Starting phenix.real_space_refine on Thu Jun 19 09:55:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fs5_29414/06_2025/8fs5_29414.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fs5_29414/06_2025/8fs5_29414.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fs5_29414/06_2025/8fs5_29414.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fs5_29414/06_2025/8fs5_29414.map" model { file = "/net/cci-nas-00/data/ceres_data/8fs5_29414/06_2025/8fs5_29414.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fs5_29414/06_2025/8fs5_29414.cif" } resolution = 2.76 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= -0.000 sd= 0.047 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 71 5.49 5 Mg 4 5.21 5 S 115 5.16 5 C 13862 2.51 5 N 3821 2.21 5 O 4338 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 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: 22211 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3559 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 17, 'TRANS': 417} Chain breaks: 2 Chain: "B" Number of atoms: 2490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2490 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 9, 'TRANS': 307} Chain: "C" Number of atoms: 2586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2586 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 12, 'TRANS': 314} Chain: "D" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2616 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain: "E" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2787 Classifications: {'peptide': 353} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 338} Chain: "F" Number of atoms: 2337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2337 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 9, 'TRANS': 282} Chain breaks: 5 Chain: "G" Number of atoms: 2322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2322 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 4, 'TRANS': 288} Chain breaks: 1 Chain: "H" Number of atoms: 2193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2193 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 10, 'TRANS': 261} Chain breaks: 6 Chain: "I" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 652 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain breaks: 1 Chain: "J" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 313 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DA:plan': 1, ' DA:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "K" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 201 Classifications: {'DNA': 10} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 9} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 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, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.07, per 1000 atoms: 0.63 Number of scatterers: 22211 At special positions: 0 Unit cell: (116.748, 137.448, 139.104, 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 115 16.00 P 71 15.00 Mg 4 11.99 O 4338 8.00 N 3821 7.00 C 13862 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: 5.82 Conformation dependent library (CDL) restraints added in 2.5 seconds 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5008 Finding SS restraints... Secondary structure from input PDB file: 123 helices and 18 sheets defined 52.7% alpha, 15.3% beta 22 base pairs and 46 stacking pairs defined. Time for finding SS restraints: 7.94 Creating SS restraints... Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 74 through 78 removed outlier: 3.508A pdb=" N GLN A 77 " --> pdb=" O CYS A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 96 Processing helix chain 'A' and resid 114 through 131 removed outlier: 3.631A pdb=" N ILE A 119 " --> pdb=" O LYS A 115 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU A 121 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) Proline residue: A 128 - end of helix Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 164 through 174 Processing helix chain 'A' and resid 194 through 210 Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 269 through 283 Processing helix chain 'A' and resid 284 through 291 Processing helix chain 'A' and resid 296 through 308 removed outlier: 3.575A pdb=" N VAL A 300 " --> pdb=" O LYS A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 323 Processing helix chain 'A' and resid 338 through 349 Processing helix chain 'A' and resid 355 through 367 Processing helix chain 'A' and resid 367 through 372 Processing helix chain 'A' and resid 373 through 384 removed outlier: 3.959A pdb=" N LYS A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 387 No H-bonds generated for 'chain 'A' and resid 385 through 387' Processing helix chain 'A' and resid 393 through 408 Processing helix chain 'A' and resid 413 through 431 removed outlier: 3.950A pdb=" N ASN A 417 " --> pdb=" O LEU A 413 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU A 418 " --> pdb=" O PRO A 414 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG A 422 " --> pdb=" O GLU A 418 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN A 430 " --> pdb=" O LYS A 426 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE A 431 " --> pdb=" O THR A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 470 removed outlier: 4.356A pdb=" N TYR A 469 " --> pdb=" O ASN A 465 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LYS A 470 " --> pdb=" O VAL A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 484 removed outlier: 3.502A pdb=" N LEU A 482 " --> pdb=" O ARG A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 497 removed outlier: 3.973A pdb=" N CYS A 494 " --> pdb=" O LEU A 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 19 through 23 Processing helix chain 'B' and resid 26 through 40 Processing helix chain 'B' and resid 54 through 68 Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 85 through 99 removed outlier: 3.854A pdb=" N ILE B 93 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LYS B 94 " --> pdb=" O ARG B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 119 Processing helix chain 'B' and resid 120 through 134 removed outlier: 3.938A pdb=" N ARG B 129 " --> pdb=" O GLN B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 150 Processing helix chain 'B' and resid 151 through 157 removed outlier: 3.909A pdb=" N ARG B 157 " --> pdb=" O PRO B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 183 Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 201 through 216 Processing helix chain 'B' and resid 220 through 228 removed outlier: 3.622A pdb=" N ILE B 227 " --> pdb=" O ASN B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 241 Processing helix chain 'B' and resid 244 through 255 removed outlier: 3.770A pdb=" N SER B 248 " --> pdb=" O ASN B 244 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN B 250 " --> pdb=" O GLU B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 277 removed outlier: 3.538A pdb=" N ARG B 272 " --> pdb=" O THR B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 301 Processing helix chain 'B' and resid 305 through 322 removed outlier: 3.717A pdb=" N LEU B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 13 removed outlier: 3.576A pdb=" N ASN C 12 " --> pdb=" O SER C 9 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU C 13 " --> pdb=" O LYS C 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 9 through 13' Processing helix chain 'C' and resid 14 through 19 Processing helix chain 'C' and resid 23 through 27 removed outlier: 3.559A pdb=" N VAL C 27 " --> pdb=" O LEU C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 44 removed outlier: 3.763A pdb=" N ILE C 34 " --> pdb=" O GLN C 30 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS C 39 " --> pdb=" O THR C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 72 Processing helix chain 'C' and resid 74 through 78 Processing helix chain 'C' and resid 89 through 103 removed outlier: 3.909A pdb=" N ILE C 97 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N LYS C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 122 Processing helix chain 'C' and resid 123 through 130 Processing helix chain 'C' and resid 130 through 135 Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.739A pdb=" N LYS C 152 " --> pdb=" O TYR C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 160 Processing helix chain 'C' and resid 170 through 186 Processing helix chain 'C' and resid 190 through 202 removed outlier: 3.783A pdb=" N ASN C 202 " --> pdb=" O ILE C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 219 Processing helix chain 'C' and resid 228 through 237 Processing helix chain 'C' and resid 240 through 253 removed outlier: 3.764A pdb=" N LYS