Starting phenix.real_space_refine on Mon Sep 30 05:38:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh9_34756/09_2024/8hh9_34756.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh9_34756/09_2024/8hh9_34756.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh9_34756/09_2024/8hh9_34756.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh9_34756/09_2024/8hh9_34756.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh9_34756/09_2024/8hh9_34756.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh9_34756/09_2024/8hh9_34756.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 5 5.21 5 S 77 5.16 5 C 15277 2.51 5 N 4214 2.21 5 O 4661 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 189 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 24250 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 23, 'TRANS': 454} Chain: "B" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 23, 'TRANS': 454} Chain: "C" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 23, 'TRANS': 454} Chain: "D" 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: "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: 2218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2218 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 10, 'TRANS': 272} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 15.67, per 1000 atoms: 0.65 Number of scatterers: 24250 At special positions: 0 Unit cell: (129.36, 122.32, 151.36, 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 77 16.00 P 16 15.00 Mg 5 11.99 O 4661 8.00 N 4214 7.00 C 15277 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.10 Conformation dependent library (CDL) restraints added in 3.1 seconds 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5712 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 18 sheets defined 48.3% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.92 Creating SS restraints... Processing helix chain 'A' and resid 78 through 82 removed outlier: 4.197A pdb=" N GLY A 81 " --> pdb=" O PRO A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 104 removed outlier: 3.555A pdb=" N LEU A 103 " --> pdb=" O GLY A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 139 removed outlier: 4.020A pdb=" N ARG A 139 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 174 through 186 removed outlier: 3.653A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 189 No H-bonds generated for 'chain 'A' and resid 187 through 189' Processing helix chain 'A' and resid 201 through 216 Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 231 through 251 removed outlier: 3.599A pdb=" N LEU A 235 " --> pdb=" O PRO A 231 " (cutoff:3.500A) Proline residue: A 239 - end of helix removed outlier: 3.708A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 277 removed outlier: 3.875A pdb=" N GLN A 266 " --> pdb=" O ASP A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 289 through 299 Processing helix chain 'A' and resid 328 through 338 Processing helix chain 'A' and resid 345 through 352 Processing helix chain 'A' and resid 372 through 393 removed outlier: 3.983A pdb=" N VAL A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLY A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N THR A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 421 removed outlier: 3.529A pdb=" N GLN A 407 " --> pdb=" O ASP A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 442 Processing helix chain 'A' and resid 449 through 468 removed outlier: 4.298A pdb=" N ARG A 454 " --> pdb=" O VAL A 450 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ARG A 455 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS A 458 " --> pdb=" O ARG A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 479 Processing helix chain 'A' and resid 483 through 496 Processing helix chain 'B' and resid 100 through 104 Processing helix chain 'B' and resid 150 through 157 removed outlier: 4.167A pdb=" N LEU B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 186 removed outlier: 3.507A pdb=" N GLN B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 216 Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 231 through 253 removed outlier: 3.721A pdb=" N LEU B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Proline residue: B 239 - end of helix removed outlier: 3.742A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.233A 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 287 through 288 No H-bonds generated for 'chain 'B' and resid 287 through 288' Processing helix chain 'B' and resid 289 through 300 removed outlier: 3.781A pdb=" N HIS B 294 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG B 300 " --> pdb=" O ARG B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 336 Processing helix chain 'B' and resid 345 through 350 Processing helix chain 'B' and resid 372 through 396 removed outlier: 4.038A pdb=" N GLY B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N THR B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU B 382 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU B 384 " --> pdb=" O GLY B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 420 removed outlier: 3.576A pdb=" N GLN B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 442 removed outlier: 3.905A pdb=" N LEU B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 468 removed outlier: 4.571A pdb=" N ARG B 454 " --> pdb=" O VAL B 450 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ARG B 455 " --> pdb=" O GLU B 451 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR B 461 " --> pdb=" O GLU B 457 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU B 462 " --> pdb=" O LYS B 458 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN B 466 " --> pdb=" O LEU B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 479 Processing helix chain 'B' and resid 483 through 498 Processing helix chain 'C' and resid 100 through 104 removed outlier: 3.676A pdb=" N LEU C 103 " --> pdb=" O GLY C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 157 Processing helix chain 'C' and resid 174 through 186 removed outlier: 3.582A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 215 Processing helix chain 'C' and resid 216 through 219 Processing helix chain 'C' and resid 231 through 251 removed outlier: 3.599A pdb=" N LEU C 235 " --> pdb=" O PRO C 231 " (cutoff:3.500A) Proline residue: C 239 - end of helix removed outlier: 3.798A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 277 Processing helix chain 'C' and resid 282 through 286 Processing helix chain 'C' and resid 287 through 288 No H-bonds generated for 'chain 'C' and resid 287 through 288' Processing helix chain 'C' and resid 289 through 299 Processing helix chain 'C' and resid 328 through 