Starting phenix.real_space_refine on Fri Sep 19 08:36:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yh8_39284/09_2025/8yh8_39284.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yh8_39284/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8yh8_39284/09_2025/8yh8_39284.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yh8_39284/09_2025/8yh8_39284.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yh8_39284/09_2025/8yh8_39284.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yh8_39284/09_2025/8yh8_39284.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 5.17, per 1000 atoms: 0.21 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: 2.06 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.64 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: 4.05 Time building geometry restraints manager: 2.65 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: 2.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.360 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.030 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:6.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.400 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.009 0.001 ARG D 404 TYR 0.072 0.004 TYR C 220 PHE 0.060 0.005 PHE F 96 HIS 0.013 0.002 HIS E 363 Details of bonding type rmsd covalent geometry : bond 0.00863 (25124) covalent geometry : angle 1.31364 (34048) hydrogen bonds : bond 0.15871 ( 1199) hydrogen bonds : angle 6.59222 ( 3396) 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 : 1.013 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: 0.8368 (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: 0.7554 (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: 0.6311 time to fit residues: 291.1578 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 : 0.607 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.6980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 0.1980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3285 r_free = 0.3285 target = 0.084447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.065463 restraints weight = 50563.728| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 2.46 r_work: 0.2809 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.148 25125 Z= 0.167 Angle : 0.716 30.937 34048 Z= 0.371 Chirality : 0.049 0.537 3932 Planarity : 0.005 0.135 4454 Dihedral : 8.223 141.510 3582 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.39 % Favored : 96.21 % Rotamer: Outliers : 3.52 % Allowed : 16.13 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 1.32 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.15), residues: 3189 helix: 1.27 (0.14), residues: 1246 sheet: 0.13 (0.22), residues: 526 loop : -0.27 (0.17), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 203 TYR 0.022 0.001 TYR G 206 PHE 0.015 0.001 PHE D 257 HIS 0.015 0.001 HIS E 401 Details of bonding type rmsd covalent geometry : bond 0.00385 (25124) covalent geometry : angle 0.71647 (34048) hydrogen bonds : bond 0.05213 ( 1199) hydrogen bonds : angle 5.12635 ( 3396) Misc. bond : bond 0.00307 ( 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 307 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 215 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 LEU cc_start: 0.8340 (mp) cc_final: 0.8122 (mt) REVERT: A 402 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8228 (mm) REVERT: A 492 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8366 (mp0) REVERT: D 311 ASP cc_start: 0.8927 (m-30) cc_final: 0.8671 (m-30) REVERT: D 397 LYS cc_start: 0.8355 (tptt) cc_final: 0.8059 (tptt) REVERT: G 204 THR cc_start: 0.5181 (OUTLIER) cc_final: 0.4967 (p) REVERT: G 213 GLU cc_start: 0.7531 (mt-10) cc_final: 0.7180 (mm-30) REVERT: G 276 GLU cc_start: 0.8577 (tt0) cc_final: 0.8298 (tp30) REVERT: H 1 MET cc_start: 0.6493 (pp-130) cc_final: 0.5580 (tmt) REVERT: H 24 SER cc_start: 0.7813 (m) cc_final: 0.7503 (t) outliers start: 92 outliers final: 27 residues processed: 289 average time/residue: 0.6179 time to fit residues: 205.2898 Evaluate side-chains 211 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 181 time to evaluate : 0.796 ------------------------------------------------------------------------------- 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 97 VAL 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 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 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 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 236 optimal weight: 0.8980 chunk 226 optimal weight: 10.0000 chunk 228 optimal weight: 0.9980 chunk 173 optimal weight: 7.9990 chunk 169 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 204 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 148 optimal weight: 6.9990 chunk 302 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN A 467 ASN B 425 HIS C 185 ASN C 474 HIS E 253 ASN F 38 ASN F 40 ASN G 177 HIS ** H 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.076885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.057774 restraints weight = 51563.648| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 2.52 r_work: 0.2648 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2520 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9039 