Starting phenix.real_space_refine on Fri Mar 6 03:26:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vmd_21240/03_2026/6vmd_21240.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vmd_21240/03_2026/6vmd_21240.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6vmd_21240/03_2026/6vmd_21240.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vmd_21240/03_2026/6vmd_21240.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vmd_21240/03_2026/6vmd_21240.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vmd_21240/03_2026/6vmd_21240.map" } resolution = 4.53 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians P 14 5.49 5 S 106 5.16 5 C 17268 2.51 5 N 4746 2.21 5 O 5367 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 138 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27501 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3850 Classifications: {'peptide': 501} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 483} Chain: "B" Number of atoms: 3862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 3862 Classifications: {'peptide': 503} Link IDs: {'PTRANS': 17, 'TRANS': 485} Chain: "C" Number of atoms: 3843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3843 Classifications: {'peptide': 500} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 482} Chain: "D" Number of atoms: 3619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3619 Classifications: {'peptide': 478} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 452} Chain: "E" Number of atoms: 3645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3645 Classifications: {'peptide': 481} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 455} Chain: "F" Number of atoms: 3636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3636 Classifications: {'peptide': 480} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 454} Chain: "d" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1384 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 4, 'TRANS': 174} Chain: "e" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1007 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 126} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "g" Number of atoms: 2504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2504 Classifications: {'peptide': 323} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 310} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.01, per 1000 atoms: 0.25 Number of scatterers: 27501 At special positions: 0 Unit cell: (155.76, 148.68, 128.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 106 16.00 P 14 15.00 O 5367 8.00 N 4746 7.00 C 17268 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS g 240 " - pdb=" SG CYS g 246 " distance=2.04 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: 2.47 Conformation dependent library (CDL) restraints added in 1.2 seconds 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6574 Finding SS restraints... Secondary structure from input PDB file: 123 helices and 28 sheets defined 46.3% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 6 through 25 removed outlier: 3.597A pdb=" N SER A 10 " --> pdb=" O ALA A 6 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ARG A 16 " --> pdb=" O ILE A 12 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N GLY A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 177 through 186 Processing helix chain 'A' and resid 187 through 191 removed outlier: 3.848A pdb=" N GLN A 190 " --> pdb=" O GLN A 187 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASN A 191 " --> pdb=" O GLN A 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 187 through 191' Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 232 through 253 Proline residue: A 240 - end of helix Processing helix chain 'A' and resid 263 through 277 Processing helix chain 'A' and resid 283 through 287 Processing helix chain 'A' and resid 288 through 289 No H-bonds generated for 'chain 'A' and resid 288 through 289' Processing helix chain 'A' and resid 290 through 300 Processing helix chain 'A' and resid 323 through 326 Processing helix chain 'A' and resid 329 through 339 removed outlier: 4.000A pdb=" N THR A 333 " --> pdb=" O ALA A 329 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN A 334 " --> pdb=" O TYR A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 353 Processing helix chain 'A' and resid 367 through 372 removed outlier: 4.060A pdb=" N ALA A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 381 removed outlier: 3.550A pdb=" N LYS A 377 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 399 removed outlier: 4.602A pdb=" N PHE A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 421 Processing helix chain 'A' and resid 430 through 443 removed outlier: 4.245A pdb=" N THR A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 468 removed outlier: 4.241A pdb=" N TYR A 457 " --> pdb=" O GLN A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 480 removed outlier: 4.192A pdb=" N GLN A 473 " --> pdb=" O LYS A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 505 Processing helix chain 'B' and resid 9 through 18 Processing helix chain 'B' and resid 101 through 105 removed outlier: 4.128A pdb=" N TYR B 104 " --> pdb=" O SER B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 177 through 187 removed outlier: 3.719A pdb=" N GLN B 187 " --> pdb=" O THR B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 216 removed outlier: 3.595A pdb=" N VAL B 206 " --> pdb=" O LYS B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 252 Proline residue: B 240 - end of helix removed outlier: 3.665A pdb=" N PHE B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 278 Processing helix chain 'B' and resid 283 through 287 removed outlier: 3.870A pdb=" N ALA B 286 " --> pdb=" O GLY B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 300 Processing helix chain 'B' and resid 329 through 339 Processing helix chain 'B' and resid 346 through 353 removed outlier: 3.531A pdb=" N PHE B 350 " --> pdb=" O SER B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 371 removed outlier: 4.252A pdb=" N ALA B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 396 removed outlier: 5.552A pdb=" N LYS B 382 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU B 392 " --> pdb=" O ALA B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 421 Processing helix chain 'B' and resid 430 through 444 removed outlier: 3.842A pdb=" N VAL B 435 " --> pdb=" O VAL B 431 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N THR B 440 " --> pdb=" O MET B 436 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N GLY B 441 " --> pdb=" O THR B 437 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR B 442 " --> pdb=" O ILE B 438 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN B 443 " --> pdb=" O TYR B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 469 removed outlier: 3.857A pdb=" N LYS B 466 " --> pdb=" O ARG B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 479 removed outlier: 4.278A pdb=" N GLN B 473 " --> pdb=" O LYS B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 503 removed outlier: 3.992A pdb=" N GLU B 496 " --> pdb=" O GLU B 492 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN B 497 " --> pdb=" O ALA B 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 20 Processing helix chain 'C' and resid 101 through 105 removed outlier: 4.117A pdb=" N TYR C 104 " --> pdb=" O SER C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 157 Processing helix chain 'C' and resid 175 through 187 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 218 through 221 Processing helix chain 'C' and resid 232 through 253 removed outlier: 3.668A pdb=" N GLN C 236 " --> pdb=" O PRO C 232 " (cutoff:3.500A) Proline residue: C 240 - end of helix Processing helix chain 'C' and resid 263 through 278 Processing helix chain 'C' and resid 283 through 287 removed outlier: 3.591A pdb=" N ALA C 286 " --> pdb=" O GLY C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 289 No H-bonds generated for 'chain 'C' and resid 288 through 289' Processing helix chain 'C' and resid 290 through 300 Processing helix chain 'C' and resid 329 through 339 Processing helix chain 'C' and resid 346 through 352 Processing helix chain 'C' and resid 373 through 393 removed outlier: 3.812A pdb=" N LYS C 378 " --> pdb=" O LYS C 374 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N LYS C 382 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU C 383 " --> pdb=" O VAL C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 399 removed outlier: 3.649A pdb=" N GLN C 398 " --> pdb=" O ALA C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 421 removed outlier: 4.110A pdb=" N GLN C 410 " --> pdb=" O ALA C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 444 removed outlier: 4.100A pdb=" N MET C 436 " --> pdb=" O GLU C 432 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR C 437 " --> pdb=" O GLU C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 469 Processing helix chain 'C' and resid 469 through 480 Processing helix chain 'C' and resid 483 through 504 Processing helix chain 'D' and resid 103 through 107 removed outlier: 