336 removed outlier: 3.536A pdb=" N SER C 336 " --> pdb=" O THR C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 352 removed outlier: 3.687A pdb=" N GLY C 352 " --> pdb=" O LEU C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 396 removed outlier: 3.533A pdb=" N LYS C 377 " --> pdb=" O LYS C 373 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL C 378 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY C 380 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N THR C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLU C 391 " --> pdb=" O ALA C 387 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU C 392 " --> pdb=" O ALA C 388 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU C 393 " --> pdb=" O TYR C 389 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ALA C 394 " --> pdb=" O ARG C 390 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE C 395 " --> pdb=" O GLU C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 420 removed outlier: 4.036A pdb=" N LYS C 409 " --> pdb=" O ALA C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 442 removed outlier: 3.658A pdb=" N ILE C 436 " --> pdb=" O LYS C 432 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE C 437 " --> pdb=" O GLN C 433 " (cutoff:3.500A) 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 removed outlier: 3.687A pdb=" N ALA C 490 " --> pdb=" O ASP C 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'D' and resid 124 through 128 removed outlier: 3.525A pdb=" N LEU D 128 " --> pdb=" O PHE D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 145 Processing helix chain 'D' and resid 163 through 179 Processing helix chain 'D' and resid 191 through 206 removed outlier: 3.508A pdb=" N GLY D 195 " --> pdb=" O ARG D 191 " (cutoff:3.500A) 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 243 removed outlier: 3.533A pdb=" N ARG D 225 " --> pdb=" O PRO D 221 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ALA D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N LEU D 230 " --> pdb=" O MET D 226 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET D 235 " --> pdb=" O THR D 231 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 269 removed outlier: 3.823A pdb=" N THR D 258 " --> pdb=" O ILE D 254 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA D 266 " --> pdb=" O SER D 262 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LEU D 267 " --> pdb=" O GLU D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 290 removed outlier: 3.738A pdb=" N LEU D 288 " --> pdb=" O GLU D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 312 Processing helix chain 'D' and resid 315 through 321 removed outlier: 3.964A pdb=" N THR D 321 " --> pdb=" O ALA D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 325 Processing helix chain 'D' and resid 335 through 339 Processing helix chain 'D' and resid 355 through 360 Processing helix chain 'D' and resid 360 through 387 removed outlier: 3.893A pdb=" N TYR D 377 " --> pdb=" O THR D 373 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS D 378 " --> pdb=" O LEU D 374 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU D 379 " --> pdb=" O GLN D 375 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU D 380 " --> pdb=" O ARG D 376 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASP D 382 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 410 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 removed outlier: 3.865A pdb=" N PHE D 453 " --> pdb=" O PRO D 449 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG D 454 " --> pdb=" O GLU D 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 449 through 454' Processing helix chain 'D' and resid 458 through 471 Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'E' and resid 124 through 128 Processing helix chain 'E' and resid 139 through 146 Processing helix chain 'E' and resid 159 through 162 Processing helix chain 'E' and resid 163 through 180 removed outlier: 3.657A pdb=" N LEU E 167 " --> pdb=" O GLY E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 206 Processing helix chain 'E' and resid 207 through 209 No H-bonds generated for 'chain 'E' and resid 207 through 209' Processing helix chain 'E' and resid 221 through 242 removed outlier: 5.274A pdb=" N ALA E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU E 230 " --> pdb=" O MET E 226 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TYR E 238 " --> pdb=" O THR E 234 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N PHE E 239 " --> pdb=" O MET E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 269 removed outlier: 4.090A pdb=" N PHE E 257 " --> pdb=" O ASN E 253 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR E 258 " --> pdb=" O ILE E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 290 Processing helix chain 'E' and resid 308 through 312 removed outlier: 3.682A pdb=" N ASP E 311 " --> pdb=" O VAL E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 323 removed outlier: 3.744A pdb=" N SER E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 338 Processing helix chain 'E' and resid 355 through 360 Processing helix chain 'E' and resid 360 through 387 removed outlier: 3.505A pdb=" N GLU E 379 " --> pdb=" O GLN E 375 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU E 387 " --> pdb=" O ILE E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 410 removed outlier: 3.910A pdb=" N ARG E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 422 Processing helix chain 'E' and resid 429 through 442 Processing helix chain 'E' and resid 449 through 454 removed outlier: 3.624A pdb=" N PHE E 453 " --> pdb=" O GLU E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 459 through 468 removed outlier: 3.747A pdb=" N VAL E 463 " --> pdb=" O ILE E 459 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA E 468 " --> pdb=" O GLU E 464 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'F' and resid 124 through 128 removed outlier: 3.760A pdb=" N GLU F 127 " --> pdb=" O LYS F 124 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU F 128 " --> pdb=" O PHE F 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 124 through 128' Processing helix chain 'F' and resid 139 through 145 Processing helix chain 'F' and resid 163 through 176 Processing helix chain 'F' and resid 177 through 179 No H-bonds generated for 'chain 'F' and resid 177 through 179' Processing helix chain 'F' and resid 191 through 206 Processing helix chain 'F' and resid 207 through 209 No H-bonds generated for 'chain 'F' and resid 207 through 209' Processing helix chain 'F' and resid 221 through 243 removed outlier: 5.316A pdb=" N ALA F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LEU F 230 " --> pdb=" O