Starting phenix.real_space_refine on Sat Jul 4 16:41:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wf3_32459/07_2026/7wf3_32459_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wf3_32459/07_2026/7wf3_32459.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wf3_32459/07_2026/7wf3_32459.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wf3_32459/07_2026/7wf3_32459.map" model { file = "/net/cci-nas-00/data/ceres_data/7wf3_32459/07_2026/7wf3_32459_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wf3_32459/07_2026/7wf3_32459_neut.cif" } resolution = 3.4 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= -0.041 sd= 1.215 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 4 8.98 5 P 12 5.49 5 S 116 5.16 5 C 14164 2.51 5 N 3720 2.21 5 O 4084 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 128 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22100 Number of models: 1 Model: "" Number of chains: 25 Chain: "B" Number of atoms: 2002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2002 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 13, 'TRANS': 238} Chain breaks: 2 Chain: "C" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2557 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 315} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 2002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2002 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 13, 'TRANS': 238} Chain breaks: 2 Chain: "F" Number of atoms: 2002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2002 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 13, 'TRANS': 238} Chain breaks: 2 Chain: "G" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2557 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 315} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 2002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2002 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 13, 'TRANS': 238} Chain breaks: 2 Chain: "I" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2557 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 315} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 13 Chain: "J" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 888 Classifications: {'peptide': 106} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "M" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2557 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 315} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 13 Chain: "N" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 888 Classifications: {'peptide': 106} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "O" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 888 Classifications: {'peptide': 106} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "P" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 888 Classifications: {'peptide': 106} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 0 Ad-hoc single atom residues: {' K': 4} Chain breaks: 4 Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "F" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "G" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "H" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "I" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "M" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Time building chain proxies: 5.16, per 1000 atoms: 0.23 Number of scatterers: 22100 At special positions: 0 Unit cell: (131.274, 131.274, 159.588, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 4 19.00 S 116 16.00 P 12 15.00 O 4084 8.00 N 3720 7.00 C 14164 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS J 101 " - pdb=" SG CYS J 123 " distance=2.03 Simple disulfide: pdb=" SG CYS N 101 " - pdb=" SG CYS N 123 " distance=2.03 Simple disulfide: pdb=" SG CYS O 101 " - pdb=" SG CYS O 123 " distance=2.03 Simple disulfide: pdb=" SG CYS P 101 " - pdb=" SG CYS P 123 " distance=2.03 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: 1.63 Conformation dependent library (CDL) restraints added in 873.7 milliseconds 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5072 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 12 sheets defined 62.2% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'B' and resid 217 through 226 Processing helix chain 'B' and resid 230 through 254 Processing helix chain 'B' and resid 294 through 316 removed outlier: 3.568A pdb=" N THR B 300 " --> pdb=" O PHE B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 326 removed outlier: 3.534A pdb=" N PHE B 323 " --> pdb=" O SER B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 352 removed outlier: 3.594A pdb=" N ILE B 337 " --> pdb=" O ILE B 333 " (cutoff:3.500A) Proline residue: B 338 - end of helix Processing helix chain 'B' and resid 360 through 370 removed outlier: 3.604A pdb=" N ARG B 370 " --> pdb=" O ILE B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 380 removed outlier: 3.610A pdb=" N ARG B 379 " --> pdb=" O LYS B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 393 removed outlier: 3.785A pdb=" N GLN B 385 " --> pdb=" O SER B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 419 removed outlier: 3.575A pdb=" N LEU B 398 " --> pdb=" O SER B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 440 removed outlier: 3.572A pdb=" N PHE B 435 " --> pdb=" O ILE B 431 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N TRP B 436 " --> pdb=" O PRO B 432 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N TRP B 437 " --> pdb=" O ASP B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 474 removed outlier: 3.803A pdb=" N LYS B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL B 469 " --> pdb=" O ALA B 465 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 492 removed outlier: 4.134A pdb=" N ILE B 479 " --> pdb=" O PRO B 475 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLU B 490 " --> pdb=" O PHE B 486 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N THR B 491 " --> pdb=" O TYR B 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 79 removed outlier: 3.696A pdb=" N ASN C 79 " --> pdb=" O LEU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 92 removed outlier: 3.650A pdb=" N ALA C 92 " --> pdb=" O VAL C 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 89 through 92' Processing helix chain 'C' and resid 93 through 107 removed outlier: 3.518A pdb=" N ILE C 103 " --> pdb=" O LEU C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 113 removed outlier: 3.523A pdb=" N SER C 112 " --> pdb=" O ARG C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 129 removed outlier: 4.004A pdb=" N ARG C 129 " --> pdb=" O GLU C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 148 Processing helix chain 'C' and resid 165 through 179 removed outlier: 3.590A pdb=" N THR C 169 " --> pdb=" O PRO C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 205 Processing helix chain 'C' and resid 222 through 228 removed outlier: 3.680A pdb=" N GLU C 226 " --> pdb=" O ARG C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 236 removed outlier: 4.030A pdb=" N LEU C 232 " --> pdb=" O GLN C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 250 Processing helix chain 'C' and resid 270 through 278 removed outlier: 3.665A pdb=" N LYS C 274 " --> pdb=" O TYR C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 300 removed outlier: 3.920A pdb=" N ARG C 283 " --> pdb=" O SER C 279 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ARG C 284 " --> pdb=" O GLU C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 311 removed outlier: 3.980A pdb=" N CYS C 311 " --> pdb=" O ALA C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 335 removed outlier: 3.881A pdb=" N GLY C 335 " --> pdb=" O MET C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 343 removed outlier: 3.589A pdb=" N LEU C 343 " --> pdb=" O LEU C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 356 Processing helix chain 'D' and resid 217 through 226 Processing helix chain 'D' and resid 230 through 254 Processing helix chain 'D' and resid 294 through 316 removed outlier: 3.569A pdb=" N THR D 300 " --> pdb=" O PHE D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 326 removed outlier: 3.535A pdb=" N PHE D 323 " --> pdb=" O SER D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 352 removed outlier: 3.594A pdb=" N ILE D 337 " --> pdb=" O ILE D 333 " (cutoff:3.500A) Proline residue: D 338 - end of helix Processing helix chain 'D' and resid 360 through 370 removed outlier: 3.604A pdb=" N ARG D 370 " --> pdb=" O ILE D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 380 removed outlier: 3.611A pdb=" N ARG D 379 " --> pdb=" O LYS D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 393 removed outlier: 3.785A pdb=" N GLN D 385 " --> pdb=" O SER D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 419 removed outlier: 3.574A pdb=" N LEU D 398 " --> pdb=" O SER D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 440 removed outlier: 3.571A pdb=" N PHE D 435 " --> pdb=" O ILE D 431 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N TRP D 436 " --> pdb=" O PRO D 432 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N TRP D 437 " --> pdb=" O ASP D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 474 removed outlier: 3.804A pdb=" N LYS D 458 " --> pdb=" O THR D 454 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL D 469 " --> pdb=" O ALA D 465 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU D 470 " --> pdb=" O ILE D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 492 removed outlier: 4.134A pdb=" N ILE D 479 " --> pdb=" O PRO D 475 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLU D 490 " --> pdb=" O PHE D 486 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N THR D 491 " --> pdb=" O TYR D 487 " (cutoff:3.500A) Processing helix chain 'F' and resid 217 through 226 Processing helix chain 'F' and resid 230 through 254 Processing helix chain 'F' and resid 294 through 316 removed outlier: 3.567A pdb=" N THR F 300 " --> pdb=" O PHE F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 326 removed outlier: 3.536A pdb=" N PHE F 323 " --> pdb=" O SER F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 352 removed outlier: 3.594A pdb=" N ILE F 337 " --> pdb=" O ILE F 333 " (cutoff:3.500A) Proline residue: F 338 - end of helix Processing helix chain 'F' and resid 360 through 370 removed outlier: 3.605A pdb=" N ARG F 370 " --> pdb=" O ILE F 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 371 through 380 removed outlier: 3.611A pdb=" N ARG F 379 " --> pdb=" O LYS F 376 " (cutoff:3.500A) Processing helix chain 'F' and resid 381 through 393 removed outlier: 3.785A pdb=" N GLN F 385 " --> pdb=" O SER F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 419 removed outlier: 3.575A pdb=" N LEU F 398 " --> pdb=" O SER F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 430 through 440 removed outlier: 3.571A pdb=" N PHE F 435 " --> pdb=" O ILE F 431 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N TRP F 436 " --> pdb=" O PRO F 432 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N TRP F 437 " --> pdb=" O ASP F 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 454 through 474 removed outlier: 3.803A pdb=" N LYS F 458 " --> pdb=" O THR F 454 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL F 469 " --> pdb=" O ALA F 465 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU F 470 " --> pdb=" O ILE F 466 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 