3.650A pdb=" N LEU D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 159 Processing helix chain 'D' and resid 177 through 190 removed outlier: 3.818A pdb=" N ILE D 182 " --> pdb=" O LYS D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 220 Processing helix chain 'D' and resid 245 through 263 removed outlier: 4.604A pdb=" N GLY D 250 " --> pdb=" O ARG D 246 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N LEU D 251 " --> pdb=" O MET D 247 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE D 260 " --> pdb=" O MET D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 289 removed outlier: 3.933A pdb=" N PHE D 278 " --> pdb=" O ASN D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 311 Processing helix chain 'D' and resid 336 through 344 removed outlier: 4.012A pdb=" N THR D 342 " --> pdb=" O ALA D 338 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ALA D 344 " --> pdb=" O ALA D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 358 removed outlier: 3.935A pdb=" N ALA D 357 " --> pdb=" O SER D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 381 Processing helix chain 'D' and resid 381 through 408 removed outlier: 5.218A pdb=" N ASP D 403 " --> pdb=" O LYS D 399 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ILE D 404 " --> pdb=" O GLU D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 413 removed outlier: 3.504A pdb=" N GLU D 412 " --> pdb=" O GLY D 409 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU D 413 " --> pdb=" O LEU D 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 409 through 413' Processing helix chain 'D' and resid 414 through 431 Processing helix chain 'D' and resid 436 through 440 removed outlier: 3.664A pdb=" N GLU D 439 " --> pdb=" O PHE D 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 463 Processing helix chain 'D' and resid 470 through 475 removed outlier: 3.774A pdb=" N PHE D 474 " --> pdb=" O GLU D 471 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 492 Processing helix chain 'E' and resid 153 through 159 Processing helix chain 'E' and resid 177 through 192 removed outlier: 3.749A pdb=" N LEU E 181 " --> pdb=" O GLY E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 220 removed outlier: 3.642A pdb=" N GLY E 220 " --> pdb=" O MET E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 265 removed outlier: 4.156A pdb=" N ARG E 246 " --> pdb=" O PRO E 242 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG E 248 " --> pdb=" O GLY E 244 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLY E 250 " --> pdb=" O ARG E 246 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N LEU E 251 " --> pdb=" O MET E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 290 removed outlier: 3.598A pdb=" N PHE E 278 " --> pdb=" O ASN E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 311 Processing helix chain 'E' and resid 329 through 333 removed outlier: 3.769A pdb=" N ASP E 332 " --> pdb=" O VAL E 329 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP E 333 " --> pdb=" O PRO E 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 329 through 333' Processing helix chain 'E' and resid 336 through 344 Processing helix chain 'E' and resid 353 through 360 removed outlier: 4.305A pdb=" N LYS E 359 " --> pdb=" O GLY E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 376 through 381 Processing helix chain 'E' and resid 381 through 409 removed outlier: 4.892A pdb=" N ASP E 403 " --> pdb=" O LYS E 399 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ILE E 404 " --> pdb=" O GLU E 400 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA E 406 " --> pdb=" O GLN E 402 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE E 407 " --> pdb=" O ASP E 403 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU E 408 " --> pdb=" O ILE E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 431 Processing helix chain 'E' and resid 451 through 463 Processing helix chain 'E' and resid 470 through 474 Processing helix chain 'E' and resid 479 through 496 removed outlier: 3.595A pdb=" N LYS E 495 " --> pdb=" O GLU E 491 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 158 Processing helix chain 'F' and resid 179 through 193 removed outlier: 4.566A pdb=" N LYS F 191 " --> pdb=" O ASN F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 220 Processing helix chain 'F' and resid 242 through 247 Processing helix chain 'F' and resid 248 through 263 removed outlier: 3.567A pdb=" N PHE F 260 " --> pdb=" O MET F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 287 removed outlier: 3.969A pdb=" N PHE F 278 " --> pdb=" O ASN F 274 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ALA F 287 " --> pdb=" O SER F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 312 removed outlier: 3.998A pdb=" N GLU F 305 " --> pdb=" O THR F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 333 removed outlier: 3.878A pdb=" N ASP F 332 " --> pdb=" O VAL F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 346 removed outlier: 3.628A pdb=" N ALA F 344 " --> pdb=" O ALA F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 359 removed outlier: 4.037A pdb=" N ALA F 357 " --> pdb=" O SER F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 381 Processing helix chain 'F' and resid 382 through 406 removed outlier: 4.564A pdb=" N ASP F 403 " --> pdb=" O LYS F 399 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ILE F 404 " --> pdb=" O GLU F 400 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA F 406 " --> pdb=" O GLN F 402 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 431 Processing helix chain 'F' and resid 437 through 441 removed outlier: 3.868A pdb=" N VAL F 440 " --> pdb=" O VAL F 437 " (cutoff:3.500A) Processing helix chain 'F' and resid 451 through 463 Processing helix chain 'F' and resid 479 through 496 removed outlier: 4.342A pdb=" N LYS F 495 " --> pdb=" O GLU F 491 " (cutoff:3.500A) Processing helix chain 'd' and resid 73 through 89 removed outlier: 3.926A pdb=" N TYR d 78 " --> pdb=" O THR d 74 " (cutoff:3.500A) Processing helix chain 'd' and resid 91 through 106 removed outlier: 3.692A pdb=" N ARG d 104 " --> pdb=" O GLU d 100 " (cutoff:3.500A) Processing helix chain 'd' and resid 109 through 117 Processing helix chain 'd' and resid 121 through 137 removed outlier: 3.662A pdb=" N GLY d 137 " --> pdb=" O ILE d 133 " (cutoff:3.500A) Processing helix chain 'd' and resid 139 through 152 removed outlier: 3.907A pdb=" N ILE d 146 " --> pdb=" O THR d 142 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASN d 147 " --> pdb=" O ALA d 143 " (cutoff:3.500A) Processing helix chain 'd' and resid 154 through 156 No H-bonds generated for 'chain 'd' and resid 154 through 156' Processing helix chain 'd' and resid 157 through 174 removed outlier: 4.488A pdb=" N GLU d 166 " --> pdb=" O LEU d 162 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ASP d 167 " --> pdb=" O ASN d 163 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL d 168 " --> pdb=" O GLU d 164 " (cutoff:3.500A) Processing helix chain 'd' and resid 187 through 202 Processing helix chain 'd' and resid 237 through 249 removed outlier: 4.027A pdb=" N GLU d 243 " --> pdb=" O LYS d 239 " (cutoff:3.500A) Processing helix chain 'e' and resid 88 through 103 Processing helix chain 'e' and resid 109 through 131 removed outlier: 3.797A pdb=" N ILE e 113 " --> pdb=" O LYS e 109 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU e 114 " --> pdb=" O ARG e 110 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU e 127 " --> pdb=" O ARG e 123 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA e 128 " --> pdb=" O THR e 124 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER e 129 " --> pdb=" O ARG e 125 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR e 131 " --> pdb=" O GLU e 127 " (cutoff:3.500A) Processing helix chain 'g' and resid 42 through 100 Proline residue: g 84 - end of helix Processing helix chain 'g' and resid 133 through 152 removed outlier: 3.685A pdb=" N LEU g 151 " --> pdb=" O GLU g 147 " (cutoff:3.500A) Processing helix chain 'g' and resid 163 through 171 removed outlier: 3.709A pdb=" N ARG g 171 " --> pdb=" O TYR g 167 " (cutoff:3.500A) Processing helix chain 'g' and resid 187 through 204 removed outlier: 3.604A pdb=" N SER g 204 " --> pdb=" O SER g 200 " (cutoff:3.500A) Processing helix chain 'g' and resid 287 through 361 removed outlier: 3.515A pdb=" N LEU g 292 " --> pdb=" O PRO g 288 " (cutoff:3.500A) Proline residue: g 297 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 55 removed outlier: 3.507A pdb=" N GLY A 30 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ARG A 41 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL A 35 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE A 39 " --> pdb=" O VAL A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 98 removed outlier: 3.548A pdb=" N ILE A 98 " --> pdb=" O ARG A 128 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG A 128 " --> pdb=" O ILE A 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 108 through 109 removed outlier: 6.018A pdb=" N ILE A 109 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE A 193 