MET F 226 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR F 238 " --> pdb=" O THR F 234 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN F 243 " --> pdb=" O PHE F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 266 removed outlier: 3.974A pdb=" N THR F 258 " --> pdb=" O ILE F 254 " (cutoff:3.500A) removed outlier: 3.918A 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 Processing helix chain 'F' and resid 309 through 312 Processing helix chain 'F' and resid 315 through 321 removed outlier: 3.748A pdb=" N THR F 321 " --> pdb=" O ALA F 317 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 324 No H-bonds generated for 'chain 'F' and resid 322 through 324' Processing helix chain 'F' and resid 332 through 338 removed outlier: 3.619A pdb=" N MET F 338 " --> pdb=" O LYS F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 360 Processing helix chain 'F' and resid 360 through 388 removed outlier: 4.579A pdb=" N ASP F 382 " --> pdb=" O LYS F 378 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ILE F 383 " --> pdb=" O GLU F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 410 removed outlier: 3.830A pdb=" N ARG F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 420 removed outlier: 3.606A pdb=" N GLN F 419 " --> pdb=" O VAL F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 442 Processing helix chain 'F' and resid 449 through 454 removed outlier: 3.596A pdb=" N ARG F 454 " --> pdb=" O ASP F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 458 through 469 removed outlier: 3.973A pdb=" N VAL F 462 " --> pdb=" O ARG F 458 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL F 463 " --> pdb=" O ILE F 459 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 57 removed outlier: 3.521A pdb=" N ARG G 34 " --> pdb=" O SER G 30 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLN G 37 " --> pdb=" O ASN G 33 " (cutoff:3.500A) Proline residue: G 44 - end of helix removed outlier: 4.155A pdb=" N ASN G 55 " --> pdb=" O GLU G 51 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL G 56 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA G 57 " --> pdb=" O VAL G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 107 removed outlier: 3.619A pdb=" N VAL G 95 " --> pdb=" O TYR G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 111 No H-bonds generated for 'chain 'G' and resid 109 through 111' Processing helix chain 'G' and resid 119 through 129 Processing helix chain 'G' and resid 145 through 162 removed outlier: 3.819A pdb=" N ILE G 149 " --> pdb=" O SER G 145 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU G 151 " --> pdb=" O ALA G 147 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ILE G 152 " --> pdb=" O ASP G 148 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS G 155 " --> pdb=" O GLU G 151 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE G 160 " --> pdb=" O THR G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 189 through 192 Processing helix chain 'G' and resid 208 through 284 Proline residue: G 218 - end of helix removed outlier: 3.714A pdb=" N ALA G 283 " --> pdb=" O ALA G 279 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU G 284 " --> pdb=" O GLY G 280 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 66 removed outlier: 3.928A pdb=" N GLU A 51 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU A 52 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ARG A 40 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N VAL A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ASN A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N LEU A 66 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLY A 72 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N GLU E 75 " --> pdb=" O GLN E 33 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N GLN E 33 " --> pdb=" O GLU E 75 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N HIS E 53 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N THR E 58 " --> pdb=" O HIS E 53 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL E 13 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL E 9 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASP E 15 " --> pdb=" O ILE E 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 99 removed outlier: 3.938A pdb=" N GLU A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 108 removed outlier: 6.551A pdb=" N SER A 193 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL A 224 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N TYR A 195 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ALA A 226 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ALA A 197 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR A 260 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N PHE A 343 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU A 361 " --> pdb=" O PHE A 343 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 60 through 66 removed outlier: 4.241A pdb=" N GLU B 51 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ARG B 93 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N GLU B 54 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N THR B 91 " --> pdb=" O GLU B 54 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ARG B 40 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL B 34 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL B 74 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ALA B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N GLU F 75 " --> pdb=" O GLN F 33 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N GLN F 33 " --> pdb=" O GLU F 75 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N HIS F 53 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N THR F 58 " --> pdb=" O HIS F 53 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN F 8 " --> pdb=" O ASP F 15 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LYS F 17 " --> pdb=" O VAL F 6 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N VAL F 6 " --> pdb=" O LYS F 17 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 96 through 99 removed outlier: 3.517A pdb=" N ARG B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 107 through 108 removed outlier: 6.412A pdb=" N VAL B 108 " --> pdb=" O THR B 225 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE B 192 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N VAL B 259 " --> pdb=" O ILE B 192 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE B 194 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ASP B 261 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N VAL B 196 " --> pdb=" O ASP B 261 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR B 260 " --> pdb=" O LEU B 316 