492 removed outlier: 4.135A pdb=" N ILE F 479 " --> pdb=" O PRO F 475 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLU F 490 " --> pdb=" O PHE F 486 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N THR F 491 " --> pdb=" O TYR F 487 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 79 removed outlier: 3.696A pdb=" N ASN G 79 " --> pdb=" O LEU G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 92 removed outlier: 3.650A pdb=" N ALA G 92 " --> pdb=" O VAL G 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 89 through 92' Processing helix chain 'G' and resid 93 through 107 removed outlier: 3.518A pdb=" N ILE G 103 " --> pdb=" O LEU G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 113 removed outlier: 3.524A pdb=" N SER G 112 " --> pdb=" O ARG G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 129 removed outlier: 4.004A pdb=" N ARG G 129 " --> pdb=" O GLU G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 148 Processing helix chain 'G' and resid 165 through 179 removed outlier: 3.589A pdb=" N THR G 169 " --> pdb=" O PRO G 165 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 205 Processing helix chain 'G' and resid 222 through 228 removed outlier: 3.680A pdb=" N GLU G 226 " --> pdb=" O ARG G 222 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 236 removed outlier: 4.031A pdb=" N LEU G 232 " --> pdb=" O GLN G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 250 Processing helix chain 'G' and resid 270 through 278 removed outlier: 3.664A pdb=" N LYS G 274 " --> pdb=" O TYR G 270 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 300 removed outlier: 3.921A pdb=" N ARG G 283 " --> pdb=" O SER G 279 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG G 284 " --> pdb=" O GLU G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 302 through 311 removed outlier: 3.980A pdb=" N CYS G 311 " --> pdb=" O ALA G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 326 through 335 removed outlier: 3.880A pdb=" N GLY G 335 " --> pdb=" O MET G 331 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 343 removed outlier: 3.588A pdb=" N LEU G 343 " --> pdb=" O LEU G 340 " (cutoff:3.500A) Processing helix chain 'G' and resid 344 through 356 Processing helix chain 'H' and resid 217 through 226 Processing helix chain 'H' and resid 230 through 254 Processing helix chain 'H' and resid 294 through 316 removed outlier: 3.568A pdb=" N THR H 300 " --> pdb=" O PHE H 296 " (cutoff:3.500A) Processing helix chain 'H' and resid 319 through 326 removed outlier: 3.535A pdb=" N PHE H 323 " --> pdb=" O SER H 319 " (cutoff:3.500A) Processing helix chain 'H' and resid 327 through 352 removed outlier: 3.595A pdb=" N ILE H 337 " --> pdb=" O ILE H 333 " (cutoff:3.500A) Proline residue: H 338 - end of helix Processing helix chain 'H' and resid 360 through 370 removed outlier: 3.605A pdb=" N ARG H 370 " --> pdb=" O ILE H 366 " (cutoff:3.500A) Processing helix chain 'H' and resid 371 through 380 removed outlier: 3.611A pdb=" N ARG H 379 " --> pdb=" O LYS H 376 " (cutoff:3.500A) Processing helix chain 'H' and resid 381 through 393 removed outlier: 3.785A pdb=" N GLN H 385 " --> pdb=" O SER H 381 " (cutoff:3.500A) Processing helix chain 'H' and resid 394 through 419 removed outlier: 3.574A pdb=" N LEU H 398 " --> pdb=" O SER H 394 " (cutoff:3.500A) Processing helix chain 'H' and resid 430 through 440 removed outlier: 3.571A pdb=" N PHE H 435 " --> pdb=" O ILE H 431 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N TRP H 436 " --> pdb=" O PRO H 432 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N TRP H 437 " --> pdb=" O ASP H 433 " (cutoff:3.500A) Processing helix chain 'H' and resid 454 through 474 removed outlier: 3.803A pdb=" N LYS H 458 " --> pdb=" O THR H 454 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL H 469 " --> pdb=" O ALA H 465 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU H 470 " --> pdb=" O ILE H 466 " (cutoff:3.500A) Processing helix chain 'H' and resid 475 through 492 removed outlier: 4.134A pdb=" N ILE H 479 " --> pdb=" O PRO H 475 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLU H 490 " --> pdb=" O PHE H 486 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N THR H 491 " --> pdb=" O TYR H 487 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 79 removed outlier: 3.697A pdb=" N ASN I 79 " --> pdb=" O LEU I 75 " (cutoff:3.500A) Processing helix chain 'I' and resid 89 through 92 removed outlier: 3.650A pdb=" N ALA I 92 " --> pdb=" O VAL I 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 89 through 92' Processing helix chain 'I' and resid 93 through 107 removed outlier: 3.518A pdb=" N ILE I 103 " --> pdb=" O LEU I 99 " (cutoff:3.500A) Processing helix chain 'I' and resid 109 through 113 removed outlier: 3.524A pdb=" N SER I 112 " --> pdb=" O ARG I 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 125 through 129 removed outlier: 4.004A pdb=" N ARG I 129 " --> pdb=" O GLU I 126 " (cutoff:3.500A) Processing helix chain 'I' and resid 132 through 148 Processing helix chain 'I' and resid 165 through 179 removed outlier: 3.588A pdb=" N THR I 169 " --> pdb=" O PRO I 165 " (cutoff:3.500A) Processing helix chain 'I' and resid 191 through 205 Processing helix chain 'I' and resid 222 through 228 removed outlier: 3.680A pdb=" N GLU I 226 " --> pdb=" O ARG I 222 " (cutoff:3.500A) Processing helix chain 'I' and resid 228 through 236 removed outlier: 4.030A pdb=" N LEU I 232 " --> pdb=" O GLN I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 246 through 250 Processing helix chain 'I' and resid 270 through 278 removed outlier: 3.665A pdb=" N LYS I 274 " --> pdb=" O TYR I 270 " (cutoff:3.500A) Processing helix chain 'I' and resid 279 through 300 removed outlier: 3.921A pdb=" N ARG I 283 " --> pdb=" O SER I 279 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ARG I 284 " --> pdb=" O GLU I 280 " (cutoff:3.500A) Processing helix chain 'I' and resid 302 through 311 removed outlier: 3.980A pdb=" N CYS I 311 " --> pdb=" O ALA I 307 " (cutoff:3.500A) Processing helix chain 'I' and resid 326 through 335 removed outlier: 3.880A pdb=" N GLY I 335 " --> pdb=" O MET I 331 " (cutoff:3.500A) Processing helix chain 'I' and resid 339 through 343 removed outlier: 3.590A pdb=" N LEU I 343 " --> pdb=" O LEU I 340 " (cutoff:3.500A) Processing helix chain 'I' and resid 344 through 356 Processing helix chain 'J' and resid 119 through 123 Processing helix chain 'J' and resid 135 through 138 removed outlier: 4.243A pdb=" N ARG J 138 " --> pdb=" O ARG J 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 135 through 138' Processing helix chain 'J' and resid 155 through 165 removed outlier: 3.625A pdb=" N TYR J 163 " --> pdb=" O ILE J 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 176 through 188 Processing helix chain 'J' and resid 191 through 201 Processing helix chain 'M' and resid 65 through 79 removed outlier: 3.695A pdb=" N ASN M 79 " --> pdb=" O LEU M 75 " (cutoff:3.500A) Processing helix chain 'M' and resid 89 through 92 removed outlier: 3.650A pdb=" N ALA M 92 " --> pdb=" O VAL M 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 89 through 92' Processing helix chain 'M' and resid 93 through 107 removed outlier: 3.518A pdb=" N ILE M 103 " --> pdb=" O LEU M 99 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 113 removed outlier: 3.524A pdb=" N SER M 112 " --> pdb=" O ARG M 109 " (cutoff:3.500A) Processing helix chain 'M' and resid 125 through 129 removed outlier: 4.004A pdb=" N ARG M 129 " --> pdb=" O GLU M 126 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 148 Processing helix chain 'M' and resid 165 through 179 removed outlier: 3.589A pdb=" N THR M 169 " --> pdb=" O PRO M 165 " (cutoff:3.500A) Processing helix chain 'M' and resid 191 through 205 Processing helix chain 'M' and resid 222 through 228 removed outlier: 3.680A pdb=" N GLU M 226 " --> pdb=" O ARG M 222 " (cutoff:3.500A) Processing helix chain 'M' and resid 228 through 236 removed outlier: 4.031A pdb=" N LEU M 232 " --> pdb=" O GLN M 228 " (cutoff:3.500A) Processing helix chain 'M' and resid 246 through 250 Processing helix chain 'M' and resid 270 through 278 removed outlier: 3.666A pdb=" N LYS M 274 " --> pdb=" O TYR M 270 " (cutoff:3.500A) Processing helix chain 'M' and resid 279 through 300 removed outlier: 3.922A pdb=" N ARG M 283 " --> pdb=" O SER M 279 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG M 284 " --> pdb=" O GLU M 280 " (cutoff:3.500A) Processing helix chain 'M' and resid 302 through 311 removed outlier: 3.979A pdb=" N CYS M 311 " --> pdb=" O ALA M 307 " (cutoff:3.500A) Processing helix chain 'M' and resid 326 through 335 removed outlier: 3.879A pdb=" N GLY M 335 " --> pdb=" O MET M 331 " (cutoff:3.500A) Processing helix chain 'M' and resid 339 through 343 removed outlier: 3.588A pdb=" N LEU M 343 " --> pdb=" O LEU M 340 " (cutoff:3.500A) Processing helix chain 'M' and resid 344 through 356 Processing helix chain 'N' and resid 119 through 123 Processing helix chain 'N' and resid 135 through 138 removed outlier: 4.244A pdb=" N ARG N 138 " --> pdb=" O ARG N 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 135 through 138' Processing helix chain 'N' and resid 155 through 165 removed outlier: 3.626A pdb=" N TYR N 163 " --> pdb=" O ILE N 159 " (cutoff:3.500A) Processing helix chain 'N' and resid 176 through 188 Processing helix chain 'N' and resid 191 through 201 Processing helix chain 'O' and resid 119 through 123 Processing helix chain 'O' and resid 135 through 138 removed outlier: 4.244A pdb=" N ARG O 138 " --> pdb=" O ARG O 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 135 through 138' Processing helix chain 'O' and resid 155 through 165 removed outlier: 3.626A pdb=" N TYR O 163 " --> pdb=" O ILE O 159 " (cutoff:3.500A) Processing helix chain 'O' and resid 176 through 188 Processing helix chain 'O' and resid 191 through 201 Processing helix chain 'P' and resid 119 through 123 Processing helix chain 'P' and resid 135 through 138 removed outlier: 4.244A pdb=" N ARG P 138 " --> pdb=" O ARG P 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 135 through 138' Processing helix chain 'P' and resid 155 through 165 removed outlier: 3.626A pdb=" N TYR P 163 " --> pdb=" O ILE P 159 " (cutoff:3.500A) Processing helix chain 'P' and resid 176 through 188 Processing helix chain 'P' and resid 191 through 201 Processing sheet with id=AA1, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AA2, first strand: chain 'C' and resid 52 through 55 removed outlier: 4.983A pdb=" N LEU C 83 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE C 115 " --> pdb=" O VAL C 154 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N PHE C 156 " --> pdb=" O ILE C 115 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N THR C 117 " --> pdb=" O PHE C 156 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N VAL C 155 " --> pdb=" O GLY C 186 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N SER C 188 " --> pdb=" O VAL C 155 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ALA C 157 " --> pdb=" O SER C 188 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N CYS C 212 " --> pdb=" O TRP C 185 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLU C 213 " --> pdb=" O MET C 241 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ALA C 240 " --> pdb=" O SER C 318 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL C 320 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR C 242 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LEU C 322 " --> pdb=" O THR C 242 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLY C 53 " --> pdb=" O LEU C 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'G' and resid 52 through 55 removed outlier: 4.983A pdb=" N LEU G 83 " --> pdb=" O LEU G 52 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE G 115 " --> pdb=" O VAL G 154 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N PHE G 156 " --> pdb=" O ILE G 115 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N THR G 117 " --> pdb=" O PHE G 156 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N VAL G 155 " --> pdb=" O GLY G 186 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N SER G 188 " --> pdb=" O VAL G 155 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ALA G 157 " --> pdb=" O SER G 188 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N CYS G 212 " --> pdb=" O TRP G 185 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLU G 213 " --> pdb=" O MET G 241 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ALA G 240 " --> pdb=" O SER G 318 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL G 320 " --> pdb=" O ALA G 240 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N THR G 242 " --> pdb=" O VAL G 320 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LEU G 322 " --> pdb=" O THR G 242 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY G 53 " --> pdb=" O LEU G 322 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 39 through 41 Processing sheet with id=AA6, first strand: chain 'I' and resid 52 through 55 removed outlier: 4.983A pdb=" N LEU I 83 " --> pdb=" O LEU I 52 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE I 115 " --> pdb=" O VAL I 154 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N PHE I 156 " --> pdb=" O ILE I 115 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N THR I 117 " --> pdb=" O PHE I 156 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N VAL I 155 " --> pdb=" O GLY I 186 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N SER I 188 " --> pdb=" O VAL I 155 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ALA I 157 " --> pdb=" O SER I 188 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N CYS I 212 " --> pdb=" O TRP I 185 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLU I 213 " --> pdb=" O MET I 241 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ALA I 240 " --> pdb=" O SER I 318 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL I 320 " --> pdb=" O ALA I 240 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N THR I 242 " --> pdb=" O VAL I 320 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU I 322 " --> pdb=" O THR I 242 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLY I 53 " --> pdb=" O LEU I 322 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 113 through 118 removed outlier: 3.595A pdb=" N GLU J 146 " --> pdb=" O ASP J 141 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 39 through 41 Processing sheet with id=AA9, first strand: chain 'M' and resid 52 through 55 removed outlier: 4.983A pdb=" N LEU M 83 " --> pdb=" O LEU M 52 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE M 115 " --> pdb=" O VAL M 154 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N PHE M 156 " --> pdb=" O ILE M 115 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N THR M 117 " --> pdb=" O PHE M 156 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N VAL M 155 " --> pdb=" O GLY M 186 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N SER M 188 " --> pdb=" O VAL M 155 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ALA M 157 " --> pdb=" O SER M 188 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N CYS M 212 " --> pdb=" O TRP M 185 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLU M 213 " --> pdb=" O MET M 241 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ALA M 240 " --> pdb=" O SER M 318 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL M 320 " --> pdb=" O ALA M 240 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N THR M 242 " --> pdb=" O VAL M 320 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU M 322 " --> pdb=" O THR M 242 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLY M 53 " --> pdb=" O LEU M 322 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 113 through 118 removed outlier: 3.594A pdb=" N GLU N 146 " --> pdb=" O ASP N 141 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'O' and resid 113 through 118 removed outlier: 3.594A pdb=" N GLU O 146 " --> pdb=" O ASP O 141 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'P' and resid 113 through 118 removed outlier: 3.593A pdb=" N GLU P 146 " --> pdb=" O ASP P 141 " (cutoff:3.500A) 1124 hydrogen bonds defined for protein. 3228 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: 3.34 Time building geometry restraints manager: 2.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 3492 1.28 - 1.42: 5961 1.42 - 1.55: 12754 1.55 - 1.68: 97 1.68 - 1.81: 184 Bond restraints: 22488 Sorted by residual: bond pdb=" CA ILE B 337 " pdb=" CB ILE B 337 " ideal model delta sigma weight residual 1.534 1.433 0.101 6.80e-03 2.16e+04 2.22e+02 bond pdb=" CA ILE D 337 " pdb=" CB ILE D 337 " ideal model delta sigma weight residual 1.534 1.434 0.101 6.80e-03 2.16e+04 2.20e+02 bond pdb=" CA ILE H 337 " pdb=" CB ILE H 337 " ideal model delta sigma weight residual 1.534 1.434 0.100 6.80e-03 2.16e+04 2.17e+02 bond pdb=" CA ILE F 337 " pdb=" CB ILE F 337 " ideal model delta sigma weight residual 1.534 1.434 0.100 6.80e-03 2.16e+04 2.17e+02 bond pdb=" C ALA F 335 " pdb=" O ALA F 335 " ideal model delta sigma weight residual 1.236 1.397 -0.160 1.15e-02 7.56e+03 1.94e+02 ... (remaining 22483 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.65: 30312 6.65 - 13.31: 132 13.31 - 19.96: 12 19.96 - 26.61: 0 26.61 - 33.27: 4 Bond angle restraints: 30460 Sorted by residual: angle pdb=" C ASP D 293 " pdb=" N PRO D 294 " pdb=" CA PRO D 294 " ideal model delta sigma weight residual 119.28 135.94 -16.66 1.10e+00 8.26e-01 2.29e+02 angle pdb=" C ASP B 293 " pdb=" N PRO B 294 " pdb=" CA PRO B 294 " ideal model delta sigma weight residual 119.28 135.93 -16.65 1.10e+00 8.26e-01 2.29e+02 angle pdb=" C ASP H 293 " pdb=" N PRO H 294 " pdb=" CA PRO H 294 " ideal model delta sigma weight residual 119.28 135.89 -16.61 1.10e+00 8.26e-01 2.28e+02 angle pdb=" C ASP F 293 " pdb=" N PRO F 294 " pdb=" CA PRO F 294 " ideal model delta sigma weight residual 119.28 135.86 -16.58 1.10e+00 8.26e-01 2.27e+02 angle pdb=" CA LEU B 347 " pdb=" CB LEU B 347 " pdb=" CG LEU B 347 " ideal model delta sigma weight residual 116.30 83.03 33.27 3.50e+00 8.16e-02 9.03e+01 ... (remaining 30455 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.00: 12038 17.00 - 34.00: 1027 34.00 - 51.01: 335 51.01 - 68.01: 96 68.01 - 85.01: 52 Dihedral angle restraints: 13548 sinusoidal: 5660 harmonic: 7888 Sorted by residual: dihedral pdb=" C PHE F 296 " pdb=" N PHE F 296 " pdb=" CA PHE F 296 " pdb=" CB PHE F 296 " ideal model delta harmonic sigma weight residual -122.60 -145.09 22.49 0 2.50e+00 1.60e-01 8.09e+01 dihedral pdb=" C PHE D 296 " pdb=" N PHE D 296 " pdb=" CA PHE D 296 " pdb=" CB PHE D 296 " ideal model delta harmonic sigma weight residual -122.60 -145.08 22.48 0 2.50e+00 1.60e-01 8.09e+01 dihedral pdb=" C PHE B 296 " pdb=" N PHE B 296 " pdb=" CA PHE B 296 " pdb=" CB PHE B 296 " ideal model delta harmonic sigma weight residual -122.60 -145.04 22.44 0 2.50e+00 1.60e-01 8.06e+01 ... (remaining 13545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.199: 3288 0.199 - 0.399: 57 0.399 - 0.598: 23 0.598 - 0.797: 8 0.797 - 0.996: 4 Chirality restraints: 3380 Sorted by residual: chirality pdb=" CA PHE D 296 " pdb=" N PHE D 296 " pdb=" C PHE D 296 " pdb=" CB PHE D 296 " both_signs ideal model delta sigma weight residual False 2.51 1.51 1.00 2.00e-01 2.50e+01 2.48e+01 chirality pdb=" CA PHE F 296 " pdb=" N PHE F 296 " pdb=" C PHE F 296 " pdb=" CB PHE F 296 " both_signs ideal model delta sigma weight residual False 2.51 1.51 1.00 2.00e-01 2.50e+01 2.48e+01 chirality pdb=" CA PHE B 296 " pdb=" N PHE B 296 " pdb=" C PHE B 296 " pdb=" CB PHE B 296 " both_signs ideal model delta sigma weight residual False 2.51 1.52 0.99 2.00e-01 2.50e+01 2.47e+01 ... (remaining 3377 not shown) Planarity restraints: 3844 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 337 " -0.070 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO B 338 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO B 338 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO B 338 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE F 337 " 0.069 5.00e-02 4.00e+02 1.03e-01 1.70e+01 pdb=" N PRO F 338 " -0.178 5.00e-02 4.00e+02 pdb=" CA PRO F 338 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO F 338 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE H 337 " -0.069 5.00e-02 4.00e+02 1.03e-01 1.69e+01 pdb=" N PRO H 338 " 0.178 5.00e-02 4.00e+02 pdb=" CA PRO H 338 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO H 338 " -0.055 5.00e-02 4.00e+02 ... (remaining 3841 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.69: 672 2.69 - 3.30: 22829 3.30 - 3.91: 40552 3.91 - 4.53: 55993 4.53 - 5.14: 87949 Nonbonded interactions: 207995 Sorted by model distance: nonbonded pdb=" OG1 THR B 300 " pdb=" OH TYR B 339 " model vdw 2.074 3.040 nonbonded pdb=" OG1 THR D 300 " pdb=" OH TYR D 339 " model vdw 2.074 3.040 nonbonded pdb=" OG1 THR H 300 " pdb=" OH TYR H 339 " model vdw 2.075 3.040 nonbonded pdb=" OG1 THR F 300 " pdb=" OH TYR F 339 " model vdw 2.076 3.040 nonbonded pdb=" OE2 GLU G 138 " pdb=" OH TYR M 151 " model vdw 2.307 3.040 ... (remaining 207990 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 'B' and resid 208 through 493) selection = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'I' selection = chain 'M' } ncs_group { reference = chain 'J' selection = chain 'N' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.300 Find NCS groups from input model: 0.380 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: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 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 : 0.012 0.219 22492 Z= 0.697 Angle : 1.224 33.268 30468 Z= 0.710 Chirality : 0.091 0.996 3380 Planarity : 0.008 0.103 3844 Dihedral : 15.743 85.011 8464 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.74 % Favored : 96.12 % Rotamer: Outliers : 7.69 % Allowed : 9.10 % Favored : 83.21 % Cbeta Deviations : 1.26 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.54 (0.14), residues: 2704 helix: -0.32 (0.12), residues: 1516 sheet: 0.87 (0.39), residues: 172 loop : -2.41 (0.15), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 298 TYR 0.047 0.003 TYR B 339 PHE 0.039 0.003 PHE B 296 TRP 0.019 0.002 TRP I 185 HIS 0.010 0.002 HIS M 135 Details of bonding type rmsd/Z covalent geometry : bond 0.01177 / 0.70 (22488) covalent geometry : angle 1.22443 / 0.71 (30460) SS BOND : bond 0.00204 / 0.10 ( 4) SS BOND : angle 1.00002 / 0.48 ( 8) hydrogen bonds : bond 0.17453 / 11.22 ( 1124) hydrogen bonds : angle 5.76853 / 4.31 ( 3228) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 426 time to evaluate : 0.886 Fit side-chains REVERT: B 242 LEU cc_start: 0.7272 (mt) cc_final: 0.7021 (mt) REVERT: B 296 PHE cc_start: 0.7049 (OUTLIER) cc_final: 0.6292 (t80) REVERT: B 466 ILE cc_start: 0.7777 (mm) cc_final: 0.7559 (mt) REVERT: C 70 GLU cc_start: 0.7126 (tt0) cc_final: 0.6901 (tt0) REVERT: C 94 LYS cc_start: 0.7545 (mtpt) cc_final: 0.7038 (mttp) REVERT: C 104 LYS cc_start: 0.7859 (tttp) cc_final: 0.7624 (ttmm) REVERT: C 105 LYS cc_start: 0.7841 (tttt) cc_final: 0.7613 (tttm) REVERT: C 129 ARG cc_start: 0.7343 (ptm160) cc_final: 0.7005 (ptt-90) REVERT: C 223 GLU cc_start: 0.7494 (tp30) cc_final: 0.7064 (tm-30) REVERT: C 290 LYS cc_start: 0.6517 (mtmt) cc_final: 0.6192 (mttm) REVERT: C 315 GLU cc_start: 0.6933 (mm-30) cc_final: 0.6363 (mp0) REVERT: D 222 LEU cc_start: 0.6141 (OUTLIER) cc_final: 0.5935 (mm) REVERT: D 242 LEU cc_start: 0.7276 (mt) cc_final: 0.7014 (mt) REVERT: D 296 PHE cc_start: 0.6996 (OUTLIER) cc_final: 0.5752 (t80) REVERT: D 391 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7684 (mp) REVERT: F 244 ILE cc_start: 0.6477 (mt) cc_final: 0.6129 (mt) REVERT: F 340 PHE cc_start: 0.8282 (m-10) cc_final: 0.8057 (m-80) REVERT: G 70 GLU cc_start: 0.6867 (tt0) cc_final: 0.6633 (tt0) REVERT: G 94 LYS cc_start: 0.7314 (mtpt) cc_final: 0.6923 (mttp) REVERT: G 124 LYS cc_start: 0.7721 (OUTLIER) cc_final: 0.7500 (mmmm) REVERT: G 129 ARG cc_start: 0.7454 (ptm160) cc_final: 0.7027 (ptt-90) REVERT: G 223 GLU cc_start: 0.7558 (tp30) cc_final: 0.6960 (tm-30) REVERT: G 270 TYR cc_start: 0.7868 (m-80) cc_final: 0.7398 (m-80) REVERT: G 315 GLU cc_start: 0.7310 (mm-30) cc_final: 0.6755 (mp0) REVERT: G 350 GLU cc_start: 0.7203 (tt0) cc_final: 0.6988 (tt0) REVERT: G 353 SER cc_start: 0.8002 (t) cc_final: 0.7758 (p) REVERT: H 222 LEU cc_start: 0.6335 (OUTLIER) cc_final: 0.6065 (mm) REVERT: H 296 PHE cc_start: 0.6987 (OUTLIER) cc_final: 0.6239 (t80) REVERT: H 386 ILE cc_start: 0.7985 (mt) cc_final: 0.7695 (mt) REVERT: I 70 GLU cc_start: 0.6917 (tt0) cc_final: 0.6464 (tt0) REVERT: I 94 LYS cc_start: 0.7588 (mtpt) cc_final: 0.7079 (mttp) REVERT: I 104 LYS cc_start: 0.7773 (tttp) cc_final: 0.7507 (ttmm) REVERT: I 105 LYS cc_start: 0.7735 (tttt) cc_final: 0.7365 (tttt) REVERT: I 124 LYS cc_start: 0.7770 (OUTLIER) cc_final: 0.7557 (mttp) REVERT: I 129 ARG cc_start: 0.7361 (ptm160) cc_final: 0.7035 (ptt-90) REVERT: I 223 GLU cc_start: 0.7552 (tp30) cc_final: 0.7252 (tm-30) REVERT: I 241 MET cc_start: 0.8768 (ttm) cc_final: 0.8543 (ttm) REVERT: I 290 LYS cc_start: 0.6740 (mtmt) cc_final: 0.6528 (mmtt) REVERT: I 315 GLU cc_start: 0.7147 (mm-30) cc_final: 0.6532 (mp0) REVERT: J 104 GLU cc_start: 0.7428 (tt0) cc_final: 0.7181 (tt0) REVERT: J 170 ARG cc_start: 0.7400 (OUTLIER) cc_final: 0.6744 (mtt-85) REVERT: M 70 GLU cc_start: 0.6884 (tt0) cc_final: 0.6674 (tt0) REVERT: M 94 LYS cc_start: 0.7330 (mtpt) cc_final: 0.6933 (mttp) REVERT: M 129 ARG cc_start: 0.7485 (ptm160) cc_final: 0.7220 (ptt-90) REVERT: M 223 GLU cc_start: 0.7625 (tp30) cc_final: 0.7099 (tm-30) REVERT: M 270 TYR cc_start: 0.7871 (m-80) cc_final: 0.7456 (m-80) REVERT: M 315 GLU cc_start: 0.7391 (mm-30) cc_final: 0.6835 (mp0) REVERT: N 104 GLU cc_start: 0.7495 (tt0) cc_final: 0.7274 (tt0) REVERT: N 157 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7592 (m-30) REVERT: N 170 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.6841 (mtt-85) REVERT: O 104 GLU cc_start: 0.7485 (tt0) cc_final: 0.7273 (tt0) REVERT: O 170 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.6923 (mtt-85) REVERT: O 171 ARG cc_start: 0.7989 (ttp80) cc_final: 0.7780 (ttp80) REVERT: P 104 GLU cc_start: 0.7492 (tt0) cc_final: 0.7220 (tt0) REVERT: P 135 ARG cc_start: 0.8517 (mtt180) cc_final: 0.8078 (mtt180) REVERT: P 170 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.6935 (mtt-85) outliers start: 180 outliers final: 77 residues processed: 561 average time/residue: 0.1752 time to fit residues: 146.2075 Evaluate side-chains 455 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 365 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 296 PHE Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 338 PRO Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 290 SER Chi-restraints excluded: chain D residue 291 PHE Chi-restraints excluded: chain D residue 296 PHE Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 338 PRO Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain D residue 491 THR Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 290 SER Chi-restraints excluded: chain F residue 296 PHE Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 338 PRO Chi-restraints excluded: chain F residue 342 THR Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 349 GLU Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 476 VAL Chi-restraints excluded: chain F residue 491 THR Chi-restraints excluded: chain G residue 124 LYS Chi-restraints excluded: chain G residue 289 LEU Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 337 ILE Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain H residue 290 SER Chi-restraints excluded: chain H residue 296 PHE Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain H residue 303 ILE Chi-restraints excluded: chain H residue 338 PRO Chi-restraints excluded: chain H residue 342 THR Chi-restraints excluded: chain H residue 343 LEU Chi-restraints excluded: chain H residue 349 GLU Chi-restraints excluded: chain H residue 384 LEU Chi-restraints excluded: chain H residue 440 VAL Chi-restraints excluded: chain H residue 476 VAL Chi-restraints excluded: chain H residue 491 THR Chi-restraints excluded: chain I residue 124 LYS Chi-restraints excluded: chain I residue 127 THR Chi-restraints excluded: chain I residue 227 VAL Chi-restraints excluded: chain I residue 289 LEU Chi-restraints excluded: chain I residue 302 THR Chi-restraints excluded: chain I residue 337 ILE Chi-restraints excluded: chain J residue 101 CYS Chi-restraints excluded: chain J residue 157 ASP Chi-restraints excluded: chain J residue 170 ARG Chi-restraints excluded: chain J residue 174 ASN Chi-restraints excluded: chain M residue 227 VAL Chi-restraints excluded: chain M residue 289 LEU Chi-restraints excluded: chain M residue 302 THR Chi-restraints excluded: chain M residue 337 ILE Chi-restraints excluded: chain N residue 101 CYS Chi-restraints excluded: chain N residue 157 ASP Chi-restraints excluded: chain N residue 170 ARG Chi-restraints excluded: chain N residue 174 ASN Chi-restraints excluded: chain O residue 101 CYS Chi-restraints excluded: chain O residue 170 ARG Chi-restraints excluded: chain O residue 174 ASN Chi-restraints excluded: chain O residue 199 GLU Chi-restraints excluded: chain P residue 101 CYS Chi-restraints excluded: chain P residue 157 ASP Chi-restraints excluded: chain P residue 170 ARG Chi-restraints excluded: chain P residue 174 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 385 GLN C 293 GLN G 158 ASN I 293 GLN M 158 ASN M 293 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.134659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.097922 restraints weight = 25125.349| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 2.13 r_work: 0.2504 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 22492 Z= 0.134 Angle : 0.557 5.819 30468 Z= 0.298 Chirality : 0.042 0.142 3380 Planarity : 0.005 0.050 3844 Dihedral : 12.323 87.254 3427 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.25 % Allowed : 11.58 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.01 (0.16), residues: 2704 helix: 1.03 (0.13), residues: 1568 sheet: 0.71 (0.35), residues: 216 loop : -2.05 (0.17), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 218 TYR 0.016 0.002 TYR B 447 PHE 0.046 0.002 PHE D 216 TRP 0.013 0.002 TRP G 185 HIS 0.005 0.001 HIS G 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (22488) covalent geometry : angle 0.55741 / 0.30 (30460) SS BOND : bond 0.00259 / 0.13 ( 4) SS BOND : angle 0.53164 / 0.25 ( 8) hydrogen bonds : bond 0.05751 / 3.86 ( 1124) hydrogen bonds : angle 3.98555 / 2.94 ( 3228) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 356 time to evaluate : 0.841 Fit side-chains REVERT: C 94 LYS cc_start: 0.8153 (mtpt) cc_final: 0.7721 (mttp) REVERT: C 104 LYS cc_start: 0.8075 (tttp) cc_final: 0.7828 (ttmm) REVERT: C 129 ARG cc_start: 0.8300 (ptm160) cc_final: 0.7862 (ptt-90) REVERT: C 223 GLU cc_start: 0.8165 (tp30) cc_final: 0.7743 (tm-30) REVERT: C 290 LYS cc_start: 0.7357 (mtmt) cc_final: 0.7027 (mttp) REVERT: C 315 GLU cc_start: 0.7315 (mm-30) cc_final: 0.6980 (mm-30) REVERT: C 347 ILE cc_start: 0.8120 (OUTLIER) cc_final: 0.7912 (mm) REVERT: F 225 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7369 (tp30) REVERT: G 70 GLU cc_start: 0.7995 (tt0) cc_final: 0.7761 (tt0) REVERT: G 94 LYS cc_start: 0.8073 (mtpt) cc_final: 0.7663 (mttp) REVERT: G 129 ARG cc_start: 0.8415 (ptm160) cc_final: 0.7948 (ptt-90) REVERT: G 270 TYR cc_start: 0.8407 (m-80) cc_final: 0.8099 (m-80) REVERT: G 315 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7185 (mp0) REVERT: H 367 ARG cc_start: 0.8554 (mtp180) cc_final: 0.8339 (mtp180) REVERT: I 94 LYS cc_start: 0.8159 (mtpt) cc_final: 0.7769 (mttp) REVERT: I 105 LYS cc_start: 0.8342 (tttt) cc_final: 0.8082 (tttm) REVERT: I 129 ARG cc_start: 0.8271 (ptm160) cc_final: 0.7819 (ptt-90) REVERT: I 290 LYS cc_start: 0.7554 (mtmt) cc_final: 0.7232 (mmtt) REVERT: J 170 ARG cc_start: 0.7605 (OUTLIER) cc_final: 0.6787 (mtt-85) REVERT: M 94 LYS cc_start: 0.8256 (mtpt) cc_final: 0.7836 (mttp) REVERT: M 129 ARG cc_start: 0.8427 (ptm160) cc_final: 0.7964 (ptt-90) REVERT: M 223 GLU cc_start: 0.8149 (tp30) cc_final: 0.7776 (tm-30) REVERT: M 270 TYR cc_start: 0.8430 (m-80) cc_final: 0.8099 (m-80) REVERT: M 315 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7186 (mp0) REVERT: N 170 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.6855 (mtt-85) REVERT: O 168 ARG cc_start: 0.8346 (mtm180) cc_final: 0.8029 (mtm-85) REVERT: O 170 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.6996 (mmt-90) REVERT: O 171 ARG cc_start: 0.8204 (ttp80) cc_final: 0.7997 (ttp80) REVERT: P 135 ARG cc_start: 0.8866 (mtt180) cc_final: 0.8579 (mtt180) REVERT: P 170 ARG cc_start: 0.7714 (OUTLIER) cc_final: 0.6913 (mtt-85) outliers start: 76 outliers final: 44 residues processed: 409 average time/residue: 0.1853 time to fit residues: 111.6443 Evaluate side-chains 380 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 331 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain D residue 291 PHE Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 315 PHE Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 317 CYS Chi-restraints excluded: chain F residue 336 ILE Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 349 GLU Chi-restraints excluded: chain G residue 289 LEU Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 346 SER Chi-restraints excluded: chain H residue 303 ILE Chi-restraints excluded: chain H residue 315 PHE Chi-restraints excluded: chain H residue 343 LEU Chi-restraints excluded: chain H residue 476 VAL Chi-restraints excluded: chain I residue 145 GLU Chi-restraints excluded: chain I residue 289 LEU Chi-restraints excluded: chain I residue 302 THR Chi-restraints excluded: chain J residue 101 CYS Chi-restraints excluded: chain J residue 170 ARG Chi-restraints excluded: chain J residue 174 ASN Chi-restraints excluded: chain M residue 289 LEU Chi-restraints excluded: chain M residue 302 THR Chi-restraints excluded: chain M residue 346 SER Chi-restraints excluded: chain M residue 347 ILE Chi-restraints excluded: chain N residue 101 CYS Chi-restraints excluded: chain N residue 170 ARG Chi-restraints excluded: chain N residue 174 ASN