Starting phenix.real_space_refine on Sat Jun 21 06:10:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yh8_39284/06_2025/8yh8_39284.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yh8_39284/06_2025/8yh8_39284.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yh8_39284/06_2025/8yh8_39284.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yh8_39284/06_2025/8yh8_39284.map" model { file = "/net/cci-nas-00/data/ceres_data/8yh8_39284/06_2025/8yh8_39284.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yh8_39284/06_2025/8yh8_39284.cif" } resolution = 2.7 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= 0.001 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 7 5.49 5 Mg 3 5.21 5 S 80 5.16 5 C 15601 2.51 5 N 4305 2.21 5 O 4716 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 193 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24712 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3624 Classifications: {'peptide': 474} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 451} Chain: "B" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3631 Classifications: {'peptide': 475} Link IDs: {'PTRANS': 22, 'TRANS': 452} Chain: "C" Number of atoms: 3637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3637 Classifications: {'peptide': 476} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 453} Chain: "D" Number of atoms: 3622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3622 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Chain: "E" Number of atoms: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3623 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Chain: "F" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3630 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 447} Chain: "G" Number of atoms: 2211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2211 Classifications: {'peptide': 282} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 271} Chain: "H" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 646 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 6, 'TRANS': 80} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 15.04, per 1000 atoms: 0.61 Number of scatterers: 24712 At special positions: 0 Unit cell: (132, 127.6, 156.64, 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 80 16.00 P 7 15.00 Mg 3 11.99 O 4716 8.00 N 4305 7.00 C 15601 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.69 Conformation dependent library (CDL) restraints added in 3.4 seconds 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5848 Finding SS restraints... Secondary structure from input PDB file: 133 helices and 26 sheets defined 48.6% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.24 Creating SS restraints... Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 175 through 185 removed outlier: 4.352A pdb=" N ALA A 179 " --> pdb=" O ALA A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 189 Processing helix chain 'A' and resid 201 through 215 Processing helix chain 'A' and resid 216 through 220 Processing helix chain 'A' and resid 231 through 253 removed outlier: 3.530A pdb=" N LEU A 235 " --> pdb=" O PRO A 231 " (cutoff:3.500A) Proline residue: A 239 - end of helix removed outlier: 3.713A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 277 removed outlier: 3.757A pdb=" N GLN A 266 " --> pdb=" O ALA A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 299 removed outlier: 3.520A pdb=" N HIS A 294 " --> pdb=" O ILE A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 328 through 338 Processing helix chain 'A' and resid 345 through 351 Processing helix chain 'A' and resid 372 through 393 removed outlier: 3.556A pdb=" N VAL A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N GLY A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N THR A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 402 removed outlier: 4.075A pdb=" N GLN A 397 " --> pdb=" O ALA A 394 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N SER A 400 " --> pdb=" O GLN A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 420 Processing helix chain 'A' and resid 429 through 442 Processing helix chain 'A' and resid 452 through 468 Processing helix chain 'A' and resid 468 through 479 Processing helix chain 'A' and resid 483 through 496 Processing helix chain 'B' and resid 78 through 82 removed outlier: 4.225A pdb=" N GLY B 81 " --> pdb=" O PRO B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 104 removed outlier: 3.577A pdb=" N ILE B 104 " --> pdb=" O GLU B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 139 removed outlier: 3.892A pdb=" N ARG B 139 " --> pdb=" O VAL B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 174 through 186 removed outlier: 3.762A pdb=" N VAL B 178 " --> pdb=" O GLY B 174 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA B 179 " --> pdb=" O ALA B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 189 No H-bonds generated for 'chain 'B' and resid 187 through 189' Processing helix chain 'B' and resid 201 through 215 Processing helix chain 'B' and resid 216 through 220 Processing helix chain 'B' and resid 231 through 253 Proline residue: B 239 - end of helix removed outlier: 3.719A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 277 Processing helix chain 'B' and resid 282 through 286 Processing helix chain 'B' and resid 289 through 299 removed outlier: 3.533A pdb=" N HIS B 294 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 309 removed outlier: 3.522A pdb=" N GLY B 309 " --> pdb=" O ASP B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 338 Processing helix chain 'B' and resid 345 through 351 Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'B' and resid 372 through 399 removed outlier: 3.813A pdb=" N VAL B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLY B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N THR B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 382 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLU B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU B 392 " --> pdb=" O ALA B 388 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ALA B 394 " --> pdb=" O ARG B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 421 removed outlier: 3.589A pdb=" N LYS B 421 " --> pdb=" O VAL B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 442 Processing helix chain 'B' and resid 452 through 468 Processing helix chain 'B' and resid 468 through 479 Processing helix chain 'B' and resid 483 through 496 Processing helix chain 'C' and resid 100 through 104 Processing helix chain 'C' and resid 135 through 139 removed outlier: 3.949A pdb=" N ARG C 139 " --> pdb=" O VAL C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 157 Processing helix chain 'C' and resid 174 through 186 removed outlier: 4.272A pdb=" N ALA C 179 " --> pdb=" O ALA C 175 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ILE C 180 " --> pdb=" O ALA C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 189 No H-bonds generated for 'chain 'C' and resid 187 through 189' Processing helix chain 'C' and resid 201 through 215 Processing helix chain 'C' and resid 216 through 220 Processing helix chain 'C' and resid 231 through 251 removed outlier: 3.535A pdb=" N LEU C 235 " --> pdb=" O PRO C 231 " (cutoff:3.500A) Proline residue: C 239 - end of helix removed outlier: 3.671A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 278 removed outlier: 3.744A pdb=" N GLN C 266 " --> pdb=" O ALA C 262 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA C 267 " --> pdb=" O LEU C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 300 removed outlier: 3.933A pdb=" N HIS C 294 " --> pdb=" O ILE C 290 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG C 300 " --> pdb=" O ARG C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 309 Processing helix chain 'C' and resid 328 through 338 Processing helix chain 'C' and resid 345 through 351 Processing helix chain 'C' and resid 372 through 379 Processing helix chain 'C' and resid 381 through 399 removed outlier: 3.709A pdb=" N GLN C 397 " --> pdb=" O GLU C 393 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N PHE C 398 " --> pdb=" O ALA C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 420 Processing helix chain 'C' and resid 429 through 442 Processing helix chain 'C' and resid 449 through 451 No H-bonds generated for 'chain 'C' and resid 449 through 451' Processing helix chain 'C' and resid 452 through 468 Processing helix chain 'C' and resid 468 through 479 Processing helix chain 'C' and resid 483 through 498 Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'D' and