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 60 through 66 removed outlier: 4.259A pdb=" N GLU C 51 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ARG C 93 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N GLU C 54 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N THR C 91 " --> pdb=" O GLU C 54 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ARG C 40 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ASN C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N LEU C 66 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLY C 72 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLU D 75 " --> pdb=" O GLN D 33 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N GLN D 33 " --> pdb=" O GLU D 75 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N HIS D 53 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N THR D 58 " --> pdb=" O HIS D 53 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL D 13 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N VAL D 9 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ASP D 15 " --> pdb=" O ILE D 7 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 96 through 99 removed outlier: 4.053A pdb=" N GLU C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 107 through 108 removed outlier: 6.159A pdb=" N VAL C 108 " --> pdb=" O THR C 225 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N SER C 193 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N VAL C 224 " --> pdb=" O SER C 193 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TYR C 195 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ALA C 226 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA C 197 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR C 260 " --> pdb=" O LEU C 316 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 84 through 86 Processing sheet with id=AB2, first strand: chain 'D' and resid 95 through 96 removed outlier: 6.872A pdb=" N SER D 183 " --> pdb=" O ALA D 212 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N VAL D 214 " --> pdb=" O SER D 183 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N PHE D 185 " --> pdb=" O VAL D 214 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N GLY D 216 " --> pdb=" O PHE D 185 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N GLY D 187 " --> pdb=" O GLY D 216 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL D 184 " --> pdb=" O PHE D 250 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ASP D 252 " --> pdb=" O VAL D 184 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ALA D 186 " --> pdb=" O ASP D 252 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N VAL D 247 " --> pdb=" O THR D 301 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ILE D 303 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU D 249 " --> pdb=" O ILE D 303 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N ALA D 305 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ILE D 251 " --> pdb=" O ALA D 305 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA D 327 " --> pdb=" O LYS D 153 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 84 through 86 Processing sheet with id=AB4, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.398A pdb=" N PHE E 96 " --> pdb=" O PHE E 215 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N GLN E 217 " --> pdb=" O PHE E 96 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY E 298 " --> pdb=" O THR E 295 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.398A pdb=" N PHE E 96 " --> pdb=" O PHE E 215 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N GLN E 217 " --> pdb=" O PHE E 96 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LYS E 153 " --> pdb=" O ASP E 326 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N THR E 328 " --> pdb=" O LYS E 153 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLY E 155 " --> pdb=" O THR E 328 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N ASN E 330 " --> pdb=" O GLY E 155 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N PHE E 157 " --> pdb=" O ASN E 330 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 134 through 135 removed outlier: 4.042A pdb=" N TYR E 148 " --> pdb=" O LEU E 135 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 84 through 86 Processing sheet with id=AB8, first strand: chain 'F' and resid 95 through 96 removed outlier: 6.787A pdb=" N SER F 183 " --> pdb=" O ALA F 212 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N VAL F 214 " --> pdb=" O SER F 183 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N PHE F 185 " --> pdb=" O VAL F 214 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP F 252 " --> pdb=" O ALA F 186 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE F 154 " --> pdb=" O GLN F 304 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ILE F 306 " --> pdb=" O ILE F 154 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N LEU F 156 " --> pdb=" O ILE F 306 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LYS F 153 " --> pdb=" O ALA F 327 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N THR F 329 " --> pdb=" O LYS F 153 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLY F 155 " --> pdb=" O THR F 329 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 133 through 137 removed outlier: 6.923A pdb=" N VAL G 133 " --> pdb=" O TYR G 113 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ILE G 115 " --> pdb=" O VAL G 133 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU G 135 " --> pdb=" O ILE G 115 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N THR G 76 " --> pdb=" O ALA G 114 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ILE G 116 " --> pdb=" O THR G 76 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N TYR G 78 " --> pdb=" O ILE G 116 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ILE G 118 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL G 80 " --> pdb=" O ILE G 118 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N GLY G 77 " --> pdb=" O TYR G 169 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N TYR G 171 " --> pdb=" O GLY G 77 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU G 79 " --> pdb=" O TYR G 171 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N ASN G 173 " --> pdb=" O LEU G 79 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N ILE G 81 " --> pdb=" O ASN G 173 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET G 170 " --> pdb=" O ARG G 186 " (cutoff:3.500A) 1163 hydrogen bonds defined for protein. 3318 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: 8.72 Time building geometry restraints manager: 7.