Starting phenix.real_space_refine on Thu Jun 19 06:14:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wf3_32459/06_2025/7wf3_32459_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wf3_32459/06_2025/7wf3_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_32459/06_2025/7wf3_32459.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wf3_32459/06_2025/7wf3_32459.map" model { file = "/net/cci-nas-00/data/ceres_data/7wf3_32459/06_2025/7wf3_32459_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wf3_32459/06_2025/7wf3_32459_neut.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.041 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 2, 'ARG:plan': 1} 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: {'GLN:plan1': 2, 'ARG:plan': 1} 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: {'GLN:plan1': 2, 'ARG:plan': 1} 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: {'GLN:plan1': 2, 'ARG:plan': 1} 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, 4 Unusual residues: {' K': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: 14.86, per 1000 atoms: 0.67 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: 5.39 Conformation dependent library (CDL) restraints added in 2.8 seconds 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: 2.25 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: 8.95 Time building geometry restraints manager: 6.12 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: 45.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.950 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 52.530 Find NCS groups from input model: 1.590 Set up NCS constraints: 0.270 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: 0.020 Load rotamer database and sin/cos tables:3.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (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 TRP 0.019 0.002 TRP I 185 HIS 0.010 0.002 HIS M 135 PHE 0.039 0.003 PHE B 296 TYR 0.047 0.003 TYR B 339 ARG 0.004 0.001 ARG C 298 Details of bonding type rmsd hydrogen bonds : bond 0.17453 ( 1124) hydrogen bonds : angle 5.76853 ( 3228) SS BOND : bond 0.00204 ( 4) SS BOND : angle 1.00002 ( 8) covalent geometry : bond 0.01177 (22488) covalent geometry : angle 1.22443 (30460) *********************** 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 : 2.354 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: 0.7125 (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: 0.6128 (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: 0.6334 (OUTLIER) cc_final: 0.6065 (mm) REVERT: H 296 PHE cc_start: 0.6987 (OUTLIER) cc_final: 0.6240 (t80) REVERT: H 386 ILE cc_start: 0.7984 (mt) cc_final: 0.7695 (mt) REVERT: I 70 GLU cc_start: 0.6918 (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: 0.4064 time to fit residues: 334.5383 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 : 3.674 ------------------------------------------------------------------------------- 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 226 optimal weight: 0.0020 chunk 203 optimal weight: 0.3980 chunk 112 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 137 optimal weight: 0.7980 chunk 108 optimal weight: 0.8980 chunk 210 optimal weight: 0.0050 chunk 81 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 156 optimal weight: 0.6980 chunk 243 optimal weight: 1.9990 overall best weight: 0.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3375 r_free = 0.3375 target = 0.137475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.102969 restraints weight = 24911.006| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 2.02 r_work: 0.2565 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 22492 Z= 0.116 Angle : 0.530 5.735 30468 Z= 0.283 Chirality : 0.041 0.136 3380 Planarity : 0.005 0.050 3844 Dihedral : 11.963 88.776 3427 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.12 % Allowed : 11.