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N ILE A 260 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N VAL A 195 " --> pdb=" O ILE A 260 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 319 through 321 Processing sheet with id=AA5, first strand: chain 'B' and resid 39 through 43 removed outlier: 7.550A pdb=" N ASN B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N LEU B 67 " --> pdb=" O ASN B 71 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N GLY B 73 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU B 65 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLU B 52 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LEU B 53 " --> pdb=" O THR B 92 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 39 through 43 removed outlier: 7.550A pdb=" N ASN B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N LEU B 67 " --> pdb=" O ASN B 71 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N GLY B 73 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU B 65 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN D 25 " --> pdb=" O ASP D 32 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ARG D 73 " --> pdb=" O LEU D 69 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN D 67 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL D 77 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL D 65 " --> pdb=" O VAL D 77 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 147 removed outlier: 4.170A pdb=" N VAL B 160 " --> pdb=" O LEU B 147 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 168 through 170 removed outlier: 3.656A pdb=" N VAL B 320 " --> pdb=" O ILE B 168 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 222 through 223 removed outlier: 5.840A pdb=" N ILE B 193 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE B 260 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL B 195 " --> pdb=" O ILE B 260 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N LEU B 317 " --> pdb=" O THR B 257 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE B 259 " --> pdb=" O LEU B 317 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 91 through 93 removed outlier: 3.877A pdb=" N ASN E 45 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL E 65 " --> pdb=" O ASN E 45 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL E 65 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N VAL E 77 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN E 67 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ALA E 34 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ILE E 23 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ASN C 28 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ALA d 178 " --> pdb=" O LYS d 210 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL d 212 " --> pdb=" O ALA d 178 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N VAL d 180 " --> pdb=" O VAL d 212 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 91 through 93 removed outlier: 3.877A pdb=" N ASN E 45 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL E 65 " --> pdb=" O ASN E 45 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL E 65 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N VAL E 77 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN E 67 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ALA E 34 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ILE E 23 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLY C 73 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N LEU C 67 " --> pdb=" O ASN C 71 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ASN C 71 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N HIS C 43 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL C 32 " --> pdb=" O HIS C 43 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ALA d 178 " --> pdb=" O LYS d 210 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL d 212 " --> pdb=" O ALA d 178 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N VAL d 180 " --> pdb=" O VAL d 212 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 98 through 100 Processing sheet with id=AB4, first strand: chain 'C' and resid 108 through 109 removed outlier: 3.645A pdb=" N ILE C 109 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA C 226 " --> pdb=" O ILE C 109 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N VAL C 225 " --> pdb=" O CYS C 194 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N TYR C 196 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N GLU C 227 " --> pdb=" O TYR C 196 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA C 198 " --> pdb=" O GLU C 227 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE C 193 " --> pdb=" O LEU C 258 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N ILE C 260 " --> pdb=" O ILE C 193 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N VAL C 195 " --> pdb=" O ILE C 260 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 146 through 147 removed outlier: 4.643A pdb=" N VAL C 160 " --> pdb=" O LEU C 147 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 99 through 101 Processing sheet with id=AB7, first strand: chain 'D' and resid 110 through 111 removed outlier: 7.739A pdb=" N LEU D 234 " --> pdb=" O PHE D 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 148 through 149 removed outlier: 3.586A pdb=" N PHE D 149 " --> pdb=" O TYR D 162 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N TYR D 162 " --> pdb=" O PHE D 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 197 through 199 removed outlier: 7.286A pdb=" N LEU D 270 " --> pdb=" O ILE D 324 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N ALA D 326 " --> pdb=" O LEU D 270 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N ILE D 272 " --> pdb=" O ALA D 326 " (cutoff:3.500A) removed outlier: 9.026A pdb=" N TYR D 328 " --> pdb=" O ILE D 272 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY D 172 " --> pdb=" O VAL D 327 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N PHE D 171 " --> pdb=" O LEU D 352 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 99 through 100 Processing sheet with id=AC2, first strand: chain 'E' and resid 110 through 111 removed outlier: 3.877A pdb=" N ALA E 233 " --> pdb=" O SER E 197 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL E 198 " --> pdb=" O PHE E 271 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N VAL E 268 " --> pdb=" O THR E 322 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE E 324 " --> pdb=" O VAL E 268 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU E 270 " --> pdb=" O ILE E 324 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ILE E 168 " --> pdb=" O GLN E 325 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N THR E 350 " --> pdb=" O LYS E 167 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N GLY E 169 " --> pdb=" O THR E 350 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 30 through 31 removed outlier: 3.534A pdb=" N GLN F 67 " --> pdb=" O ARG F 75 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL F 77 " --> pdb=" O VAL F 65 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N VAL F 65 " --> pdb=" O VAL F 77 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 99 through 101 Processing sheet with id=AC5, first strand: chain 'F' and resid 110 through 111 removed outlier: 6.186A pdb=" N VAL F 198 " --> pdb=" O PHE F 271 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE F 168 " --> pdb=" O GLN F 325 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 148 through 149 removed outlier: 4.307A pdb=" N TYR F 162 " --> pdb=" O PHE F 149 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'e' and resid 13 through 14 removed outlier: 6.009A pdb=" N LEU e 8 " --> pdb=" O VAL e 78 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'e' and resid 48 through 52 removed outlier: 3.525A pdb=" N ALA e 61 " --> pdb=" O GLU e 82 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'g' and resid 156 through 159 removed outlier: 3.576A pdb=" N ILE g 158 " --> pdb=" O LEU g 120 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU g 211 " --> pdb=" O ALA g 119 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HIS g 228 " --> pdb=" O MET g 212 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS g 216 " --> pdb=" O ASP g 224 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ASP g 224 " --> pdb=" O LYS g 216 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'g' and resid 251 through 257 1269 hydrogen bonds defined for protein. 