moved from start: 0.4870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 25125 Z= 0.208 Angle : 0.688 16.662 34048 Z= 0.362 Chirality : 0.049 0.287 3932 Planarity : 0.005 0.072 4454 Dihedral : 7.642 132.245 3552 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.34 % Allowed : 3.70 % Favored : 95.95 % Rotamer: Outliers : 3.90 % Allowed : 16.59 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 2.65 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.15), residues: 3189 helix: 1.48 (0.15), residues: 1234 sheet: -0.04 (0.22), residues: 543 loop : -0.36 (0.17), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 132 TYR 0.027 0.001 TYR G 206 PHE 0.021 0.002 PHE D 257 HIS 0.011 0.001 HIS E 401 Details of bonding type rmsd covalent geometry : bond 0.00494 (25124) covalent geometry : angle 0.68833 (34048) hydrogen bonds : bond 0.05978 ( 1199) hydrogen bonds : angle 5.04692 ( 3396) Misc. bond : bond 0.00326 ( 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 282 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 180 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8240 (mm) REVERT: A 492 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.7749 (mp0) REVERT: B 385 ASP cc_start: 0.8082 (m-30) cc_final: 0.7841 (m-30) REVERT: C 67 GLU cc_start: 0.9184 (mt-10) cc_final: 0.8966 (mt-10) REVERT: D 120 ARG cc_start: 0.8908 (OUTLIER) cc_final: 0.8391 (ttp-170) REVERT: D 397 LYS cc_start: 0.8365 (tptt) cc_final: 0.8076 (tptt) REVERT: E 253 ASN cc_start: 0.8089 (OUTLIER) cc_final: 0.7829 (t0) REVERT: E 384 ILE cc_start: 0.8559 (tt) cc_final: 0.8291 (mm) REVERT: E 467 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8589 (tmtm) REVERT: F 242 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8517 (mm-30) REVERT: G 77 LYS cc_start: 0.8720 (mptt) cc_final: 0.8483 (mmtm) REVERT: G 115 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8198 (mt-10) REVERT: G 206 TYR cc_start: 0.7277 (m-10) cc_final: 0.5498 (t80) REVERT: G 213 GLU cc_start: 0.7448 (mt-10) cc_final: 0.7036 (mm-30) REVERT: H 24 SER cc_start: 0.7706 (m) cc_final: 0.7505 (t) REVERT: H 28 LYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7790 (pptt) REVERT: H 39 ILE cc_start: 0.6982 (OUTLIER) cc_final: 0.6468 (mp) outliers start: 102 outliers final: 31 residues processed: 264 average time/residue: 0.7314 time to fit residues: 220.0677 Evaluate side-chains 195 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 156 time to evaluate : 0.851 ------------------------------------------------------------------------------- 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 320 GLU 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 314 THR 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 C residue 484 GLU Chi-restraints excluded: chain D residue 120 ARG Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 253 ASN Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 386 ILE Chi-restraints excluded: chain E residue 389 MET Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 464 GLU Chi-restraints excluded: chain E residue 467 LYS Chi-restraints excluded: chain F residue 43 ASP Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 242 GLU 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 145 ASP Chi-restraints excluded: chain G residue 215 CYS Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain H residue 39 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 272 optimal weight: 0.6980 chunk 31 optimal weight: 6.9990 chunk 300 optimal weight: 4.9990 chunk 203 optimal weight: 0.9990 chunk 307 optimal weight: 1.9990 chunk 227 optimal weight: 9.9990 chunk 294 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 128 optimal weight: 0.0670 chunk 145 optimal weight: 8.9990 overall best weight: 1.5524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN B 407 GLN F 253 ASN G 40 GLN H 59 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.078288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.059345 restraints weight = 50616.464| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 2.44 r_work: 0.2686 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2558 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9029 moved from start: 0.5081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 25125 Z= 0.142 Angle : 0.586 9.965 34048 Z= 0.306 Chirality : 0.045 0.309 3932 Planarity : 0.005 0.075 4454 Dihedral : 7.245 135.634 3550 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.20 % Favored : 96.61 % Rotamer: Outliers : 3.10 % Allowed : 17.28 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 1.32 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.15), residues: 3189 helix: 1.76 (0.15), residues: 1245 sheet: 0.23 (0.22), residues: 536 loop : -0.33 (0.17), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 142 TYR 0.010 0.001 TYR A 248 PHE 0.016 0.001 PHE D 257 HIS 0.009 0.001 HIS E 401 Details of bonding type rmsd covalent geometry : bond 0.00333 (25124) covalent geometry : angle 0.58649 (34048) hydrogen bonds : bond 0.04859 ( 1199) hydrogen bonds : angle 4.79371 ( 3396) Misc. bond : bond 0.00166 ( 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 242 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 161 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8209 (mm) REVERT: A 492 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7607 (mp0) REVERT: B 385 ASP cc_start: 0.8133 (m-30) cc_final: 0.7799 (m-30) REVERT: E 5 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.8117 (mtp85) REVERT: E 384 ILE cc_start: 0.8590 (tt) cc_final: 0.8127 (mm) REVERT: E 467 LYS cc_start: 0.8835 (ptmm) cc_final: 0.8620 (tmtm) REVERT: F 235 MET cc_start: 0.9094 (OUTLIER) cc_final: 0.8830 (mtt) REVERT: F 242 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8340 (mm-30) REVERT: G 115 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8211 (mt-10) REVERT: G 213 GLU cc_start: 0.7346 (mt-10) cc_final: 0.6617 (tp30) REVERT: H 21 GLU cc_start: 0.7335 (mm-30) cc_final: 0.6789 (tp30) REVERT: H 24 SER cc_start: 0.7722 (m) cc_final: 0.7518 (t) REVERT: H 39 ILE cc_start: 0.6993 (OUTLIER) cc_final: 0.6617 (mt) outliers start: 81 outliers final: 37 residues processed: 226 average time/residue: 0.7648 time to fit residues: 196.3225 Evaluate side-chains 198 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 155 time to evaluate : 0.870 ------------------------------------------------------------------------------- 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 189 GLN 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 53 VAL 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 462 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 386 ILE 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 386 ILE Chi-restraints excluded: chain E residue 464 GLU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 118 ILE 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 G residue 83 VAL Chi-restraints excluded: chain G residue 108 LYS Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain G residue 215 CYS Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain H residue 39 ILE 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 284 optimal weight: 3.9990 chunk 225 optimal weight: 7.9990 chunk 300 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 121 optimal weight: 6.9990 chunk 288 optimal weight: 20.0000 chunk 292 optimal weight: 8.9990 chunk 143 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN C 322 GLN D 22 HIS D 243 GLN D 363 HIS ** E 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.073390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.054525 restraints weight = 51565.046| |-----------------------------------------------------------------------------| r_work (start): 0.2701 rms_B_bonded: 2.48 r_work: 0.2573 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2444 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9132 moved from start: 0.5437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.078 25125 Z= 0.311 Angle : 0.712 9.209 34048 Z= 0.373 Chirality : 0.051 0.246 3932 Planarity : 0.005 0.077 4454 Dihedral : 7.649 156.331 3550 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.36 % Favored : 96.43 % Rotamer: Outliers : 3.75 % Allowed : 16.97 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 1.99 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.15), residues: 3189 helix: 1.37 (0.14), residues: 1256 sheet: 0.12 (0.22), residues: 535 loop : -0.50 (0.17), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 352 TYR 0.015 0.002 TYR A 251 PHE 0.026 0.002 PHE F 257 HIS 0.012 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00763 (25124) covalent geometry : angle 0.71242 (34048) hydrogen bonds : bond 0.06787 ( 1199) hydrogen bonds : angle 5.13238 ( 3396) Misc. bond : bond 0.00055 ( 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 254 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 156 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 402 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8330 (mm) REVERT: A 492 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.7807 (mp0) REVERT: B 385 ASP cc_start: 0.8151 (m-30) cc_final: 0.7839 (m-30) REVERT: D 387 LEU cc_start: 0.7107 (OUTLIER) cc_final: 0.6893 (mt) REVERT: E 5 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.8167 (mtp85) REVERT: E 464 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8152 (mp0) REVERT: E 467 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8687 (tmtm) REVERT: F 1 MET cc_start: 0.7554 (OUTLIER) cc_final: 0.7306 (mtp) REVERT: F 213 MET cc_start: 0.7544 (mpp) cc_final: 0.7321 (mpp) REVERT: F 389 MET cc_start: 0.8970 (OUTLIER) cc_final: 0.8752 (mpp) REVERT: G 213 GLU cc_start: 0.7561 (mt-10) cc_final: 0.6818 (tp30) REVERT: H 1 MET cc_start: 0.7501 (pp-130) cc_final: 0.7068 (tmm) REVERT: H 21 GLU cc_start: 0.7547 (mm-30) cc_final: 0.6138 (tp30) outliers start: 98 outliers final: 41 residues processed: 232 average time/residue: 0.7657 time to fit residues: 203.1194 Evaluate side-chains 196 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 147 time to evaluate : 1.269 ------------------------------------------------------------------------------- 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 256 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 404 LYS 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 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 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 C residue 484 