C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 271 removed outlier: 3.596A pdb=" N HIS C 260 " --> pdb=" O TRP C 256 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LYS C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 287 removed outlier: 4.031A pdb=" N LEU C 277 " --> pdb=" O ALA C 273 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASP C 287 " --> pdb=" O LYS C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 312 removed outlier: 3.901A pdb=" N VAL C 297 " --> pdb=" O GLU C 293 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS C 312 " --> pdb=" O TYR C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 335 removed outlier: 3.949A pdb=" N ASN C 333 " --> pdb=" O ALA C 329 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU C 334 " --> pdb=" O SER C 330 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N THR C 335 " --> pdb=" O PHE C 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 31 Processing helix chain 'D' and resid 42 through 55 removed outlier: 3.710A pdb=" N VAL D 46 " --> pdb=" O GLN D 42 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL D 48 " --> pdb=" O HIS D 44 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR D 52 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LYS D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 84 Processing helix chain 'D' and resid 84 through 91 removed outlier: 4.257A pdb=" N LYS D 89 " --> pdb=" O PRO D 85 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N SER D 90 " --> pdb=" O ASP D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 116 removed outlier: 3.935A pdb=" N VAL D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N LYS D 111 " --> pdb=" O ARG D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 141 through 145 Processing helix chain 'D' and resid 146 through 152 Processing helix chain 'D' and resid 153 through 160 removed outlier: 3.522A pdb=" N TYR D 160 " --> pdb=" O THR D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 176 Processing helix chain 'D' and resid 177 through 184 removed outlier: 3.505A pdb=" N ARG D 183 " --> pdb=" O PRO D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 208 Processing helix chain 'D' and resid 218 through 224 Processing helix chain 'D' and resid 227 through 246 removed outlier: 3.540A pdb=" N GLY D 231 " --> pdb=" O ASP D 227 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR D 244 " --> pdb=" O LYS D 240 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY D 246 " --> pdb=" O ALA D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 261 removed outlier: 3.552A pdb=" N GLY D 261 " --> pdb=" O GLU D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 278 removed outlier: 3.629A pdb=" N GLY D 278 " --> pdb=" O LYS D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 292 removed outlier: 3.764A pdb=" N LYS D 292 " --> pdb=" O ASN D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 311 removed outlier: 3.585A pdb=" N ASN D 311 " --> pdb=" O TYR D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 335 removed outlier: 3.603A pdb=" N TRP D 324 " --> pdb=" O ASN D 320 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN D 335 " --> pdb=" O SER D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 352 Processing helix chain 'E' and resid 3 through 8 Processing helix chain 'E' and resid 12 through 16 removed outlier: 3.783A pdb=" N LEU E 16 " --> pdb=" O LEU E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 32 removed outlier: 3.601A pdb=" N THR E 23 " --> pdb=" O ASN E 19 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE E 25 " --> pdb=" O GLU E 21 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLN E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 36 Processing helix chain 'E' and resid 48 through 62 Processing helix chain 'E' and resid 98 through 103 removed outlier: 7.372A pdb=" N ASN E 103 " --> pdb=" O ASP E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 119 removed outlier: 3.806A pdb=" N VAL E 108 " --> pdb=" O ASN E 104 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU E 113 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LYS E 114 " --> pdb=" O GLN E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 146 removed outlier: 3.716A pdb=" N LEU E 146 " --> pdb=" O ALA E 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 143 through 146' Processing helix chain 'E' and resid 151 through 161 removed outlier: 3.873A pdb=" N ARG E 155 " --> pdb=" O GLN E 151 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ARG E 156 " --> pdb=" O ALA E 152 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR E 157 " --> pdb=" O ALA E 153 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU E 159 " --> pdb=" O ARG E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 184 Processing helix chain 'E' and resid 194 through 209 Processing helix chain 'E' and resid 216 through 227 removed outlier: 3.583A pdb=" N LYS E 220 " --> pdb=" O LYS E 216 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN E 227 " --> pdb=" O ALA E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 243 Processing helix chain 'E' and resid 257 through 273 Processing helix chain 'E' and resid 275 through 291 Processing helix chain 'E' and resid 295 through 308 Processing helix chain 'E' and resid 314 through 334 Processing helix chain 'E' and resid 337 through 354 removed outlier: 4.645A pdb=" N HIS E 341 " --> pdb=" O LYS E 337 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE E 346 " --> pdb=" O LEU E 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 30 removed outlier: 3.502A pdb=" N THR F 22 " --> pdb=" O LEU F 18 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA F 27 " --> pdb=" O ILE F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 62 removed outlier: 3.903A pdb=" N LEU F 61 " --> pdb=" O ASN F 57 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG F 62 " --> pdb=" O GLY F 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 57 through 62' Processing helix chain 'F' and resid 75 through 77 No H-bonds generated for 'chain 'F' and resid 75 through 77' Processing helix chain 'F' and resid 86 through 90 Processing helix chain 'F' and resid 96 through 113 removed outlier: 4.086A pdb=" N LEU F 100 " --> pdb=" O ASN F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 219 removed outlier: 3.537A pdb=" N ARG F 219 " --> pdb=" O ALA F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 252 removed outlier: 4.254A pdb=" N SER F 244 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ALA F 245 " --> pdb=" O GLU F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 256 removed outlier: 4.003A pdb=" N TYR F 256 " --> pdb=" O VAL F 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 253 through 256' Processing helix chain 'F' and resid 412 through 424 removed outlier: 3.625A pdb=" N CYS F 418 " --> pdb=" O ASP F 414 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 27 removed outlier: 4.067A pdb=" N ILE G 21 " --> pdb=" O HIS G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 67 No H-bonds generated for 'chain 'G' and resid 65 through 67' Processing helix chain 'G' and resid 86 through 97 removed outlier: 4.136A pdb=" N VAL G 95 " --> pdb=" O ASP G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 100 No H-bonds generated for 'chain 'G' and resid 98 through 100' Processing helix chain 'G' and resid 160 through 173 Processing helix chain 'G' and resid 239 through 243 Processing helix chain 'G' and resid 245 through 250 removed outlier: 3.533A pdb=" N LYS G 250 " --> pdb=" O ARG G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 319 through 330 Processing helix chain 'H' and resid 10 through 27 removed outlier: 3.542A pdb=" N TRP H 16 " --> pdb=" O LYS H 12 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 61 No H-bonds generated for 'chain 'H' and resid 59 through 61' Processing helix chain 'H' and resid 98 through 105 removed outlier: 3.983A pdb=" N THR H 103 " --> pdb=" O ARG H 99 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE H 104 " --> pdb=" O HIS H 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 233 through 243 removed outlier: 3.726A pdb=" N LEU H 237 " --> pdb=" O ASN H 233 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N PHE H 240 " --> pdb=" O LEU H 236 " (cutoff:3.500A) Processing helix chain 'H' and resid 326 through 336 removed outlier: 4.115A pdb=" N ASN H 331 " --> pdb=" O LYS H 327 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLY H 336 " --> pdb=" O PHE H 332 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 148 through 150 removed outlier: 6.268A pdb=" N LEU A 105 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ILE A 223 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU A 107 