Chi-restraints excluded: chain O residue 101 CYS Chi-restraints excluded: chain O residue 157 ASP Chi-restraints excluded: chain O residue 170 ARG Chi-restraints excluded: chain O residue 174 ASN Chi-restraints excluded: chain P residue 101 CYS Chi-restraints excluded: chain P residue 170 ARG Chi-restraints excluded: chain P residue 174 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 100 optimal weight: 0.4980 chunk 180 optimal weight: 2.9990 chunk 232 optimal weight: 5.9990 chunk 199 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 127 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 385 GLN G 293 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.129314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.094801 restraints weight = 25162.645| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 2.28 r_work: 0.2398 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 22492 Z= 0.189 Angle : 0.602 5.875 30468 Z= 0.321 Chirality : 0.045 0.161 3380 Planarity : 0.005 0.051 3844 Dihedral : 11.345 86.622 3338 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.02 % Allowed : 11.24 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.35 (0.16), residues: 2704 helix: 1.39 (0.13), residues: 1584 sheet: 0.57 (0.34), residues: 212 loop : -2.01 (0.17), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 40 TYR 0.018 0.002 TYR F 447 PHE 0.027 0.002 PHE D 216 TRP 0.016 0.002 TRP I 185 HIS 0.009 0.002 HIS F 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.19 (22488) covalent geometry : angle 0.60236 / 0.32 (30460) SS BOND : bond 0.00415 / 0.21 ( 4) SS BOND : angle 0.52475 / 0.25 ( 8) hydrogen bonds : bond 0.06838 / 4.61 ( 1124) hydrogen bonds : angle 3.97579 / 2.91 ( 3228) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 329 time to evaluate : 0.901 Fit side-chains REVERT: B 433 ASP cc_start: 0.9145 (t0) cc_final: 0.8781 (t0) REVERT: B 485 TYR cc_start: 0.8991 (t80) cc_final: 0.8638 (t80) REVERT: C 94 LYS cc_start: 0.8418 (mtpt) cc_final: 0.7976 (mttp) REVERT: C 104 LYS cc_start: 0.8301 (tttp) cc_final: 0.8060 (ttmm) REVERT: C 129 ARG cc_start: 0.8411 (ptm160) cc_final: 0.7998 (ptt-90) REVERT: C 223 GLU cc_start: 0.8300 (tp30) cc_final: 0.7881 (tm-30) REVERT: C 290 LYS cc_start: 0.7517 (mtmt) cc_final: 0.7152 (mmtt) REVERT: D 420 GLU cc_start: 0.8986 (tt0) cc_final: 0.8692 (tt0) REVERT: F 303 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8654 (mp) REVERT: G 94 LYS cc_start: 0.8378 (mtpt) cc_final: 0.8024 (mttp) REVERT: G 129 ARG cc_start: 0.8499 (ptm160) cc_final: 0.8092 (ptt-90) REVERT: G 315 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7138 (mp0) REVERT: H 485 TYR cc_start: 0.9038 (t80) cc_final: 0.8588 (t80) REVERT: I 94 LYS cc_start: 0.8368 (mtpt) cc_final: 0.7982 (mttp) REVERT: I 105 LYS cc_start: 0.8479 (tttt) cc_final: 0.8253 (tttm) REVERT: I 129 ARG cc_start: 0.8384 (ptm160) cc_final: 0.7977 (ptt-90) REVERT: I 290 LYS cc_start: 0.7801 (mtmt) cc_final: 0.7471 (mmtt) REVERT: J 170 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.6783 (mtt-85) REVERT: M 94 LYS cc_start: 0.8408 (mtpt) cc_final: 0.8054 (mttp) REVERT: M 105 LYS cc_start: 0.8516 (tttt) cc_final: 0.8214 (tttm) REVERT: M 129 ARG cc_start: 0.8477 (ptm160) cc_final: 0.8061 (ptt-90) REVERT: M 223 GLU cc_start: 0.8267 (tp30) cc_final: 0.7834 (tm-30) REVERT: M 315 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7121 (mp0) REVERT: N 170 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.6853 (mtt-85) REVERT: O 170 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.6881 (mtt-85) REVERT: P 170 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.6862 (mtt-85) outliers start: 94 outliers final: 67 residues processed: 396 average time/residue: 0.1780 time to fit residues: 104.3949 Evaluate side-chains 392 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 320 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 414 SER Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain D residue 291 PHE Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 315 PHE Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 317 CYS Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 349 GLU Chi-restraints excluded: chain F residue 410 ILE Chi-restraints excluded: chain F residue 414 SER Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 476 VAL Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 145 GLU Chi-restraints excluded: chain G residue 223 GLU Chi-restraints excluded: chain G residue 289 LEU Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 337 ILE Chi-restraints excluded: chain G residue 346 SER Chi-restraints excluded: chain G residue 353 SER Chi-restraints excluded: chain H residue 303 ILE Chi-restraints excluded: chain H residue 331 ILE Chi-restraints excluded: chain H residue 336 ILE Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 343 LEU Chi-restraints excluded: chain H residue 345 THR Chi-restraints excluded: chain H residue 440 VAL Chi-restraints excluded: chain H residue 476 VAL Chi-restraints excluded: chain I residue 145 GLU Chi-restraints excluded: chain I residue 289 LEU Chi-restraints excluded: chain I residue 302 THR Chi-restraints excluded: chain I residue 337 ILE Chi-restraints excluded: chain J residue 101 CYS Chi-restraints excluded: chain J residue 157 ASP Chi-restraints excluded: chain J residue 170 ARG Chi-restraints excluded: chain J residue 174 ASN Chi-restraints excluded: chain M residue 127 THR Chi-restraints excluded: chain M residue 145 GLU Chi-restraints excluded: chain M residue 289 LEU Chi-restraints excluded: chain M residue 302 THR Chi-restraints excluded: chain M residue 337 ILE Chi-restraints excluded: chain M residue 346 SER Chi-restraints excluded: chain N residue 101 CYS Chi-restraints excluded: chain N residue 157 ASP Chi-restraints excluded: chain N residue 170 ARG Chi-restraints excluded: chain N residue 174 ASN Chi-restraints excluded: chain O residue 101 CYS Chi-restraints excluded: chain O residue 157 ASP Chi-restraints excluded: chain O residue 170 ARG Chi-restraints excluded: chain O residue 174 ASN Chi-restraints excluded: chain P residue 101 CYS Chi-restraints excluded: chain P residue 157 ASP Chi-restraints excluded: chain P residue 170 ARG Chi-restraints excluded: chain P residue 174 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 204 optimal weight: 0.7980 chunk 256 optimal weight: 0.9990 chunk 131 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 172 optimal weight: 0.7980 chunk 238 optimal weight: 3.9990 chunk 245 optimal weight: 1.9990 chunk 78 optimal weight: 0.1980 chunk 47 optimal weight: 0.0060 chunk 203 optimal weight: 0.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 293 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.134644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.098206 restraints weight = 25100.656| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 1.95 r_work: 0.2486 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 22492 Z= 0.102 Angle : 0.479 5.502 30468 Z= 0.255 Chirality : 0.040 0.135 3380 Planarity : 0.004 0.047 3844 Dihedral : 10.200 88.375 3332 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.52 % Allowed : 12.65 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.88 (0.16), residues: 2704 helix: 1.91 (0.14), residues: 1568 sheet: 0.11 (0.37), residues: 152 loop : -1.62 (0.17), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 40 TYR 0.006 0.001 TYR H 487 PHE 0.019 0.001 PHE B 308 TRP 0.010 0.001 TRP C 185 HIS 0.004 0.001 HIS G 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.10 (22488) covalent geometry : angle 0.47851 / 0.25 (30460) SS BOND : bond 0.00242 / 0.12 ( 4) SS BOND : angle 0.51513 / 0.26 ( 8) hydrogen bonds : bond 0.04293 / 2.92 ( 1124) hydrogen bonds : angle 3.55761 / 2.61 ( 3228) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 342 time to evaluate : 0.872 Fit side-chains REVERT: B 433 ASP cc_start: 0.9105 (t0) cc_final: 0.8700 (t0) REVERT: B 485 TYR cc_start: 0.8931 (t80) cc_final: 0.8576 (t80) REVERT: C 94 LYS cc_start: 0.8135 (mtpt) cc_final: 0.7731 (mttp) REVERT: C 104 LYS cc_start: 0.8105 (tttp) cc_final: 0.7593 (tppt) REVERT: C 129 ARG cc_start: 0.8257 (ptm160) cc_final: 0.7793 (ptt-90) REVERT: C 223 GLU cc_start: 0.8215 (tp30) cc_final: 0.7766 (tm-30) REVERT: C 290 LYS cc_start: 0.7410 (mtmt) cc_final: 0.7044 (mmtt) REVERT: F 330 LEU cc_start: 0.8464 (mt) cc_final: 0.8117 (tp) REVERT: G 94 LYS cc_start: 0.8132 (mtpt) cc_final: 0.7753 (mttp) REVERT: G 105 LYS cc_start: 0.8338 (tttt) cc_final: 0.8063 (tttm) REVERT: G 129 ARG cc_start: 0.8335 (ptm160) cc_final: 0.7891 (ptt-90) REVERT: G 315 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7084 (mp0) REVERT: H 485 TYR cc_start: 0.8970 (t80) cc_final: 0.8668 (t80) REVERT: I 94 LYS cc_start: 0.8082 (mtpt) cc_final: 0.7676 (mttp) REVERT: I 129 ARG cc_start: 0.8230 (ptm160) cc_final: 0.7729 (ptt-90) REVERT: I 290 LYS cc_start: 0.7422 (mtmt) cc_final: 0.7133 (mmtt) REVERT: J 170 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.6714 (mtt-85) REVERT: M 94 LYS cc_start: 0.8141 (mtpt) cc_final: 0.7775 (mttp) REVERT: M 105 LYS cc_start: 0.8356 (tttt) cc_final: 0.8036 (tttm) REVERT: M 129 ARG cc_start: 0.8306 (ptm160) cc_final: 0.7796 (ptt-90) REVERT: M 223 GLU cc_start: 0.8241 (tp30) cc_final: 0.7813 (tm-30) REVERT: M 289 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7318 (mp) REVERT: M 290 LYS cc_start: 0.7339 (mttp) cc_final: 0.6999 (mmtt) REVERT: M 315 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7127 (mp0) REVERT: N 170 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.6662 (mmt-90) REVERT: O 170 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.6844 (mmt-90) REVERT: P 170 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.6805 (mtt-85) outliers start: 59 outliers final: 38 residues processed: 390 average time/residue: 0.1800 time to fit residues: 103.5683 Evaluate side-chains 370 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 327 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 315 PHE Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 488 HIS Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 349 GLU Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain H residue 303 ILE Chi-restraints excluded: chain H residue 315 PHE Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 440 VAL Chi-restraints excluded: chain H residue 488 HIS Chi-restraints excluded: chain I residue 289 LEU Chi-restraints excluded: chain I residue 302 THR Chi-restraints excluded: chain J residue 101 CYS Chi-restraints excluded: chain J residue 170 ARG Chi-restraints excluded: chain M residue 127 THR Chi-restraints excluded: chain M residue 158 ASN Chi-restraints excluded: chain M residue 289 LEU Chi-restraints excluded: chain M residue 302 THR Chi-restraints excluded: chain N residue 101 CYS Chi-restraints excluded: chain N residue 170 ARG Chi-restraints excluded: chain O residue 101 CYS Chi-restraints excluded: chain O residue 157 ASP Chi-restraints excluded: chain O residue 170 ARG Chi-restraints excluded: chain P residue 101 CYS Chi-restraints excluded: chain P residue 170 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 166 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 254 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 234 optimal weight: 0.0470 chunk 170 optimal weight: 1.9990 chunk 256 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 overall best weight: 