GLU Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 387 LEU 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 328 THR Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 386 ILE Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 464 GLU Chi-restraints excluded: chain E residue 467 LYS 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 F residue 359 VAL Chi-restraints excluded: chain F residue 389 MET Chi-restraints excluded: chain G residue 83 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 28 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 246 optimal weight: 10.0000 chunk 204 optimal weight: 0.9990 chunk 178 optimal weight: 0.7980 chunk 184 optimal weight: 0.9990 chunk 237 optimal weight: 6.9990 chunk 230 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 272 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 G 212 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.077108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.058160 restraints weight = 50766.558| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 2.48 r_work: 0.2656 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2528 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9058 moved from start: 0.5558 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= 0.131 Angle : 0.571 8.264 34048 Z= 0.297 Chirality : 0.045 0.372 3932 Planarity : 0.004 0.084 4454 Dihedral : 7.120 154.486 3550 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.85 % Favored : 96.96 % Rotamer: Outliers : 2.64 % Allowed : 18.27 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 1.32 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.15), residues: 3189 helix: 1.78 (0.15), residues: 1248 sheet: 0.15 (0.22), residues: 558 loop : -0.30 (0.17), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 405 TYR 0.011 0.001 TYR A 248 PHE 0.016 0.001 PHE D 257 HIS 0.018 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00302 (25124) covalent geometry : angle 0.57056 (34048) hydrogen bonds : bond 0.04693 ( 1199) hydrogen bonds : angle 4.73964 ( 3396) Misc. bond : bond 0.00111 ( 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 226 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 157 time to evaluate : 1.133 Fit side-chains revert: symmetry clash REVERT: A 402 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8285 (mm) REVERT: A 492 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.7615 (mp0) REVERT: B 62 MET cc_start: 0.9426 (ttm) cc_final: 0.9209 (ttm) REVERT: B 385 ASP cc_start: 0.8175 (m-30) cc_final: 0.7899 (m-30) REVERT: D 464 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8384 (mt-10) REVERT: E 37 ARG cc_start: 0.8964 (mtp180) cc_final: 0.8740 (mtt180) REVERT: E 464 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8222 (mm-30) REVERT: E 467 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8655 (tmtm) REVERT: F 235 MET cc_start: 0.9109 (OUTLIER) cc_final: 0.8817 (mtt) REVERT: F 389 MET cc_start: 0.8907 (mpp) cc_final: 0.8698 (mpp) REVERT: G 108 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8584 (tmtt) REVERT: G 213 GLU cc_start: 0.7457 (mt-10) cc_final: 0.6583 (tp30) REVERT: H 1 MET cc_start: 0.7555 (pp-130) cc_final: 0.7226 (tmm) REVERT: H 21 GLU cc_start: 0.7669 (mm-30) cc_final: 0.6370 (tp30) REVERT: H 28 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7586 (pptt) REVERT: H 68 LEU cc_start: 0.8647 (tp) cc_final: 0.8375 (tm) outliers start: 69 outliers final: 26 residues processed: 206 average time/residue: 0.7663 time to fit residues: 180.9168 Evaluate side-chains 185 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 151 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU 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 289 ASP 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 97 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 328 THR 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 26 ILE 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 359 VAL Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 108 LYS Chi-restraints excluded: chain H residue 15 VAL 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 206 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 160 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 chunk 105 optimal weight: 0.0970 chunk 61 optimal weight: 6.9990 chunk 156 optimal weight: 4.9990 chunk 295 optimal weight: 4.9990 chunk 188 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 253 ASN ** 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 = 0.3107 r_free = 0.3107 target = 0.074311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.055381 restraints weight = 51222.818| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 2.48 r_work: 0.2593 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2464 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9119 moved from start: 0.5629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 25125 Z= 0.236 Angle : 0.647 10.613 34048 Z= 0.336 Chirality : 0.048 0.358 3932 Planarity : 0.005 0.088 4454 Dihedral : 7.416 164.358 3549 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.20 % Favored : 96.64 % Rotamer: Outliers : 3.13 % Allowed : 17.85 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.15), residues: 3189 helix: 1.64 (0.15), residues: 1252 sheet: -0.00 (0.22), residues: 565 loop : -0.38 (0.17), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 352 TYR 0.013 0.001 TYR A 251 PHE 0.022 0.002 PHE F 257 HIS 0.016 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00579 (25124) covalent geometry : angle 0.64713 (34048) hydrogen bonds : bond 0.05962 ( 1199) hydrogen bonds : angle 4.90055 ( 3396) Misc. bond : bond 0.00091 ( 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 230 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 148 time to evaluate : 1.066 Fit side-chains revert: symmetry clash REVERT: A 402 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8370 (mm) REVERT: A 492 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.7693 (mp0) REVERT: B 62 MET cc_start: 0.9424 (OUTLIER) cc_final: 0.9196 (ttm) REVERT: B 188 ASP cc_start: 0.8991 (OUTLIER) cc_final: 0.8700 (p0) REVERT: B 385 ASP cc_start: 0.8192 (m-30) cc_final: 0.7897 (m-30) REVERT: D 397 LYS cc_start: 0.8404 (tppt) cc_final: 0.7921 (tptp) REVERT: E 5 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.8188 (mtp85) REVERT: E 37 ARG cc_start: 0.8972 (mtp180) cc_final: 0.8746 (mtt180) REVERT: E 464 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8244 (mm-30) REVERT: E 467 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8652 (tmtm) REVERT: F 1 MET cc_start: 0.7620 (OUTLIER) cc_final: 0.7272 (mtp) REVERT: F 213 MET cc_start: 0.7533 (mpp) cc_final: 0.7313 (mpp) REVERT: G 213 GLU cc_start: 0.7515 (mt-10) cc_final: 0.6737 (tp30) REVERT: H 1 MET cc_start: 0.7515 (pp-130) cc_final: 0.7246 (tmm) REVERT: H 21 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.6054 (tp30) REVERT: H 28 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7640 (pptt) REVERT: H 53 LYS cc_start: 0.8047 (mmtt) cc_final: 0.7726 (mmmm) outliers start: 82 outliers final: 35 residues processed: 211 average time/residue: 0.7741 time to fit residues: 186.7477 Evaluate side-chains 191 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 146 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 320 GLU 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 62 MET Chi-restraints excluded: chain B residue 108 VAL 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 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 484 GLU Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain E residue 5 ARG Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 328 THR 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 E residue 467 LYS 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 358 ILE Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 79 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 287 optimal weight: 0.0470 chunk 281 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 273 optimal weight: 0.9980 chunk 29 optimal weight: 7.9990 chunk 279 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 188 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 268 optimal weight: 5.9990 overall best weight: 1.0082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 253 ASN ** 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 = 0.3172 r_free = 0.3172 target = 0.077799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.058839 restraints weight = 50677.777| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 2.48 r_work: 0.2672 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2544 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9047 moved from start: 0.5732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25125 Z= 0.117 Angle : 0.562 9.313 34048 Z= 0.289 Chirality : 0.044 0.276 3932 Planarity : 0.004 0.088 4454 Dihedral : 6.984 156.858 3549 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.76 % Favored : 97.08 % Rotamer: Outliers : 1.83 % Allowed : 19.15 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 1.32 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.15), residues: 3189 helix: 1.99 (0.15), residues: 1240 sheet: 0.11 (0.22), residues: 572 loop : -0.23 (0.17), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 84 TYR 0.011 0.001 TYR A 248 PHE 0.014 0.001 PHE D 257 HIS 0.019 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00263 (25124) covalent geometry : angle 0.56179 (34048) hydrogen bonds : bond 0.04317 ( 1199) hydrogen bonds : angle 4.60655 ( 3396) Misc. bond : bond 0.00119 ( 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 202 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 154 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 492 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.7747 (mp0) REVERT: B 62 MET cc_start: 0.9417 (OUTLIER) cc_final: 0.9189 (ttm) REVERT: B 188 ASP cc_start: 0.8962 (t0) cc_final: 0.8643 (p0) REVERT: B 385 ASP cc_start: 0.8206 (m-30) cc_final: 0.7933 (m-30) REVERT: D 397 LYS cc_start: 0.8471 (tppt) cc_final: 0.8018 (tptp) REVERT: E 5 ARG cc_start: 0.8725 (ptt180) cc_final: 0.8158 (mtp85) REVERT: E 37 ARG cc_start: 0.8984 (mtp180) cc_final: 0.8675 (mtt180) REVERT: E 386 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7993 (mt) REVERT: E 464 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8194 (mm-30) REVERT: E 467 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8621 (tmtm) REVERT: F 213 MET cc_start: 0.7599 (mpp) cc_final: 