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE A 104 " --> pdb=" O LYS A 261 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N ILE A 263 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU A 106 " --> pdb=" O ILE A 263 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 226 through 227 Processing sheet with id=AA3, first strand: chain 'B' and resid 75 through 78 removed outlier: 6.213A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ILE B 46 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 185 through 186 removed outlier: 7.584A pdb=" N LYS B 185 " --> pdb=" O VAL B 219 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 79 through 82 removed outlier: 6.061A pdb=" N LEU C 50 " --> pdb=" O PHE C 164 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 188 through 189 removed outlier: 7.057A pdb=" N LYS C 188 " --> pdb=" O ILE C 227 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 92 through 95 removed outlier: 6.241A pdb=" N LYS D 135 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N CYS D 167 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE D 137 " --> pdb=" O CYS D 167 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N ILE D 169 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEU D 139 " --> pdb=" O ILE D 169 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 69 through 76 removed outlier: 3.643A pdb=" N LEU E 85 " --> pdb=" O ARG E 73 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU E 94 " --> pdb=" O ILE E 139 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ASN E 141 " --> pdb=" O LEU E 94 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE E 96 " --> pdb=" O ASN E 141 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N LYS E 136 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE E 168 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N VAL E 138 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL E 170 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE E 140 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU E 39 " --> pdb=" O MET E 169 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N CYS E 171 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N LEU E 41 " --> pdb=" O CYS E 171 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 79 through 83 removed outlier: 3.973A pdb=" N LEU F 79 " --> pdb=" O ILE F 6 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE F 6 " --> pdb=" O LEU F 79 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR F 81 " --> pdb=" O LYS F 4 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS F 4 " --> pdb=" O THR F 81 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 72 through 73 removed outlier: 3.594A pdb=" N LEU F 35 " --> pdb=" O MET F 93 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 72 through 73 removed outlier: 4.115A pdb=" N ILE F 44 " --> pdb=" O CYS F 70 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLU F 427 " --> pdb=" O SER F 443 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N VAL F 428 " --> pdb=" O LEU F 235 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE F 432 " --> pdb=" O MET F 231 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET F 231 " --> pdb=" O ILE F 432 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 405 through 411 removed outlier: 4.568A pdb=" N LEU F 281 " --> pdb=" O TRP F 296 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLU G 122 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N SER G 69 " --> pdb=" O SER G 14 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 80 through 85 removed outlier: 7.207A pdb=" N ASP G 36 " --> pdb=" O GLU G 51 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N GLU G 51 " --> pdb=" O ASP G 36 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL G 264 " --> pdb=" O ASP G 260 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU G 270 " --> pdb=" O LYS G 254 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS G 254 " --> pdb=" O LEU G 270 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE G 154 " --> pdb=" O MET G 259 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS G 216 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N LYS G 159 " --> pdb=" O LEU G 214 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LEU G 214 " --> pdb=" O LYS G 159 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 232 through 238 removed outlier: 4.671A pdb=" N PHE G 192 " --> pdb=" O LEU G 207 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR H 148 " --> pdb=" O VAL H 136 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL H 136 " --> pdb=" O TYR H 148 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLU H 63 " --> pdb=" O THR H 6 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 78 through 79 Processing sheet with id=AB7, first strand: chain 'H' and resid 78 through 79 removed outlier: 7.275A pdb=" N ASP H 29 " --> pdb=" O MET H 44 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N MET H 44 " --> pdb=" O ASP H 29 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE H 353 " --> pdb=" O ASN H 228 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 283 through 289 Processing sheet with id=AB9, first strand: chain 'H' and resid 270 through 271 removed outlier: 6.266A pdb=" N VAL H 270 " --> pdb=" O LEU H 278 " (cutoff:3.500A) 1086 hydrogen bonds defined for protein. 3102 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 55 hydrogen bonds 110 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 46 stacking parallelities Total time for adding SS restraints: 8.04 Time building geometry restraints manager: 6.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 7206 1.36 - 1.51: 5995 1.51 - 1.65: 9333 1.65 - 1.80: 74 1.80 - 1.95: 97 Bond restraints: 22705 Sorted by residual: bond pdb=" C SER E 175 " pdb=" N PRO E 176 " ideal model delta sigma weight residual 1.334 1.366 -0.032 8.40e-03 1.42e+04 1.47e+01 bond pdb=" CA SER F 51 " pdb=" CB SER F 51 " ideal model delta sigma weight residual 1.539 1.494 0.045 1.20e-02 6.94e+03 1.40e+01 bond pdb=" N HIS E 18 " pdb=" CA HIS E 18 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.31e-02 5.83e+03 8.30e+00 bond pdb=" N ILE F 468 " pdb=" CA ILE F 468 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.20e-02 6.94e+03 8.24e+00 bond pdb=" N LEU G 28 " pdb=" CA LEU G 28 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.27e-02 6.20e+03 7.24e+00 ... (remaining 22700 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 30112 1.84 - 3.68: 707 3.68 - 5.52: 91 5.52 - 7.36: 16 7.36 - 9.20: 5 Bond angle restraints: 30931 Sorted by residual: angle pdb=" N GLU E 21 " pdb=" CA GLU E 21 " pdb=" C GLU E 21 " ideal model delta sigma weight residual 112.54 107.31 5.23 1.22e+00 6.72e-01 1.84e+01 angle pdb=" N GLU A 68 " pdb=" CA GLU A 68 " pdb=" C GLU A 68 " ideal model delta sigma weight residual 113.88 108.85 5.03 1.23e+00 6.61e-01 1.67e+01 angle pdb=" CA GLY G 303 " pdb=" C GLY G 303 " pdb=" O GLY G 303 " ideal model delta sigma weight residual 122.78 117.99 4.79 1.20e+00 6.94e-01 1.59e+01 angle pdb=" CA GLN A 65 " pdb=" C GLN A 65 " pdb=" O GLN A 65 " ideal model delta sigma weight residual 121.47 117.10 4.37 1.15e+00 7.56e-01 1.44e+01 angle pdb=" N TYR A 67 " pdb=" CA TYR A 67 " pdb=" C TYR A 67 " ideal model delta sigma weight residual 113.16 108.51 4.65 1.24e+00 6.50e-01 1.41e+01 ... (remaining 30926 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.10: 13003 35.10 - 70.20: 699 70.20 - 105.30: 22 105.30 - 140.40: 2 140.40 - 175.50: 1 Dihedral angle restraints: 13727 sinusoidal: 6045 harmonic: 7682 Sorted by residual: dihedral pdb=" C5' ADP E 500 " pdb=" O5' ADP E 500 " pdb=" PA ADP E 500 " pdb=" O2A ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 115.50 -175.50 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O2A ADP E 500 " pdb=" O3A ADP E 500 " pdb=" PA ADP E 500 " pdb=" PB ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 80.07 -140.07 1 2.00e+01 2.50e-03 4.24e+01 dihedral pdb=" O1B ADP E 500 " pdb=" O3A ADP E 500 " pdb=" PB ADP E 500 " pdb=" PA ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 62.73 -122.73 1 2.00e+01 2.50e-03 3.70e+01 ... (remaining 13724 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2781 0.046 - 0.092: 609 0.092 - 0.138: 174 0.138 - 0.183: 7 0.183 - 0.229: 3 Chirality restraints: 3574 Sorted by residual: chirality pdb=" CA ILE F 468 " pdb=" N ILE F 468 " pdb=" C ILE F 468 " pdb=" CB ILE F 468 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CB ILE E 211 " pdb=" CA ILE E 211 " pdb=" CG1 ILE E 211 " pdb=" CG2 ILE E 211 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA VAL C 133 " pdb=" N VAL C 133 " pdb=" C VAL C 133 " pdb=" CB VAL C 133 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.31e-01 ... (remaining 3571 not shown) Planarity restraints: 3703 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY E 62 " 0.080 5.00e-02 4.00e+02 1.21e-01 2.33e+01 pdb=" N PRO E 63 " -0.208 5.00e-02 4.00e+02 pdb=" CA PRO E 63 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO E 63 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY H 336 " -0.054 5.00e-02 4.00e+02 8.25e-02 1.09e+01 pdb=" N PRO H 337 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO H 337 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO H 337 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 235 " 0.036 5.00e-02 4.00e+02 5.41e-02 4.67e+00 pdb=" N PRO F 236 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO F 236 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO F 236 " 0.030 5.00e-02 4.00e+02 ... (remaining 3700 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 262 2.63 - 3.19: 18785 3.19 - 3.76: 35597 3.76 - 4.33: 50262 4.33 - 4.90: 82510 Nonbonded interactions: 187416 Sorted by model distance: nonbonded pdb=" O2G AGS B 401 " pdb="MG MG B 402 " model vdw 2.057 2.170 nonbonded pdb=" O2G AGS C 401 " pdb="MG MG C 402 " model vdw 2.066 2.170 nonbonded pdb=" OE2 GLU A 187 " pdb="MG MG A 602 " model vdw 2.087 2.170 nonbonded pdb=" OG1 THR D 72 " pdb="MG MG D 402 " model vdw 2.095 2.170 nonbonded pdb=" O3G AGS D 401 " pdb="MG MG D 402 " model vdw 2.122 2.170 ... (remaining 187411 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: 34.600 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: 0.900 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 56.920 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.100 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:13.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 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 : 0.003 0.060 22705 Z= 0.192 Angle : 0.687 9.200 30931 Z= 0.432 Chirality : 0.042 0.229 3574 Planarity : 0.005 0.121 3703 Dihedral : 18.408 175.496 8719 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.77 % Allowed : 23.84 % Favored : 74.39 % 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: -0.31 (0.17), residues: 2575 helix: 0.33 (0.15), residues: 1216 sheet: -0.31 (0.23), residues: 542 loop : -0.71 (0.22), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 463 HIS 0.009 0.001 HIS E 18 PHE 0.012 0.001 PHE G 140 TYR 0.013 0.001 TYR A 67 ARG 0.007 0.000 ARG E 67 Details of bonding type rmsd hydrogen bonds : bond 0.18282 ( 1137) hydrogen bonds : angle 7.06931 ( 3212) covalent geometry : bond 0.00318 (22705) covalent geometry : angle 0.68684 (30931) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 292 time to evaluate : 3.862 Fit side-chains REVERT: A 131 ARG cc_start: 0.7729 (ttm-80) cc_final: 0.7500 (ttm-80) REVERT: B 183 ASP cc_start: 0.7421 (m-30) cc_final: 0.7172 (m-30) REVERT: C 199 GLU cc_start: 0.7383 (mp0) cc_final: 0.7002 (mp0) REVERT: D 80 LYS cc_start: 0.8105 (ttmt) cc_final: 0.7662 (mmmt) REVERT: E 67 ARG cc_start: 0.7310 (ttm-80) cc_final: 0.7063 (tpp80) REVERT: E 104 ASN cc_start: 0.7054 (m-40) cc_final: 0.6631 (m110) REVERT: E 142 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7558 (mm-30) REVERT: E 221 ARG cc_start: 0.6979 (mtp-110) cc_final: 0.6691 (mtm110) REVERT: G 35 ASP cc_start: 0.6732 (t0) cc_final: 0.6442 (t0) REVERT: G 314 GLU cc_start: 0.7158 (mm-30) cc_final: 0.6894 (mm-30) REVERT: H 133 ARG cc_start: 0.6594 (mtt90) cc_final: 0.6358 (mtt90) outliers start: 42 outliers final: 31 residues processed: 325 average time/residue: 1.5035 time to fit residues: 556.6215 Evaluate side-chains 301 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 270 time to evaluate : 2.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 471 TYR Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 256 TRP Chi-restraints excluded: chain E residue 18 HIS Chi-restraints excluded: chain E residue 19 ASN Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain H residue 2 SER Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 252 VAL Chi-restraints excluded: chain H residue 264 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 7.9990 chunk 200 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 206 optimal weight: 0.0670 chunk 80 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 154 optimal weight: 0.0070 chunk 239 optimal weight: 2.9990 overall best weight: 1.4142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 495 GLN B 35 GLN C 184 HIS D 128 ASN E 19 ASN E 243 ASN F 57 ASN G 9 ASN G 52 ASN G 53 ASN G 87 ASN G 218 GLN H 100 HIS H 151 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.175162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.127239 restraints weight = 23285.841| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.76 r_work: 0.3351 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22705 Z= 0.176 Angle : 0.564 7.713 30931 Z= 0.301 Chirality : 0.043 0.171 3574 Planarity : 0.005 0.078 3703 Dihedral : 16.195 147.153 3550 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.97 % Allowed : 20.80 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.08 (0.17), residues: 2575 helix: 0.51 (0.15), residues: 1218 sheet: -0.21 (0.23), residues: 553 loop : -0.57 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 463 HIS 0.010 0.001 HIS E 18 PHE 0.015 0.002 PHE G 154 TYR 0.021 0.001 TYR E 135 ARG 0.005 0.001 ARG E 34 Details of bonding type rmsd hydrogen bonds : bond 0.04784 ( 1137) hydrogen bonds : angle 5.06493 ( 3212) covalent geometry : bond 0.00415 (22705) covalent geometry : angle 0.56439 (30931) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 286 time to evaluate : 2.650 Fit side-chains REVERT: A 68 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7802 (tt0) REVERT: A 131 ARG cc_start: 0.7731 (ttm-80) cc_final: 0.7489 (ttm-80) REVERT: A 273 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7711 (mp) REVERT: D 126 LEU cc_start: 0.8600 (mt) cc_final: 0.8399 (mt) REVERT: D 175 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.7586 (mmp80) REVERT: E 19 ASN cc_start: 0.7368 (OUTLIER) cc_final: 0.7127 (t0) REVERT: E 69 LYS cc_start: 0.7405 (OUTLIER) cc_final: 0.6822 (ptmm) REVERT: E 230 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7696 (tt) REVERT: G 95 VAL cc_start: 0.7722 (OUTLIER) cc_final: 0.7424 (p) REVERT: G 122 GLU cc_start: 0.6599 (OUTLIER) cc_final: 0.6151 (pm20) REVERT: G 215 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7485 (mp0) REVERT: G 216 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7341 (pptt) REVERT: G 258 ARG cc_start: 0.8538 (mtm180) cc_final: 0.8274 (mtp180) REVERT: G 323 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.6541 (tm-30) REVERT: H 276 ASP cc_start: 0.6682 (t70) cc_final: 0.6278 (m-30) outliers start: 94 outliers final: 40 residues processed: 361 average time/residue: 1.3380 time to fit residues: 551.9516 Evaluate side-chains 320 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 269 time to evaluate : 2.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 471 TYR Chi-restraints excluded: chain B residue 27 LYS Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 175 ARG Chi-restraints excluded: chain E residue 19 ASN Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 103 ASN Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 122 GLU Chi-restraints excluded: chain G residue 133 SER Chi-restraints excluded: chain G residue 154 PHE Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 215 GLU Chi-restraints excluded: chain G residue 216 LYS Chi-restraints excluded: chain G residue 323 GLU Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 252 VAL Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 263 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 58 optimal weight: 0.7980 chunk 146 optimal weight: 9.9990 chunk 140 optimal weight: 1.9990 chunk 220 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 180 optimal weight: 8.9990 chunk 13 optimal weight: 0.8980 chunk 206 optimal weight: 0.4980 chunk 159 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN A 99 ASN B 35 GLN ** C 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN E 224 GLN G 218 GLN H 14 ASN H 151 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.176401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.129191 restraints weight = 23292.899| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.81 r_work: 0.3360 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22705 Z= 0.121 Angle : 0.499 7.240 30931 Z= 0.266 Chirality : 0.041 0.157 3574 Planarity : 0.004 0.075 3703 Dihedral : 15.972 130.629 3535 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.01 % Allowed : 20.93 % Favored : 75.06 % 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: 0.22 (0.17), residues: 