resid 124 through 128 removed outlier: 3.760A pdb=" N LEU D 128 " --> pdb=" O PHE D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 146 Processing helix chain 'D' and resid 163 through 176 Processing helix chain 'D' and resid 191 through 206 Processing helix chain 'D' and resid 207 through 209 No H-bonds generated for 'chain 'D' and resid 207 through 209' Processing helix chain 'D' and resid 221 through 242 removed outlier: 5.209A pdb=" N ALA D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N LEU D 230 " --> pdb=" O MET D 226 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 269 removed outlier: 4.071A pdb=" N THR D 258 " --> pdb=" O ILE D 254 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ALA D 266 " --> pdb=" O SER D 262 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N LEU D 267 " --> pdb=" O GLU D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 277 Processing helix chain 'D' and resid 280 through 290 removed outlier: 3.547A pdb=" N LEU D 288 " --> pdb=" O GLU D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 322 Processing helix chain 'D' and resid 323 through 325 No H-bonds generated for 'chain 'D' and resid 323 through 325' Processing helix chain 'D' and resid 332 through 339 Processing helix chain 'D' and resid 351 through 355 Processing helix chain 'D' and resid 356 through 361 removed outlier: 4.254A pdb=" N GLU D 361 " --> pdb=" O GLU D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 386 removed outlier: 4.042A pdb=" N GLN D 365 " --> pdb=" O GLU D 361 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL D 366 " --> pdb=" O GLU D 362 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASP D 382 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA D 385 " --> pdb=" O GLN D 381 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ILE D 386 " --> pdb=" O ASP D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 392 Processing helix chain 'D' and resid 394 through 410 removed outlier: 3.967A pdb=" N LEU D 398 " --> pdb=" O ASP D 394 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL D 399 " --> pdb=" O GLU D 395 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG D 402 " --> pdb=" O LEU D 398 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 416 No H-bonds generated for 'chain 'D' and resid 414 through 416' Processing helix chain 'D' and resid 417 through 422 Processing helix chain 'D' and resid 429 through 443 Processing helix chain 'D' and resid 449 through 454 Processing helix chain 'D' and resid 458 through 470 removed outlier: 3.543A pdb=" N VAL D 462 " --> pdb=" O ARG D 458 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'E' and resid 139 through 146 Processing helix chain 'E' and resid 163 through 179 Processing helix chain 'E' and resid 191 through 205 Processing helix chain 'E' and resid 206 through 210 Processing helix chain 'E' and resid 221 through 243 removed outlier: 5.242A pdb=" N ALA E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N LEU E 230 " --> pdb=" O MET E 226 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE E 239 " --> pdb=" O MET E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 269 removed outlier: 3.623A pdb=" N PHE E 257 " --> pdb=" O ASN E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 277 Processing helix chain 'E' and resid 280 through 290 Processing helix chain 'E' and resid 315 through 323 Processing helix chain 'E' and resid 332 through 339 Processing helix chain 'E' and resid 347 through 353 removed outlier: 4.260A pdb=" N SER E 351 " --> pdb=" O LEU E 347 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG E 352 " --> pdb=" O ALA E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 385 removed outlier: 3.929A pdb=" N GLN E 365 " --> pdb=" O GLU E 361 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASP E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE E 383 " --> pdb=" O GLU E 379 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA E 385 " --> pdb=" O GLN E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 410 removed outlier: 3.813A pdb=" N SER E 393 " --> pdb=" O MET E 389 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ASP E 394 " --> pdb=" O ASP E 390 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLU E 395 " --> pdb=" O GLU E 391 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LYS E 397 " --> pdb=" O SER E 393 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU E 398 " --> pdb=" O ASP E 394 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N VAL E 399 " --> pdb=" O GLU E 395 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG E 402 " --> pdb=" O LEU E 398 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 420 removed outlier: 3.799A pdb=" N GLN E 419 " --> pdb=" O VAL E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 429 through 443 Processing helix chain 'E' and resid 449 through 454 Processing helix chain 'E' and resid 458 through 470 removed outlier: 3.888A pdb=" N VAL E 462 " --> pdb=" O ARG E 458 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'F' and resid 124 through 128 removed outlier: 3.724A pdb=" N LEU F 128 " --> pdb=" O PHE F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 146 Processing helix chain 'F' and resid 163 through 176 Processing helix chain 'F' and resid 191 through 205 Processing helix chain 'F' and resid 206 through 212 removed outlier: 3.998A pdb=" N LYS F 210 " --> pdb=" O GLY F 206 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 226 Processing helix chain 'F' and resid 227 through 244 removed outlier: 3.638A pdb=" N PHE F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 266 removed outlier: 3.988A pdb=" N THR F 258 " --> pdb=" O ILE F 254 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA F 266 " --> pdb=" O SER F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 277 Processing helix chain 'F' and resid 280 through 290 removed outlier: 3.511A pdb=" N LEU F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 322 Processing helix chain 'F' and resid 323 through 325 No H-bonds generated for 'chain 'F' and resid 323 through 325' Processing helix chain 'F' and resid 332 through 339 Processing helix chain 'F' and resid 350 through 355 removed outlier: 3.673A pdb=" N LEU F 354 " --> pdb=" O THR F 350 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA F 355 " --> pdb=" O SER F 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 350 through 355' Processing helix chain 'F' and resid 361 through 388 removed outlier: 3.754A pdb=" N GLN F 365 " --> pdb=" O GLU F 361 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL F 366 " --> pdb=" O GLU F 362 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASP F 382 " --> pdb=" O LYS F 378 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ILE F 383 " --> pdb=" O GLU F 379 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE F 386 " --> pdb=" O ASP F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 392 removed outlier: 3.837A pdb=" N LEU F 392 " --> pdb=" O MET F 389 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 389 through 392' Processing helix chain 'F' and resid 393 through 410 removed outlier: 3.626A pdb=" N LEU F 398 " --> pdb=" O ASP F 394 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL F 399 " --> pdb=" O GLU F 395 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL F 400 " --> pdb=" O ASP F 396 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 420 removed outlier: 3.913A pdb=" N GLN F 419 " --> pdb=" O VAL F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 443 Processing helix chain 'F' and resid 449 through 454 Processing helix chain 'F' and resid 458 through 470 removed outlier: 3.816A pdb=" N VAL F 462 " --> pdb=" O ARG F 458 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL F 463 " --> pdb=" O ILE F 459 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 45 removed outlier: 3.630A pdb=" N PHE G 45 " --> pdb=" O ASN G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 61 Processing helix chain 'G' and resid 68 through 72 Processing helix chain 'G' and resid 93 through 109 removed outlier: 4.097A pdb=" N VAL G 98 " --> pdb=" O TYR G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 114 No H-bonds generated for 'chain 'G' and resid 112 through 114' Processing helix chain 'G' and resid 122 through 131 Processing helix chain 'G' and resid 152 through 165 Processing helix chain 'G' and resid 211 through 287 removed outlier: 3.719A pdb=" N VAL G 218 " --> pdb=" O GLU G 214 " (cutoff:3.500A) Proline residue: G 221 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 