0.7377 (mpp) REVERT: F 235 MET cc_start: 0.9071 (OUTLIER) cc_final: 0.8801 (mtt) REVERT: G 108 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8620 (tmtt) REVERT: G 213 GLU cc_start: 0.7368 (mt-10) cc_final: 0.6631 (mm-30) REVERT: H 1 MET cc_start: 0.7490 (pp-130) cc_final: 0.7254 (tmm) REVERT: H 21 GLU cc_start: 0.7609 (mm-30) cc_final: 0.6175 (tp30) REVERT: H 53 LYS cc_start: 0.8041 (mmtt) cc_final: 0.7593 (mmmm) outliers start: 48 outliers final: 28 residues processed: 193 average time/residue: 0.7094 time to fit residues: 156.2136 Evaluate side-chains 185 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 150 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 320 GLU 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 62 MET Chi-restraints excluded: chain B residue 108 VAL 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 381 THR Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 484 GLU 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 328 THR 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 235 MET 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 79 THR Chi-restraints excluded: chain G residue 108 LYS Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 212 GLN Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 28 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 286 optimal weight: 6.9990 chunk 310 optimal weight: 9.9990 chunk 214 optimal weight: 2.9990 chunk 315 optimal weight: 7.9990 chunk 170 optimal weight: 0.0570 chunk 146 optimal weight: 0.9990 chunk 240 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 171 optimal weight: 2.9990 chunk 136 optimal weight: 8.9990 chunk 96 optimal weight: 2.9990 overall best weight: 1.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 57 ASN ** E 253 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.076736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.057873 restraints weight = 50742.683| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 2.44 r_work: 0.2654 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2527 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9061 moved from start: 0.5757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25125 Z= 0.143 Angle : 0.586 12.314 34048 Z= 0.299 Chirality : 0.045 0.272 3932 Planarity : 0.004 0.090 4454 Dihedral : 6.984 158.781 3548 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.92 % Favored : 96.96 % Rotamer: Outliers : 1.72 % Allowed : 19.27 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 1.32 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.15), residues: 3189 helix: 1.99 (0.15), residues: 1245 sheet: 0.08 (0.22), residues: 587 loop : -0.21 (0.17), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 405 TYR 0.012 0.001 TYR A 248 PHE 0.017 0.001 PHE D 257 HIS 0.022 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00339 (25124) covalent geometry : angle 0.58641 (34048) hydrogen bonds : bond 0.04739 ( 1199) hydrogen bonds : angle 4.62039 ( 3396) 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 193 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 148 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 492 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.7760 (mp0) REVERT: B 62 MET cc_start: 0.9411 (OUTLIER) cc_final: 0.9184 (ttm) REVERT: B 188 ASP cc_start: 0.8924 (t0) cc_final: 0.8637 (p0) REVERT: B 385 ASP cc_start: 0.8199 (m-30) cc_final: 0.7909 (m-30) REVERT: E 37 ARG cc_start: 0.8981 (mtp180) cc_final: 0.8771 (mtt180) REVERT: E 464 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8208 (mm-30) REVERT: E 467 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8627 (tmtm) REVERT: F 1 MET cc_start: 0.7625 (OUTLIER) cc_final: 0.7283 (mtp) REVERT: G 108 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8602 (tmtt) REVERT: G 212 GLN cc_start: 0.6228 (OUTLIER) cc_final: 0.5915 (tt0) REVERT: G 213 GLU cc_start: 0.7409 (mt-10) cc_final: 0.6843 (mm-30) REVERT: H 1 MET cc_start: 0.7465 (pp-130) cc_final: 0.7227 (tmm) REVERT: H 21 GLU cc_start: 0.7578 (mm-30) cc_final: 0.6121 (tp30) REVERT: H 53 LYS cc_start: 0.8063 (mmtt) cc_final: 0.7610 (mmmm) outliers start: 45 outliers final: 28 residues processed: 184 average time/residue: 0.7238 time to fit residues: 152.7319 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 : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 320 GLU 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 62 MET Chi-restraints excluded: chain B residue 108 VAL 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 381 THR Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 484 GLU 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 328 THR Chi-restraints excluded: chain E residue 464 GLU Chi-restraints excluded: chain E residue 467 LYS Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 26 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 G residue 76 VAL Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 108 LYS Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 212 GLN Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 28 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 272 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 164 optimal weight: 4.9990 chunk 256 optimal weight: 2.9990 chunk 262 