1.1882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 293 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.130979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.096339 restraints weight = 24996.587| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 2.34 r_work: 0.2467 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 22492 Z= 0.147 Angle : 0.529 5.566 30468 Z= 0.281 Chirality : 0.042 0.138 3380 Planarity : 0.005 0.047 3844 Dihedral : 10.399 86.925 3310 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.38 % Allowed : 12.56 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.96 (0.16), residues: 2704 helix: 1.97 (0.14), residues: 1568 sheet: 0.24 (0.38), residues: 172 loop : -1.63 (0.17), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 40 TYR 0.011 0.001 TYR H 487 PHE 0.017 0.001 PHE D 406 TRP 0.014 0.001 TRP I 185 HIS 0.005 0.001 HIS G 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (22488) covalent geometry : angle 0.52857 / 0.28 (30460) SS BOND : bond 0.00361 / 0.18 ( 4) SS BOND : angle 0.49292 / 0.24 ( 8) hydrogen bonds : bond 0.05580 / 3.78 ( 1124) hydrogen bonds : angle 3.68405 / 2.70 ( 3228) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 321 time to evaluate : 1.022 Fit side-chains REVERT: B 433 ASP cc_start: 0.9086 (t0) cc_final: 0.8685 (t0) REVERT: B 485 TYR cc_start: 0.8967 (t80) cc_final: 0.8631 (t80) REVERT: C 94 LYS cc_start: 0.8282 (mtpt) cc_final: 0.7909 (mttp) REVERT: C 129 ARG cc_start: 0.8308 (ptm160) cc_final: 0.7887 (ptt-90) REVERT: C 223 GLU cc_start: 0.8236 (tp30) cc_final: 0.7809 (tm-30) REVERT: C 290 LYS cc_start: 0.7404 (mtmt) cc_final: 0.7061 (mmtt) REVERT: F 330 LEU cc_start: 0.8489 (mt) cc_final: 0.8155 (tp) REVERT: G 94 LYS cc_start: 0.8281 (mtpt) cc_final: 0.7940 (mttp) REVERT: G 105 LYS cc_start: 0.8409 (tttt) cc_final: 0.8082 (tttm) REVERT: G 129 ARG cc_start: 0.8405 (ptm160) cc_final: 0.7965 (ptt-90) REVERT: H 485 TYR cc_start: 0.8968 (t80) cc_final: 0.8523 (t80) REVERT: I 94 LYS cc_start: 0.8274 (mtpt) cc_final: 0.7909 (mttp) REVERT: I 105 LYS cc_start: 0.8395 (tttt) cc_final: 0.8121 (tttm) REVERT: I 129 ARG cc_start: 0.8294 (ptm160) cc_final: 0.7860 (ptt-90) REVERT: I 290 LYS cc_start: 0.7644 (mtmt) cc_final: 0.7337 (mmtt) REVERT: J 170 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.6775 (mtt-85) REVERT: M 94 LYS cc_start: 0.8287 (mtpt) cc_final: 0.7953 (mttp) REVERT: M 105 LYS cc_start: 0.8399 (tttt) cc_final: 0.8112 (tttm) REVERT: M 129 ARG cc_start: 0.8374 (ptm160) cc_final: 0.7896 (ptt-90) REVERT: M 223 GLU cc_start: 0.8238 (tp30) cc_final: 0.7789 (tm-30) REVERT: M 290 LYS cc_start: 0.7448 (mttp) cc_final: 0.7121 (mmtt) REVERT: N 170 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.6752 (mmt-90) REVERT: O 170 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.6892 (mtt-85) REVERT: P 170 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.6875 (mtt-85) outliers start: 79 outliers final: 61 residues processed: 380 average time/residue: 0.1705 time to fit residues: 96.3290 Evaluate side-chains 385 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 320 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 414 SER Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 315 PHE Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 488 HIS Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 291 PHE Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 336 ILE Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 349 GLU Chi-restraints excluded: chain F residue 410 ILE Chi-restraints excluded: chain F residue 414 SER Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 476 VAL Chi-restraints excluded: chain G residue 145 GLU Chi-restraints excluded: chain G residue 223 GLU Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 337 ILE Chi-restraints excluded: chain G residue 346 SER Chi-restraints excluded: chain H residue 303 ILE Chi-restraints excluded: chain H residue 315 PHE Chi-restraints excluded: chain H residue 336 ILE Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 362 ILE Chi-restraints excluded: chain H residue 384 LEU Chi-restraints excluded: chain H residue 440 VAL Chi-restraints excluded: chain H residue 488 HIS Chi-restraints excluded: chain I residue 127 THR Chi-restraints excluded: chain I residue 289 LEU Chi-restraints excluded: chain I residue 302 THR Chi-restraints excluded: chain I residue 337 ILE Chi-restraints excluded: chain J residue 101 CYS Chi-restraints excluded: chain J residue 170 ARG Chi-restraints excluded: chain M residue 127 THR Chi-restraints excluded: chain M residue 145 GLU Chi-restraints excluded: chain M residue 289 LEU Chi-restraints excluded: chain M residue 302 THR Chi-restraints excluded: chain M residue 337 ILE Chi-restraints excluded: chain M residue 346 SER Chi-restraints excluded: chain N residue 101 CYS Chi-restraints excluded: chain N residue 170 ARG Chi-restraints excluded: chain O residue 101 CYS Chi-restraints excluded: chain O residue 157 ASP Chi-restraints excluded: chain O residue 170 ARG Chi-restraints excluded: chain P residue 101 CYS Chi-restraints excluded: chain P residue 170 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 212 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 200 optimal weight: 0.6980 chunk 149 optimal weight: 3.9990 chunk 67 optimal weight: 0.3980 chunk 3 optimal weight: 2.9990 chunk 257 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 169 optimal weight: 4.9990 chunk 193 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.132975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.098762 restraints weight = 25174.243| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 2.42 r_work: 0.2511 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 22492 Z= 0.113 Angle : 0.486 5.547 30468 Z= 0.258 Chirality : 0.040 0.138 3380 Planarity : 0.004 0.046 3844 Dihedral : 9.966 86.676 3310 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.12 % Allowed : 13.25 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.06 (0.17), residues: 2704 helix: 2.01 (0.14), residues: 1592 sheet: 0.36 (0.37), residues: 176 loop : -1.62 (0.18), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 40 TYR 0.012 0.001 TYR F 485 PHE 0.017 0.001 PHE B 308 TRP 0.012 0.001 TRP C 185 HIS 0.005 0.001 HIS G 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (22488) covalent geometry : angle 0.48570 / 0.26 (30460) SS BOND : bond 0.00287 / 0.14 ( 4) SS BOND : angle 0.49545 / 0.24 ( 8) hydrogen bonds : bond 0.04668 / 3.18 ( 1124) hydrogen bonds : angle 3.54117 / 2.59 ( 3228) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 327 time to evaluate : 0.889 Fit side-chains REVERT: B 433 ASP cc_start: 0.9064 (t0) cc_final: 0.8661 (t0) REVERT: B 485 TYR cc_start: 0.8962 (t80) cc_final: 0.8631 (t80) REVERT: C 94 LYS cc_start: 0.8181 (mtpt) cc_final: 0.7746 (mttp) REVERT: C 129 ARG cc_start: 0.8221 (ptm160) cc_final: 0.7777 (ptt-90) REVERT: C 223 GLU cc_start: 0.8208 (tp30) cc_final: 0.7783 (tm-30) REVERT: C 290 LYS cc_start: 0.7423 (mtmt) cc_final: 0.7084 (mmtt) REVERT: G 94 LYS cc_start: 0.8128 (mtpt) cc_final: 0.7776 (mttp) REVERT: G 105 LYS cc_start: 0.8350 (tttt) cc_final: 0.8023 (tttm) REVERT: G 129 ARG cc_start: 0.8292 (ptm160) cc_final: 0.7842 (ptt-90) REVERT: H 485 TYR cc_start: 0.8942 (t80) cc_final: 0.8697 (t80) REVERT: I 94 LYS cc_start: 0.8175 (mtpt) cc_final: 0.7802 (mttp) REVERT: I 129 ARG cc_start: 0.8207 (ptm160) cc_final: 0.7733 (ptt-90) REVERT: I 290 LYS cc_start: 0.7442 (mtmt) cc_final: 0.7161 (mmtt) REVERT: J 170 ARG cc_start: 0.7580 (OUTLIER) cc_final: 0.6743 (mtt-85) REVERT: M 94 LYS cc_start: 0.8138 (mtpt) cc_final: 0.7793 (mttp) REVERT: M 105 LYS cc_start: 0.8336 (tttt) cc_final: 0.8064 (tttm) REVERT: M 129 ARG cc_start: 0.8282 (ptm160) cc_final: 0.7788 (ptt-90) REVERT: M 223 GLU cc_start: 0.8194 (tp30) cc_final: 0.7754 (tm-30) REVERT: M 290 LYS cc_start: 0.7327 (mttp) cc_final: 0.6990 (mmtt) REVERT: N 170 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.6748 (mmt-90) REVERT: O 170 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.6918 (mtt-85) REVERT: P 170 ARG cc_start: 0.7689 (OUTLIER) cc_final: 0.6838 (mtt-85) outliers start: 73 outliers final: 58 residues processed: 382 average time/residue: 0.1701 time to fit residues: 97.4542 Evaluate side-chains 382 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 320 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 414 SER Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 315 PHE Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 488 HIS Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 291 PHE Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 336 ILE Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 349 GLU Chi-restraints excluded: chain F residue 410 ILE Chi-restraints excluded: chain F residue 414 SER Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 476 VAL Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 337 ILE Chi-restraints excluded: chain G residue 346 SER Chi-restraints excluded: chain H residue 303 ILE Chi-restraints excluded: chain H residue 315 PHE Chi-restraints excluded: chain H residue 336 ILE Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 362 ILE Chi-restraints excluded: chain H residue 384 LEU Chi-restraints excluded: chain H residue 440 VAL Chi-restraints excluded: chain H residue 488 HIS Chi-restraints excluded: chain I residue 289 LEU Chi-restraints excluded: chain I residue 302 THR Chi-restraints excluded: chain I residue 337 ILE Chi-restraints excluded: chain I residue 353 SER Chi-restraints excluded: chain J residue 101 CYS Chi-restraints excluded: chain J residue 157 ASP Chi-restraints excluded: chain J residue 170 ARG Chi-restraints excluded: chain M residue 127 THR Chi-restraints excluded: chain M residue 145 GLU Chi-restraints excluded: chain M residue 302 THR Chi-restraints excluded: chain M residue 337 ILE Chi-restraints excluded: chain M residue 346 SER Chi-restraints excluded: chain N residue 101 CYS Chi-restraints excluded: chain N residue 170 ARG Chi-restraints excluded: chain O residue 101 CYS Chi-restraints excluded: chain O residue 157 ASP Chi-restraints excluded: chain O residue 170 ARG Chi-restraints excluded: chain P residue 101 CYS Chi-restraints excluded: chain P residue 157 ASP Chi-restraints excluded: chain P residue 170 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 26 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 224 optimal weight: 0.9980 chunk 261 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 142 optimal weight: 3.9990 chunk 82 optimal weight: 10.0000 chunk 117 optimal weight: 0.6980 chunk 249 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 293 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.132017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.097689 restraints weight = 25073.901| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 2.28 r_work: 0.2471 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22492 Z= 0.124 Angle : 0.503 5.697 30468 Z= 0.267 Chirality : 0.041 0.140 3380 Planarity : 0.004 0.046 3844 Dihedral : 9.953 85.728 3306 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.29 % Favored : 96.63 % Rotamer: Outliers : 3.33 % Allowed : 12.99 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.07 (0.17), residues: 2704 helix: 2.03 (0.14), residues: 1592 sheet: 0.26 (0.38), residues: 172 loop : -1.62 (0.18), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 40 TYR 0.013 