35 removed outlier: 6.617A pdb=" N ARG A 40 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N VAL A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU A 51 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N LEU A 52 " --> pdb=" O THR A 91 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 99 removed outlier: 4.088A pdb=" N GLU A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 224 through 226 removed outlier: 6.619A pdb=" N VAL A 256 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N LEU A 316 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL A 258 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N PHE A 318 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N TYR A 260 " --> pdb=" O PHE A 318 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N GLU A 320 " --> pdb=" O TYR A 260 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 60 through 66 removed outlier: 4.054A pdb=" N GLU B 51 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N LEU B 52 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ARG B 40 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N VAL B 34 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLU F 75 " --> pdb=" O GLN F 33 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLN F 33 " --> pdb=" O GLU F 75 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N HIS F 53 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N THR F 58 " --> pdb=" O HIS F 53 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL F 13 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL F 9 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ASP F 15 " --> pdb=" O ILE F 7 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 96 through 99 removed outlier: 3.994A pdb=" N GLU B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 108 through 109 Processing sheet with id=AA7, first strand: chain 'B' and resid 224 through 226 removed outlier: 7.614A pdb=" N VAL B 224 " --> pdb=" O SER B 193 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N TYR B 195 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ALA B 226 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ALA B 197 " --> pdb=" O ALA B 226 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 28 through 35 removed outlier: 6.270A pdb=" N ARG C 40 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU C 51 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N LEU C 52 " --> pdb=" O THR C 91 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 96 through 99 removed outlier: 4.113A pdb=" N GLU C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 224 through 226 removed outlier: 6.517A pdb=" N ILE C 192 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N VAL C 259 " --> pdb=" O ILE C 192 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE C 194 " --> pdb=" O VAL C 259 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N ALA C 261 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N VAL C 196 " --> pdb=" O ALA C 261 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 224 through 226 removed outlier: 6.517A pdb=" N ILE C 192 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N VAL C 259 " --> pdb=" O ILE C 192 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE C 194 " --> pdb=" O VAL C 259 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N ALA C 261 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N VAL C 196 " --> pdb=" O ALA C 261 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU C 166 " --> pdb=" O ILE C 342 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 3 through 10 removed outlier: 6.517A pdb=" N ASP D 15 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VAL D 9 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N VAL D 13 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N THR D 58 " --> pdb=" O HIS D 53 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N HIS D 53 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLN D 33 " --> pdb=" O GLU D 75 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLU D 75 " --> pdb=" O GLN D 33 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 84 through 86 Processing sheet with id=AB5, first strand: chain 'D' and resid 95 through 96 removed outlier: 6.773A pdb=" N ILE D 182 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N PHE D 250 " --> pdb=" O ILE D 182 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL D 184 " --> pdb=" O PHE D 250 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ASP D 252 " --> pdb=" O VAL D 184 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ALA D 186 " --> pdb=" O ASP D 252 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL D 247 " --> pdb=" O THR D 301 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ILE D 303 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU D 249 " --> pdb=" O ILE D 303 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ALA D 305 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ILE D 251 " --> pdb=" O ALA D 305 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N TYR D 307 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE D 154 " --> pdb=" O GLN D 304 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ILE D 306 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N LEU D 156 " --> pdb=" O ILE D 306 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LYS D 153 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N THR D 329 " --> pdb=" O LYS D 153 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLY D 155 " --> pdb=" O THR D 329 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 134 through 135 removed outlier: 4.162A pdb=" N TYR D 148 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 3 through 10 removed outlier: 6.540A pdb=" N ASP E 15 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N VAL E 9 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL E 13 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N THR E 58 " --> pdb=" O HIS E 53 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N HIS E 53 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N GLN E 33 " --> pdb=" O GLU E 75 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N GLU E 75 " --> pdb=" O GLN E 33 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 84 through 86 Processing sheet with id=AB9, first strand: chain 'E' and resid 134 through 135 removed outlier: 4.178A pdb=" N TYR E 148 " --> pdb=" O LEU E 135 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 214 through 217 removed outlier: 8.067A pdb=" N VAL E 214 " --> pdb=" O SER E 183 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N PHE E 185 " --> pdb=" O VAL E 214 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N GLY E 216 " --> pdb=" O PHE E 185 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLY E 187 " --> pdb=" O GLY E 216 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY E 298 " --> pdb=" O THR E 295 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 214 through 217 removed outlier: 8.067A pdb=" N VAL E 214 " --> pdb=" O SER E 183 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N PHE E 185 " --> pdb=" O VAL E 214 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N GLY E 216 " --> pdb=" O PHE E 185 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLY E 187 " --> pdb=" O GLY E 216 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 84 through 86 Processing sheet with id=AC4, first strand: chain 'F' and resid 95 through 96 removed outlier: 6.724A pdb=" N PHE F 96 " --> pdb=" O PHE F 215 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N VAL F 214 " --> pdb=" O SER F 183 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N PHE F 185 " --> pdb=" O VAL F 214 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N GLY F 216 " --> pdb=" O PHE F 185 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N GLY F 187 " --> pdb=" O GLY F 216 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL F 184 " --> pdb=" O PHE F 250 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL F 247 " --> pdb=" O THR F 301 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ILE F 303 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU F 249 " --> pdb=" O ILE F 303 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N ALA F 305 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE F 251 " --> pdb=" O ALA F 305 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N TYR F 307 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ILE F 154 " --> pdb=" O GLN F 304 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ILE F 306 " --> pdb=" O ILE