5345 (mtt) REVERT: E 92 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7689 (tm-30) REVERT: E 94 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8324 (mt-10) REVERT: E 155 LYS cc_start: 0.7854 (mtmm) cc_final: 0.7539 (mtmm) REVERT: F 83 GLU cc_start: 0.7151 (mm-30) cc_final: 0.6739 (mm-30) REVERT: F 163 GLU cc_start: 0.7525 (mm-30) cc_final: 0.7218 (mm-30) REVERT: G 111 TYR cc_start: 0.7751 (m-80) cc_final: 0.7308 (m-80) REVERT: H 82 MET cc_start: 0.5716 (tpt) cc_final: 0.5029 (tpt) REVERT: H 147 ARG cc_start: 0.7975 (mtm110) cc_final: 0.7643 (ptp-110) REVERT: H 155 SER cc_start: 0.8447 (m) cc_final: 0.8131 (t) REVERT: H 195 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7565 (tm-30) REVERT: H 214 GLU cc_start: 0.7251 (mt-10) cc_final: 0.6763 (mt-10) REVERT: H 215 LYS cc_start: 0.8523 (ptpp) cc_final: 0.8159 (ptpp) REVERT: H 285 CYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8282 (m) REVERT: H 288 ASP cc_start: 0.8067 (m-30) cc_final: 0.7728 (t0) REVERT: H 300 SER cc_start: 0.9039 (t) cc_final: 0.8568 (m) REVERT: I 21 ILE cc_start: 0.8560 (tp) cc_final: 0.8235 (tp) REVERT: I 56 GLN cc_start: 0.7462 (tp-100) cc_final: 0.6789 (tp-100) REVERT: I 58 ASN cc_start: 0.8123 (m110) cc_final: 0.7744 (m110) REVERT: I 59 MET cc_start: 0.7740 (mpp) cc_final: 0.7383 (mpp) REVERT: I 122 GLU cc_start: 0.7518 (mm-30) cc_final: 0.7039 (mm-30) REVERT: I 134 ASP cc_start: 0.6916 (p0) cc_final: 0.6671 (p0) REVERT: I 138 ASN cc_start: 0.7381 (t0) cc_final: 0.7087 (t0) REVERT: I 167 ASN cc_start: 0.7888 (t0) cc_final: 0.7329 (t0) REVERT: I 238 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7467 (mm-30) REVERT: I 318 LYS cc_start: 0.8213 (mmpt) cc_final: 0.7977 (mmtt) REVERT: I 321 LYS cc_start: 0.8585 (tttm) cc_final: 0.8279 (tttm) REVERT: J 31 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8180 (tt) REVERT: J 76 SER cc_start: 0.7948 (t) cc_final: 0.7473 (p) REVERT: J 122 TRP cc_start: 0.7810 (m100) cc_final: 0.7599 (m-10) REVERT: J 151 ILE cc_start: 0.8770 (mt) cc_final: 0.8512 (mm) outliers start: 72 outliers final: 60 residues processed: 610 average time/residue: 0.4035 time to fit residues: 362.0001 Evaluate side-chains 642 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 578 time to evaluate : 2.199 ------------------------------------------------------------------------------- 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 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 19 LYS Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 100 ILE 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 317 LEU Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 126 GLU 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 204 GLU Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 105 ILE 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 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 186 THR Chi-restraints excluded: chain H residue 190 MET Chi-restraints excluded: chain H residue 198 TYR Chi-restraints excluded: chain H residue 242 LEU 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 H residue 318 THR Chi-restraints excluded: chain I residue 32 VAL 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 26 SER Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 134 ILE Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain J residue 187 MET Chi-restraints excluded: chain J residue 210 ILE Chi-restraints excluded: chain J residue 226 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 4 optimal weight: 0.9980 chunk 146 optimal weight: 0.0020 chunk 254 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 240 optimal weight: 0.2980 chunk 171 optimal weight: 7.9990 chunk 250 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 overall best weight: 0.4988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 HIS C 75 