0.001 TYR F 485 PHE 0.016 0.001 PHE D 406 TRP 0.013 0.001 TRP I 185 HIS 0.005 0.001 HIS M 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (22488) covalent geometry : angle 0.50302 / 0.27 (30460) SS BOND : bond 0.00319 / 0.16 ( 4) SS BOND : angle 0.47805 / 0.23 ( 8) hydrogen bonds : bond 0.04983 / 3.39 ( 1124) hydrogen bonds : angle 3.57122 / 2.62 ( 3228) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 325 time to evaluate : 0.856 Fit side-chains REVERT: B 433 ASP cc_start: 0.9104 (t0) cc_final: 0.8711 (t0) REVERT: B 485 TYR cc_start: 0.9020 (t80) cc_final: 0.8683 (t80) REVERT: C 94 LYS cc_start: 0.8263 (mtpt) cc_final: 0.7928 (mttp) REVERT: C 129 ARG cc_start: 0.8295 (ptm160) cc_final: 0.7860 (ptt-90) REVERT: C 223 GLU cc_start: 0.8270 (tp30) cc_final: 0.7855 (tm-30) REVERT: C 290 LYS cc_start: 0.7359 (mtmt) cc_final: 0.7028 (mmtt) REVERT: F 485 TYR cc_start: 0.8983 (t80) cc_final: 0.8672 (t80) REVERT: G 94 LYS cc_start: 0.8238 (mtpt) cc_final: 0.7894 (mttp) REVERT: G 105 LYS cc_start: 0.8419 (tttt) cc_final: 0.8100 (tttm) REVERT: G 129 ARG cc_start: 0.8357 (ptm160) cc_final: 0.7954 (ptt-90) REVERT: H 485 TYR cc_start: 0.8979 (t80) cc_final: 0.8539 (t80) REVERT: I 94 LYS cc_start: 0.8277 (mtpt) cc_final: 0.7913 (mttp) REVERT: I 129 ARG cc_start: 0.8273 (ptm160) cc_final: 0.7805 (ptt-90) REVERT: I 290 LYS cc_start: 0.7615 (mtmt) cc_final: 0.7312 (mmtt) REVERT: J 170 ARG cc_start: 0.7697 (OUTLIER) cc_final: 0.6824 (mtt-85) REVERT: M 94 LYS cc_start: 0.8249 (mtpt) cc_final: 0.7911 (mttp) REVERT: M 129 ARG cc_start: 0.8361 (ptm160) cc_final: 0.7876 (ptt-90) REVERT: M 290 LYS cc_start: 0.7404 (mttp) cc_final: 0.7061 (mmtt) REVERT: N 170 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.6790 (mmt-90) REVERT: O 170 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.6952 (mtt-85) REVERT: P 170 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.6861 (mtt-85) outliers start: 78 outliers final: 69 residues processed: 382 average time/residue: 0.1717 time to fit residues: 97.8761 Evaluate side-chains 393 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 320 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 414 SER Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 488 HIS Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 315 PHE Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 488 HIS Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 291 PHE Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 317 CYS Chi-restraints excluded: chain F residue 336 ILE Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 349 GLU Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 410 ILE Chi-restraints excluded: chain F residue 414 SER Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 476 VAL Chi-restraints excluded: chain F residue 488 HIS Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 145 GLU Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 337 ILE Chi-restraints excluded: chain G residue 346 SER Chi-restraints excluded: chain G residue 353 SER Chi-restraints excluded: chain G residue 354 ILE Chi-restraints excluded: chain H residue 303 ILE Chi-restraints excluded: chain H residue 315 PHE Chi-restraints excluded: chain H residue 336 ILE Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 362 ILE Chi-restraints excluded: chain H residue 384 LEU Chi-restraints excluded: chain H residue 440 VAL Chi-restraints excluded: chain H residue 488 HIS Chi-restraints excluded: chain I residue 127 THR Chi-restraints excluded: chain I residue 145 GLU Chi-restraints excluded: chain I residue 289 LEU Chi-restraints excluded: chain I residue 302 THR Chi-restraints excluded: chain I residue 337 ILE Chi-restraints excluded: chain I residue 353 SER Chi-restraints excluded: chain J residue 101 CYS Chi-restraints excluded: chain J residue 157 ASP Chi-restraints excluded: chain J residue 170 ARG Chi-restraints excluded: chain M residue 127 THR Chi-restraints excluded: chain M residue 145 GLU Chi-restraints excluded: chain M residue 302 THR Chi-restraints excluded: chain M residue 337 ILE Chi-restraints excluded: chain M residue 346 SER Chi-restraints excluded: chain N residue 101 CYS Chi-restraints excluded: chain N residue 157 ASP Chi-restraints excluded: chain N residue 170 ARG Chi-restraints excluded: chain O residue 101 CYS Chi-restraints excluded: chain O residue 157 ASP Chi-restraints excluded: chain O residue 170 ARG Chi-restraints excluded: chain P residue 101 CYS Chi-restraints excluded: chain P residue 157 ASP Chi-restraints excluded: chain P residue 170 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 92 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 99 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 231 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 240 optimal weight: 0.0070 chunk 128 optimal weight: 0.8980 chunk 191 optimal weight: 0.9990 chunk 241 optimal weight: 0.6980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 293 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.133640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.103559 restraints weight = 25036.199| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.03 r_work: 0.2483 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 22492 Z= 0.107 Angle : 0.480 5.425 30468 Z= 0.253 Chirality : 0.040 0.130 3380 Planarity : 0.004 0.045 3844 Dihedral : 9.565 85.011 3306 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.33 % Favored : 97.60 % Rotamer: Outliers : 3.12 % Allowed : 13.38 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.20 (0.17), residues: 2704 helix: 2.13 (0.14), residues: 1592 sheet: 0.36 (0.37), residues: 176 loop : -1.57 (0.18), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 260 TYR 0.011 0.001 TYR F 485 PHE 0.016 0.001 PHE D 406 TRP 0.012 0.001 TRP C 185 HIS 0.004 0.001 HIS G 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (22488) covalent geometry : angle 0.47982 / 0.25 (30460) SS BOND : bond 0.00288 / 0.14 ( 4) SS BOND : angle 0.44960 / 0.22 ( 8) hydrogen bonds : bond 0.04381 / 2.99 ( 1124) hydrogen bonds : angle 3.46926 / 2.54 ( 3228) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 335 time to evaluate : 0.929 Fit side-chains REVERT: B 433 ASP cc_start: 0.9120 (t0) cc_final: 0.8754 (t0) REVERT: B 485 TYR cc_start: 0.9020 (t80) cc_final: 0.8695 (t80) REVERT: C 94 LYS cc_start: 0.8220 (mtpt) cc_final: 0.7882 (mttp) REVERT: C 129 ARG cc_start: 0.8258 (ptm160) cc_final: 0.7808 (ptt-90) REVERT: C 223 GLU cc_start: 0.8292 (tp30) cc_final: 0.7885 (tm-30) REVERT: C 290 LYS cc_start: 0.7466 (mtmt) cc_final: 0.7135 (mmtt) REVERT: F 367 ARG cc_start: 0.8522 (ttt180) cc_final: 0.8209 (ttt-90) REVERT: G 94 LYS cc_start: 0.8205 (mtpt) cc_final: 0.7850 (mttp) REVERT: G 105 LYS cc_start: 0.8400 (tttt) cc_final: 0.8129 (tttm) REVERT: G 129 ARG cc_start: 0.8320 (ptm160) cc_final: 0.7867 (ptt-90) REVERT: H 485 TYR cc_start: 0.8979 (t80) cc_final: 0.8739 (t80) REVERT: I 94 LYS cc_start: 0.8237 (mtpt) cc_final: 0.7864 (mttp) REVERT: I 129 ARG cc_start: 0.8237 (ptm160) cc_final: 0.7750 (ptt-90) REVERT: I 290 LYS cc_start: 0.7499 (mtmt) cc_final: 0.7203 (mmtt) REVERT: J 170 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.6869 (mtt-85) REVERT: M 94 LYS cc_start: 0.8193 (mtpt) cc_final: 0.7848 (mttp) REVERT: M 129 ARG cc_start: 0.8316 (ptm160) cc_final: 0.7813 (ptt-90) REVERT: M 290 LYS cc_start: 0.7409 (mttp) cc_final: 0.7080 (mmtt) REVERT: N 170 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.6817 (mmt-90) REVERT: O 170 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.6978 (mmt-90) REVERT: P 170 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.6872 (mtt-85) outliers start: 73 outliers final: 60 residues processed: 390 average time/residue: 0.1851 time to fit residues: 106.9193 Evaluate side-chains 393 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 329 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 414 SER Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 488 HIS Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 315 PHE Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 488 HIS Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 291 PHE Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 349 GLU Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 410 ILE Chi-restraints excluded: chain F residue 414 SER Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 488 HIS Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 145 GLU Chi-restraints excluded: chain G residue 158 ASN Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 346 SER Chi-restraints excluded: chain G residue 353 SER Chi-restraints excluded: chain G residue 354 ILE Chi-restraints excluded: chain H residue 303 ILE Chi-restraints excluded: chain H residue 315 PHE Chi-restraints excluded: chain H residue 336 ILE Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 362 ILE Chi-restraints excluded: chain H residue 384 LEU Chi-restraints excluded: chain H residue 440 VAL Chi-restraints excluded: chain H residue 488 HIS Chi-restraints excluded: chain I residue 127 THR Chi-restraints excluded: chain I residue 302 THR Chi-restraints excluded: chain I residue 337 ILE Chi-restraints excluded: chain I residue 353 SER Chi-restraints excluded: chain J residue 101 CYS Chi-restraints excluded: chain J residue 157 ASP Chi-restraints excluded: chain J residue 170 ARG Chi-restraints excluded: chain M residue 127 THR Chi-restraints excluded: chain M residue 145 GLU Chi-restraints excluded: chain M residue 302 THR Chi-restraints excluded: chain M residue 337 ILE Chi-restraints excluded: chain M residue 346 SER Chi-restraints excluded: chain N residue 101 CYS Chi-restraints excluded: chain N residue 170 ARG Chi-restraints excluded: chain O residue 101 CYS Chi-restraints excluded: chain O residue 157 ASP Chi-restraints excluded: chain O residue 170 ARG Chi-restraints excluded: chain P residue 101 CYS Chi-restraints excluded: chain P residue 157 ASP Chi-restraints excluded: chain P residue 170 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 250 optimal weight: 0.9980 chunk 194 optimal weight: 0.0170 chunk 9 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 101 optimal weight: 0.4980 chunk 79 optimal weight: 0.8980 chunk 201 optimal weight: 0.3980 chunk 22 optimal weight: 2.9990 chunk 162 optimal weight: 0.9980 chunk 155 optimal weight: 0.8980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 293 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.134154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.099523 restraints weight = 25037.274| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 2.62 r_work: 0.2522 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 22492 Z= 0.101 Angle : 0.475 6.040 30468 Z= 0.250 Chirality : 0.040 0.129 3380 Planarity : 0.004 0.044 3844 Dihedral : 9.107 84.192 3301 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.81 % Favored : 97.12 % Rotamer: Outliers : 2.78 % Allowed : 13.50 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.31 (0.17), residues: 2704 helix: 2.31 (0.14), residues: 1568 sheet: 0.35 (0.37), residues: 176 loop : -1.60 (0.18), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 40 TYR 0.014 0.001 TYR F 485 PHE 0.016 0.001 PHE D 406 TRP 0.011 0.001 TRP I 185 HIS 0.004 0.001 HIS M 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (22488) covalent geometry : angle 0.47509 / 0.25 (30460) SS BOND : bond 0.00304 / 0.15 ( 4) SS BOND : angle 