F 154 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N LEU F 156 " --> pdb=" O ILE F 306 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LYS F 153 " --> pdb=" O ALA F 327 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N THR F 329 " --> pdb=" O LYS F 153 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLY F 155 " --> pdb=" O THR F 329 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N LEU F 331 " --> pdb=" O GLY F 155 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N PHE F 157 " --> pdb=" O LEU F 331 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ASN F 330 " --> pdb=" O ASP F 345 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 134 through 135 removed outlier: 4.341A pdb=" N TYR F 148 " --> pdb=" O LEU F 135 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 136 through 140 removed outlier: 7.378A pdb=" N ILE G 137 " --> pdb=" O TYR G 116 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ILE G 118 " --> pdb=" O ILE G 137 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N ASP G 139 " --> pdb=" O ILE G 118 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL G 120 " --> pdb=" O ASP G 139 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N THR G 79 " --> pdb=" O ALA G 117 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ILE G 119 " --> pdb=" O THR G 79 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N TYR G 81 " --> pdb=" O ILE G 119 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ILE G 121 " --> pdb=" O TYR G 81 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL G 83 " --> pdb=" O ILE G 121 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLY G 80 " --> pdb=" O TYR G 172 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N TYR G 174 " --> pdb=" O GLY G 80 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU G 82 " --> pdb=" O TYR G 174 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N ASN G 176 " --> pdb=" O LEU G 82 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N ILE G 84 " --> pdb=" O ASN G 176 " (cutoff:3.500A) removed outlier: 10.882A pdb=" N TYR G 178 " --> pdb=" O ILE G 84 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU G 171 " --> pdb=" O LEU G 191 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 13 through 18 removed outlier: 4.961A pdb=" N THR H 10 " --> pdb=" O PRO H 14 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N HIS H 5 " --> pdb=" O VAL H 75 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ILE H 77 " --> pdb=" O HIS H 5 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N SER H 7 " --> pdb=" O ILE H 77 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 31 through 33 removed outlier: 3.509A pdb=" N LYS H 53 " --> pdb=" O MET H 22 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LYS H 26 " --> pdb=" O ALA H 49 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ALA H 49 " --> pdb=" O LYS H 26 " (cutoff:3.500A) 1219 hydrogen bonds defined for protein. 3396 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.64 Time building geometry restraints manager: 7.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 4274 1.29 - 1.43: 5837 1.43 - 1.56: 14832 1.56 - 1.69: 23 1.69 - 1.83: 158 Bond restraints: 25124 Sorted by residual: bond pdb=" C GLY D 189 " pdb=" N GLU D 190 " ideal model delta sigma weight residual 1.332 1.156 0.176 1.02e-02 9.61e+03 2.98e+02 bond pdb=" C4 ADP E 501 " pdb=" C5 ADP E 501 " ideal model delta sigma weight residual 1.490 1.349 0.141 2.00e-02 2.50e+03 4.96e+01 bond pdb=" C GLU D 190 " pdb=" N ARG D 191 " ideal model delta sigma weight residual 1.330 1.407 -0.077 1.39e-02 5.18e+03 3.08e+01 bond pdb=" C5 ADP E 501 " pdb=" C6 ADP E 501 " ideal model delta sigma weight residual 1.490 1.385 0.105 2.00e-02 2.50e+03 2.75e+01 bond pdb=" CA ILE A 222 " pdb=" C ILE A 222 " ideal model delta sigma weight residual 1.523 1.587 -0.064 1.27e-02 6.20e+03 2.53e+01 ... (remaining 25119 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.74: 33273 3.74 - 7.48: 683 7.48 - 11.21: 71 11.21 - 14.95: 12 14.95 - 18.69: 9 Bond angle restraints: 34048 Sorted by residual: angle pdb=" CA GLU D 190 " pdb=" C GLU D 190 " pdb=" N ARG D 191 " ideal model delta sigma weight residual 116.93 132.73 -15.80 9.00e-01 1.23e+00 3.08e+02 angle pdb=" O GLU D 190 " pdb=" C GLU D 190 " pdb=" N ARG D 191 " ideal model delta sigma weight residual 123.13 106.26 16.87 1.07e+00 8.73e-01 2.49e+02 angle pdb=" O GLY D 189 " pdb=" C GLY D 189 " pdb=" N GLU D 190 " ideal model delta sigma weight residual 122.41 109.91 12.50 9.80e-01 1.04e+00 1.63e+02 angle pdb=" C LEU G 143 " pdb=" N PRO G 144 " pdb=" CA PRO G 144 " ideal model delta sigma weight residual 119.84 132.11 -12.27 1.25e+00 6.40e-01 9.63e+01 angle pdb=" C GLU D 190 " pdb=" N ARG D 191 " pdb=" CA ARG D 191 " ideal model delta sigma weight residual 122.72 134.75 -12.03 1.38e+00 5.25e-01 7.59e+01 ... (remaining 34043 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.04: 14632 32.04 - 64.08: 612 64.08 - 96.13: 54 96.13 - 128.17: 1 128.17 - 160.21: 2 Dihedral angle restraints: 15301 sinusoidal: 6163 harmonic: 9138 Sorted by residual: dihedral pdb=" C ASN E 253 " pdb=" N ASN E 253 " pdb=" CA ASN E 253 " pdb=" CB ASN E 253 " ideal model delta harmonic sigma weight residual -122.60 -144.97 22.37 0 2.50e+00 1.60e-01 8.01e+01 dihedral pdb=" N ASN E 253 " pdb=" C ASN E 253 " pdb=" CA ASN E 253 " pdb=" CB ASN E 253 " ideal model delta harmonic sigma weight residual 122.80 140.61 -17.81 0 2.50e+00 1.60e-01 5.08e+01 dihedral pdb=" C HIS A 215 " pdb=" N HIS A 215 " pdb=" CA HIS A 215 " pdb=" CB HIS A 215 " ideal model delta harmonic sigma weight residual -122.60 -140.06 17.46 0 2.50e+00 1.60e-01 4.88e+01 ... (remaining 15298 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.164: 3808 0.164 - 0.329: 98 0.329 - 0.493: 11 0.493 - 0.658: 11 0.658 - 0.822: 4 Chirality restraints: 3932 Sorted by residual: chirality pdb=" CA ASN E 253 " pdb=" N ASN E 253 " pdb=" C ASN E 253 " pdb=" CB ASN E 253 " both_signs ideal model delta sigma weight residual False 2.51 1.69 0.82 2.00e-01 2.50e+01 1.69e+01 chirality pdb=" CA HIS A 215 " pdb=" N HIS A 215 " pdb=" C HIS A 215 " pdb=" CB HIS A 215 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.12e+01 chirality pdb=" CA HIS C 215 " pdb=" N HIS C 215 " pdb=" C HIS C 215 " pdb=" CB HIS C 215 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.10e+01 ... (remaining 3929 not shown) Planarity restraints: 4454 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS F 363 " -0.094 2.00e-02 2.50e+03 6.99e-02 7.33e+01 pdb=" CG HIS F 363 " 0.112 2.00e-02 2.50e+03 pdb=" ND1 HIS F 363 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 HIS F 363 " 0.039 2.00e-02 2.50e+03 pdb=" CE1 HIS F 363 " -0.053 2.00e-02 2.50e+03 pdb=" NE2 HIS F 363 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 363 " -0.084 2.00e-02 2.50e+03 6.32e-02 5.98e+01 pdb=" CG HIS E 363 " 0.105 2.00e-02 2.50e+03 pdb=" ND1 HIS E 363 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 HIS E 363 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 HIS E 363 " -0.051 2.00e-02 2.50e+03 pdb=" NE2 HIS E 363 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 401 " 0.075 2.00e-02 2.50e+03 5.62e-02 4.74e+01 pdb=" CG HIS E 401 " -0.078 2.00e-02 2.50e+03 pdb=" ND1 HIS E 401 " -0.045 2.00e-02 2.50e+03 pdb=" CD2 HIS E 401 " -0.037 2.00e-02 2.50e+03 pdb=" CE1 HIS E 401 " 0.050 2.00e-02 2.50e+03 pdb=" NE2 HIS E 401 " 0.035 2.00e-02 2.50e+03 ... (remaining 4451 not shown) Histogram of nonbonded interaction distances: 0.39 - 1.29: 28 1.29 - 2.20: 71 2.20 - 3.10: 18084 3.10 - 4.00: 63701 4.00 - 4.90: 122036 Warning: very small nonbonded interaction distances. Nonbonded interactions: 203920 Sorted by model distance: nonbonded pdb=" O VAL G 205 " pdb=" C PRO H 40 " model vdw 0.393 3.270 nonbonded pdb=" CB GLU G 207 " pdb=" CD1 LEU H 41 " model vdw 0.482 3.860 nonbonded pdb=" CE LYS G 51 " pdb=" CG LEU H 78 " model vdw 0.539 3.870 nonbonded pdb=" CG2 VAL G 205 " pdb=" C ILE H 39 " model vdw 0.540 3.690 nonbonded pdb=" NZ LYS G 51 " pdb=" CB LEU H 78 " model vdw 0.576 3.520 ... (remaining 203915 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 27 through 499) selection = (chain 'B' and resid 27 through 499) selection = (chain 'C' and resid 27 through 499) } ncs_group { reference = (chain 'D' and resid 2 through 470) selection = (chain 'E' and resid 2 through 470) selection = (chain 'F' and resid 2 through 470) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.340 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: 1.020 Check model and map are aligned: 0.180 Set scattering table: 0.210 Process input model: 59.130 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.130 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:40.