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.16), residues: 2704 helix: 1.20 (0.13), residues: 1532 sheet: 0.74 (0.36), residues: 216 loop : -2.06 (0.16), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 305 HIS 0.005 0.001 HIS B 451 PHE 0.046 0.001 PHE D 216 TYR 0.014 0.001 TYR B 447 ARG 0.003 0.000 ARG G 40 Details of bonding type rmsd hydrogen bonds : bond 0.05088 ( 1124) hydrogen bonds : angle 3.92336 ( 3228) SS BOND : bond 0.00172 ( 4) SS BOND : angle 0.64055 ( 8) covalent geometry : bond 0.00229 (22488) covalent geometry : angle 0.52970 (30460) *********************** 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 435 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 362 time to evaluate : 2.703 Fit side-chains REVERT: C 104 LYS cc_start: 0.8108 (tttp) cc_final: 0.7878 (ttmm) REVERT: C 105 LYS cc_start: 0.8510 (tttt) cc_final: 0.8293 (tttm) REVERT: C 129 ARG cc_start: 0.8370 (ptm160) cc_final: 0.7931 (ptt-90) REVERT: C 223 GLU cc_start: 0.8203 (tp30) cc_final: 0.7803 (tm-30) REVERT: C 290 LYS cc_start: 0.7503 (mtmt) cc_final: 0.7181 (mttp) REVERT: C 315 GLU cc_start: 0.7343 (mm-30) cc_final: 0.7062 (mm-30) REVERT: C 347 ILE cc_start: 0.8283 (OUTLIER) cc_final: 0.8068 (mm) REVERT: D 433 ASP cc_start: 0.8754 (t0) cc_final: 0.8548 (t0) REVERT: F 225 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7360 (tp30) REVERT: G 70 GLU cc_start: 0.8082 (tt0) cc_final: 0.7846 (tt0) REVERT: G 129 ARG cc_start: 0.8449 (ptm160) cc_final: 0.7976 (ptt-90) REVERT: G 270 TYR cc_start: 0.8411 (m-80) cc_final: 0.8091 (m-80) REVERT: G 315 GLU cc_start: 0.7645 (mm-30) cc_final: 0.7218 (mp0) REVERT: I 94 LYS cc_start: 0.8154 (mtpt) cc_final: 0.7790 (mttp) REVERT: I 105 LYS cc_start: 0.8397 (tttt) cc_final: 0.8150 (tttm) REVERT: I 129 ARG cc_start: 0.8312 (ptm160) cc_final: 0.7854 (ptt-90) REVERT: I 290 LYS cc_start: 0.7664 (mtmt) cc_final: 0.7326 (mmtt) REVERT: I 315 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7102 (mp0) REVERT: J 170 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.6884 (mtt-85) REVERT: M 70 GLU cc_start: 0.8128 (tt0) cc_final: 0.7922 (tt0) REVERT: M 129 ARG cc_start: 0.8452 (ptm160) cc_final: 0.7990 (ptt-90) REVERT: M 223 GLU cc_start: 0.8192 (tp30) cc_final: 0.7861 (tm-30) REVERT: M 270 TYR cc_start: 0.8443 (m-80) cc_final: 0.8177 (m-80) REVERT: M 315 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7263 (mp0) REVERT: N 170 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.6940 (mtt-85) REVERT: O 168 ARG cc_start: 0.8407 (mtm180) cc_final: 0.8102 (mtm-85) REVERT: O 170 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7042 (mmt-90) REVERT: P 135 ARG cc_start: 0.8857 (mtt180) cc_final: 0.8571 (mtt180) REVERT: P 170 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.7019 (mtt-85) outliers start: 73 outliers final: 44 residues processed: 413 average time/residue: 0.3965 time to fit residues: 240.4678 Evaluate side-chains 375 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 326 time to evaluate : 2.458 ------------------------------------------------------------------------------- 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 391 LEU Chi-restraints excluded: chain B residue 454 THR 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 454 THR 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 454 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 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 97 optimal weight: 2.9990 chunk 34 optimal weight: 0.0470 chunk 4 optimal weight: 3.9990 chunk 195 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 239 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 120 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 overall best weight: 0.9680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 293 GLN M 293 