0.43282 / 0.21 ( 8) hydrogen bonds : bond 0.04177 / 2.85 ( 1124) hydrogen bonds : angle 3.42255 / 2.51 ( 3228) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 337 time to evaluate : 1.009 Fit side-chains REVERT: B 433 ASP cc_start: 0.9033 (t0) cc_final: 0.8707 (t0) REVERT: B 485 TYR cc_start: 0.8978 (t80) cc_final: 0.8655 (t80) REVERT: C 94 LYS cc_start: 0.8160 (mtpt) cc_final: 0.7754 (mttp) REVERT: C 129 ARG cc_start: 0.8190 (ptm160) cc_final: 0.7724 (ptt-90) REVERT: C 223 GLU cc_start: 0.8188 (tp30) cc_final: 0.7751 (tm-30) REVERT: C 290 LYS cc_start: 0.7386 (mtmt) cc_final: 0.7075 (mmtt) REVERT: F 367 ARG cc_start: 0.8488 (ttt180) cc_final: 0.8246 (mtp180) REVERT: F 392 LYS cc_start: 0.8726 (tttm) cc_final: 0.8464 (tptm) REVERT: G 94 LYS cc_start: 0.8131 (mtpt) cc_final: 0.7778 (mttp) REVERT: G 129 ARG cc_start: 0.8249 (ptm160) cc_final: 0.7776 (ptt-90) REVERT: H 485 TYR cc_start: 0.8937 (t80) cc_final: 0.8684 (t80) REVERT: I 94 LYS cc_start: 0.8175 (mtpt) cc_final: 0.7801 (mttp) REVERT: I 129 ARG cc_start: 0.8205 (ptm160) cc_final: 0.7697 (ptt-90) REVERT: I 290 LYS cc_start: 0.7442 (mtmt) cc_final: 0.7157 (mmtt) REVERT: J 170 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.6810 (mmt-90) REVERT: M 94 LYS cc_start: 0.8138 (mtpt) cc_final: 0.7792 (mttp) REVERT: M 129 ARG cc_start: 0.8241 (ptm160) cc_final: 0.7730 (ptt-90) REVERT: M 290 LYS cc_start: 0.7299 (mttp) cc_final: 0.6965 (mmtt) REVERT: N 170 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.6787 (mmt-90) REVERT: O 170 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.6904 (mmt-90) REVERT: P 170 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.6798 (mmt-90) outliers start: 65 outliers final: 59 residues processed: 388 average time/residue: 0.1781 time to fit residues: 103.2374 Evaluate side-chains 392 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 329 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 414 SER Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 488 HIS Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 488 HIS Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 291 PHE Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 336 ILE Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 349 GLU Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 410 ILE Chi-restraints excluded: chain F residue 414 SER Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 476 VAL Chi-restraints excluded: chain F residue 488 HIS Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 145 GLU Chi-restraints excluded: chain G residue 158 ASN Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 346 SER Chi-restraints excluded: chain G residue 353 SER Chi-restraints excluded: chain G residue 354 ILE Chi-restraints excluded: chain H residue 303 ILE Chi-restraints excluded: chain H residue 315 PHE Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 362 ILE Chi-restraints excluded: chain H residue 384 LEU Chi-restraints excluded: chain H residue 440 VAL Chi-restraints excluded: chain H residue 488 HIS Chi-restraints excluded: chain I residue 127 THR Chi-restraints excluded: chain I residue 302 THR Chi-restraints excluded: chain I residue 353 SER Chi-restraints excluded: chain J residue 101 CYS Chi-restraints excluded: chain J residue 157 ASP Chi-restraints excluded: chain J residue 170 ARG Chi-restraints excluded: chain M residue 127 THR Chi-restraints excluded: chain M residue 145 GLU Chi-restraints excluded: chain M residue 158 ASN Chi-restraints excluded: chain M residue 302 THR Chi-restraints excluded: chain M residue 337 ILE Chi-restraints excluded: chain M residue 346 SER Chi-restraints excluded: chain N residue 101 CYS Chi-restraints excluded: chain N residue 170 ARG Chi-restraints excluded: chain O residue 101 CYS Chi-restraints excluded: chain O residue 157 ASP Chi-restraints excluded: chain O residue 170 ARG Chi-restraints excluded: chain P residue 101 CYS Chi-restraints excluded: chain P residue 157 ASP Chi-restraints excluded: chain P residue 170 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 15 optimal weight: 2.9990 chunk 230 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 chunk 218 optimal weight: 0.1980 chunk 106 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 186 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 217 optimal weight: 0.8980 chunk 82 optimal weight: 10.0000 chunk 161 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 293 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.132680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.098496 restraints weight = 25139.735| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 2.28 r_work: 0.2457 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22492 Z= 0.116 Angle : 0.495 7.398 30468 Z= 0.260 Chirality : 0.040 0.132 3380 Planarity : 0.004 0.045 3844 Dihedral : 9.335 82.902 3301 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.96 % Favored : 96.93 % Rotamer: Outliers : 2.82 % Allowed : 13.68 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.27 (0.17), residues: 2704 helix: 2.28 (0.14), residues: 1568 sheet: 0.26 (0.37), residues: 172 loop : -1.60 (0.18), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 40 TYR 0.015 0.001 TYR F 485 PHE 0.017 0.001 PHE D 406 TRP 0.013 0.001 TRP I 185 HIS 0.005 0.001 HIS G 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (22488) covalent geometry : angle 0.49497 / 0.26 (30460) SS BOND : bond 0.00308 / 0.15 ( 4) SS BOND : angle 0.45552 / 0.22 ( 8) hydrogen bonds : bond 0.04663 / 3.18 ( 1124) hydrogen bonds : angle 3.48210 / 2.55 ( 3228) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5408 Ramachandran restraints generated. 2704 Oldfield, 0 Emsley, 2704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 331 time to evaluate : 0.912 Fit side-chains revert: symmetry clash REVERT: B 433 ASP cc_start: 0.9122 (t0) cc_final: 0.8739 (t0) REVERT: B 485 TYR cc_start: 0.9069 (t80) cc_final: 0.8745 (t80) REVERT: C 94 LYS cc_start: 0.8291 (mtpt) cc_final: 0.7941 (mttp) REVERT: C 129 ARG cc_start: 0.8281 (ptm160) cc_final: 0.7851 (ptt-90) REVERT: C 223 GLU cc_start: 0.8331 (tp30) cc_final: 0.7915 (tm-30) REVERT: C 290 LYS cc_start: 0.7469 (mtmt) cc_final: 0.7146 (mmtt) REVERT: F 367 ARG cc_start: 0.8592 (ttt180) cc_final: 0.8370 (mtp180) REVERT: F 392 LYS cc_start: 0.8722 (tttm) cc_final: 0.8469 (tptm) REVERT: G 94 LYS cc_start: 0.8250 (mtpt) cc_final: 0.7912 (mttp) REVERT: G 105 LYS cc_start: 0.8444 (tttt) cc_final: 0.8177 (tttm) REVERT: G 129 ARG cc_start: 0.8346 (ptm160) cc_final: 0.7943 (ptt-90) REVERT: H 485 TYR cc_start: 0.8992 (t80) cc_final: 0.8746 (t80) REVERT: I 94 LYS cc_start: 0.8308 (mtpt) cc_final: 0.7940 (mttp) REVERT: I 129 ARG cc_start: 0.8274 (ptm160) cc_final: 0.7815 (ptt-90) REVERT: I 290 LYS cc_start: 0.7655 (mtmt) cc_final: 0.7347 (mmtt) REVERT: J 170 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.6848 (mtt-85) REVERT: M 94 LYS cc_start: 0.8254 (mtpt) cc_final: 0.7923 (mttp) REVERT: M 129 ARG cc_start: 0.8345 (ptm160) cc_final: 0.7867 (ptt-90) REVERT: M 290 LYS cc_start: 0.7402 (mttp) cc_final: 0.7056 (mmtt) REVERT: N 170 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.6812 (mmt-90) REVERT: O 170 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.6967 (mmt-90) REVERT: P 170 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.6868 (mtt-85) outliers start: 66 outliers final: 61 residues processed: 381 average time/residue: 0.1774 time to fit residues: 100.8482 Evaluate side-chains 395 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 330 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 414 SER Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 488 HIS Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 488 HIS Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 291 PHE Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 303 ILE Chi-restraints excluded: chain F residue 336 ILE Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 349 GLU Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 410 ILE Chi-restraints excluded: chain F residue 414 SER Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 476 VAL Chi-restraints excluded: chain F residue 488 HIS Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 145 GLU Chi-restraints excluded: chain G residue 158 ASN Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 346 SER Chi-restraints excluded: chain G residue 353 SER Chi-restraints excluded: chain G residue 354 ILE Chi-restraints excluded: chain H residue 303 ILE Chi-restraints excluded: chain H residue 315 PHE Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 362 ILE Chi-restraints excluded: chain H residue 384 LEU Chi-restraints excluded: chain H residue 440 VAL Chi-restraints excluded: chain H residue 488 HIS Chi-restraints excluded: chain I residue 127 THR Chi-restraints excluded: chain I residue 302 THR Chi-restraints excluded: chain I residue 337 ILE Chi-restraints excluded: chain I residue 353 SER Chi-restraints excluded: chain J residue 101 CYS Chi-restraints excluded: chain J residue 157 ASP Chi-restraints excluded: chain J residue 170 ARG Chi-restraints excluded: chain M residue 127 THR Chi-restraints excluded: chain M residue 145 GLU Chi-restraints excluded: chain M residue 158 ASN Chi-restraints excluded: chain M residue 302 THR Chi-restraints excluded: chain M residue 337 ILE Chi-restraints excluded: chain M residue 346 SER Chi-restraints excluded: chain N residue 101 CYS Chi-restraints excluded: chain N residue 170 ARG Chi-restraints excluded: chain O residue 101 CYS Chi-restraints excluded: chain O residue 157 ASP Chi-restraints excluded: chain O residue 170 ARG Chi-restraints excluded: chain P residue 101 CYS Chi-restraints excluded: chain P residue 157 ASP Chi-restraints excluded: chain P residue 170 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 233 optimal weight: 0.5980 chunk 160 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 145 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 264 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 197 optimal weight: 0.6980 chunk 262 optimal weight: 0.6980 chunk 146 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 293 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.133064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.099441 restraints weight = 25147.194| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 2.23 r_work: 0.2456 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 22492 Z= 0.111 Angle : 0.488 7.153 30468 Z= 0.256 Chirality : 0.040 0.131 3380 Planarity : 0.004 0.044 3844 Dihedral : 9.289 81.537 3301 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.81 % Favored : 97.08 % Rotamer: Outliers : 2.99 % Allowed : 13.55 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.31 (0.17), residues: 2704 helix: 2.31 (0.14), residues: 1568 sheet: 0.35 (0.37), residues: 176 loop : -1.58 (0.18), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 40 TYR 0.014 0.001 TYR F 485 PHE 0.020 0.001 PHE B 308 TRP 0.012 0.001 TRP C 185 HIS 0.004 0.001 HIS G 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (22488) covalent geometry : angle 0.48801 / 0.26 (30460) SS BOND : bond 0.00295 / 0.15 ( 4) SS BOND : angle 0.43439 / 0.21 ( 8) hydrogen bonds : bond 0.04486 / 3.06 ( 1124) hydrogen bonds : angle 3.45725 / 2.53 ( 3228) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4884.23 seconds wall clock time: 84 minutes 24.80 seconds (5064.80 seconds total)