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 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 : 0.009 0.176 25125 Z= 0.492 Angle : 1.314 18.691 34048 Z= 0.846 Chirality : 0.078 0.822 3932 Planarity : 0.010 0.165 4454 Dihedral : 16.530 160.209 9453 Min Nonbonded Distance : 0.393 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 1.25 % Allowed : 4.05 % Favored : 94.70 % Rotamer: Outliers : 3.63 % Allowed : 15.86 % Favored : 80.50 % Cbeta Deviations : 0.72 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.66 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.14), residues: 3189 helix: 0.25 (0.14), residues: 1262 sheet: -0.16 (0.22), residues: 543 loop : -0.55 (0.17), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.002 HIS E 363 PHE 0.060 0.005 PHE F 96 TYR 0.072 0.004 TYR C 220 ARG 0.009 0.001 ARG D 404 Details of bonding type rmsd hydrogen bonds : bond 0.15871 ( 1199) hydrogen bonds : angle 6.59222 ( 3396) covalent geometry : bond 0.00863 (25124) covalent geometry : angle 1.31364 (34048) Misc. bond : bond 0.06724 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 326 time to evaluate : 3.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 392 LEU cc_start: 0.8712 (tp) cc_final: 0.8386 (tp) REVERT: H 16 TYR cc_start: 0.7727 (t80) cc_final: 0.7512 (t80) REVERT: H 32 LEU cc_start: 0.7912 (mt) cc_final: 0.7553 (mt) REVERT: H 69 GLU cc_start: 0.8365 (tm-30) cc_final: 0.8147 (tm-30) outliers start: 95 outliers final: 28 residues processed: 402 average time/residue: 1.7060 time to fit residues: 795.8325 Evaluate side-chains 222 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 194 time to evaluate : 4.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 236 LYS Chi-restraints excluded: chain H residue 22 MET Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 34 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 3.9990 chunk 241 optimal weight: 0.9990 chunk 133 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 162 optimal weight: 0.6980 chunk 128 optimal weight: 2.9990 chunk 249 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 151 optimal weight: 7.9990 chunk 185 optimal weight: 0.9980 chunk 288 optimal weight: 10.0000 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 ASN B 185 ASN C 425 HIS E 40 ASN E 253 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.083740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.064754 restraints weight = 50424.555| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.46 r_work: 0.2796 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.188 25125 Z= 0.182 Angle : 0.708 24.550 34048 Z= 0.369 Chirality : 0.048 0.600 3932 Planarity : 0.006 0.135 4454 Dihedral : 8.180 139.412 3582 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.26 % Favored : 96.33 % Rotamer: Outliers : 3.67 % Allowed : 15.90 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 1.32 % Twisted General : 0.16 % 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 (0.15), residues: 3189 helix: 1.30 (0.14), residues: 1245 sheet: 0.10 (0.22), residues: 535 loop : -0.27 (0.17), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.015 0.001 HIS H 38 PHE 0.021 0.001 PHE G 208 TYR 0.035 0.001 TYR G 206 ARG 0.025 0.001 ARG G 203 Details of bonding type rmsd hydrogen bonds : bond 0.05088 ( 1199) hydrogen bonds : angle 5.10143 ( 3396) covalent geometry : bond 0.00437 (25124) covalent geometry : angle 0.70812 (34048) Misc. bond : bond 0.00402 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 212 time to evaluate : 3.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 LEU cc_start: 0.8342 (mp) cc_final: 0.8116 (mt) REVERT: A 402 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8230 (mm) REVERT: A 492 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8398 (mp0) REVERT: B 407 GLN cc_start: 0.8647 (mt0) cc_final: 0.8387 (mt0) REVERT: D 311 ASP cc_start: 0.8986 (m-30) cc_final: 0.8758 (m-30) REVERT: D 397 LYS cc_start: 0.8318 (tptt) cc_final: 0.8055 (tptt) REVERT: E 337 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8273 (mp0) REVERT: G 115 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8210 (mt-10) REVERT: G 213 GLU cc_start: 0.7500 (mt-10) cc_final: 0.7137 (mm-30) REVERT: G 276 GLU cc_start: 0.8624 (tt0) cc_final: 0.8343 (tp30) REVERT: H 1 MET cc_start: 0.6493 (pp-130) cc_final: 0.5583 (tmt) REVERT: H 24 SER cc_start: 0.7818 (m) cc_final: 0.7587 (t) REVERT: H 32 LEU cc_start: 0.6727 (mt) cc_final: 0.6526 (mt) REVERT: H 78 LEU cc_start: 0.7660 (mt) cc_final: 0.7428 (mm) outliers start: 96 outliers final: 30 residues processed: 290 average time/residue: 1.8969 time to fit residues: 636.7992 Evaluate side-chains 209 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 177 time to evaluate : 2.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain E residue 386 ILE Chi-restraints excluded: chain E residue 464 GLU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 215 CYS Chi-restraints excluded: chain G residue 236 LYS Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 28 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 206 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 305 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 chunk 306 optimal weight: 0.8980 chunk 279 optimal weight: 5.9990 chunk 136 optimal weight: 0.9980 chunk 172 optimal weight: 0.2980 chunk 13 optimal weight: 9.9990 chunk 51 optimal weight: 0.0870 chunk 316 optimal weight: 5.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN D 8 GLN E 253 ASN H 5 HIS H 59 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.083703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.064899 restraints weight = 50273.918| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.45 r_work: 0.2804 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 25125 Z= 0.122 Angle : 0.586 17.797 34048 Z= 0.304 Chirality : 0.045 0.216 3932 Planarity : 0.005 0.078 4454 Dihedral : 7.351 132.327 3555 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.48 % Favored : 96.24 % Rotamer: Outliers : 3.36 % Allowed : 16.82 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 1.32 % Twisted General : 0.13 % 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: 0.96 (0.15), residues: 3189 helix: 1.77 (0.15), residues: 1253 sheet: 0.20 (0.22), residues: 540 loop : -0.14 (0.17), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS E 401 PHE 0.015 0.001 PHE G 208 TYR 0.021 0.001 TYR H 16 ARG 0.005 0.000 ARG E 405 Details of bonding type rmsd hydrogen bonds : bond 0.04191 ( 1199) hydrogen bonds : angle 4.71240 ( 3396) covalent geometry : bond 0.00262 (25124) covalent geometry : angle 0.58599 (34048) Misc. bond : bond 0.00247 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 189 time to evaluate : 3.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8321 (mm) REVERT: B 385 ASP cc_start: 0.8032 (m-30) cc_final: 0.7804 (m-30) REVERT: C 397 GLN cc_start: 0.8419 (mm-40) cc_final: 0.8201 (mp10) REVERT: D 397 LYS cc_start: 0.8325 (tptt) cc_final: 0.8074 (tptt) REVERT: E 64 MET cc_start: 0.9333 (mmp) cc_final: 0.9103 (mmt) REVERT: E 253 ASN cc_start: 0.7811 (OUTLIER) cc_final: 0.7546 (m110) REVERT: E 337 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8309 (mp0) REVERT: G 77 LYS cc_start: 0.8746 (mptt) cc_final: 0.8522 (mmtm) REVERT: G 108 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8141 (tmmt) REVERT: G 115 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8271 (mt-10) REVERT: G 143 LEU cc_start: 0.8139 (mt) cc_final: 0.7880 (pp) REVERT: G 206 TYR cc_start: 0.7111 (m-10) cc_final: 0.5493 (t80) REVERT: H 16 TYR cc_start: 0.7593 (t80) cc_final: 0.7347 (t80) outliers start: 88 outliers final: 37 residues processed: 260 average time/residue: 1.5060 time to fit residues: 450.3848 Evaluate side-chains 202 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 162 time to evaluate : 2.