3687 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.93 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9292 1.34 - 1.46: 5561 1.46 - 1.59: 12809 1.59 - 1.71: 21 1.71 - 1.83: 200 Bond restraints: 27883 Sorted by residual: bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.29e+01 bond pdb=" C4 ATP D 601 " pdb=" C5 ATP D 601 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.28e+01 bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.12e+01 bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 4.98e+01 bond pdb=" C5 ATP C 600 " pdb=" C6 ATP C 600 " ideal model delta sigma weight residual 1.409 1.472 -0.063 1.00e-02 1.00e+04 3.94e+01 ... (remaining 27878 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.03: 37551 5.03 - 10.05: 213 10.05 - 15.08: 13 15.08 - 20.10: 4 20.10 - 25.13: 5 Bond angle restraints: 37786 Sorted by residual: angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 114.74 25.13 1.00e+00 1.00e+00 6.31e+02 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 116.60 23.27 1.00e+00 1.00e+00 5.41e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 117.18 22.69 1.00e+00 1.00e+00 5.15e+02 angle pdb=" PA ATP B 600 " pdb=" O3A ATP B 600 " pdb=" PB ATP B 600 " ideal model delta sigma weight residual 136.83 114.63 22.20 1.00e+00 1.00e+00 4.93e+02 angle pdb=" PB ATP D 601 " pdb=" O3B ATP D 601 " pdb=" PG ATP D 601 " ideal model delta sigma weight residual 139.87 119.34 20.53 1.00e+00 1.00e+00 4.21e+02 ... (remaining 37781 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.35: 15678 22.35 - 44.70: 1273 44.70 - 67.05: 169 67.05 - 89.40: 61 89.40 - 111.74: 1 Dihedral angle restraints: 17182 sinusoidal: 6940 harmonic: 10242 Sorted by residual: dihedral pdb=" CA ALA D 295 " pdb=" C ALA D 295 " pdb=" N VAL D 296 " pdb=" CA VAL D 296 " ideal model delta harmonic sigma weight residual -180.00 -127.28 -52.72 0 5.00e+00 4.00e-02 1.11e+02 dihedral pdb=" CA ALA F 295 " pdb=" C ALA F 295 " pdb=" N VAL F 296 " pdb=" CA VAL F 296 " ideal model delta harmonic sigma weight residual -180.00 -132.27 -47.73 0 5.00e+00 4.00e-02 9.11e+01 dihedral pdb=" CA ALA E 295 " pdb=" C ALA E 295 " pdb=" N VAL E 296 " pdb=" CA VAL E 296 " ideal model delta harmonic sigma weight residual -180.00 -134.50 -45.50 0 5.00e+00 4.00e-02 8.28e+01 ... (remaining 17179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 3708 0.080 - 0.159: 676 0.159 - 0.239: 55 0.239 - 0.319: 6 0.319 - 0.398: 2 Chirality restraints: 4447 Sorted by residual: chirality pdb=" CB ILE e 23 " pdb=" CA ILE e 23 " pdb=" CG1 ILE e 23 " pdb=" CG2 ILE e 23 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.97e+00 chirality pdb=" CA ARG B 355 " pdb=" N ARG B 355 " pdb=" C ARG B 355 " pdb=" CB ARG B 355 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" CB ILE D 189 " pdb=" CA ILE D 189 " pdb=" CG1 ILE D 189 " pdb=" CG2 ILE D 189 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 4444 not shown) Planarity restraints: 4912 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR e 9 " 0.053 5.00e-02 4.00e+02 8.00e-02 1.02e+01 pdb=" N PRO e 10 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO e 10 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO e 10 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 295 " -0.014 2.00e-02 2.50e+03 2.86e-02 8.18e+00 pdb=" C ALA D 295 " 0.049 2.00e-02 2.50e+03 pdb=" O ALA D 295 " -0.019 2.00e-02 2.50e+03 pdb=" N VAL D 296 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA D 338 " 0.047 5.00e-02 4.00e+02 7.08e-02 8.01e+00 pdb=" N PRO D 339 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO D 339 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 339 " 0.040 5.00e-02 4.00e+02 ... (remaining 4909 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 3132 2.73 - 3.27: 29511 3.27 - 3.82: 50039 3.82 - 4.36: 56118 4.36 - 4.90: 91268 Nonbonded interactions: 230068 Sorted by model distance: nonbonded pdb=" OG1 THR B 177 " pdb=" O2B ATP B 600 " model vdw 2.192 3.040 nonbonded pdb=" O LEU D 47 " pdb=" OG1 THR D 62 " model vdw 2.202 3.040 nonbonded pdb=" O ASP F 366 " pdb=" OG SER F 370 " model vdw 2.220 3.040 nonbonded pdb=" OG1 THR D 179 " pdb=" O1G ATP D 601 " model vdw 2.227 3.040 nonbonded pdb=" O VAL D 102 " pdb=" OG1 THR D 128 " model vdw 2.236 3.040 ... (remaining 230063 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 6 through 503 or resid 600)) selection = (chain 'B' and resid 6 through 600) selection = (chain 'C' and (resid 6 through 503 or resid 600)) } ncs_group { reference = (chain 'D' and resid 17 through 494) selection = (chain 'E' and resid 17 through 494) selection = (chain 'F' and resid 17 through 494) } 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.030 Extract box with map and model: 0.560 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 26.960 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.060 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 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 : 0.008 0.089 27884 Z= 0.408 Angle : 1.159 25.129 37788 Z= 0.697 Chirality : 0.060 0.398 4447 Planarity : 0.007 0.080 4912 Dihedral : 16.576 111.745 10605 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.12 % Favored : 89.74 % Rotamer: Outliers : 0.78 % Allowed : 15.57 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.98 (0.12), residues: 3558 helix: -2.19 (0.11), residues: 1441 sheet: -2.82 (0.20), residues: 466 loop : -2.96 (0.13), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG F 277 TYR 0.021 0.003 TYR A 464 PHE 0.030 0.003 PHE E 430 TRP 0.005 0.001 TRP e 15 HIS 0.013 0.002 HIS B 295 Details of bonding type rmsd covalent geometry : bond 0.00798 (27883) covalent geometry : angle 1.15875 (37786) SS BOND : bond 0.00667 ( 1) SS BOND : angle 2.83779 ( 2) hydrogen bonds : bond 0.15973 ( 1236) hydrogen bonds : angle 7.23655 ( 3687) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 315 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.8908 (tp) cc_final: 0.8222 (mt) REVERT: A 157 MET cc_start: 0.8592 (ptp) cc_final: 0.7921 (mmt) REVERT: A 276 LEU cc_start: 0.9172 (tp) cc_final: 0.8939 (tp) REVERT: A 314 MET cc_start: 0.8101 (mmm) cc_final: 0.7579 (mmm) REVERT: A 338 ILE cc_start: 0.9350 (mm) cc_final: 0.9111 (mt) REVERT: A 351 ASN cc_start: 0.8598 (t0) cc_final: 0.8190 (t0) REVERT: A 376 MET cc_start: 0.8789 (tpp) cc_final: 0.8509 (mmp) REVERT: A 436 MET cc_start: 0.8677 (ptp) cc_final: 0.8099 (ptp) REVERT: A 498 MET cc_start: 0.8896 (ttm) cc_final: 0.8511 (mtp) REVERT: B 236 GLN cc_start: 0.9148 (mt0) cc_final: 0.8910 (mt0) REVERT: B 251 MET cc_start: 0.7596 (tpt) cc_final: 0.7009 (tpt) REVERT: B 314 MET cc_start: 0.7909 (tpt) cc_final: 0.6968 (tpt) REVERT: B 323 GLN cc_start: 0.8614 (mp-120) cc_final: 0.8312 (mm110) REVERT: C 235 LEU cc_start: 0.9417 (mt) cc_final: 0.9201 (mt) REVERT: C 474 GLU cc_start: 0.9100 (mm-30) cc_final: 0.8889 (mm-30) REVERT: D 256 MET cc_start: 0.8680 (mmt) cc_final: 0.8413 (mmp) REVERT: D 488 MET cc_start: 0.9184 (tmm) cc_final: 0.8928 (tmm) REVERT: E 79 MET cc_start: 0.9180 (mmt) cc_final: 0.8940 (mmp) REVERT: E 239 MET cc_start: 0.8625 (mmm) cc_final: 0.8195 (mmm) REVERT: E 247 MET cc_start: 0.8686 (tpp) cc_final: 0.8423 (tpp) REVERT: F 79 MET cc_start: 0.8503 (mpp) cc_final: 0.8029 (mpp) REVERT: F 89 MET cc_start: 0.8623 (ttm) cc_final: 0.8314 (mtp) REVERT: d 139 GLN cc_start: 0.9279 (mm110) cc_final: 0.8964 (mp10) REVERT: d 250 MET cc_start: 0.4386 (mmt) cc_final: 0.3183 (mtm) REVERT: g 62 GLU cc_start: 0.8987 (tm-30) cc_final: 0.8729 (tm-30) REVERT: g 66 LEU cc_start: 0.8732 (mt) cc_final: 0.8095 (tt) REVERT: g 133 PHE cc_start: 0.8726 (t80) cc_final: 0.8383 (t80) REVERT: g 346 GLN cc_start: 0.8521 (mm110) cc_final: 0.8038 (mt0) outliers start: 23 outliers final: 12 residues processed: 335 average time/residue: 0.1674 time to fit residues: 90.8202 Evaluate side-chains 224 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 212 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 ASN A 495 GLN B 66 ASN B 148 GLN B 186 ASN B 269 GLN B 295 HIS B 359 ASN C 34 GLN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 GLN C 423 GLN C 434 GLN C 468 ASN D 19 ASN ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN D 133 HIS D 299 GLN E 25 GLN E 120 ASN E 402 GLN E 472 GLN F 19 ASN F 193 HIS F 225 GLN F 264 ASN F 389 GLN F 402 GLN ** d 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 147 ASN d 247 GLN e 56 GLN g 81 ASN g 95 ASN g 97 ASN g 192 GLN g 228 HIS ** g 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 346 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.049871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.041100 restraints weight = 190173.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.042418 restraints weight = 116588.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.043365 restraints weight = 79464.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.044009 restraints weight = 58762.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.044542 restraints weight = 46397.173| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27884 Z= 0.149 Angle : 0.710 10.128 37788 Z= 0.369 Chirality : 0.046 0.206 4447 Planarity : 0.005 0.064 4912 Dihedral : 8.901 102.692 4023 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.09 % Favored : 91.77 % Rotamer: Outliers : 0.17 % Allowed : 5.23 % Favored : 94.