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7260 1.33 - 1.45: 3280 1.45 - 1.57: 13939 1.57 - 1.69: 22 1.69 - 1.81: 154 Bond restraints: 24655 Sorted by residual: bond pdb=" N GLY D 159 " pdb=" CA GLY D 159 " ideal model delta sigma weight residual 1.449 1.495 -0.046 1.45e-02 4.76e+03 1.01e+01 bond pdb=" N ALA D 160 " pdb=" CA ALA D 160 " ideal model delta sigma weight residual 1.455 1.495 -0.040 1.33e-02 5.65e+03 8.92e+00 bond pdb=" CZ ARG E 454 " pdb=" NH2 ARG E 454 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.62e+00 bond pdb=" CZ ARG E 404 " pdb=" NH2 ARG E 404 " ideal model delta sigma weight residual 1.330 1.293 0.037 1.30e-02 5.92e+03 8.17e+00 bond pdb=" N THR E 192 " pdb=" CA THR E 192 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.33e-02 5.65e+03 6.96e+00 ... (remaining 24650 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 32812 2.15 - 4.30: 548 4.30 - 6.45: 64 6.45 - 8.61: 5 8.61 - 10.76: 4 Bond angle restraints: 33433 Sorted by residual: angle pdb=" O GLY D 158 " pdb=" C GLY D 158 " pdb=" N GLY D 159 " ideal model delta sigma weight residual 122.70 113.47 9.23 1.30e+00 5.92e-01 5.04e+01 angle pdb=" C ASP E 252 " pdb=" CA ASP E 252 " pdb=" CB ASP E 252 " ideal model delta sigma weight residual 110.90 102.86 8.04 1.58e+00 4.01e-01 2.59e+01 angle pdb=" OE1 GLN E 412 " pdb=" CD GLN E 412 " pdb=" NE2 GLN E 412 " ideal model delta sigma weight residual 122.60 118.05 4.55 1.00e+00 1.00e+00 2.07e+01 angle pdb=" CA ASP E 252 " pdb=" C ASP E 252 " pdb=" O ASP E 252 " ideal model delta sigma weight residual 120.70 116.25 4.45 1.03e+00 9.43e-01 1.87e+01 angle pdb=" OD1 ASN E 413 " pdb=" CG ASN E 413 " pdb=" ND2 ASN E 413 " ideal model delta sigma weight residual 122.60 118.32 4.28 1.00e+00 1.00e+00 1.83e+01 ... (remaining 33428 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.71: 14181 22.71 - 45.41: 741 45.41 - 68.11: 100 68.11 - 90.82: 36 90.82 - 113.52: 1 Dihedral angle restraints: 15059 sinusoidal: 6134 harmonic: 8925 Sorted by residual: dihedral pdb=" C5' ADP D 603 " pdb=" O5' ADP D 603 " pdb=" PA ADP D 603 " pdb=" O2A ADP D 603 " ideal model delta sinusoidal sigma weight residual -60.00 53.53 -113.52 1 2.00e+01 2.50e-03 3.36e+01 dihedral pdb=" CA LYS D 334 " pdb=" C LYS D 334 " pdb=" N LEU D 335 " pdb=" CA LEU D 335 " ideal model delta harmonic sigma weight residual 180.00 153.87 26.13 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA TYR E 341 " pdb=" C TYR E 341 " pdb=" N PRO E 342 " pdb=" CA PRO E 342 " ideal model delta harmonic sigma weight residual 0.00 23.60 -23.60 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 15056 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 3284 0.064 - 0.128: 543 0.128 - 0.193: 21 0.193 - 0.257: 3 0.257 - 0.321: 1 Chirality restraints: 3852 Sorted by residual: chirality pdb=" CA ALA E 343 " pdb=" N ALA E 343 " pdb=" C ALA E 343 " pdb=" CB ALA E 343 " both_signs ideal model delta sigma weight residual False 2.48 2.16 0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CA PRO E 342 " pdb=" N PRO E 342 " pdb=" C PRO E 342 " pdb=" CB PRO E 342 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CB VAL D 162 " pdb=" CA VAL D 162 " pdb=" CG1 VAL D 162 " pdb=" CG2 VAL D 162 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 3849 not shown) Planarity restraints: 4362 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 341 " -0.088 2.00e-02 2.50e+03 5.16e-02 5.32e+01 pdb=" CG TYR E 341 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR E 341 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 TYR E 341 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 TYR E 341 " 0.031 2.00e-02 2.50e+03 pdb=" CE2 TYR E 341 " 0.039 2.00e-02 2.50e+03 pdb=" CZ TYR E 341 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR E 341 " -0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 414 " 0.079 2.00e-02 2.50e+03 5.12e-02 4.58e+01 pdb=" CG PHE E 414 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE E 414 " -0.041 2.00e-02 2.50e+03 pdb=" CD2 PHE E 414 " -0.063 2.00e-02 2.50e+03 pdb=" CE1 PHE E 414 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE E 414 " 0.011 2.00e-02 2.50e+03 pdb=" CZ PHE E 414 " 0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 377 " 0.078 2.00e-02 2.50e+03 3.96e-02 3.14e+01 pdb=" CG TYR E 377 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR E 377 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 TYR E 377 " -0.037 2.00e-02 2.50e+03 pdb=" CE1 TYR E 377 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR E 377 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR E 377 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR E 377 " 0.044 2.00e-02 2.50e+03 ... (remaining 4359 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 101 2.44 - 3.06: 16003 3.06 - 3.67: 36395 3.67 - 4.29: 53030 4.29 - 4.90: 90561 Nonbonded interactions: 196090 Sorted by model distance: nonbonded pdb=" OE2 GLU E 190 " pdb=" CE1 PHE E 215 " model vdw 1.830 3.340 nonbonded pdb=" CB ALA D 160 " pdb=" O2 PO4 D 602 " model vdw 1.920 3.460 nonbonded pdb=" CA ALA D 160 " pdb=" O2 PO4 D 602 " model vdw 1.929 3.470 nonbonded pdb=" O2G ATP F 501 " pdb="MG MG F 502 " model vdw 1.971 2.170 nonbonded pdb=" OG1 THR F 165 " pdb="MG MG F 502 " model vdw 2.006 2.170 ... (remaining 196085 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 24 through 501) selection = (chain 'B' and resid 24 through 501) selection = (chain 'C' and resid 24 through 501) } ncs_group { reference = (chain 'D' and resid 1 through 470) selection = (chain 'E' and resid 1 through 470) selection = (chain 'F' and resid 1 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.010 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 55.050 Find NCS groups from input model: 1.570 Set up NCS constraints: 0.110 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 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 : 0.004 0.048 24655 Z= 0.262 Angle : 0.667 10.757 33433 Z= 0.388 Chirality : 0.046 0.321 3852 Planarity : 0.005 0.052 4362 Dihedral : 13.989 113.525 9347 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.89 % Favored : 97.05 % Rotamer: Outliers : 0.19 % Allowed : 0.43 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.15), residues: 3115 helix: 1.09 (0.15), residues: 1249 sheet: 0.67 (0.24), residues: 505 loop : -0.04 (0.17), residues: 1361 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS B 470 PHE 0.079 0.002 PHE E 414 TYR 0.088 0.002 TYR E 341 ARG 0.009 0.000 ARG E 454 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 130 time to evaluate : 2.812 Fit side-chains REVERT: B 62 MET cc_start: 0.8191 (tpt) cc_final: 0.7708 (tpt) REVERT: B 455 ARG cc_start: 0.8911 (ttp80) cc_final: 0.8545 (ttp80) REVERT: D 164 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7561 (mtpt) REVERT: D 378 LYS cc_start: 0.6753 (mmtp) cc_final: 0.6490 (ptmt) REVERT: D 389 MET cc_start: 0.6715 (ttt) cc_final: 0.6020 (tmm) REVERT: D 462 VAL cc_start: 0.4425 (t) cc_final: 0.4221 (t) REVERT: G 67 MET cc_start: 0.7535 (mmm) cc_final: 0.7119 (mmp) outliers start: 5 outliers final: 2 residues processed: 135 average time/residue: 0.3277 time to fit residues: 74.4983 Evaluate side-chains 107 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 104 time to evaluate : 2.