2575 helix: 0.83 (0.15), residues: 1224 sheet: -0.15 (0.22), residues: 546 loop : -0.49 (0.23), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 463 HIS 0.009 0.001 HIS H 89 PHE 0.011 0.001 PHE E 328 TYR 0.015 0.001 TYR E 135 ARG 0.006 0.000 ARG E 67 Details of bonding type rmsd hydrogen bonds : bond 0.03832 ( 1137) hydrogen bonds : angle 4.63553 ( 3212) covalent geometry : bond 0.00272 (22705) covalent geometry : angle 0.49864 (30931) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 278 time to evaluate : 2.782 Fit side-chains REVERT: A 68 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7803 (tt0) REVERT: A 131 ARG cc_start: 0.7714 (ttm-80) cc_final: 0.7423 (ttm-80) REVERT: A 227 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7313 (tp30) REVERT: A 250 MET cc_start: 0.8092 (mmt) cc_final: 0.7722 (mmt) REVERT: A 273 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7743 (mp) REVERT: A 437 ASN cc_start: 0.7737 (t0) cc_final: 0.6751 (m110) REVERT: D 148 ASP cc_start: 0.8020 (OUTLIER) cc_final: 0.7666 (p0) REVERT: D 175 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.7848 (mmp80) REVERT: E 19 ASN cc_start: 0.7375 (OUTLIER) cc_final: 0.7128 (t0) REVERT: E 67 ARG cc_start: 0.7484 (ttm-80) cc_final: 0.7248 (tpp80) REVERT: E 69 LYS cc_start: 0.7279 (ptpt) cc_final: 0.6734 (ptmm) REVERT: E 142 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7648 (mm-30) REVERT: E 230 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7655 (tt) REVERT: E 311 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7485 (mm-30) REVERT: F 280 GLU cc_start: 0.7105 (tt0) cc_final: 0.6335 (pt0) REVERT: G 16 VAL cc_start: 0.7312 (m) cc_final: 0.7061 (p) REVERT: G 26 SER cc_start: 0.7611 (m) cc_final: 0.6788 (p) REVERT: G 35 ASP cc_start: 0.6869 (t0) cc_final: 0.6654 (t0) REVERT: G 216 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7403 (pptt) REVERT: G 258 ARG cc_start: 0.8560 (mtm180) cc_final: 0.8267 (mtp180) REVERT: H 276 ASP cc_start: 0.6677 (t70) cc_final: 0.6273 (m-30) outliers start: 95 outliers final: 37 residues processed: 357 average time/residue: 1.3541 time to fit residues: 550.1998 Evaluate side-chains 315 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 269 time to evaluate : 2.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 457 LYS Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 471 TYR Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 175 ARG Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain E residue 19 ASN Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 311 GLU Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 216 LYS Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 252 VAL Chi-restraints excluded: chain H residue 263 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 162 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 182 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 118 optimal weight: 0.0870 chunk 81 optimal weight: 2.9990 chunk 201 optimal weight: 9.9990 chunk 251 optimal weight: 0.9990 chunk 60 optimal weight: 0.2980 overall best weight: 1.0762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 162 GLN A 298 GLN A 411 ASN B 35 GLN ** C 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 GLN E 224 GLN G 218 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.174554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.126731 restraints weight = 23360.449| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.74 r_work: 0.3341 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22705 Z= 0.142 Angle : 0.515 7.165 30931 Z= 0.273 Chirality : 0.041 0.156 3574 Planarity : 0.004 0.073 3703 Dihedral : 15.976 134.872 3531 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.80 % Allowed : 21.52 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.32 (0.17), residues: 2575 helix: 0.94 (0.15), residues: 1212 sheet: -0.11 (0.22), residues: 547 loop : -0.48 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 463 HIS 0.007 0.001 HIS E 18 PHE 0.012 0.001 PHE E 328 TYR 0.018 0.001 TYR C 75 ARG 0.004 0.000 ARG D 183 Details of bonding type rmsd hydrogen bonds : bond 0.03826 ( 1137) hydrogen bonds : angle 4.54375 ( 3212) covalent geometry : bond 0.00334 (22705) covalent geometry : angle 0.51532 (30931) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 285 time to evaluate : 2.732 Fit side-chains REVERT: A 68 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7756 (tt0) REVERT: A 131 ARG cc_start: 0.7700 (ttm-80) cc_final: 0.7385 (ttm-80) REVERT: A 227 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7337 (tp30) REVERT: A 273 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7701 (mp) REVERT: A 293 LYS cc_start: 0.6424 (OUTLIER) cc_final: 0.4502 (ptpt) REVERT: B 301 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7358 (mt-10) REVERT: C 38 ARG cc_start: 0.7391 (OUTLIER) cc_final: 0.6548 (mtm180) REVERT: D 148 ASP cc_start: 0.8026 (OUTLIER) cc_final: 0.7677 (p0) REVERT: D 175 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.7857 (mmp80) REVERT: D 274 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.6961 (mptm) REVERT: E 19 ASN cc_start: 0.7364 (OUTLIER) cc_final: 0.7135 (t0) REVERT: E 69 LYS cc_start: 0.7305 (ptpt) cc_final: 0.6772 (ptmm) REVERT: E 230 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7707 (tt) REVERT: F 280 GLU cc_start: 0.7126 (tt0) cc_final: 0.6362 (pt0) REVERT: G 26 SER cc_start: 0.7716 (m) cc_final: 0.6891 (p) REVERT: G 35 ASP cc_start: 0.6884 (t0) cc_final: 0.6659 (t0) REVERT: G 95 VAL cc_start: 0.7773 (OUTLIER) cc_final: 0.7491 (p) REVERT: G 122 GLU cc_start: 0.6580 (OUTLIER) cc_final: 0.6205 (pm20) REVERT: G 215 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7454 (mp0) REVERT: G 216 LYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7447 (pptt) REVERT: G 258 ARG cc_start: 0.8578 (mtm180) cc_final: 0.8377 (mtp-110) REVERT: H 276 ASP cc_start: 0.6709 (t70) cc_final: 0.6292 (m-30) outliers start: 90 outliers final: 47 residues processed: 360 average time/residue: 1.3941 time to fit residues: 570.0053 Evaluate side-chains 332 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 271 time to evaluate : 2.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 457 LYS Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 471 TYR Chi-restraints excluded: chain B residue 27 LYS Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 175 ARG Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain E residue 19 ASN Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 297 ASN Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 122 GLU Chi-restraints excluded: chain G residue 133 SER Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 215 GLU Chi-restraints excluded: chain G residue 216 LYS Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 252 VAL Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain H residue 333 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 57 optimal weight: 0.8980 chunk 141 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 206 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 251 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 230 optimal weight: 4.9990 chunk 168 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 149 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 298 GLN A 411 ASN B 35 GLN B 145 ASN ** C 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 218 GLN H 228 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.175548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.129193 restraints weight = 23191.956| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.69 r_work: 0.3346 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22705 Z= 0.126 Angle : 0.501 7.030 30931 Z= 0.266 Chirality : 0.041 0.155 3574 Planarity : 0.004 0.070 3703 Dihedral : 15.946 139.760 3531 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.18 % Allowed : 21.39 % Favored : 74.43 % 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: 2575 helix: 1.05 (0.15), residues: 1217 sheet: -0.07 (0.22), residues: 540 loop : -0.42 (0.23), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 463 HIS 0.007 0.001 HIS E 18 PHE 0.014 0.001 PHE G 202 TYR 0.017 0.001 TYR E 135 ARG 0.006 0.000 ARG E 67 Details of bonding type rmsd hydrogen bonds : bond 0.03595 ( 1137) hydrogen bonds : angle 4.42911 ( 3212) covalent geometry : bond 0.00292 (22705) covalent geometry : angle 0.50067 (30931) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 278 time to evaluate : 2.786 Fit side-chains REVERT: A 68 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7749 (tt0) REVERT: A 131 ARG cc_start: 0.7650 (ttm-80) cc_final: 0.7322 (ttm-80) REVERT: A 227 GLU cc_start: 0.7775 (tt0) cc_final: 0.7316 (tp30) REVERT: A 250 