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 253 ASN Chi-restraints excluded: chain E residue 386 ILE Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 464 GLU Chi-restraints excluded: chain F residue 43 ASP Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 396 ASP Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 108 LYS Chi-restraints excluded: chain G residue 215 CYS Chi-restraints excluded: chain G residue 217 ASP Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 41 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 5 optimal weight: 4.9990 chunk 92 optimal weight: 9.9990 chunk 182 optimal weight: 6.9990 chunk 251 optimal weight: 5.9990 chunk 154 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 133 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 chunk 81 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 ASN B 425 HIS D 8 GLN F 38 ASN F 40 ASN G 177 HIS ** H 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.073246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.054403 restraints weight = 51708.253| |-----------------------------------------------------------------------------| r_work (start): 0.2700 rms_B_bonded: 2.46 r_work: 0.2573 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2444 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9134 moved from start: 0.5284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.113 25125 Z= 0.407 Angle : 0.804 13.771 34048 Z= 0.421 Chirality : 0.055 0.251 3932 Planarity : 0.006 0.085 4454 Dihedral : 7.927 145.046 3547 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.83 % Favored : 95.95 % Rotamer: Outliers : 3.59 % Allowed : 16.67 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 1.32 % Twisted General : 0.13 % 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: 0.38 (0.15), residues: 3189 helix: 1.22 (0.14), residues: 1252 sheet: 0.09 (0.22), residues: 523 loop : -0.49 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.002 HIS F 363 PHE 0.027 0.002 PHE F 257 TYR 0.017 0.002 TYR A 251 ARG 0.007 0.001 ARG G 142 Details of bonding type rmsd hydrogen bonds : bond 0.07413 ( 1199) hydrogen bonds : angle 5.27239 ( 3396) covalent geometry : bond 0.01002 (25124) covalent geometry : angle 0.80414 (34048) Misc. bond : bond 0.00121 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 156 time to evaluate : 3.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 402 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8222 (mm) REVERT: A 492 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.7768 (mp0) REVERT: B 385 ASP cc_start: 0.8110 (m-30) cc_final: 0.7805 (m-30) REVERT: E 5 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.8187 (mtp85) REVERT: E 384 ILE cc_start: 0.8421 (OUTLIER) cc_final: 0.7893 (mm) REVERT: E 467 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8640 (tmtm) REVERT: F 1 MET cc_start: 0.7570 (OUTLIER) cc_final: 0.7291 (mtp) REVERT: G 77 LYS cc_start: 0.8735 (mptt) cc_final: 0.8510 (mmtm) REVERT: G 206 TYR cc_start: 0.7096 (m-10) cc_final: 0.5366 (t80) REVERT: H 21 GLU cc_start: 0.7652 (mm-30) cc_final: 0.6135 (tp30) outliers start: 94 outliers final: 36 residues processed: 235 average time/residue: 1.5117 time to fit residues: 408.6105 Evaluate side-chains 188 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 146 time to evaluate : 2.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 110 PRO Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain E residue 5 ARG Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain E residue 386 ILE Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 467 LYS Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain G residue 108 LYS Chi-restraints excluded: chain G residue 215 CYS Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain H residue 41 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 299 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 270 optimal weight: 4.9990 chunk 303 optimal weight: 0.9990 chunk 104 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 242 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 307 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 185 ASN C 322 GLN D 22 HIS D 243 GLN ** D 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 ASN G 40 GLN G 212 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.077116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.058212 restraints weight = 51114.503| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 2.48 r_work: 0.2658 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2528 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9066 moved from start: 0.5395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 25125 Z= 0.144 Angle : 0.592 8.956 34048 Z= 0.308 Chirality : 0.045 0.176 3932 Planarity : 0.005 0.082 4454 Dihedral : 7.208 144.555 3547 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.01 % Favored : 96.80 % Rotamer: Outliers : 2.79 % Allowed : 18.16 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 1.32 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.15), residues: 3189 helix: 1.69 (0.15), residues: 1248 sheet: 0.12 (0.22), residues: 552 loop : -0.32 (0.17), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS E 401 PHE 0.017 0.001 PHE D 257 TYR 0.011 0.001 TYR F 238 ARG 0.004 0.000 ARG E 405 Details of bonding type rmsd hydrogen bonds : bond 0.04896 ( 1199) hydrogen bonds : angle 4.82867 ( 3396) covalent geometry : bond 0.00337 (25124) covalent geometry : angle 0.59152 (34048) Misc. bond : bond 0.00088 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 158 time to evaluate : 3.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8194 (mm) REVERT: A 492 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.7680 (mp0) REVERT: B 385 ASP cc_start: 0.8158 (m-30) cc_final: 0.7896 (m-30) REVERT: C 397 GLN cc_start: 0.8557 (mm-40) cc_final: 0.8351 (mp10) REVERT: D 387 LEU cc_start: 0.6513 (OUTLIER) cc_final: 0.6281 (mt) REVERT: E 464 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8268 (mm-30) REVERT: E 467 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8600 (tmtm) REVERT: F 213 MET cc_start: 0.7535 (OUTLIER) cc_final: 0.7306 (mpp) REVERT: F 235 MET cc_start: 0.9219 (OUTLIER) cc_final: 0.8911 (mtt) REVERT: G 206 TYR cc_start: 0.6992 (m-10) cc_final: 0.5239 (t80) REVERT: G 213 GLU cc_start: 0.6681 (mm-30) cc_final: 0.5719 (tp30) REVERT: H 1 MET cc_start: 0.7140 (tmm) cc_final: 0.6781 (tmm) REVERT: H 21 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7450 (tp30) outliers start: 73 outliers final: 27 residues processed: 215 average time/residue: 1.4683 time to fit residues: 364.5754 Evaluate side-chains 181 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 146 time to evaluate : 2.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 386 ILE Chi-restraints excluded: chain E residue 464 GLU Chi-restraints excluded: chain E residue 467 LYS Chi-restraints excluded: chain F residue 213 MET Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 235 MET Chi-restraints excluded: chain F residue 242 GLU Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 108 LYS Chi-restraints excluded: chain G residue 173 MET Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 21 GLU Chi-restraints excluded: chain H residue 28 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 51 optimal weight: 0.9990 chunk 61 optimal weight: 8.9990 chunk 58 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 chunk 310 optimal weight: 20.0000 chunk 174 optimal weight: 4.9990 chunk 94 optimal weight: 7.9990 chunk 296 optimal weight: 0.0470 chunk 11 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 overall best weight: 1.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 212 GLN ** H 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.076405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.057481 restraints weight = 51047.918| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 2.43 r_work: 0.2640 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2512 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9043 moved from start: 0.5485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 25125 Z= 0.155 Angle : 0.597 10.859 34048 Z= 0.308 Chirality : 0.046 0.395 3932 Planarity : 0.005 0.089 4454 Dihedral : 7.125 149.820 3547 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.26 % Favored : 96.55 % Rotamer: Outliers : 2.68 % Allowed : 18.46 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 1.32 % Twisted General : 0.07 % 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: 0.91 (0.15), residues: 3189 helix: 1.80 (0.15), residues: 1249 sheet: 0.30 (0.22), residues: 534 loop : -0.32 (0.17), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS E 401 PHE 0.017 0.001 PHE D 257 TYR 0.010 0.001 TYR A 248 ARG 0.010 0.000 ARG H 84 Details of bonding type rmsd hydrogen bonds : bond 0.05024 ( 1199) hydrogen bonds : angle 4.75770 ( 3396) covalent geometry : bond 0.00368 (25124) covalent geometry : angle 0.59680 (34048) Misc. bond : bond 0.00125 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 153 time to evaluate : 2.