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.132732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.096464 restraints weight = 24952.970| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 2.18 r_work: 0.2443 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22492 Z= 0.138 Angle : 0.543 5.693 30468 Z= 0.287 Chirality : 0.042 0.159 3380 Planarity : 0.005 0.047 3844 Dihedral : 10.195 87.380 3335 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.16 % Allowed : 11.32 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.16), residues: 2704 helix: 1.66 (0.13), residues: 1568 sheet: 0.30 (0.37), residues: 176 loop : -1.68 (0.17), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 185 HIS 0.008 0.001 HIS F 451 PHE 0.027 0.001 PHE D 216 TYR 0.021 0.002 TYR F 447 ARG 0.011 0.000 ARG G 40 Details of bonding type rmsd hydrogen bonds : bond 0.05570 ( 1124) hydrogen bonds : angle 3.73083 ( 3228) SS BOND : bond 0.00370 ( 4) SS BOND : angle 0.53654 ( 8) covalent geometry : bond 0.00312 (22488) covalent geometry : angle 0.54294 (30460) *********************** 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 415 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 341 time to evaluate : 2.562 Fit side-chains REVERT: B 433 ASP cc_start: 0.9063 (t0) cc_final: 0.8676 (t0) REVERT: C 94 LYS cc_start: 0.8269 (mtpt) cc_final: 0.7843 (mttp) REVERT: C 104 LYS cc_start: 0.8181 (tttp) cc_final: 0.7914 (ttmm) REVERT: C 129 ARG cc_start: 0.8364 (ptm160) cc_final: 0.7921 (ptt-90) REVERT: C 223 GLU cc_start: 0.8202 (tp30) cc_final: 0.7772 (tm-30) REVERT: C 290 LYS cc_start: 0.7444 (mtmt) cc_final: 0.7018 (mmtt) REVERT: C 347 ILE cc_start: 0.8134 (mt) cc_final: 0.7922 (mm) REVERT: D 433 ASP cc_start: 0.8918 (t0) cc_final: 0.8713 (t0) REVERT: F 303 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8483 (mp) REVERT: G 51 CYS cc_start: 0.8356 (m) cc_final: 0.8125 (m) REVERT: G 70 GLU cc_start: 0.8115 (tt0) cc_final: 0.7912 (tt0) REVERT: G 94 LYS cc_start: 0.8180 (mtpt) cc_final: 0.7796 (mttp) REVERT: G 105 LYS cc_start: 0.8423 (tttt) cc_final: 0.8119 (tttm) REVERT: G 129 ARG cc_start: 0.8454 (ptm160) cc_final: 0.7991 (ptt-90) REVERT: G 270 TYR cc_start: 0.8439 (m-80) cc_final: 0.8149 (m-80) REVERT: G 315 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7194 (mp0) REVERT: H 367 ARG cc_start: 0.8593 (mtp180) cc_final: 0.8362 (mtp180) REVERT: I 94 LYS cc_start: 0.8215 (mtpt) cc_final: 0.7799 (mttp) REVERT: I 105 LYS cc_start: 0.8362 (tttt) cc_final: 0.8146 (tttm) REVERT: I 129 ARG cc_start: 0.8302 (ptm160) cc_final: 0.7862 (ptt-90) REVERT: I 290 LYS cc_start: 0.7553 (mtmt) cc_final: 0.7236 (mmtt) REVERT: J 170 ARG cc_start: 0.7624 (OUTLIER) cc_final: 0.6762 (mtt-85) REVERT: M 94 LYS cc_start: 0.8188 (mtpt) cc_final: 0.7824 (mttp) REVERT: M 105 LYS cc_start: 0.8425 (tttt) cc_final: 0.8140 (tttm) REVERT: M 129 ARG cc_start: 0.8424 (ptm160) cc_final: 0.7992 (ptt-90) REVERT: M 270 TYR cc_start: 0.8466 (m-80) cc_final: 0.8166 (m-80) REVERT: M 315 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7170 (mp0) REVERT: N 170 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.6839 (mmt-90) REVERT: O 170 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.6943 (mmt-90) REVERT: P 170 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.6819 (mtt-85) outliers start: 74 outliers final: 50 residues processed: 400 average time/residue: 0.4265 time to fit residues: 252.6373 Evaluate side-chains 382 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 327 time to evaluate : 2.451 ------------------------------------------------------------------------------- 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 349 GLU Chi-restraints excluded: chain B residue 414 SER Chi-restraints excluded: chain B residue 471 THR 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 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 342 THR