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.82 (0.13), residues: 3558 helix: -0.88 (0.12), residues: 1462 sheet: -2.32 (0.21), residues: 458 loop : -2.67 (0.14), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 462 TYR 0.017 0.001 TYR D 362 PHE 0.027 0.001 PHE C 482 TRP 0.005 0.001 TRP e 15 HIS 0.004 0.001 HIS D 384 Details of bonding type rmsd covalent geometry : bond 0.00314 (27883) covalent geometry : angle 0.71029 (37786) SS BOND : bond 0.00310 ( 1) SS BOND : angle 2.22730 ( 2) hydrogen bonds : bond 0.04691 ( 1236) hydrogen bonds : angle 5.62357 ( 3687) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 313 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.8937 (tp) cc_final: 0.8560 (tp) REVERT: A 157 MET cc_start: 0.8940 (ptp) cc_final: 0.7947 (mmt) REVERT: A 251 MET cc_start: 0.8208 (ptp) cc_final: 0.7734 (ppp) REVERT: A 314 MET cc_start: 0.8059 (mmm) cc_final: 0.7698 (mmm) REVERT: B 82 MET cc_start: 0.8681 (mmp) cc_final: 0.8474 (mmp) REVERT: B 131 GLU cc_start: 0.8711 (mp0) cc_final: 0.8381 (tp30) REVERT: B 236 GLN cc_start: 0.9166 (mt0) cc_final: 0.8678 (mm-40) REVERT: B 355 ARG cc_start: 0.9000 (mmp-170) cc_final: 0.8172 (mmm160) REVERT: C 182 ASP cc_start: 0.8146 (m-30) cc_final: 0.7910 (m-30) REVERT: C 251 MET cc_start: 0.8837 (ttt) cc_final: 0.8612 (ttt) REVERT: C 295 HIS cc_start: 0.8877 (m-70) cc_final: 0.8671 (m-70) REVERT: D 64 GLU cc_start: 0.5784 (tp30) cc_final: 0.5282 (tp30) REVERT: D 183 MET cc_start: 0.8941 (mmp) cc_final: 0.8595 (mmm) REVERT: D 256 MET cc_start: 0.8788 (mmt) cc_final: 0.8542 (mmp) REVERT: D 488 MET cc_start: 0.9205 (tmm) cc_final: 0.8910 (tmm) REVERT: E 79 MET cc_start: 0.9288 (mmt) cc_final: 0.8954 (mmp) REVERT: E 239 MET cc_start: 0.8754 (mmm) cc_final: 0.8441 (mmm) REVERT: E 247 MET cc_start: 0.8652 (tpp) cc_final: 0.8343 (tpp) REVERT: F 79 MET cc_start: 0.8690 (mpp) cc_final: 0.7939 (mpp) REVERT: d 139 GLN cc_start: 0.9333 (mm110) cc_final: 0.9075 (mp10) REVERT: d 250 MET cc_start: 0.4395 (mmt) cc_final: 0.3512 (mtm) REVERT: e 95 THR cc_start: 0.8838 (t) cc_final: 0.8448 (p) REVERT: g 62 GLU cc_start: 0.9065 (tm-30) cc_final: 0.8846 (tm-30) REVERT: g 66 LEU cc_start: 0.8454 (mt) cc_final: 0.8042 (tt) REVERT: g 133 PHE cc_start: 0.8495 (t80) cc_final: 0.8159 (t80) REVERT: g 295 LEU cc_start: 0.9302 (mt) cc_final: 0.9049 (mt) REVERT: g 346 GLN cc_start: 0.8549 (mm-40) cc_final: 0.7888 (mt0) outliers start: 5 outliers final: 1 residues processed: 317 average time/residue: 0.1810 time to fit residues: 91.6427 Evaluate side-chains 209 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 208 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 216 optimal weight: 0.9980 chunk 277 optimal weight: 2.9990 chunk 222 optimal weight: 0.0970 chunk 266 optimal weight: 0.2980 chunk 313 optimal weight: 0.8980 chunk 263 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 68 optimal weight: 4.9990 chunk 247 optimal weight: 1.9990 chunk 41 optimal weight: 8.9990 chunk 67 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 GLN A 190 GLN ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 GLN B 323 GLN ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN ** D 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 GLN E 19 ASN ** F 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 238 GLN ** d 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.050552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.041761 restraints weight = 188880.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.043056 restraints weight = 115925.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.044003 restraints weight = 79541.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.044644 restraints weight = 59108.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.045177 restraints weight = 46823.682| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27884 Z= 0.135 Angle : 0.670 9.915 37788 Z= 0.348 Chirality : 0.045 0.198 4447 Planarity : 0.005 0.077 4912 Dihedral : 8.511 93.924 4023 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.01 % Favored : 91.91 % Rotamer: Outliers : 0.10 % Allowed : 5.40 % Favored : 94.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.13), residues: 3558 helix: -0.30 (0.13), residues: 1466 sheet: -1.96 (0.23), residues: 453 loop : -2.45 (0.14), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 418 TYR 0.015 0.001 TYR C 330 PHE 0.051 0.002 PHE B 213 TRP 0.004 0.001 TRP e 57 HIS 0.005 0.001 HIS E 133 Details of bonding type rmsd covalent geometry : bond 0.00293 (27883) covalent geometry : angle 0.66973 (37786) SS BOND : bond 0.00327 ( 1) SS BOND : angle 2.26404 ( 2) hydrogen bonds : bond 0.04231 ( 1236) hydrogen bonds : angle 5.27152 ( 3687) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 299 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.8949 (tp) cc_final: 0.8595 (tp) REVERT: A 157 MET cc_start: 0.8884 (ptp) cc_final: 0.7972 (mmt) REVERT: A 164 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7884 (pp30) REVERT: A 251 MET cc_start: 0.8146 (ptp) cc_final: 0.7598 (ppp) REVERT: A 314 MET cc_start: 0.8220 (mmm) cc_final: 0.7737 (mmm) REVERT: A 498 MET cc_start: 0.8896 (mtm) cc_final: 0.8395 (mtp) REVERT: B 82 MET cc_start: 0.8694 (mmp) cc_final: 0.8459 (mmp) REVERT: B 131 GLU cc_start: 0.8724 (mp0) cc_final: 0.8462 (tp30) REVERT: B 236 GLN cc_start: 0.9212 (mt0) cc_final: 0.8722 (mm-40) REVERT: B 251 MET cc_start: 0.7374 (tpt) cc_final: 0.6788 (tpt) REVERT: B 314 MET cc_start: 0.7947 (tpt) cc_final: 0.7278 (tpt) REVERT: B 355 ARG cc_start: 0.8960 (mmp-170) cc_final: 0.8097 (mmm160) REVERT: C 182 ASP cc_start: 0.8103 (m-30) cc_final: 0.7893 (m-30) REVERT: C 235 LEU cc_start: 0.9417 (mt) cc_final: 0.9175 (mt) REVERT: C 251 MET cc_start: 0.8923 (ttt) cc_final: 0.8658 (ttt) REVERT: C 295 HIS cc_start: 0.8842 (m-70) cc_final: 0.8572 (m-70) REVERT: D 64 GLU cc_start: 0.5813 (tp30) cc_final: 0.5607 (tp30) REVERT: D 89 MET cc_start: 0.7550 (mtp) cc_final: 0.7196 (mtp) REVERT: D 183 MET cc_start: 0.8885 (mmp) cc_final: 0.8649 (mmm) REVERT: D 488 MET cc_start: 0.9208 (tmm) cc_final: 0.8933 (tmm) REVERT: E 79 MET cc_start: 0.9298 (mmt) cc_final: 0.8921 (mmp) REVERT: F 79 MET cc_start: 0.8877 (mpp) cc_final: 0.8018 (mpp) REVERT: d 139 GLN cc_start: 0.9327 (mm110) cc_final: 0.9042 (mp10) REVERT: d 250 MET cc_start: 0.4774 (mmt) cc_final: 0.3659 (mtm) REVERT: e 112 LYS cc_start: 0.8735 (mmmm) cc_final: 0.8376 (mmmm) REVERT: g 66 LEU cc_start: 0.8315 (mt) cc_final: 0.7817 (tt) REVERT: g 133 PHE cc_start: 0.8448 (t80) cc_final: 0.8200 (t80) REVERT: g 284 PHE cc_start: 0.8404 (m-10) cc_final: 0.8061 (m-10) REVERT: g 295 LEU cc_start: 0.9312 (mt) cc_final: 0.8972 (mt) REVERT: g 346 GLN cc_start: 0.8532 (mm-40) cc_final: 0.7921 (mt0) outliers start: 3 outliers final: 1 residues processed: 302 average time/residue: 0.1801 time to fit residues: 88.5459 Evaluate side-chains 207 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 205 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 242 optimal weight: 7.9990 chunk 213 optimal weight: 5.9990 chunk 114 optimal weight: 9.9990 chunk 60 optimal weight: 0.9980 chunk 187 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 116 optimal weight: 0.9990 chunk 308 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 288 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 GLN B 269 GLN B 351 ASN C 34 GLN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN ** D 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 GLN ** F 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.050481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.041632 restraints weight = 189068.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.042943 restraints weight = 116947.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.043867 restraints weight = 80493.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.044567 restraints weight = 59921.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.045065 restraints weight = 47433.246| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27884 Z= 0.135 Angle : 0.652 10.250 37788 Z= 0.339 Chirality : 0.045 0.243 4447 Planarity : 0.005 0.081 4912 Dihedral : 8.306 94.134 4023 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.67 % Favored : 92.24 % Rotamer: Outliers : 0.07 % Allowed : 4.01 % Favored : 95.