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8247 (mm) REVERT: A 492 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.7650 (mp0) REVERT: B 95 MET cc_start: 0.9213 (mmm) cc_final: 0.9005 (ttp) REVERT: B 385 ASP cc_start: 0.8101 (m-30) cc_final: 0.7824 (m-30) REVERT: C 397 GLN cc_start: 0.8572 (mm-40) cc_final: 0.8310 (mp10) REVERT: D 464 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8458 (mt-10) REVERT: E 464 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8240 (mm-30) REVERT: E 467 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8618 (tmtm) REVERT: F 213 MET cc_start: 0.7484 (OUTLIER) cc_final: 0.7252 (mpp) REVERT: F 235 MET cc_start: 0.9235 (OUTLIER) cc_final: 0.8943 (mtt) REVERT: G 206 TYR cc_start: 0.6900 (m-10) cc_final: 0.5050 (t80) REVERT: G 213 GLU cc_start: 0.6699 (mm-30) cc_final: 0.6224 (mm-30) REVERT: H 1 MET cc_start: 0.7237 (tmm) cc_final: 0.6904 (tmm) REVERT: H 21 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7203 (tp30) outliers start: 70 outliers final: 31 residues processed: 205 average time/residue: 1.4087 time to fit residues: 332.7410 Evaluate side-chains 184 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 145 time to evaluate : 2.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 386 ILE Chi-restraints excluded: chain E residue 464 GLU Chi-restraints excluded: chain E residue 467 LYS Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 213 MET Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 235 MET Chi-restraints excluded: chain F residue 242 GLU Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 108 LYS Chi-restraints excluded: chain G residue 215 CYS Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 21 GLU Chi-restraints excluded: chain H residue 28 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 239 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 chunk 127 optimal weight: 7.9990 chunk 202 optimal weight: 4.9990 chunk 238 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 296 optimal weight: 0.5980 chunk 188 optimal weight: 6.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 253 ASN G 146 GLN G 212 GLN ** H 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.076153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.057184 restraints weight = 51128.756| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 2.49 r_work: 0.2635 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2505 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9079 moved from start: 0.5566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25125 Z= 0.168 Angle : 0.601 9.801 34048 Z= 0.310 Chirality : 0.046 0.318 3932 Planarity : 0.005 0.091 4454 Dihedral : 7.113 156.852 3546 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.14 % Favored : 96.71 % Rotamer: Outliers : 2.29 % Allowed : 18.85 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 1.32 % Twisted General : 0.03 % 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: 0.91 (0.15), residues: 3189 helix: 1.80 (0.15), residues: 1250 sheet: 0.27 (0.22), residues: 554 loop : -0.31 (0.17), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS E 401 PHE 0.018 0.001 PHE D 257 TYR 0.012 0.001 TYR A 248 ARG 0.009 0.000 ARG H 84 Details of bonding type rmsd hydrogen bonds : bond 0.05158 ( 1199) hydrogen bonds : angle 4.73723 ( 3396) covalent geometry : bond 0.00403 (25124) covalent geometry : angle 0.60098 (34048) Misc. bond : bond 0.00119 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 148 time to evaluate : 3.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8344 (mm) REVERT: A 492 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.7700 (mp0) REVERT: B 385 ASP cc_start: 0.8154 (m-30) cc_final: 0.7864 (m-30) REVERT: C 397 GLN cc_start: 0.8635 (mm-40) cc_final: 0.8392 (mp10) REVERT: C 426 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.8534 (mp10) REVERT: D 397 LYS cc_start: 0.8379 (tppt) cc_final: 0.7884 (tptp) REVERT: E 464 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8263 (mm-30) REVERT: F 395 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8758 (mp0) REVERT: G 213 GLU cc_start: 0.6742 (mm-30) cc_final: 0.6246 (mm-30) REVERT: H 1 MET cc_start: 0.7155 (tmm) cc_final: 0.6853 (tmm) REVERT: H 21 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7142 (tp30) outliers start: 60 outliers final: 32 residues processed: 198 average time/residue: 1.5755 time to fit residues: 357.2691 Evaluate side-chains 184 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 146 time to evaluate : 3.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 426 GLN Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 386 ILE Chi-restraints excluded: chain E residue 464 GLU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 395 GLU Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 108 LYS Chi-restraints excluded: chain G residue 145 ASP Chi-restraints excluded: chain G residue 173 MET Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 21 GLU Chi-restraints excluded: chain H residue 28 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 27 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 233 optimal weight: 5.9990 chunk 273 optimal weight: 4.9990 chunk 231 optimal weight: 4.9990 chunk 212 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 165 optimal weight: 7.9990 chunk 205 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 363 HIS E 253 ASN G 212 GLN H 59 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.074104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.055226 restraints weight = 51193.936| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 2.48 r_work: 0.2590 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2461 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9122 moved from start: 0.5656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 25125 Z= 0.245 Angle : 0.659 14.018 34048 Z= 0.341 Chirality : 0.048 0.298 3932 Planarity : 0.005 0.091 4454 Dihedral : 7.453 165.715 3546 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.39 % Favored : 96.49 % Rotamer: Outliers : 2.75 % Allowed : 18.23 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 1.32 % Twisted General : 0.10 % 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: 0.70 (0.15), residues: 3189 helix: 1.61 (0.15), residues: 1252 sheet: 0.12 (0.22), residues: 547 loop : -0.38 (0.17), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS E 401 PHE 0.023 0.002 PHE F 257 TYR 0.014 0.001 TYR A 251 ARG 0.006 0.000 ARG H 84 Details of bonding type rmsd hydrogen bonds : bond 0.06089 ( 1199) hydrogen bonds : angle 4.90609 ( 3396) covalent geometry : bond 0.00601 (25124) covalent geometry : angle 0.65868 (34048) Misc. bond : bond 0.00093 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 150 time to evaluate : 3.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 492 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.7678 (mp0) REVERT: B 188 ASP cc_start: 0.8944 (OUTLIER) cc_final: 0.8722 (p0) REVERT: B 385 ASP cc_start: 0.8172 (m-30) cc_final: 0.7861 (m-30) REVERT: C 397 GLN cc_start: 0.8684 (mm-40) cc_final: 0.8428 (mp10) REVERT: D 397 LYS cc_start: 0.8423 (tppt) cc_final: 0.7972 (tptp) REVERT: E 37 ARG cc_start: 0.8992 (mtp180) cc_final: 0.8769 (mtt180) REVERT: E 386 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.8116 (mt) REVERT: E 464 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8182 (mp0) REVERT: F 395 GLU cc_start: 0.9025 (pm20) cc_final: 0.8802 (mp0) REVERT: H 1 MET cc_start: 0.7113 (tmm) cc_final: 0.6816 (tmm) REVERT: H 21 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.6679 (tp30) REVERT: H 53 LYS cc_start: 0.8089 (mmtt) cc_final: 0.7641 (mmmm) REVERT: H 59 GLN cc_start: 0.6182 (OUTLIER) cc_final: 0.5908 (tp40) REVERT: H 68 LEU cc_start: 0.8689 (tp) cc_final: 0.8403 (tm) outliers start: 72 outliers final: 38 residues processed: 203 average time/residue: 1.5978 time to fit residues: 372.7774 Evaluate side-chains 190 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 146 time to evaluate : 2.