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 164 LYS Chi-restraints excluded: chain E residue 251 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 261 optimal weight: 10.0000 chunk 234 optimal weight: 9.9990 chunk 130 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 chunk 158 optimal weight: 10.0000 chunk 125 optimal weight: 4.9990 chunk 242 optimal weight: 3.9990 chunk 94 optimal weight: 11.9990 chunk 147 optimal weight: 7.9990 chunk 180 optimal weight: 8.9990 chunk 281 optimal weight: 2.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN A 425 HIS C 189 GLN C 470 HIS D 53 HIS D 375 GLN E 179 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 24655 Z= 0.485 Angle : 0.691 11.645 33433 Z= 0.360 Chirality : 0.049 0.159 3852 Planarity : 0.005 0.053 4362 Dihedral : 8.452 121.349 3553 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.40 % Favored : 96.57 % Rotamer: Outliers : 0.62 % Allowed : 6.85 % Favored : 92.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.15), residues: 3115 helix: 0.69 (0.14), residues: 1267 sheet: 0.46 (0.23), residues: 508 loop : -0.37 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 470 PHE 0.017 0.002 PHE D 125 TYR 0.016 0.002 TYR A 329 ARG 0.008 0.001 ARG D 376 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 110 time to evaluate : 3.082 Fit side-chains revert: symmetry clash REVERT: B 375 MET cc_start: 0.8717 (tpp) cc_final: 0.8288 (tmm) REVERT: F 64 MET cc_start: 0.9297 (mmt) cc_final: 0.9017 (mmt) REVERT: G 131 MET cc_start: 0.6915 (mmm) cc_final: 0.6511 (mmm) outliers start: 16 outliers final: 9 residues processed: 119 average time/residue: 0.3140 time to fit residues: 64.1971 Evaluate side-chains 114 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 105 time to evaluate : 2.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain G residue 191 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 156 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 234 optimal weight: 5.9990 chunk 191 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 282 optimal weight: 2.9990 chunk 304 optimal weight: 10.0000 chunk 251 optimal weight: 0.9990 chunk 279 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 226 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN D 375 GLN G 107 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 24655 Z= 0.282 Angle : 0.571 11.096 33433 Z= 0.296 Chirality : 0.045 0.152 3852 Planarity : 0.004 0.056 4362 Dihedral : 8.077 127.604 3547 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.92 % Favored : 97.05 % Rotamer: Outliers : 1.05 % Allowed : 9.35 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.15), residues: 3115 helix: 1.06 (0.15), residues: 1239 sheet: 0.39 (0.23), residues: 518 loop : -0.33 (0.17), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 363 PHE 0.018 0.001 PHE B 395 TYR 0.014 0.001 TYR B 248 ARG 0.003 0.000 ARG E 454 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 118 time to evaluate : 2.998 Fit side-chains revert: symmetry clash REVERT: B 62 MET cc_start: 0.8612 (tpp) cc_final: 0.8139 (ttt) REVERT: B 407 GLN cc_start: 0.8149 (mt0) cc_final: 0.7875 (mp10) REVERT: D 389 MET cc_start: 0.6683 (ttt) cc_final: 0.6067 (tmm) REVERT: D 462 VAL cc_start: 0.4464 (t) cc_final: 0.4146 (t) REVERT: F 64 MET cc_start: 0.9324 (mmt) cc_final: 0.9022 (mmt) REVERT: G 67 MET cc_start: 0.7524 (mmm) cc_final: 0.7119 (mmp) REVERT: G 131 MET cc_start: 0.7028 (mmm) cc_final: 0.6658 (mmm) outliers start: 27 outliers final: 19 residues processed: 137 average time/residue: 0.3125 time to fit residues: 73.6001 Evaluate side-chains 125 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 106 time to evaluate : 2.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain G residue 191 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 278 optimal weight: 9.9990 chunk 212 optimal weight: 6.9990 chunk 146 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 134 optimal weight: 5.9990 chunk 189 optimal weight: 5.9990 chunk 283 optimal weight: 10.0000 chunk 299 optimal weight: 10.0000 chunk 147 optimal weight: 0.9990 chunk 268 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN D 375 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 24655 Z= 0.404 Angle : 0.629 10.982 33433 Z= 0.326 Chirality : 0.047 0.165 3852 Planarity : 0.005 0.061 4362 Dihedral : 8.065 131.408 3547 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.87 % Allowed : 10.32 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.15), residues: 3115 helix: 0.89 (0.14), residues: 1240 sheet: 0.35 (0.23), residues: 512 loop : -0.46 (0.17), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 363 PHE 0.019 0.002 PHE B 395 TYR 0.016 0.002 TYR B 248 ARG 0.004 0.000 ARG E 3 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 110 time to evaluate : 2.726 Fit side-chains revert: symmetry clash REVERT: A 157 VAL cc_start: 0.8780 (OUTLIER) cc_final: 0.8537 (m) REVERT: B 62 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.8289 (ttt) REVERT: D 376 ARG cc_start: 0.8183 (tpt90) cc_final: 0.7850 (tpt90) REVERT: D 462 VAL cc_start: 0.4350 (t) cc_final: 0.4146 (t) REVERT: G 25 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7471 (tt0) REVERT: G 131 MET cc_start: 0.7031 (mmm) cc_final: 0.6707 (mmm) outliers start: 48 outliers final: 32 residues processed: 149 average time/residue: 0.3170 time to fit residues: 79.9372 Evaluate side-chains 141 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 106 time to evaluate : 2.