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.14), residues: 3558 helix: 0.03 (0.13), residues: 1453 sheet: -1.82 (0.23), residues: 479 loop : -2.23 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 462 TYR 0.021 0.001 TYR B 457 PHE 0.028 0.001 PHE g 168 TRP 0.004 0.001 TRP e 57 HIS 0.004 0.001 HIS C 43 Details of bonding type rmsd covalent geometry : bond 0.00293 (27883) covalent geometry : angle 0.65215 (37786) SS BOND : bond 0.00280 ( 1) SS BOND : angle 2.24374 ( 2) hydrogen bonds : bond 0.03998 ( 1236) hydrogen bonds : angle 5.09659 ( 3687) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 287 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 LEU cc_start: 0.9381 (tp) cc_final: 0.9025 (tt) REVERT: A 138 MET cc_start: 0.9272 (pmm) cc_final: 0.9068 (pmm) REVERT: A 147 LEU cc_start: 0.8995 (tp) cc_final: 0.8666 (tp) REVERT: A 157 MET cc_start: 0.8978 (ptp) cc_final: 0.8079 (mmt) REVERT: A 251 MET cc_start: 0.8162 (ptp) cc_final: 0.7695 (ppp) REVERT: A 314 MET cc_start: 0.8298 (mmm) cc_final: 0.7649 (mmm) REVERT: A 326 ASP cc_start: 0.9516 (m-30) cc_final: 0.9261 (m-30) REVERT: A 498 MET cc_start: 0.8836 (mtm) cc_final: 0.8137 (mtp) REVERT: B 82 MET cc_start: 0.8736 (mmp) cc_final: 0.8520 (mmp) REVERT: B 131 GLU cc_start: 0.8791 (mp0) cc_final: 0.8503 (tp30) REVERT: B 236 GLN cc_start: 0.9257 (mt0) cc_final: 0.8777 (mm-40) REVERT: B 251 MET cc_start: 0.7474 (tpt) cc_final: 0.6899 (tpt) REVERT: B 314 MET cc_start: 0.8105 (tpt) cc_final: 0.7400 (tpt) REVERT: C 251 MET cc_start: 0.8932 (ttt) cc_final: 0.8691 (ttt) REVERT: C 295 HIS cc_start: 0.8927 (m-70) cc_final: 0.8655 (m-70) REVERT: D 44 TYR cc_start: 0.8814 (m-80) cc_final: 0.7977 (m-80) REVERT: D 89 MET cc_start: 0.7537 (mtp) cc_final: 0.7206 (mtp) REVERT: D 183 MET cc_start: 0.8971 (mmp) cc_final: 0.8746 (mmm) REVERT: D 247 MET cc_start: 0.8888 (ttt) cc_final: 0.7650 (tpp) REVERT: D 248 ARG cc_start: 0.8276 (mmt90) cc_final: 0.7901 (mmt180) REVERT: D 488 MET cc_start: 0.9204 (tmm) cc_final: 0.8924 (tmm) REVERT: E 79 MET cc_start: 0.9129 (mmt) cc_final: 0.8797 (mmp) REVERT: E 247 MET cc_start: 0.8905 (tpt) cc_final: 0.8519 (tpp) REVERT: F 79 MET cc_start: 0.8890 (mpp) cc_final: 0.7956 (mpp) REVERT: d 139 GLN cc_start: 0.9339 (mm110) cc_final: 0.9036 (mp10) REVERT: d 250 MET cc_start: 0.4810 (mmt) cc_final: 0.3637 (mtm) REVERT: g 66 LEU cc_start: 0.8456 (mt) cc_final: 0.7791 (tt) REVERT: g 133 PHE cc_start: 0.8421 (t80) cc_final: 0.8198 (t80) REVERT: g 295 LEU cc_start: 0.9293 (mt) cc_final: 0.9021 (mt) REVERT: g 346 GLN cc_start: 0.8419 (mm-40) cc_final: 0.8040 (tt0) outliers start: 2 outliers final: 0 residues processed: 288 average time/residue: 0.1727 time to fit residues: 82.5357 Evaluate side-chains 203 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 176 optimal weight: 2.9990 chunk 175 optimal weight: 4.9990 chunk 57 optimal weight: 20.0000 chunk 281 optimal weight: 1.9990 chunk 306 optimal weight: 0.0000 chunk 66 optimal weight: 3.9990 chunk 318 optimal weight: 5.9990 chunk 297 optimal weight: 0.2980 chunk 69 optimal weight: 3.9990 chunk 330 optimal weight: 8.9990 chunk 248 optimal weight: 9.9990 overall best weight: 1.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 GLN B 43 HIS B 164 GLN B 389 GLN C 34 GLN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN D 299 GLN ** E 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.050137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.041294 restraints weight = 192045.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.042573 restraints weight = 118610.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.043512 restraints weight = 81927.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.044147 restraints weight = 61184.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.044681 restraints weight = 48701.730| |-----------------------------------------------------------------------------| r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27884 Z= 0.150 Angle : 0.654 10.271 37788 Z= 0.339 Chirality : 0.045 0.199 4447 Planarity : 0.005 0.054 4912 Dihedral : 8.183 96.015 4023 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.18 % Favored : 91.74 % Rotamer: Outliers : 0.07 % Allowed : 3.67 % Favored : 96.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.14), residues: 3558 helix: 0.19 (0.13), residues: 1459 sheet: -1.81 (0.23), residues: 481 loop : -2.15 (0.15), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 462 TYR 0.015 0.001 TYR B 457 PHE 0.034 0.002 PHE g 168 TRP 0.009 0.001 TRP e 57 HIS 0.012 0.001 HIS B 43 Details of bonding type rmsd covalent geometry : bond 0.00325 (27883) covalent geometry : angle 0.65391 (37786) SS BOND : bond 0.00243 ( 1) SS BOND : angle 2.11762 ( 2) hydrogen bonds : bond 0.03939 ( 1236) hydrogen bonds : angle 5.01652 ( 3687) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 272 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.8965 (tp) cc_final: 0.8629 (tp) REVERT: A 157 MET cc_start: 0.8913 (ptp) cc_final: 0.7948 (mmt) REVERT: A 251 MET cc_start: 0.8188 (ptp) cc_final: 0.7725 (ppp) REVERT: A 314 MET cc_start: 0.8434 (mmm) cc_final: 0.7836 (mmm) REVERT: A 498 MET cc_start: 0.8768 (mtm) cc_final: 0.8135 (mtp) REVERT: B 82 MET cc_start: 0.8777 (mmp) cc_final: 0.8545 (mmp) REVERT: B 131 GLU cc_start: 0.8780 (mp0) cc_final: 0.8501 (tp30) REVERT: B 236 GLN cc_start: 0.9309 (mt0) cc_final: 0.8764 (mm-40) REVERT: B 251 MET cc_start: 0.7478 (tpt) cc_final: 0.6853 (tpt) REVERT: B 276 LEU cc_start: 0.9122 (tp) cc_final: 0.8436 (tp) REVERT: B 314 MET cc_start: 0.8146 (tpt) cc_final: 0.7420 (tpt) REVERT: C 251 MET cc_start: 0.8908 (ttt) cc_final: 0.8607 (ttt) REVERT: C 295 HIS cc_start: 0.8987 (m-70) cc_final: 0.8671 (m-70) REVERT: D 89 MET cc_start: 0.7585 (mtp) cc_final: 0.7243 (mtp) REVERT: D 488 MET cc_start: 0.9181 (tmm) cc_final: 0.8890 (tmm) REVERT: E 59 MET cc_start: 0.8624 (ptp) cc_final: 0.8291 (ptp) REVERT: E 79 MET cc_start: 0.9178 (mmt) cc_final: 0.8833 (mmp) REVERT: E 89 MET cc_start: 0.8223 (tpt) cc_final: 0.7961 (tpt) REVERT: E 214 MET cc_start: 0.9341 (mmp) cc_final: 0.9027 (mmm) REVERT: E 247 MET cc_start: 0.9005 (tpt) cc_final: 0.8557 (tpp) REVERT: E 273 ASP cc_start: 0.8691 (t0) cc_final: 0.8467 (t70) REVERT: E 335 THR cc_start: 0.8650 (t) cc_final: 0.7800 (t) REVERT: F 79 MET cc_start: 0.8880 (mpp) cc_final: 0.7917 (mpp) REVERT: d 250 MET cc_start: 0.4860 (mmt) cc_final: 0.3814 (mtm) REVERT: g 66 LEU cc_start: 0.8279 (mt) cc_final: 0.7877 (tt) REVERT: g 282 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7520 (pp) REVERT: g 295 LEU cc_start: 0.9232 (mt) cc_final: 0.8825 (mt) REVERT: g 346 GLN cc_start: 0.8440 (mm-40) cc_final: 0.7919 (mt0) outliers start: 2 outliers final: 0 residues processed: 273 average time/residue: 0.1738 time to fit residues: 78.0665 Evaluate side-chains 198 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 197 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 174 optimal weight: 2.9990 chunk 326 optimal weight: 2.9990 chunk 220 optimal weight: 4.9990 chunk 330 optimal weight: 7.9990 chunk 143 optimal weight: 0.8980 chunk 150 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 221 optimal weight: 1.9990 chunk 260 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 443 ASN B 43 HIS B 164 GLN B 269 GLN C 34 GLN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN D 299 GLN ** E 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.050405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.041572 restraints weight = 190497.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.042856 restraints weight = 118194.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.043795 restraints weight = 81605.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.044433 restraints weight = 61000.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.044962 restraints weight = 48506.606| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27884 Z= 0.140 Angle : 0.653 10.823 37788 Z= 0.335 Chirality : 0.044 0.194 4447 Planarity : 0.004 0.050 4912 Dihedral : 8.059 95.841 4023 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.76 % Favored : 92.16 % Rotamer: Outliers : 0.07 % Allowed : 3.16 % Favored : 96.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.14), residues: 3558 helix: 0.29 (0.13), residues: 1462 sheet: -1.71 (0.23), residues: 477 loop : -2.09 (0.15), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 141 TYR 0.015 0.001 TYR g 167 PHE 0.033 0.001 PHE B 213 TRP 0.006 0.001 TRP e 57 HIS 0.010 0.001 HIS B 43 Details of bonding type rmsd covalent geometry : bond 0.00306 (27883) covalent geometry : angle 0.65243 (37786) SS BOND : bond 0.01753 ( 1) SS BOND : angle 2.77063 ( 2) hydrogen bonds : bond 0.03833 ( 1236) hydrogen bonds : angle 4.88186 ( 3687) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 273 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.8968 (tp) cc_final: 0.8674 (tp) REVERT: A 157 MET cc_start: 0.8882 (ptp) cc_final: 0.7956 (mmt) REVERT: A 251 MET cc_start: 0.8199 (ptp) cc_final: 0.7768 (ppp) REVERT: A 314 MET cc_start: 0.8474 (mmm) cc_final: 0.7864 (mmm) REVERT: A 498 MET cc_start: 0.8711 (mtm) cc_final: 0.8039 (mtp) REVERT: B 82 MET cc_start: 0.8808 (mmp) cc_final: 0.8585 (mmp) REVERT: B 236 GLN cc_start: 0.9318 (mt0) cc_final: 0.8759 (mm-40) REVERT: B 251 MET cc_start: 0.7521 (tpt) cc_final: 0.6930 (tpt) REVERT: B 314 MET cc_start: 0.8174 (tpt) cc_final: 0.7433 (tpt) REVERT: C 251 MET cc_start: 0.8915 (ttt) cc_final: 0.8604 (ttt) REVERT: C 295 HIS cc_start: 0.8962 (m-70) cc_final: 0.8656 (m-70) REVERT: D 85 LEU cc_start: 0.9441 (mt) cc_final: 0.9022 (mt) REVERT: D 247 MET cc_start: 0.8789 (ttt) cc_final: 0.8469 (ttt) REVERT: D 488 MET cc_start: 0.9155 (tmm) cc_final: 0.8926 (tmm) REVERT: E 79 MET cc_start: 0.9089 (mmt) cc_final: 0.8777 (mmp) REVERT: E 89 MET cc_start: 0.8111 (tpt) cc_final: 0.7827 (tpt) REVERT: E 214 MET cc_start: 0.9281 (mmp) cc_final: 0.9029 (mmm) REVERT: E 247 MET cc_start: 0.8971 (tpt) cc_final: 0.8537 (tpp) REVERT: E 335 THR cc_start: 0.8641 (t) cc_final: 0.7928 (t) REVERT: F 79 MET cc_start: 0.8926 (mpp) cc_final: 0.7918 (mpp) REVERT: F 167 LYS cc_start: 0.9193 (mppt) cc_final: 0.8874 (mtmt) REVERT: d 250 MET cc_start: 0.4832 (mmt) cc_final: 0.3905 (mtm) REVERT: e 90 GLN cc_start: 0.9376 (tm-30) cc_final: 0.9165 (tm-30) REVERT: g 66 LEU cc_start: 0.8188 (mt) cc_final: 0.7812 (tt) REVERT: g 133 PHE cc_start: 0.8393 (t80) cc_final: 0.7890 (t80) REVERT: g 295 LEU cc_start: 0.9352 (mt) cc_final: 0.9045 (mt) REVERT: g 323 MET cc_start: 0.9358 (mmp) cc_final: 0.8875 (mmm) REVERT: g 346 GLN cc_start: 0.8430 (mm-40) cc_final: 0.7972 (mt0) outliers start: 2 outliers final: 0 residues processed: 275 average time/residue: 0.1736 time to fit residues: 78.9801 Evaluate side-chains 203 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 71 optimal weight: 2.9990 chunk 175 optimal weight: 6.9990 chunk 243 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 59 optimal weight: 0.3980 chunk 190 optimal weight: 9.9990 chunk 147 optimal weight: 2.9990 chunk 281 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 349 optimal weight: 6.9990 chunk 276 optimal weight: 0.7980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 HIS B 164 GLN B 269 GLN C 34 GLN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN ** F 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.050709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.041843 restraints weight = 189076.