Chi-restraints excluded: chain D residue 471 THR 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 414 SER Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 471 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 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 440 VAL Chi-restraints excluded: chain H residue 476 VAL Chi-restraints excluded: chain H residue 488 HIS 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 260 optimal weight: 1.9990 chunk 233 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 180 optimal weight: 2.9990 chunk 187 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 47 optimal weight: 0.0980 chunk 259 optimal weight: 0.5980 chunk 178 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.130497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.096282 restraints weight = 25124.870| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 2.32 r_work: 0.2419 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22492 Z= 0.160 Angle : 0.557 6.977 30468 Z= 0.296 Chirality : 0.043 0.156 3380 Planarity : 0.005 0.048 3844 Dihedral : 10.515 87.285 3314 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.76 % Allowed : 11.37 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.16), residues: 2704 helix: 1.75 (0.14), residues: 1576 sheet: 0.23 (0.38), residues: 172 loop : -1.71 (0.17), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 185 HIS 0.006 0.001 HIS M 135 PHE 0.017 0.001 PHE D 216 TYR 0.012 0.002 TYR H 487 ARG 0.006 0.000 ARG C 40 Details of bonding type rmsd hydrogen bonds : bond 0.05894 ( 1124) hydrogen bonds : angle 3.76932 ( 3228) SS BOND : bond 0.00329 ( 4) SS BOND : angle 0.52417 ( 8) covalent geometry : bond 0.00380 (22488) covalent geometry : angle 0.55698 (30460) *********************** 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 420 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 332 time to evaluate : 2.961 Fit side-chains REVERT: B 433 ASP cc_start: 0.9147 (t0) cc_final: 0.8775 (t0) REVERT: B 485 TYR cc_start: 0.9009 (t80) cc_final: 0.8724 (t80) REVERT: C 94 LYS cc_start: 0.8318 (mtpt) cc_final: 0.7915 (mttp) REVERT: C 129 ARG cc_start: 0.8399 (ptm160) cc_final: 0.7967 (ptt-90) REVERT: C 223 GLU cc_start: 0.8298 (tp30) cc_final: 0.7879 (tm-30) REVERT: C 290 LYS cc_start: 0.7467 (mtmt) cc_final: 0.7102 (mmtt) REVERT: F 330 LEU cc_start: 0.8483 (mt) cc_final: 0.8201 (tp) REVERT: G 94 LYS cc_start: 0.8302 (mtpt) cc_final: 0.7956 (mttp) REVERT: G 129 ARG cc_start: 0.8476 (ptm160) cc_final: 0.8059 (ptt-90) REVERT: G 270 TYR cc_start: 0.8462 (m-80) cc_final: 0.8258 (m-80) REVERT: G 315 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7124 (mp0) REVERT: H 485 TYR cc_start: 0.9028 (t80) cc_final: 0.8745 (t80) REVERT: I 94 LYS cc_start: 0.8270 (mtpt) cc_final: 0.7928 (mttp) REVERT: I 105 LYS cc_start: 0.8454 (tttt) cc_final: 0.8182 (tttm) REVERT: I 129 ARG cc_start: 0.8367 (ptm160) cc_final: 0.7934 (ptt-90) REVERT: I 290 LYS cc_start: 0.7733 (mtmt) cc_final: 0.7412 (mmtt) REVERT: J 170 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.6774 (mtt-85) REVERT: M 94 LYS cc_start: 0.8386 (mtpt) cc_final: 0.8018 (mttp) REVERT: M 129 ARG cc_start: 0.8468 (ptm160) cc_final: 0.8019 (ptt-90) REVERT: M 270 TYR cc_start: 0.8466 (m-80) cc_final: 0.8259 (m-80) REVERT: M 315 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7154 (mp0) REVERT: M 331 MET cc_start: 0.8217 (mmp) cc_final: 0.8009 (mmp) REVERT: N 170 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.6817 (mtt-85) REVERT: O 170 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.6936 (mmt-90) REVERT: P 170 ARG cc_start: 0.7624 (OUTLIER) cc_final: 0.6874 (mtt-85) outliers start: 88 outliers final: 62 residues processed: 395 average time/residue: 0.3926 time to fit residues: 229.7332 Evaluate side-chains 388 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 322 time