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 191 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 249 optimal weight: 1.9990 chunk 170 optimal weight: 0.2980 chunk 4 optimal weight: 3.9990 chunk 223 optimal weight: 0.4980 chunk 123 optimal weight: 4.9990 chunk 255 optimal weight: 2.9990 chunk 207 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 153 optimal weight: 4.9990 chunk 268 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN G 107 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24655 Z= 0.196 Angle : 0.527 11.370 33433 Z= 0.272 Chirality : 0.044 0.153 3852 Planarity : 0.004 0.064 4362 Dihedral : 7.502 127.004 3547 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.64 % Allowed : 11.21 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.15), residues: 3115 helix: 1.30 (0.15), residues: 1237 sheet: 0.39 (0.23), residues: 522 loop : -0.28 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS G 107 PHE 0.018 0.001 PHE B 395 TYR 0.013 0.001 TYR B 248 ARG 0.003 0.000 ARG A 354 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 120 time to evaluate : 3.045 Fit side-chains REVERT: A 157 VAL cc_start: 0.8645 (OUTLIER) cc_final: 0.8355 (m) REVERT: B 375 MET cc_start: 0.8848 (mmm) cc_final: 0.8629 (tmm) REVERT: B 407 GLN cc_start: 0.8151 (mt0) cc_final: 0.7869 (mp10) REVERT: B 455 ARG cc_start: 0.8971 (ttp80) cc_final: 0.8562 (ttp80) REVERT: D 376 ARG cc_start: 0.8150 (tpt90) cc_final: 0.7816 (tpt170) REVERT: D 381 GLN cc_start: 0.6046 (mm-40) cc_final: 0.5761 (mm110) REVERT: D 462 VAL cc_start: 0.4439 (t) cc_final: 0.4133 (t) REVERT: G 25 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7393 (tt0) REVERT: G 67 MET cc_start: 0.7416 (mmm) cc_final: 0.7053 (mmp) outliers start: 42 outliers final: 25 residues processed: 154 average time/residue: 0.3324 time to fit residues: 86.0228 Evaluate side-chains 138 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 111 time to evaluate : 2.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 202 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 100 optimal weight: 9.9990 chunk 269 optimal weight: 6.9990 chunk 59 optimal weight: 7.9990 chunk 175 optimal weight: 9.9990 chunk 73 optimal weight: 5.9990 chunk 299 optimal weight: 0.0270 chunk 248 optimal weight: 10.0000 chunk 138 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 99 optimal weight: 0.0970 chunk 157 optimal weight: 8.9990 overall best weight: 4.2242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN A 294 HIS D 375 GLN ** G 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 24655 Z= 0.357 Angle : 0.595 11.106 33433 Z= 0.308 Chirality : 0.046 0.155 3852 Planarity : 0.005 0.066 4362 Dihedral : 7.572 129.426 3547 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.41 % Allowed : 11.72 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.15), residues: 3115 helix: 1.10 (0.15), residues: 1239 sheet: 0.34 (0.23), residues: 523 loop : -0.39 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 363 PHE 0.018 0.001 PHE B 395 TYR 0.014 0.001 TYR B 248 ARG 0.003 0.000 ARG D 405 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 110 time to evaluate : 2.932 Fit side-chains revert: symmetry clash REVERT: A 157 VAL cc_start: 0.8804 (OUTLIER) cc_final: 0.8549 (m) REVERT: B 407 GLN cc_start: 0.8136 (mt0) cc_final: 0.7873 (mp10) REVERT: D 376 ARG cc_start: 0.8163 (tpt90) cc_final: 0.7758 (tpt90) REVERT: D 381 GLN cc_start: 0.6184 (mm-40) cc_final: 0.5880 (mm110) REVERT: D 462 VAL cc_start: 0.4391 (t) cc_final: 0.4067 (t) REVERT: F 136 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8165 (pt0) REVERT: G 25 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7443 (tt0) REVERT: G 67 MET cc_start: 0.7568 (mmm) cc_final: 0.7142 (mmp) outliers start: 62 outliers final: 49 residues processed: 166 average time/residue: 0.3348 time to fit residues: 92.7885 Evaluate side-chains 159 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 107 time to evaluate : 2.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 404 ARG Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 202 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 289 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 170 optimal weight: 6.9990 chunk 219 optimal weight: 5.9990 chunk 169 optimal weight: 2.9990 chunk 252 optimal weight: 3.9990 chunk 167 optimal weight: 0.9990 chunk 298 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 chunk 182 optimal weight: 4.9990 chunk 137 optimal weight: 10.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN G 107 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 24655 Z= 0.234 Angle : 0.543 11.279 33433 Z= 0.280 Chirality : 0.044 0.152 3852 Planarity : 0.004 0.066 4362 Dihedral : 7.318 128.428 3547 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.26 % Allowed : 12.23 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.15), residues: 3115 helix: 1.23 (0.15), residues: 1239 sheet: 0.38 (0.23), residues: 522 loop : -0.32 (0.17), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 363 PHE 0.020 0.001 PHE G 165 TYR 0.014 0.001 TYR B 248 ARG 0.002 0.000 ARG D 405 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 117 time to evaluate : 2.859 Fit side-chains revert: symmetry clash REVERT: A 157 VAL cc_start: 0.8732 (OUTLIER) cc_final: 0.8467 (m) REVERT: B 407 GLN cc_start: 0.8152 (mt0) cc_final: 0.7881 (mp10) REVERT: B 455 ARG cc_start: 0.8963 (ttp80) cc_final: 0.8553 (ttp80) REVERT: D 376 ARG cc_start: 0.8172 (tpt90) cc_final: 0.7889 (tpt170) REVERT: D 381 GLN cc_start: 0.6144 (mm-40) cc_final: 0.5828 (mm110) REVERT: D 462 VAL cc_start: 0.4383 (t) cc_final: 0.4079 (t) REVERT: E 101 GLU cc_start: 0.8178 (pm20) cc_final: 0.7907 (pm20) REVERT: E 407 GLN cc_start: 0.9059 (tm-30) cc_final: 0.8802 (tm-30) REVERT: F 136 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8133 (pt0) REVERT: G 25 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7428 (tt0) REVERT: G 131 MET cc_start: 0.6820 (mmm) cc_final: 0.6616 (mmm) outliers start: 58 outliers final: 42 residues processed: 168 average time/residue: 0.3207 time to fit residues: 90.4580 Evaluate side-chains 156 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 111 time to evaluate : 2.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 404 ARG Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 202 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 184 optimal weight: 10.0000 chunk 119 optimal weight: 0.6980 chunk 178 optimal weight: 0.9980 chunk 90 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 chunk 57 optimal weight: 0.0970 chunk 189 optimal weight: 6.9990 chunk 203 optimal weight: 3.9990 chunk 147 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 chunk 234 optimal weight: 10.0000 overall best weight: 2.