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.043149 restraints weight = 116719.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.044094 restraints weight = 80413.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.044742 restraints weight = 59971.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.045250 restraints weight = 47652.985| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27884 Z= 0.130 Angle : 0.654 11.330 37788 Z= 0.334 Chirality : 0.045 0.244 4447 Planarity : 0.004 0.052 4912 Dihedral : 7.931 94.766 4023 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.36 % Favored : 92.55 % Rotamer: Outliers : 0.03 % Allowed : 1.73 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.14), residues: 3558 helix: 0.40 (0.13), residues: 1464 sheet: -1.67 (0.23), residues: 492 loop : -2.02 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 500 TYR 0.017 0.001 TYR E 298 PHE 0.031 0.001 PHE g 133 TRP 0.005 0.001 TRP e 57 HIS 0.009 0.001 HIS B 43 Details of bonding type rmsd covalent geometry : bond 0.00284 (27883) covalent geometry : angle 0.65427 (37786) SS BOND : bond 0.00533 ( 1) SS BOND : angle 2.34568 ( 2) hydrogen bonds : bond 0.03766 ( 1236) hydrogen bonds : angle 4.81144 ( 3687) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 278 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.9039 (tp) cc_final: 0.8771 (tp) REVERT: A 157 MET cc_start: 0.8860 (ptp) cc_final: 0.7952 (mmt) REVERT: A 251 MET cc_start: 0.8219 (ptp) cc_final: 0.7939 (ppp) REVERT: A 314 MET cc_start: 0.8496 (mmm) cc_final: 0.7845 (mmm) REVERT: A 321 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7940 (tm-30) REVERT: A 498 MET cc_start: 0.8750 (mtm) cc_final: 0.8161 (mtp) REVERT: B 1 MET cc_start: 0.5784 (mmt) cc_final: 0.5538 (mmt) REVERT: B 236 GLN cc_start: 0.9336 (mt0) cc_final: 0.8725 (mm-40) REVERT: C 77 MET cc_start: 0.8312 (ttp) cc_final: 0.8016 (ttm) REVERT: C 157 MET cc_start: 0.8579 (mmm) cc_final: 0.8376 (mmm) REVERT: C 182 ASP cc_start: 0.8101 (m-30) cc_final: 0.7892 (m-30) REVERT: C 219 MET cc_start: 0.8479 (mpp) cc_final: 0.8145 (mpp) REVERT: C 251 MET cc_start: 0.8880 (ttt) cc_final: 0.8568 (ttt) REVERT: C 295 HIS cc_start: 0.8967 (m-70) cc_final: 0.8630 (m-70) REVERT: D 183 MET cc_start: 0.8901 (mmp) cc_final: 0.8611 (mmm) REVERT: D 343 PHE cc_start: 0.8466 (m-10) cc_final: 0.8252 (m-80) REVERT: E 79 MET cc_start: 0.9069 (mmt) cc_final: 0.8762 (mmp) REVERT: E 89 MET cc_start: 0.8107 (tpt) cc_final: 0.7804 (tpt) REVERT: E 247 MET cc_start: 0.8956 (tpt) cc_final: 0.8477 (tpp) REVERT: E 335 THR cc_start: 0.8664 (t) cc_final: 0.7881 (t) REVERT: F 167 LYS cc_start: 0.9178 (mppt) cc_final: 0.8874 (mtmt) REVERT: F 256 MET cc_start: 0.8733 (mmm) cc_final: 0.8274 (mmm) REVERT: d 250 MET cc_start: 0.5093 (mmt) cc_final: 0.4134 (mtm) REVERT: g 66 LEU cc_start: 0.8451 (mt) cc_final: 0.7816 (tt) REVERT: g 295 LEU cc_start: 0.9325 (mt) cc_final: 0.9023 (mt) REVERT: g 323 MET cc_start: 0.9338 (mmp) cc_final: 0.8894 (mmm) REVERT: g 346 GLN cc_start: 0.8410 (mm-40) cc_final: 0.7971 (mt0) outliers start: 1 outliers final: 0 residues processed: 279 average time/residue: 0.1675 time to fit residues: 77.3414 Evaluate side-chains 208 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 332 optimal weight: 4.9990 chunk 329 optimal weight: 0.5980 chunk 128 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 307 optimal weight: 7.9990 chunk 287 optimal weight: 0.7980 chunk 246 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 123 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 267 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 HIS B 164 GLN B 269 GLN C 34 GLN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN D 67 GLN ** E 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 144 ASN g 76 GLN ** g 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.051358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.042413 restraints weight = 188671.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.043745 restraints weight = 116731.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.044706 restraints weight = 80357.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.045358 restraints weight = 59774.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.045881 restraints weight = 47522.848| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27884 Z= 0.121 Angle : 0.657 11.789 37788 Z= 0.333 Chirality : 0.045 0.199 4447 Planarity : 0.004 0.068 4912 Dihedral : 7.793 92.015 4023 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.22 % Favored : 92.69 % Rotamer: Outliers : 0.03 % Allowed : 1.16 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.14), residues: 3558 helix: 0.50 (0.14), residues: 1461 sheet: -1.63 (0.23), residues: 496 loop : -2.01 (0.15), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 378 TYR 0.016 0.001 TYR E 298 PHE 0.019 0.001 PHE g 133 TRP 0.005 0.001 TRP e 57 HIS 0.008 0.001 HIS B 43 Details of bonding type rmsd covalent geometry : bond 0.00265 (27883) covalent geometry : angle 0.65680 (37786) SS BOND : bond 0.00435 ( 1) SS BOND : angle 1.94445 ( 2) hydrogen bonds : bond 0.03674 ( 1236) hydrogen bonds : angle 4.74305 ( 3687) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 281 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.9039 (tp) cc_final: 0.8802 (tp) REVERT: A 157 MET cc_start: 0.8830 (ptp) cc_final: 0.7949 (mmt) REVERT: A 219 MET cc_start: 0.8934 (mmm) cc_final: 0.7720 (mpp) REVERT: A 251 MET cc_start: 0.8190 (ptp) cc_final: 0.7915 (ppp) REVERT: A 314 MET cc_start: 0.8482 (mmm) cc_final: 0.7813 (mmm) REVERT: A 376 MET cc_start: 0.8959 (ptt) cc_final: 0.8413 (ppp) REVERT: A 498 MET cc_start: 0.8805 (mtm) cc_final: 0.8313 (mtp) REVERT: B 1 MET cc_start: 0.5729 (mmt) cc_final: 0.5483 (mmt) REVERT: B 236 GLN cc_start: 0.9306 (mt0) cc_final: 0.9008 (mt0) REVERT: B 251 MET cc_start: 0.7364 (tpt) cc_final: 0.6542 (tpt) REVERT: B 314 MET cc_start: 0.8265 (tpt) cc_final: 0.7734 (tpt) REVERT: B 355 ARG cc_start: 0.8925 (mmp-170) cc_final: 0.8337 (mmm160) REVERT: C 77 MET cc_start: 0.8382 (ttp) cc_final: 0.8068 (ttm) REVERT: C 251 MET cc_start: 0.8758 (ttt) cc_final: 0.8488 (ttt) REVERT: C 295 HIS cc_start: 0.8916 (m-70) cc_final: 0.8598 (m-70) REVERT: C 403 LEU cc_start: 0.9423 (mm) cc_final: 0.9066 (mt) REVERT: D 183 MET cc_start: 0.8937 (mmp) cc_final: 0.8601 (mmm) REVERT: D 275 ILE cc_start: 0.9385 (pt) cc_final: 0.8896 (tp) REVERT: D 374 MET cc_start: 0.8711 (mmm) cc_final: 0.8253 (mmt) REVERT: D 488 MET cc_start: 0.9195 (tmm) cc_final: 0.8950 (tmm) REVERT: E 79 MET cc_start: 0.9052 (mmt) cc_final: 0.8792 (mmp) REVERT: E 89 MET cc_start: 0.8125 (tpt) cc_final: 0.7822 (tpt) REVERT: E 247 MET cc_start: 0.8915 (tpt) cc_final: 0.8467 (tpp) REVERT: F 167 LYS cc_start: 0.9147 (mppt) cc_final: 0.8836 (mtmt) REVERT: F 256 MET cc_start: 0.8771 (mmm) cc_final: 0.8277 (mmm) REVERT: d 250 MET cc_start: 0.5368 (mmt) cc_final: 0.4504 (mtm) REVERT: g 66 LEU cc_start: 0.8470 (mt) cc_final: 0.7844 (tt) REVERT: g 295 LEU cc_start: 0.9338 (mt) cc_final: 0.9078 (mt) REVERT: g 323 MET cc_start: 0.9290 (mmp) cc_final: 0.8879 (mmm) REVERT: g 346 GLN cc_start: 0.8371 (mm-40) cc_final: 0.7982 (tt0) outliers start: 1 outliers final: 0 residues processed: 282 average time/residue: 0.1739 time to fit residues: 81.0202 Evaluate side-chains 212 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 41 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 230 optimal weight: 20.0000 chunk 299 optimal weight: 4.9990 chunk 184 optimal weight: 0.0770 chunk 194 optimal weight: 0.9980 chunk 352 optimal weight: 0.9980 chunk 142 optimal weight: 9.9990 chunk 319 optimal weight: 0.9990 chunk 280 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 overall best weight: 0.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 HIS B 164 GLN B 269 GLN C 34 GLN C 164 GLN ** C 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN ** E 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.051459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.042511 restraints weight = 189422.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.043816 restraints weight = 117575.