to evaluate : 2.338 ------------------------------------------------------------------------------- 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 349 GLU 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 476 VAL Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 302 THR 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 342 THR Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 471 THR 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 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 414 SER Chi-restraints excluded: chain F residue 471 THR 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 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 315 PHE Chi-restraints excluded: chain H residue 336 ILE Chi-restraints excluded: chain H residue 384 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 153 optimal weight: 0.9980 chunk 180 optimal weight: 2.9990 chunk 214 optimal weight: 1.9990 chunk 141 optimal weight: 7.9990 chunk 66 optimal weight: 0.8980 chunk 256 optimal weight: 3.9990 chunk 229 optimal weight: 0.0870 chunk 174 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 chunk 217 optimal weight: 0.0060 chunk 67 optimal weight: 0.7980 overall best weight: 0.5174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.134591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.100812 restraints weight = 25106.569| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 2.25 r_work: 0.2479 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 22492 Z= 0.101 Angle : 0.479 5.710 30468 Z= 0.252 Chirality : 0.040 0.127 3380 Planarity : 0.004 0.045 3844 Dihedral : 9.302 87.553 3312 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.48 % Allowed : 13.21 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.16), residues: 2704 helix: 2.08 (0.14), residues: 1568 sheet: 0.11 (0.37), residues: 152 loop : -1.54 (0.17), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 185 HIS 0.004 0.001 HIS G 135 PHE 0.015 0.001 PHE F 224 TYR 0.007 0.001 TYR G 270 ARG 0.004 0.000 ARG I 40 Details of bonding type rmsd hydrogen bonds : bond 0.04179 ( 1124) hydrogen bonds : angle 3.46984 ( 3228) SS BOND : bond 0.00263 ( 4) SS BOND : angle 0.46701 ( 8) covalent geometry : bond 0.00214 (22488) covalent geometry : angle 0.47858 (30460) *********************** 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 389 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 331 time to evaluate : 2.347 Fit side-chains REVERT: B 433 ASP cc_start: 0.9135 (t0) cc_final: 0.8748 (t0) REVERT: B 485 TYR cc_start: 0.9012 (t80) cc_final: 0.8706 (t80) REVERT: C 94 LYS cc_start: 0.8213 (mtpt) cc_final: 0.7809 (mttp) REVERT: C 129 ARG cc_start: 0.8296 (ptm160) cc_final: 0.7846 (ptt-90) REVERT: C 223 GLU cc_start: 0.8277 (tp30) cc_final: 0.7848 (tm-30) REVERT: C 290 LYS cc_start: 0.7516 (mtmt) cc_final: 0.7147 (mmtt) REVERT: F 391 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8807 (mt) REVERT: G 94 LYS cc_start: 0.8218 (mtpt) cc_final: 0.7886 (mttp) REVERT: G 105 LYS cc_start: 0.8388 (tttt) cc_final: 0.8111 (tttm) REVERT: G 129 ARG cc_start: 0.8355 (ptm160) cc_final: 0.7937 (ptt-90) REVERT: G 270 TYR cc_start: 0.8334 (m-80) cc_final: 0.8116 (m-80) REVERT: G 315 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7148 (mp0) REVERT: H 485 TYR cc_start: 0.9007 (t80) cc_final: 0.8727 (t80) REVERT: I 94 LYS cc_start: 0.8177 (mtpt) cc_final: 0.7798 (mttp) REVERT: I 129 ARG cc_start: 0.8254 (ptm160) cc_final: 0.7781 (ptt-90) REVERT: I 290 LYS cc_start: 0.7567 (mtmt) cc_final: 0.7265 (mmtt) REVERT: J 170 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.6796 (mtt-85) REVERT: M 94 LYS cc_start: 0.8247 (mtpt) cc_final: 0.7897 (mttp) REVERT: M 129 ARG cc_start: 0.8366 (ptm160) cc_final: 0.7873 (ptt-90) REVERT: M 270 TYR cc_start: 0.8382 (m-80) cc_final: 0.8151 (m-80) REVERT: M 290 LYS cc_start: 