MET cc_start: 0.8067 (mmt) cc_final: 0.7727 (mmt) REVERT: A 273 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7724 (mp) REVERT: A 293 LYS cc_start: 0.6468 (OUTLIER) cc_final: 0.4674 (ptpt) REVERT: C 38 ARG cc_start: 0.7308 (OUTLIER) cc_final: 0.6500 (mtm180) REVERT: D 148 ASP cc_start: 0.8019 (OUTLIER) cc_final: 0.7660 (p0) REVERT: D 175 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.7791 (mmp80) REVERT: E 69 LYS cc_start: 0.7239 (ptpt) cc_final: 0.6664 (ptmm) REVERT: E 142 GLU cc_start: 0.8355 (mt-10) cc_final: 0.7699 (mm-30) REVERT: E 208 ASN cc_start: 0.7559 (m-40) cc_final: 0.7347 (m-40) REVERT: E 230 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7657 (tt) REVERT: E 311 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7494 (mm-30) REVERT: F 232 MET cc_start: 0.7220 (mpt) cc_final: 0.6973 (mpp) REVERT: F 280 GLU cc_start: 0.7174 (tt0) cc_final: 0.6424 (pt0) REVERT: F 465 ILE cc_start: 0.7035 (mt) cc_final: 0.6732 (mp) REVERT: G 16 VAL cc_start: 0.7283 (m) cc_final: 0.6981 (p) REVERT: G 26 SER cc_start: 0.7711 (m) cc_final: 0.6889 (p) REVERT: G 35 ASP cc_start: 0.6917 (t0) cc_final: 0.6676 (t0) REVERT: G 95 VAL cc_start: 0.7765 (OUTLIER) cc_final: 0.7461 (p) REVERT: G 215 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7415 (mp0) REVERT: G 216 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7763 (tmtm) REVERT: G 227 VAL cc_start: 0.8308 (t) cc_final: 0.8066 (p) REVERT: G 258 ARG cc_start: 0.8615 (mtm180) cc_final: 0.8412 (mtp-110) REVERT: H 276 ASP cc_start: 0.6621 (t70) cc_final: 0.6156 (m-30) REVERT: H 298 LEU cc_start: 0.5329 (OUTLIER) cc_final: 0.5128 (mt) outliers start: 99 outliers final: 47 residues processed: 358 average time/residue: 1.4593 time to fit residues: 595.4735 Evaluate side-chains 327 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 268 time to evaluate : 2.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 457 LYS Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 471 TYR Chi-restraints excluded: chain B residue 27 LYS Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 175 ARG Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain E residue 6 ASP Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 311 GLU Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 133 SER Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 215 GLU Chi-restraints excluded: chain G residue 216 LYS Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 95 ARG Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 228 ASN Chi-restraints excluded: chain H residue 252 VAL Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain H residue 298 LEU Chi-restraints excluded: chain H residue 333 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 234 optimal weight: 0.0970 chunk 9 optimal weight: 3.9990 chunk 182 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 190 optimal weight: 8.9990 chunk 82 optimal weight: 4.9990 chunk 216 optimal weight: 0.0370 chunk 63 optimal weight: 0.7980 chunk 219 optimal weight: 6.9990 chunk 214 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 298 GLN A 411 ASN B 35 GLN ** C 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 ASN G 218 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.175777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.129467 restraints weight = 23292.282| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.68 r_work: 0.3354 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22705 Z= 0.118 Angle : 0.495 6.984 30931 Z= 0.262 Chirality : 0.041 0.157 3574 Planarity : 0.004 0.069 3703 Dihedral : 15.880 141.511 3524 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.05 % Allowed : 21.90 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.17), residues: 2575 helix: 1.14 (0.15), residues: 1217 sheet: -0.02 (0.22), residues: 539 loop : -0.39 (0.23), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 259 HIS 0.007 0.001 HIS E 18 PHE 0.014 0.001 PHE G 202 TYR 0.021 0.001 TYR C 75 ARG 0.006 0.000 ARG E 67 Details of bonding type rmsd hydrogen bonds : bond 0.03497 ( 1137) hydrogen bonds : angle 4.35373 ( 3212) covalent geometry : bond 0.00269 (22705) covalent geometry : angle 0.49478 (30931) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 274 time to evaluate : 2.575 Fit side-chains REVERT: A 68 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7779 (tt0) REVERT: A 131 ARG cc_start: 0.7685 (ttm-80) cc_final: 0.7360 (ttm-80) REVERT: A 227 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7213 (tp30) REVERT: A 273 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7816 (mp) REVERT: A 293 LYS cc_start: 0.6622 (OUTLIER) cc_final: 0.4782 (ptpt) REVERT: A 298 GLN cc_start: 0.7574 (OUTLIER) cc_final: 0.7019 (mm-40) REVERT: B 301 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7388 (mt-10) REVERT: C 38 ARG cc_start: 0.7365 (OUTLIER) cc_final: 0.6743 (mtm180) REVERT: C 332 GLU cc_start: 0.6943 (mt-10) cc_final: 0.6329 (pt0) REVERT: D 148 ASP cc_start: 0.8088 (OUTLIER) cc_final: 0.7750 (p0) REVERT: D 175 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.7836 (mmp80) REVERT: D 274 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.6996 (mptm) REVERT: D 285 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7751 (mttt) REVERT: E 69 LYS cc_start: 0.7380 (ptpt) cc_final: 0.6714 (ptmm) REVERT: E 208 ASN cc_start: 0.7589 (m-40) cc_final: 0.7383 (m-40) REVERT: E 230 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7704 (tt) REVERT: E 311 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7469 (mm-30) REVERT: F 232 MET cc_start: 0.7220 (mpt) cc_final: 0.6966 (mpp) REVERT: F 280 GLU cc_start: 0.7171 (tt0) cc_final: 0.6413 (pt0) REVERT: F 465 ILE cc_start: 0.7086 (mt) cc_final: 0.6782 (mp) REVERT: G 26 SER cc_start: 0.7867 (m) cc_final: 0.7073 (p) REVERT: G 95 VAL cc_start: 0.7801 (OUTLIER) cc_final: 0.7577 (p) REVERT: G 122 GLU cc_start: 0.6613 (OUTLIER) cc_final: 0.6366 (pm20) REVERT: G 215 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7467 (mp0) REVERT: G 216 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7767 (tmtm) REVERT: G 227 VAL cc_start: 0.8242 (t) cc_final: 0.8007 (p) REVERT: G 228 ILE cc_start: 0.7720 (OUTLIER) cc_final: 0.6883 (tp) REVERT: H 276 ASP cc_start: 0.6641 (t70) cc_final: 0.6146 (m-30) outliers start: 96 outliers final: 50 residues processed: 350 average time/residue: 1.3774 time to fit residues: 547.8997 Evaluate side-chains 333 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 266 time to evaluate : 2.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 471 TYR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 27 LYS Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 175 ARG Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 285 LYS Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 311 GLU Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 224 MET Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 470 ARG Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 122 GLU Chi-restraints excluded: chain G residue 133 SER Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 215 GLU Chi-restraints excluded: chain G residue 216 LYS Chi-restraints excluded: chain G residue 228 ILE Chi-restraints excluded: chain H residue 29 ASP Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 95 ARG Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 252 VAL Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain H residue 333 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 14 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 213 optimal weight: 0.0670 chunk 15 optimal weight: 0.0020 chunk 168 optimal weight: 0.5980 chunk 141 optimal weight: 0.7980 chunk 242 optimal weight: 6.9990 chunk 134 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.4526 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 298 GLN A 411 ASN B 35 GLN ** C 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 ASN E 32 GLN G 218 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.176962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.130575 restraints weight = 23208.031| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.72 r_work: 0.3366 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 22705 Z= 0.103 Angle : 0.487 9.135 30931 Z= 0.259 Chirality : 0.040 0.155 3574 Planarity : 0.003 0.068 3703 Dihedral : 15.810 143.022 3524 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.12 % Allowed : 22.83 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.68 (0.17), residues: 2575 helix: 1.25 (0.15), residues: 1219 sheet: 0.06 (0.22), residues: 532 loop : -0.33 (0.23), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 259 HIS 0.006 0.001 HIS E 18 PHE 0.019 0.001 PHE G 40 TYR 0.016 0.001 TYR B 186 ARG 0.007 