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 375 GLN ** G 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 24655 Z= 0.234 Angle : 0.541 11.305 33433 Z= 0.278 Chirality : 0.044 0.151 3852 Planarity : 0.004 0.063 4362 Dihedral : 7.124 126.184 3547 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.10 % Allowed : 12.38 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.15), residues: 3115 helix: 1.28 (0.15), residues: 1241 sheet: 0.41 (0.23), residues: 522 loop : -0.30 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS G 107 PHE 0.016 0.001 PHE B 395 TYR 0.017 0.001 TYR G 171 ARG 0.002 0.000 ARG G 266 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 113 time to evaluate : 3.044 Fit side-chains revert: symmetry clash REVERT: A 157 VAL cc_start: 0.8742 (OUTLIER) cc_final: 0.8480 (m) REVERT: B 407 GLN cc_start: 0.8078 (mt0) cc_final: 0.7831 (mp10) REVERT: B 455 ARG cc_start: 0.8964 (ttp80) cc_final: 0.8561 (ttp80) REVERT: D 381 GLN cc_start: 0.6067 (mm-40) cc_final: 0.5762 (mm110) REVERT: D 462 VAL cc_start: 0.4385 (t) cc_final: 0.4074 (t) REVERT: E 101 GLU cc_start: 0.8134 (pm20) cc_final: 0.7849 (pm20) REVERT: F 136 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8120 (pt0) REVERT: G 25 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7476 (tt0) REVERT: G 67 MET cc_start: 0.7555 (mmm) cc_final: 0.7157 (mmp) outliers start: 54 outliers final: 45 residues processed: 162 average time/residue: 0.3357 time to fit residues: 90.7295 Evaluate side-chains 158 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 110 time to evaluate : 2.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 404 ARG Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 202 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 271 optimal weight: 7.9990 chunk 286 optimal weight: 8.9990 chunk 261 optimal weight: 2.9990 chunk 278 optimal weight: 5.9990 chunk 167 optimal weight: 0.3980 chunk 121 optimal weight: 10.0000 chunk 218 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 251 optimal weight: 2.9990 chunk 263 optimal weight: 0.0970 chunk 277 optimal weight: 5.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 381 GLN ** G 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24655 Z= 0.203 Angle : 0.532 11.314 33433 Z= 0.272 Chirality : 0.043 0.150 3852 Planarity : 0.004 0.063 4362 Dihedral : 6.932 123.641 3547 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.02 % Allowed : 12.58 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.15), residues: 3115 helix: 1.37 (0.15), residues: 1241 sheet: 0.40 (0.23), residues: 524 loop : -0.25 (0.17), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 363 PHE 0.015 0.001 PHE G 165 TYR 0.013 0.001 TYR D 377 ARG 0.006 0.000 ARG D 376 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 113 time to evaluate : 2.881 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 VAL cc_start: 0.8736 (OUTLIER) cc_final: 0.8476 (m) REVERT: B 407 GLN cc_start: 0.8105 (mt0) cc_final: 0.7855 (mp10) REVERT: B 455 ARG cc_start: 0.8964 (ttp80) cc_final: 0.8567 (ttp80) REVERT: D 389 MET cc_start: 0.6538 (ttt) cc_final: 0.6298 (tpp) REVERT: D 462 VAL cc_start: 0.4438 (t) cc_final: 0.4138 (t) REVERT: E 101 GLU cc_start: 0.8095 (pm20) cc_final: 0.7805 (pm20) REVERT: E 407 GLN cc_start: 0.9052 (tm-30) cc_final: 0.8807 (tm-30) REVERT: F 136 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8105 (pt0) REVERT: G 25 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7472 (tt0) REVERT: G 67 MET cc_start: 0.7521 (mmm) cc_final: 0.7083 (mmp) outliers start: 52 outliers final: 46 residues processed: 161 average time/residue: 0.3233 time to fit residues: 87.7815 Evaluate side-chains 158 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 109 time to evaluate : 2.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 404 ARG Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 202 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 182 optimal weight: 10.0000 chunk 294 optimal weight: 9.9990 chunk 179 optimal weight: 10.0000 chunk 139 optimal weight: 1.9990 chunk 204 optimal weight: 8.9990 chunk 308 optimal weight: 2.9990 chunk 284 optimal weight: 6.9990 chunk 245 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 189 optimal weight: 0.7980 chunk 150 optimal weight: 4.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 375 GLN ** G 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24655 Z= 0.275 Angle : 0.561 11.181 33433 Z= 0.287 Chirality : 0.044 0.152 3852 Planarity : 0.004 0.062 4362 Dihedral : 6.906 125.468 3547 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.06 % Allowed : 12.62 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.15), residues: 3115 helix: 1.29 (0.15), residues: 1235 sheet: 0.39 (0.23), residues: 522 loop : -0.33 (0.17), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 363 PHE 0.014 0.001 PHE B 395 TYR 0.014 0.001 TYR B 248 ARG 0.003 0.000 ARG D 405 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 111 time to evaluate : 2.935 Fit side-chains revert: symmetry clash REVERT: A 157 VAL cc_start: 0.8805 (OUTLIER) cc_final: 0.8554 (m) REVERT: B 455 ARG cc_start: 0.8952 (ttp80) cc_final: 0.8552 (ttp80) REVERT: D 381 GLN cc_start: 0.6284 (mm110) cc_final: 0.5963 (mm110) REVERT: D 462 VAL cc_start: 0.4398 (t) cc_final: 0.4089 (t) REVERT: E 101 GLU cc_start: 0.8130 (pm20) cc_final: 0.7806 (pm20) REVERT: E 407 GLN cc_start: 0.9060 (tm-30) cc_final: 0.8792 (tm-30) REVERT: F 136 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8138 (pt0) REVERT: G 25 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7495 (tt0) REVERT: G 67 MET cc_start: 0.7524 (mmm) cc_final: 0.7028 (mmp) outliers start: 53 outliers final: 49 residues processed: 159 average time/residue: 0.3150 time to fit residues: 85.2073 Evaluate side-chains 161 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 109 time to evaluate : 2.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 404 ARG Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 202 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 195 optimal weight: 0.9980 chunk 261 optimal weight: 5.9990 chunk 75 optimal weight: 8.9990 chunk 226 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 246 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 252 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.070951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.055809 restraints weight = 73683.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.057648 restraints weight = 37780.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.058852 restraints weight = 24095.817| |-----------------------------------------------------------------------------| r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24655 Z= 0.262 Angle : 0.556 11.147 33433 Z= 0.285 Chirality : 0.044 0.150 3852 Planarity : 0.004 0.062 4362 Dihedral : 6.789 126.397 3547 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.22 % Allowed : 12.54 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.15), residues: 3115 helix: 1.28 (0.15), residues: 1241 sheet: 0.40 (0.23), residues: 521 loop : -0.32 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS G 107 PHE 0.014 0.001 PHE B 395 TYR 0.014 0.001 TYR B 248 ARG 0.003 0.000 ARG D 405 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3527.83 seconds wall clock time: 65 minutes 7.91 seconds (3907.91 seconds total)