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 231 optimal weight: 0.9990 chunk 116 optimal weight: 5.9990 chunk 145 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 57 ASN ** E 253 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.076840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.057883 restraints weight = 50759.141| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 2.48 r_work: 0.2652 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2523 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9066 moved from start: 0.5788 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= 0.140 Angle : 0.591 15.151 34048 Z= 0.300 Chirality : 0.045 0.267 3932 Planarity : 0.004 0.089 4454 Dihedral : 6.924 158.763 3546 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.95 % Favored : 96.93 % Rotamer: Outliers : 1.49 % Allowed : 19.50 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 1.32 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.15), residues: 3189 helix: 2.01 (0.15), residues: 1244 sheet: 0.08 (0.22), residues: 585 loop : -0.21 (0.17), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 405 TYR 0.011 0.001 TYR A 248 PHE 0.016 0.001 PHE D 257 HIS 0.021 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00331 (25124) covalent geometry : angle 0.59100 (34048) hydrogen bonds : bond 0.04675 ( 1199) hydrogen bonds : angle 4.58658 ( 3396) Misc. bond : bond 0.00118 ( 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: 39 poor density : 149 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 492 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.7792 (mp0) REVERT: B 62 MET cc_start: 0.9419 (OUTLIER) cc_final: 0.9193 (ttm) REVERT: B 188 ASP cc_start: 0.8937 (t0) cc_final: 0.8654 (p0) REVERT: B 385 ASP cc_start: 0.8203 (m-30) cc_final: 0.7913 (m-30) REVERT: E 5 ARG cc_start: 0.8749 (ptt180) cc_final: 0.8180 (mtp85) REVERT: E 37 ARG cc_start: 0.8991 (mtp180) cc_final: 0.8777 (mtt180) REVERT: E 464 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8208 (mm-30) REVERT: E 467 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8625 (tmtm) REVERT: F 1 MET cc_start: 0.7635 (OUTLIER) cc_final: 0.7295 (mtp) REVERT: G 108 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8601 (tmtt) REVERT: G 206 TYR cc_start: 0.6367 (m-10) cc_final: 0.5444 (t80) REVERT: G 213 GLU cc_start: 0.7320 (mt-10) cc_final: 0.6971 (mm-30) REVERT: H 1 MET cc_start: 0.7448 (pp-130) cc_final: 0.7223 (tmm) REVERT: H 21 GLU cc_start: 0.7593 (mm-30) cc_final: 0.6143 (tp30) REVERT: H 53 LYS cc_start: 0.8042 (mmtt) cc_final: 0.7583 (mmmm) outliers start: 39 outliers final: 29 residues processed: 181 average time/residue: 0.7960 time to fit residues: 164.5793 Evaluate side-chains 182 residues out of total 2616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 147 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 320 GLU 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 53 VAL Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 108 VAL 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 381 THR Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 484 GLU 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 328 THR Chi-restraints excluded: chain E residue 464 GLU Chi-restraints excluded: chain E residue 467 LYS Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 108 LYS Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 28 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 242 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 chunk 178 optimal weight: 4.9990 chunk 140 optimal weight: 6.9990 chunk 295 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 253 optimal weight: 7.9990 chunk 192 optimal weight: 2.9990 chunk 221 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 201 optimal weight: 0.3980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 57 ASN E 253 ASN 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 = 0.3138 r_free = 0.3138 target = 0.075959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.056972 restraints weight = 50866.280| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 2.49 r_work: 0.2630 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2501 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9083 moved from start: 0.5812 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= 0.163 Angle : 0.609 18.819 34048 Z= 0.310 Chirality : 0.045 0.274 3932 Planarity : 0.005 0.089 4454 Dihedral : 7.041 161.184 3546 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.17 % Favored : 96.71 % Rotamer: Outliers : 1.64 % Allowed : 19.42 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 1.32 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.15), residues: 3189 helix: 1.95 (0.15), residues: 1245 sheet: 0.01 (0.22), residues: 594 loop : -0.25 (0.17), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 405 TYR 0.011 0.001 TYR A 248 PHE 0.018 0.001 PHE D 257 HIS 0.019 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00391 (25124) covalent geometry : angle 0.60948 (34048) hydrogen bonds : bond 0.05036 ( 1199) hydrogen bonds : angle 4.64317 ( 3396) Misc. bond : bond 0.00082 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8301.13 seconds wall clock time: 141 minutes 57.06 seconds (8517.06 seconds total)