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.044776 restraints weight = 81256.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.045465 restraints weight = 60537.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.045921 restraints weight = 48162.684| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27884 Z= 0.122 Angle : 0.657 12.026 37788 Z= 0.333 Chirality : 0.045 0.205 4447 Planarity : 0.005 0.166 4912 Dihedral : 7.673 90.757 4023 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.25 % Favored : 92.66 % Rotamer: Outliers : 0.07 % Allowed : 0.92 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.14), residues: 3558 helix: 0.53 (0.14), residues: 1460 sheet: -1.53 (0.23), residues: 494 loop : -1.96 (0.15), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 255 TYR 0.016 0.001 TYR E 298 PHE 0.040 0.002 PHE g 168 TRP 0.005 0.001 TRP e 57 HIS 0.008 0.001 HIS B 43 Details of bonding type rmsd covalent geometry : bond 0.00268 (27883) covalent geometry : angle 0.65652 (37786) SS BOND : bond 0.00420 ( 1) SS BOND : angle 1.88068 ( 2) hydrogen bonds : bond 0.03697 ( 1236) hydrogen bonds : angle 4.70387 ( 3687) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 286 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.9039 (tp) cc_final: 0.8836 (tp) REVERT: A 157 MET cc_start: 0.8801 (ptp) cc_final: 0.7934 (mmt) REVERT: A 219 MET cc_start: 0.8869 (mmm) cc_final: 0.7735 (mpp) REVERT: A 236 GLN cc_start: 0.8993 (mt0) cc_final: 0.8614 (mm-40) REVERT: A 251 MET cc_start: 0.8171 (ptp) cc_final: 0.7947 (ppp) REVERT: A 314 MET cc_start: 0.8463 (mmm) cc_final: 0.7801 (mmm) REVERT: A 376 MET cc_start: 0.8921 (ptt) cc_final: 0.8408 (ppp) REVERT: A 498 MET cc_start: 0.8779 (mtm) cc_final: 0.8294 (mtp) REVERT: B 1 MET cc_start: 0.5721 (mmt) cc_final: 0.5421 (mmt) REVERT: B 236 GLN cc_start: 0.9275 (mt0) cc_final: 0.9016 (mt0) REVERT: B 251 MET cc_start: 0.7393 (tpt) cc_final: 0.6617 (tpt) REVERT: B 314 MET cc_start: 0.8141 (tpt) cc_final: 0.7529 (tpt) REVERT: B 355 ARG cc_start: 0.8935 (mmp-170) cc_final: 0.8290 (mmm160) REVERT: C 77 MET cc_start: 0.8290 (ttp) cc_final: 0.7976 (ttm) REVERT: C 251 MET cc_start: 0.8747 (ttt) cc_final: 0.8491 (ttt) REVERT: C 295 HIS cc_start: 0.8888 (m-70) cc_final: 0.8561 (m-70) REVERT: C 403 LEU cc_start: 0.9437 (mm) cc_final: 0.9078 (mt) REVERT: D 183 MET cc_start: 0.8897 (mmp) cc_final: 0.8558 (mmm) REVERT: E 79 MET cc_start: 0.9032 (mmt) cc_final: 0.8791 (mmp) REVERT: E 89 MET cc_start: 0.8082 (tpt) cc_final: 0.7796 (tpt) REVERT: E 247 MET cc_start: 0.8885 (tpt) cc_final: 0.8438 (tpp) REVERT: F 167 LYS cc_start: 0.9158 (mppt) cc_final: 0.8856 (mtmt) REVERT: F 256 MET cc_start: 0.8763 (mmm) cc_final: 0.8308 (mmm) REVERT: d 250 MET cc_start: 0.5304 (mmt) cc_final: 0.4459 (mtm) REVERT: e 24 LEU cc_start: 0.8728 (pt) cc_final: 0.8508 (pt) REVERT: g 66 LEU cc_start: 0.8389 (mt) cc_final: 0.7763 (tt) REVERT: g 295 LEU cc_start: 0.9335 (mt) cc_final: 0.9058 (mp) REVERT: g 346 GLN cc_start: 0.8316 (mm-40) cc_final: 0.7948 (tt0) outliers start: 2 outliers final: 1 residues processed: 288 average time/residue: 0.1724 time to fit residues: 82.4413 Evaluate side-chains 218 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 217 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 49 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 309 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 171 optimal weight: 8.9990 chunk 234 optimal weight: 0.9990 chunk 112 optimal weight: 0.0980 chunk 68 optimal weight: 0.0000 chunk 27 optimal weight: 3.9990 chunk 275 optimal weight: 6.9990 chunk 88 optimal weight: 9.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 GLN ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 HIS B 164 GLN C 34 GLN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN ** E 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.051953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.042941 restraints weight = 188983.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.044277 restraints weight = 117149.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.045242 restraints weight = 80735.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.045907 restraints weight = 60417.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.046423 restraints weight = 48065.939| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 27884 Z= 0.121 Angle : 0.671 13.958 37788 Z= 0.339 Chirality : 0.045 0.264 4447 Planarity : 0.005 0.091 4912 Dihedral : 7.594 87.799 4023 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.97 % Favored : 92.95 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.14), residues: 3558 helix: 0.57 (0.14), residues: 1459 sheet: -1.44 (0.24), residues: 486 loop : -1.93 (0.15), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG A 14 TYR 0.025 0.001 TYR C 241 PHE 0.030 0.001 PHE D 343 TRP 0.005 0.001 TRP e 57 HIS 0.008 0.001 HIS B 43 Details of bonding type rmsd covalent geometry : bond 0.00264 (27883) covalent geometry : angle 0.67117 (37786) SS BOND : bond 0.00434 ( 1) SS BOND : angle 1.91312 ( 2) hydrogen bonds : bond 0.03754 ( 1236) hydrogen bonds : angle 4.62962 ( 3687) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 MET cc_start: 0.8746 (ptp) cc_final: 0.7835 (mmt) REVERT: A 219 MET cc_start: 0.8857 (mmm) cc_final: 0.7715 (mpp) REVERT: A 236 GLN cc_start: 0.9047 (mt0) cc_final: 0.8646 (mm-40) REVERT: A 251 MET cc_start: 0.8160 (ptp) cc_final: 0.7901 (ppp) REVERT: A 314 MET cc_start: 0.8490 (mmm) cc_final: 0.7811 (mmm) REVERT: A 498 MET cc_start: 0.8786 (mtm) cc_final: 0.8285 (mtp) REVERT: B 1 MET cc_start: 0.5689 (mmt) cc_final: 0.5406 (mmt) REVERT: B 236 GLN cc_start: 0.9261 (mt0) cc_final: 0.9006 (mt0) REVERT: B 251 MET cc_start: 0.7381 (tpt) cc_final: 0.6339 (tpt) REVERT: B 314 MET cc_start: 0.8171 (tpt) cc_final: 0.7552 (tpt) REVERT: B 355 ARG cc_start: 0.8965 (mmp-170) cc_final: 0.8293 (mmm160) REVERT: C 77 MET cc_start: 0.8278 (ttp) cc_final: 0.8029 (ttm) REVERT: C 251 MET cc_start: 0.8717 (ttt) cc_final: 0.8455 (ttt) REVERT: C 295 HIS cc_start: 0.8885 (m-70) cc_final: 0.8583 (m-70) REVERT: C 403 LEU cc_start: 0.9456 (mm) cc_final: 0.9117 (mt) REVERT: D 183 MET cc_start: 0.8936 (mmp) cc_final: 0.8611 (mmm) REVERT: D 275 ILE cc_start: 0.9362 (pt) cc_final: 0.9080 (tp) REVERT: E 89 MET cc_start: 0.8130 (tpt) cc_final: 0.7868 (tpt) REVERT: E 247 MET cc_start: 0.8873 (tpt) cc_final: 0.8419 (tpp) REVERT: E 269 LEU cc_start: 0.9266 (tp) cc_final: 0.8504 (tt) REVERT: E 271 PHE cc_start: 0.7959 (m-10) cc_final: 0.7629 (m-10) REVERT: E 335 THR cc_start: 0.8473 (t) cc_final: 0.7807 (t) REVERT: F 167 LYS cc_start: 0.9142 (mppt) cc_final: 0.8764 (mtmt) REVERT: F 256 MET cc_start: 0.8755 (mmm) cc_final: 0.8288 (mmm) REVERT: F 306 MET cc_start: 0.9108 (tpp) cc_final: 0.8194 (ttp) REVERT: d 250 MET cc_start: 0.5279 (mmt) cc_final: 0.4452 (mtm) REVERT: g 66 LEU cc_start: 0.7985 (mt) cc_final: 0.7705 (tt) REVERT: g 295 LEU cc_start: 0.9339 (mt) cc_final: 0.9096 (mt) REVERT: g 346 GLN cc_start: 0.8364 (mm-40) cc_final: 0.7918 (mt0) outliers start: 0 outliers final: 0 residues processed: 290 average time/residue: 0.1668 time to fit residues: 80.4289 Evaluate side-chains 214 residues out of total 2944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 287 optimal weight: 1.9990 chunk 293 optimal weight: 3.9990 chunk 222 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 341 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 257 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 206 optimal weight: 8.9990 chunk 130 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 HIS B 164 GLN B 269 GLN C 34 GLN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.049836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.041024 restraints weight = 190250.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.042292 restraints weight = 118030.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.043204 restraints weight = 81480.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.043902 restraints weight = 61008.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.044395 restraints weight = 48301.050| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 27884 Z= 0.191 Angle : 0.708 15.585 37788 Z= 0.362 Chirality : 0.046 0.240 4447 Planarity : 0.005 0.068 4912 Dihedral : 7.672 95.630 4023 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.40 % Favored : 91.51 % Rotamer: Outliers : 0.03 % Allowed : 0.34 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.14), residues: 3558 helix: 0.56 (0.14), residues: 1470 sheet: -1.51 (0.23), residues: 493 loop : -1.94 (0.16), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 366 TYR 0.020 0.002 TYR D 298 PHE 0.034 0.002 PHE E 271 TRP 0.002 0.001 TRP e 15 HIS 0.011 0.001 HIS B 43 Details of bonding type rmsd covalent geometry : bond 0.00406 (27883) covalent geometry : angle 0.70769 (37786) SS BOND : bond 0.00420 ( 1) SS BOND : angle 2.25711 ( 2) hydrogen bonds : bond 0.03893 ( 1236) hydrogen bonds : angle 4.73961 ( 3687) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3781.17 seconds wall clock time: 66 minutes 53.70 seconds (4013.70 seconds total)