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 334 LYS Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 386 ILE Chi-restraints excluded: chain E residue 464 GLU Chi-restraints excluded: chain F residue 43 ASP Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 108 LYS Chi-restraints excluded: chain G residue 145 ASP Chi-restraints excluded: chain G residue 173 MET Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 21 GLU Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain H residue 59 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 309 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 266 optimal weight: 0.0010 chunk 152 optimal weight: 3.9990 chunk 200 optimal weight: 0.0270 chunk 241 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 271 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 overall best weight: 2.0050 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 426 GLN ** E 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 212 GLN H 59 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.075737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.056816 restraints weight = 51038.966| |-----------------------------------------------------------------------------| r_work (start): 0.2753 rms_B_bonded: 2.49 r_work: 0.2627 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2498 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9084 moved from start: 0.5716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25125 Z= 0.164 Angle : 0.615 17.414 34048 Z= 0.316 Chirality : 0.045 0.252 3932 Planarity : 0.005 0.091 4454 Dihedral : 7.232 161.923 3546 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.98 % Favored : 96.90 % Rotamer: Outliers : 1.99 % Allowed : 18.88 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 1.32 % Twisted General : 0.07 % 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: 0.86 (0.15), residues: 3189 helix: 1.82 (0.15), residues: 1243 sheet: 0.08 (0.22), residues: 577 loop : -0.31 (0.17), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS E 401 PHE 0.018 0.001 PHE D 257 TYR 0.011 0.001 TYR F 238 ARG 0.006 0.000 ARG H 84 Details of bonding type rmsd hydrogen bonds : bond 0.05127 ( 1199) hydrogen bonds : angle 4.74086 ( 3396) covalent geometry : bond 0.00392 (25124) covalent geometry : angle 0.61531 (34048) Misc. bond : bond 0.00108 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 151 time to evaluate : 2.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 492 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.7777 (mp0) REVERT: B 188 ASP cc_start: 0.8948 (t0) cc_final: 0.8695 (p0) REVERT: B 385 ASP cc_start: 0.8185 (m-30) cc_final: 0.7898 (m-30) REVERT: C 397 GLN cc_start: 0.8662 (mm-40) cc_final: 0.8411 (mp-120) REVERT: E 37 ARG cc_start: 0.8998 (mtp180) cc_final: 0.8782 (mtt180) REVERT: E 464 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8190 (mm-30) REVERT: F 1 MET cc_start: 0.7627 (OUTLIER) cc_final: 0.7269 (mtp) REVERT: F 395 GLU cc_start: 0.8969 (pm20) cc_final: 0.8746 (mp0) REVERT: H 1 MET cc_start: 0.7178 (tmm) cc_final: 0.6921 (tmm) REVERT: H 21 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.6758 (tp30) REVERT: H 53 LYS cc_start: 0.8034 (mmtt) cc_final: 0.7547 (mmmm) REVERT: H 59 GLN cc_start: 0.5896 (OUTLIER) cc_final: 0.5598 (tp40) REVERT: H 68 LEU cc_start: 0.8658 (tp) cc_final: 0.8380 (tm) outliers start: 52 outliers final: 31 residues processed: 193 average time/residue: 1.7262 time to fit residues: 379.4752 Evaluate side-chains 181 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 145 time to evaluate : 2.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 464 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 108 LYS Chi-restraints excluded: chain G residue 145 ASP Chi-restraints excluded: chain G residue 173 MET Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 21 GLU Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain H residue 59 GLN Chi-restraints excluded: chain H residue 71 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 231 optimal weight: 5.9990 chunk 248 optimal weight: 0.9990 chunk 180 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 191 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 84 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 153 optimal weight: 0.9990 chunk 187 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 253 ASN G 212 GLN H 59 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.077277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.058329 restraints weight = 50643.820| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 2.49 r_work: 0.2662 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2533 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9059 moved from start: 0.5777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25125 Z= 0.125 Angle : 0.588 17.364 34048 Z= 0.300 Chirality : 0.044 0.229 3932 Planarity : 0.004 0.091 4454 Dihedral : 7.002 159.089 3546 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.07 % Favored : 96.80 % Rotamer: Outliers : 1.53 % Allowed : 19.50 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 1.32 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.15), residues: 3189 helix: 1.98 (0.15), residues: 1243 sheet: 0.12 (0.22), residues: 579 loop : -0.23 (0.17), residues: 1367 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS E 401 PHE 0.015 0.001 PHE D 257 TYR 0.011 0.001 TYR A 248 ARG 0.004 0.000 ARG E 405 Details of bonding type rmsd hydrogen bonds : bond 0.04520 ( 1199) hydrogen bonds : angle 4.59786 ( 3396) covalent geometry : bond 0.00287 (25124) covalent geometry : angle 0.58815 (34048) Misc. bond : bond 0.00135 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 148 time to evaluate : 4.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 492 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.7774 (mp0) REVERT: B 188 ASP cc_start: 0.8944 (t0) cc_final: 0.8652 (p0) REVERT: B 385 ASP cc_start: 0.8191 (m-30) cc_final: 0.7909 (m-30) REVERT: C 397 GLN cc_start: 0.8628 (mm-40) cc_final: 0.8346 (mp10) REVERT: E 5 ARG cc_start: 0.8739 (ptt180) cc_final: 0.8183 (mtp85) REVERT: E 37 ARG cc_start: 0.9002 (mtp180) cc_final: 0.8687 (mtt180) REVERT: E 464 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8193 (mm-30) REVERT: F 1 MET cc_start: 0.7653 (OUTLIER) cc_final: 0.7298 (mtp) REVERT: F 395 GLU cc_start: 0.8958 (pm20) cc_final: 0.8748 (mp0) REVERT: G 213 GLU cc_start: 0.6788 (mm-30) cc_final: 0.6265 (mm-30) REVERT: H 21 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.6586 (tp30) REVERT: H 59 GLN cc_start: 0.5614 (OUTLIER) cc_final: 0.5276 (tm-30) REVERT: H 68 LEU cc_start: 0.8640 (tp) cc_final: 0.8346 (tm) outliers start: 40 outliers final: 31 residues processed: 182 average time/residue: 1.7110 time to fit residues: 360.1244 Evaluate side-chains 181 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 145 time to evaluate : 2.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 464 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 108 LYS Chi-restraints excluded: chain G residue 145 ASP Chi-restraints excluded: chain G residue 173 MET Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 21 GLU Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain H residue 59 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 192 optimal weight: 0.9990 chunk 293 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 98 optimal weight: 3.9990 chunk 232 optimal weight: 3.9990 chunk 179 optimal weight: 0.7980 chunk 128 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 307 optimal weight: 0.7980 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 GLN C 57 ASN ** E 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 212 GLN H 38 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.078143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.059222 restraints weight = 50409.323| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 2.48 r_work: 0.2682 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2553 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9043 moved from start: 0.5821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25125 Z= 0.114 Angle : 0.578 16.251 34048 Z= 0.294 Chirality : 0.044 0.198 3932 Planarity : 0.004 0.090 4454 Dihedral : 6.841 157.014 3546 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.01 % Favored : 96.86 % Rotamer: Outliers : 1.68 % Allowed : 19.34 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 1.32 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.15), residues: 3189 helix: 2.12 (0.15), residues: 1239 sheet: 0.22 (0.23), residues: 545 loop : -0.22 (0.17), residues: 1405 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.015 0.001 HIS H 38 PHE 0.014 0.001 PHE D 257 TYR 0.011 0.001 TYR A 248 ARG 0.004 0.000 ARG E 405 Details of bonding type rmsd hydrogen bonds : bond 0.04241 ( 1199) hydrogen bonds : angle 4.50693 ( 3396) covalent geometry : bond 0.00258 (25124) covalent geometry : angle 0.57825 (34048) Misc. bond : bond 0.00147 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18241.22 seconds wall clock time: 321 minutes 48.46 seconds (19308.46 seconds total)