0.000 ARG E 67 Details of bonding type rmsd hydrogen bonds : bond 0.03274 ( 1137) hydrogen bonds : angle 4.26310 ( 3212) covalent geometry : bond 0.00229 (22705) covalent geometry : angle 0.48746 (30931) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 283 time to evaluate : 2.773 Fit side-chains REVERT: A 68 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7767 (tt0) REVERT: A 131 ARG cc_start: 0.7654 (ttm-80) cc_final: 0.7413 (ttm-80) REVERT: A 203 GLN cc_start: 0.7189 (pt0) cc_final: 0.6550 (mm110) REVERT: A 227 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7167 (tp30) REVERT: A 250 MET cc_start: 0.8093 (mmt) cc_final: 0.7700 (mmt) REVERT: A 293 LYS cc_start: 0.6482 (OUTLIER) cc_final: 0.4642 (ptpt) REVERT: A 298 GLN cc_start: 0.7230 (tp-100) cc_final: 0.6787 (mm-40) REVERT: A 437 ASN cc_start: 0.7646 (t0) cc_final: 0.6692 (m110) REVERT: C 332 GLU cc_start: 0.6905 (mt-10) cc_final: 0.6314 (pt0) REVERT: D 148 ASP cc_start: 0.8049 (OUTLIER) cc_final: 0.7701 (p0) REVERT: D 274 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.6967 (mptm) REVERT: D 285 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7726 (mttt) REVERT: E 69 LYS cc_start: 0.7323 (ptpt) cc_final: 0.6634 (ptmm) REVERT: E 208 ASN cc_start: 0.7554 (m-40) cc_final: 0.7333 (m-40) REVERT: E 230 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7663 (tt) REVERT: E 311 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7521 (mm-30) REVERT: F 231 MET cc_start: 0.6386 (tpt) cc_final: 0.6065 (tpp) REVERT: F 232 MET cc_start: 0.7126 (mpt) cc_final: 0.6876 (mpp) REVERT: F 280 GLU cc_start: 0.7151 (tt0) cc_final: 0.6414 (pt0) REVERT: F 465 ILE cc_start: 0.7077 (mt) cc_final: 0.6773 (mp) REVERT: G 26 SER cc_start: 0.7822 (m) cc_final: 0.7032 (p) REVERT: G 95 VAL cc_start: 0.7799 (OUTLIER) cc_final: 0.7453 (p) REVERT: G 215 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7442 (mp0) REVERT: G 216 LYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7487 (pptt) REVERT: G 227 VAL cc_start: 0.8207 (t) cc_final: 0.7983 (p) REVERT: G 228 ILE cc_start: 0.7639 (OUTLIER) cc_final: 0.6819 (tp) REVERT: H 276 ASP cc_start: 0.6659 (t70) cc_final: 0.6140 (m-30) outliers start: 74 outliers final: 40 residues processed: 341 average time/residue: 1.4041 time to fit residues: 547.0731 Evaluate side-chains 321 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 269 time to evaluate : 2.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 471 TYR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 22 ASP Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 285 LYS Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 311 GLU Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 224 MET Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 68 MET Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 215 GLU Chi-restraints excluded: chain G residue 216 LYS Chi-restraints excluded: chain G residue 228 ILE Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 95 ARG Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 252 VAL Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain H residue 333 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 117 optimal weight: 0.0870 chunk 83 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 25 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 191 optimal weight: 8.9990 chunk 135 optimal weight: 0.9980 chunk 18 optimal weight: 0.0570 chunk 139 optimal weight: 0.4980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 411 ASN B 35 GLN ** C 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 ASN E 32 GLN G 218 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.176910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.130010 restraints weight = 23329.131| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.78 r_work: 0.3362 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22705 Z= 0.106 Angle : 0.488 9.704 30931 Z= 0.258 Chirality : 0.040 0.156 3574 Planarity : 0.003 0.067 3703 Dihedral : 15.784 144.288 3523 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.12 % Allowed : 23.08 % Favored : 73.80 % 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: 0.74 (0.17), residues: 2575 helix: 1.29 (0.15), residues: 1226 sheet: 0.11 (0.23), residues: 533 loop : -0.30 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 42 HIS 0.006 0.001 HIS E 18 PHE 0.019 0.001 PHE G 202 TYR 0.021 0.001 TYR C 75 ARG 0.006 0.000 ARG E 67 Details of bonding type rmsd hydrogen bonds : bond 0.03255 ( 1137) hydrogen bonds : angle 4.21462 ( 3212) covalent geometry : bond 0.00237 (22705) covalent geometry : angle 0.48786 (30931) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 278 time to evaluate : 2.484 Fit side-chains REVERT: A 68 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7776 (tt0) REVERT: A 131 ARG cc_start: 0.7658 (ttm-80) cc_final: 0.7418 (ttm-80) REVERT: A 203 GLN cc_start: 0.7247 (pt0) cc_final: 0.6620 (mm110) REVERT: A 227 GLU cc_start: 0.7670 (tt0) cc_final: 0.7132 (tp30) REVERT: A 250 MET cc_start: 0.8121 (mmt) cc_final: 0.7734 (mmt) REVERT: A 293 LYS cc_start: 0.6596 (OUTLIER) cc_final: 0.4734 (ptpt) REVERT: A 298 GLN cc_start: 0.7481 (tp-100) cc_final: 0.7080 (mm-40) REVERT: A 437 ASN cc_start: 0.7663 (t0) cc_final: 0.6721 (m110) REVERT: C 38 ARG cc_start: 0.7333 (OUTLIER) cc_final: 0.6746 (mtm180) REVERT: C 332 GLU cc_start: 0.6889 (mt-10) cc_final: 0.6356 (pt0) REVERT: D 148 ASP cc_start: 0.8066 (OUTLIER) cc_final: 0.7751 (p0) REVERT: D 274 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7003 (mptm) REVERT: D 285 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7769 (mttt) REVERT: E 69 LYS cc_start: 0.7367 (ptpt) cc_final: 0.6722 (ptmm) REVERT: E 208 ASN cc_start: 0.7561 (m-40) cc_final: 0.7341 (m-40) REVERT: E 230 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7724 (tt) REVERT: E 311 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7537 (mm-30) REVERT: F 231 MET cc_start: 0.6408 (tpt) cc_final: 0.6082 (tpp) REVERT: F 232 MET cc_start: 0.7147 (mpt) cc_final: 0.6897 (mpp) REVERT: F 280 GLU cc_start: 0.7073 (tt0) cc_final: 0.6375 (pt0) REVERT: F 465 ILE cc_start: 0.7063 (mt) cc_final: 0.6759 (mp) REVERT: G 16 VAL cc_start: 0.7187 (m) cc_final: 0.6875 (p) REVERT: G 26 SER cc_start: 0.7820 (m) cc_final: 0.7018 (p) REVERT: G 215 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7492 (mp0) REVERT: G 216 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7556 (pptt) REVERT: G 227 VAL cc_start: 0.8253 (t) cc_final: 0.8003 (p) REVERT: G 228 ILE cc_start: 0.7613 (OUTLIER) cc_final: 0.6810 (tp) REVERT: H 276 ASP cc_start: 0.6611 (t70) cc_final: 0.6107 (m-30) outliers start: 74 outliers final: 42 residues processed: 336 average time/residue: 1.4308 time to fit residues: 544.5662 Evaluate side-chains 325 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 272 time to evaluate : 2.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 471 TYR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 285 LYS Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 311 GLU Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 470 ARG Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 215 GLU Chi-restraints excluded: chain G residue 216 LYS Chi-restraints excluded: chain G residue 228 ILE Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 95 ARG Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 252 VAL Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain H residue 333 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 126 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 218 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 189 optimal weight: 0.0870 chunk 39 optimal weight: 6.9990 chunk 131 optimal weight: 0.9990 chunk 221 optimal weight: 0.9990 chunk 203 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 overall best weight: 1.