ASN ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 167 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.155258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.123231 restraints weight = 34229.646| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.96 r_work: 0.3426 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2632 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 : 0.593 13.055 29965 Z= 0.303 Chirality : 0.044 0.250 3295 Planarity : 0.004 0.063 3845 Dihedral : 5.915 83.662 3008 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.80 % Favored : 95.16 % Rotamer: Outliers : 2.66 % Allowed : 20.12 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.17), residues: 2664 helix: 0.90 (0.18), residues: 928 sheet: 0.21 (0.21), residues: 605 loop : -1.41 (0.18), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 75 HIS 0.004 0.001 HIS D 44 PHE 0.018 0.001 PHE C 111 TYR 0.024 0.001 TYR B 298 ARG 0.015 0.000 ARG C 277 Details of bonding type rmsd hydrogen bonds : bond 0.03684 ( 891) hydrogen bonds : angle 4.11838 ( 2460) covalent geometry : bond 0.00273 (22141) covalent geometry : angle 0.59251 (29965) ********************** 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 634 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 571 time to evaluate : 2.219 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 19 LEU cc_start: 0.8279 (mt) cc_final: 0.7988 (mt) REVERT: A 26 GLU cc_start: 0.7498 (mm-30) cc_final: 0.7038 (mm-30) REVERT: A 59 ASP cc_start: 0.7318 (t70) cc_final: 0.6908 (t0) REVERT: A 79 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7619 (ttt180) REVERT: A 89 MET cc_start: 0.7758 (tpp) cc_final: 0.6882 (tpp) REVERT: A 161 ARG cc_start: 0.7957 (mmt90) cc_final: 0.7361 (mmt180) REVERT: B 96 GLU cc_start: 0.7058 (tm-30) cc_final: 0.6692 (tm-30) REVERT: B 121 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7400 (mp0) REVERT: B 170 TYR cc_start: 0.7659 (t80) cc_final: 0.7203 (t80) REVERT: B 211 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7488 (mm-30) REVERT: B 227 ILE cc_start: 0.7608 (mm) cc_final: 0.7332 (mm) REVERT: B 230 GLU cc_start: 0.7362 (mm-30) cc_final: 0.7024 (mm-30) REVERT: B 242 GLU cc_start: 0.7333 (mm-30) cc_final: 0.7027 (mm-30) REVERT: B 372 TRP cc_start: 0.8524 (m100) cc_final: 0.7916 (m100) REVERT: C 161 SER cc_start: 0.8124 (OUTLIER) cc_final: 0.7885 (p) REVERT: C 257 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7638 (mm-30) REVERT: C 341 ARG cc_start: 0.7477 (tpp80) cc_final: 0.7144 (tpp80) REVERT: C 342 LYS cc_start: 0.8264 (ptpt) cc_final: 0.7763 (mtmt) REVERT: C 352 MET cc_start: 0.7442 (tmm) cc_final: 0.6714 (tmm) REVERT: D 222 TYR cc_start: 0.8555 (m-80) cc_final: 0.7794 (m-80) REVERT: E 9 MET cc_start: 0.5388 (ttm) cc_final: 0.5178 (mtt) REVERT: E 92 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7688 (tm-30) REVERT: E 94 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8295 (mt-10) REVERT: E 155 LYS cc_start: 0.7814 (mtmm) cc_final: 0.7519 (mtmm) REVERT: F 83 GLU cc_start: 0.6962 (mm-30) cc_final: 0.6630 (mm-30) REVERT: F 163 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7251 (mm-30) REVERT: G 111 TYR cc_start: 0.7666 (m-80) cc_final: 0.7287 (m-80) REVERT: H 82 MET cc_start: 0.5365 (tpt) cc_final: 0.4727 (tpt) REVERT: H 118 LYS cc_start: 0.7871 (tptp) cc_final: 0.7632 (tptp) REVERT: H 155 SER cc_start: 0.8397 (m) cc_final: 0.8102 (t) REVERT: H 195 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7553 (tm-30) REVERT: H 210 ARG cc_start: 0.8032 (ttm-80) cc_final: 0.6941 (ttp80) REVERT: H 214 GLU cc_start: 0.7218 (mt-10) cc_final: 0.6252 (mt-10) REVERT: H 215 LYS cc_start: 0.8485 (ptpp) cc_final: 0.8135 (ptpp) REVERT: H 285 CYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8053 (m) REVERT: H 288 ASP cc_start: 0.8051 (m-30) cc_final: 0.7714 (t0) REVERT: H 300 SER cc_start: 0.8916 (t) cc_final: 0.8512 (m) REVERT: H 316 GLU cc_start: 0.6193 (tm-30) cc_final: 0.5640 (mm-30) REVERT: H 325 MET cc_start: 0.6895 (ptt) cc_final: 0.6457 (ptt) REVERT: I 21 ILE cc_start: 0.8367 (tp) cc_final: 0.8068 (tp) REVERT: I 56 GLN cc_start: 0.7402 (tp-100) cc_final: 0.6766 (tp-100) REVERT: I 58 ASN cc_start: 0.8122 (m110) cc_final: 0.7761 (m110) REVERT: I 59 MET cc_start: 0.7641 (mpp) cc_final: 0.6230 (mmm) REVERT: I 134 ASP cc_start: 0.7007 (p0) cc_final: 0.6724 (p0) REVERT: I 138 ASN cc_start: 0.7333 (t0) cc_final: 0.6991 (t0) REVERT: I 167 ASN cc_start: 0.7582 (t160) cc_final: 0.7091 (t0) REVERT: I 238 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7393 (mm-30) REVERT: I 272 ASN cc_start: 0.7759 (t0) cc_final: 0.7535 (t0) REVERT: I 318 LYS cc_start: 0.8196 (mmpt) cc_final: 0.7935 (mmtt) REVERT: I 321 LYS cc_start: 0.8599 (tttm) cc_final: 0.8292 (tttm) REVERT: J 90 SER cc_start: 0.6638 (t) cc_final: 0.6437 (p) REVERT: J 122 TRP cc_start: 0.7708 (m100) cc_final: 0.7455 (m-10) REVERT: J 151 ILE cc_start: 0.8675 (mt) cc_final: 0.8408 (mm) outliers start: 63 outliers final: 49 residues processed: 598 average time/residue: 0.3918 time to fit residues: 341.3013 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 : 2.378 ------------------------------------------------------------------------------- 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 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 19 LYS Chi-restraints excluded: chain B residue 105 CYS Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 126 GLU 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 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 E residue 46 ILE Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 142 ILE 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 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 H residue 318 THR Chi-restraints excluded: chain I residue 32 VAL 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 26 SER Chi-restraints excluded: chain J residue 134 ILE Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain J residue 210 ILE Chi-restraints excluded: chain J residue 226 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 222 optimal weight: 3.9990 chunk 259 optimal weight: 3.9990 chunk 62 optimal weight: 0.4980 chunk 214 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 254 optimal weight: 4.9990 chunk 176 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 250 optimal weight: 3.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 HIS D 47 ASN D 92 ASN D 242 ASN ** I 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 209 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.150924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.119093 restraints weight = 34481.813| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.94 r_work: 0.3364 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 22141 Z= 0.289 Angle : 0.698 12.766 29965 Z= 0.363 Chirality : 0.050 0.233 3295 Planarity : 0.005 0.058 3845 Dihedral : 6.372 96.829 3008 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.21 % Favored : 92.76 % Rotamer: Outliers : 2.70 % Allowed : 20.20 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.16), residues: 2664 helix: 0.51 (0.17), residues: 941 sheet: 0.11 (0.21), residues: 604 loop : -1.52 (0.18), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 131 HIS 0.010 0.002 HIS I 135 PHE 0.032 0.003 PHE C 169 TYR 0.034 0.002 TYR B 298 ARG 0.010 0.001 ARG C 277 Details of bonding type rmsd hydrogen bonds : bond 0.05442 ( 891) hydrogen bonds : angle 4.48565 ( 2460) covalent geometry : bond 0.00685 (22141) covalent geometry : angle 0.69770 (29965) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13718.23 seconds wall clock time: 244 minutes 39.57 seconds (14679.57 seconds total)