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN B 35 GLN ** C 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN E 19 ASN E 32 GLN G 218 GLN H 228 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.173039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.126591 restraints weight = 23260.909| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.66 r_work: 0.3318 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22705 Z= 0.170 Angle : 0.549 11.590 30931 Z= 0.288 Chirality : 0.043 0.151 3574 Planarity : 0.004 0.065 3703 Dihedral : 15.981 146.969 3523 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.21 % Allowed : 23.21 % Favored : 73.59 % 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: 0.50 (0.17), residues: 2575 helix: 1.08 (0.15), residues: 1220 sheet: 0.02 (0.22), residues: 540 loop : -0.42 (0.23), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 463 HIS 0.008 0.001 HIS E 18 PHE 0.017 0.002 PHE G 40 TYR 0.023 0.001 TYR E 135 ARG 0.006 0.000 ARG E 67 Details of bonding type rmsd hydrogen bonds : bond 0.03977 ( 1137) hydrogen bonds : angle 4.38869 ( 3212) covalent geometry : bond 0.00411 (22705) covalent geometry : angle 0.54918 (30931) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 279 time to evaluate : 2.756 Fit side-chains REVERT: A 203 GLN cc_start: 0.7292 (pt0) cc_final: 0.6691 (mm110) REVERT: A 227 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7149 (tp30) REVERT: A 298 GLN cc_start: 0.7591 (tp-100) cc_final: 0.7110 (mm-40) REVERT: C 38 ARG cc_start: 0.7289 (OUTLIER) cc_final: 0.6710 (mtm180) REVERT: C 332 GLU cc_start: 0.6929 (mt-10) cc_final: 0.6380 (pt0) REVERT: C 334 GLU cc_start: 0.7459 (tt0) cc_final: 0.7224 (mt-10) REVERT: D 148 ASP cc_start: 0.8056 (OUTLIER) cc_final: 0.7717 (p0) REVERT: D 175 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.7817 (mmp80) REVERT: D 274 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.6985 (mptm) REVERT: D 353 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7487 (mp) REVERT: E 208 ASN cc_start: 0.7612 (m-40) cc_final: 0.7391 (m-40) REVERT: E 221 ARG cc_start: 0.7087 (mtm180) cc_final: 0.6821 (mtp-110) REVERT: E 230 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7728 (tt) REVERT: F 231 MET cc_start: 0.6411 (tpt) cc_final: 0.6057 (tpp) REVERT: F 280 GLU cc_start: 0.7094 (tt0) cc_final: 0.6415 (pt0) REVERT: F 465 ILE cc_start: 0.7109 (mt) cc_final: 0.6801 (mp) REVERT: G 26 SER cc_start: 0.7893 (m) cc_final: 0.7122 (p) REVERT: G 68 MET cc_start: 0.7573 (OUTLIER) cc_final: 0.7229 (mpp) REVERT: G 146 GLU cc_start: 0.7560 (mt-10) cc_final: 0.6956 (pm20) REVERT: G 215 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7625 (mp0) REVERT: G 216 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7861 (tmtm) REVERT: G 227 VAL cc_start: 0.8314 (t) cc_final: 0.8101 (p) REVERT: G 228 ILE cc_start: 0.7641 (OUTLIER) cc_final: 0.6793 (tp) REVERT: H 276 ASP cc_start: 0.6580 (t70) cc_final: 0.6059 (m-30) outliers start: 76 outliers final: 41 residues processed: 337 average time/residue: 1.4240 time to fit residues: 544.3899 Evaluate side-chains 325 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 273 time to evaluate : 2.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 471 TYR Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 175 ARG Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 68 MET Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 133 SER Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 215 GLU Chi-restraints excluded: chain G residue 216 LYS Chi-restraints excluded: chain G residue 228 ILE Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 95 ARG Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 252 VAL Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain H residue 333 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 120 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 252 optimal weight: 20.0000 chunk 115 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 172 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 164 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 411 ASN B 35 GLN ** C 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 ASN E 32 GLN G 218 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.174792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.126947 restraints weight = 23369.201| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.78 r_work: 0.3350 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22705 Z= 0.123 Angle : 0.512 10.163 30931 Z= 0.270 Chirality : 0.041 0.147 3574 Planarity : 0.004 0.066 3703 Dihedral : 15.919 152.093 3523 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.36 % Allowed : 24.22 % Favored : 73.42 % 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: 0.63 (0.17), residues: 2575 helix: 1.20 (0.15), residues: 1220 sheet: 0.07 (0.22), residues: 537 loop : -0.37 (0.23), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 259 HIS 0.006 0.001 HIS E 18 PHE 0.019 0.001 PHE G 154 TYR 0.021 0.001 TYR C 75 ARG 0.007 0.000 ARG E 67 Details of bonding type rmsd hydrogen bonds : bond 0.03486 ( 1137) hydrogen bonds : angle 4.29371 ( 3212) covalent geometry : bond 0.00283 (22705) covalent geometry : angle 0.51195 (30931) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 276 time to evaluate : 2.920 Fit side-chains REVERT: A 203 GLN cc_start: 0.7235 (pt0) cc_final: 0.6684 (mm110) REVERT: A 227 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7168 (tp30) REVERT: A 286 LYS cc_start: 0.7978 (tptm) cc_final: 0.7087 (tptt) REVERT: A 298 GLN cc_start: 0.7554 (tp-100) cc_final: 0.7092 (mm-40) REVERT: B 28 GLU cc_start: 0.8064 (mp0) cc_final: 0.7840 (mt-10) REVERT: C 38 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.6738 (mtm180) REVERT: C 332 GLU cc_start: 0.6879 (mt-10) cc_final: 0.6405 (pt0) REVERT: C 334 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.7151 (mt-10) REVERT: D 148 ASP cc_start: 0.8063 (OUTLIER) cc_final: 0.7713 (p0) REVERT: D 274 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.6984 (mptm) REVERT: D 353 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7446 (mp) REVERT: E 208 ASN cc_start: 0.7596 (m-40) cc_final: 0.7357 (m-40) REVERT: E 221 ARG cc_start: 0.7062 (mtm180) cc_final: 0.6782 (mtp-110) REVERT: E 230 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7700 (tt) REVERT: F 231 MET cc_start: 0.6265 (tpt) cc_final: 0.5933 (tpp) REVERT: F 232 MET cc_start: 0.7141 (mpt) cc_final: 0.6862 (mpp) REVERT: F 280 GLU cc_start: 0.7077 (tt0) cc_final: 0.6419 (pt0) REVERT: F 465 ILE cc_start: 0.7108 (mt) cc_final: 0.6801 (mp) REVERT: G 26 SER cc_start: 0.7868 (m) cc_final: 0.7116 (p) REVERT: G 68 MET cc_start: 0.7447 (OUTLIER) cc_final: 0.7095 (mpp) REVERT: G 73 ARG cc_start: 0.7052 (mtm180) cc_final: 0.6784 (mpp80) REVERT: G 215 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7535 (mp0) REVERT: G 216 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7844 (tmtm) REVERT: G 227 VAL cc_start: 0.8309 (t) cc_final: 0.8085 (p) REVERT: G 228 ILE cc_start: 0.7604 (OUTLIER) cc_final: 0.6772 (tp) REVERT: H 276 ASP cc_start: 0.6583 (t70) cc_final: 0.6064 (m-30) outliers start: 56 outliers final: 37 residues processed: 319 average time/residue: 1.7809 time to fit residues: 652.0436 Evaluate side-chains 317 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 269 time to evaluate : 2.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 471 TYR Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 68 MET Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 215 GLU Chi-restraints excluded: chain G residue 216 LYS Chi-restraints excluded: chain G residue 228 ILE Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 95 ARG Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 252 VAL Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain H residue 333 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 105 optimal weight: 0.9980 chunk 200 optimal weight: 10.0000 chunk 177 optimal weight: 7.9990 chunk 206 optimal weight: 0.9990 chunk 235 optimal weight: 7.9990 chunk 260 optimal weight: 6.9990 chunk 179 optimal weight: 7.9990 chunk 57 optimal weight: 0.9990 chunk 222 optimal weight: 2.9990 chunk 153 optimal weight: 0.1980 chunk 190 optimal weight: 7.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 411 ASN B 35 GLN ** C 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 ASN E 32 GLN ** F 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 218 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.173683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.125777 restraints weight = 23271.692| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.75 r_work: 0.3337 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22705 Z= 0.154 Angle : 0.541 11.008 30931 Z= 0.284 Chirality : 0.042 0.210 3574 Planarity : 0.004 0.066 3703 Dihedral : 15.978 158.761 3523 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.70 % Allowed : 23.97 % Favored : 73.33 % 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: 0.56 (0.17), residues: 2575 helix: 1.12 (0.15), residues: 1220 sheet: 0.07 (0.22), residues: 538 loop : -0.39 (0.23), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 463 HIS 0.008 0.001 HIS E 18 PHE 0.019 0.002 PHE G 154 TYR 0.021 0.001 TYR B 186 ARG 0.006 0.000 ARG E 67 Details of bonding type rmsd hydrogen bonds : bond 0.03756 ( 1137) hydrogen bonds : angle 4.33206 ( 3212) covalent geometry : bond 0.00367 (22705) covalent geometry : angle 0.54084 (30931) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19295.42 seconds wall clock time: 336 minutes 56.20 seconds (20216.20 seconds total)