0.7378 (mttp) cc_final: 0.7054 (mmtt) REVERT: M 315 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7128 (mp0) REVERT: N 170 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.6780 (mmt-90) REVERT: O 170 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.6972 (mmt-90) REVERT: P 170 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.6879 (mtt-85) outliers start: 58 outliers final: 37 residues processed: 378 average time/residue: 0.3913 time to fit residues: 215.1241 Evaluate side-chains 363 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 321 time to evaluate : 2.493 ------------------------------------------------------------------------------- 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 440 VAL 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 F residue 216 PHE Chi-restraints excluded: chain F residue 297 VAL 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 391 LEU Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 158 ASN 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 384 LEU Chi-restraints excluded: chain H residue 440 VAL Chi-restraints excluded: chain H residue 488 HIS 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 158 ASN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 255 optimal weight: 3.9990 chunk 160 optimal weight: 0.9990 chunk 111 optimal weight: 0.0570 chunk 46 optimal weight: 0.6980 chunk 247 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 194 optimal weight: 0.0270 chunk 41 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 228 optimal weight: 0.0870 chunk 8 optimal weight: 10.0000 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 293 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.135835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.102914 restraints weight = 24989.844| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.12 r_work: 0.2530 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 22492 Z= 0.094 Angle : 0.464 5.543 30468 Z= 0.243 Chirality : 0.039 0.128 3380 Planarity : 0.004 0.043 3844 Dihedral : 8.389 87.289 3304 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.44 % Allowed : 13.25 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.17), residues: 2704 helix: 2.25 (0.14), residues: 1580 sheet: 0.18 (0.40), residues: 132 loop : -1.54 (0.17), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 185 HIS 0.004 0.001 HIS G 135 PHE 0.014 0.001 PHE D 406 TYR 0.007 0.001 TYR J 161 ARG 0.002 0.000 ARG M 40 Details of bonding type rmsd hydrogen bonds : bond 0.03853 ( 1124) hydrogen bonds : angle 3.35434 ( 3228) SS BOND : bond 0.00326 ( 4) SS BOND : angle 0.40241 ( 8) covalent geometry : bond 0.00192 (22488) covalent geometry : angle 0.46412 (30460) *********************** 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 401 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 344 time to evaluate : 2.310 Fit side-chains REVERT: B 433 ASP cc_start: 0.9052 (t0) cc_final: 0.8743 (t0) REVERT: B 485 TYR cc_start: 0.8979 (t80) cc_final: 0.8686 (t80) REVERT: C 94 LYS cc_start: 0.8158 (mtpt) cc_final: 0.7744 (mttp) REVERT: C 129 ARG cc_start: 0.8199 (ptm160) cc_final: 0.7749 (ptt-90) REVERT: C 223 GLU cc_start: 0.8208 (tp30) cc_final: 0.7800 (tm-30) REVERT: C 290 LYS cc_start: 0.7431 (mtmt) cc_final: 0.7080 (mmtt) REVERT: F 391 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8770 (mt) REVERT: G 94 LYS cc_start: 0.8212 (mtpt) cc_final: 0.7865 (mttp) REVERT: G 129 ARG cc_start: 0.8280 (ptm160) cc_final: 0.7863 (ptt-90) REVERT: G 315 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7118 (mp0) REVERT: I 94 LYS cc_start: 0.8144 (mtpt) cc_final: 0.7754 (mttp) REVERT: I 129 ARG cc_start: 0.8158 (ptm160) cc_final: 0.7683 (ptt-90) REVERT: I 290 LYS cc_start: 0.7485 (mtmt) cc_final: 0.7197 (mmtt) REVERT: J 170 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.6827 (mmt-90) REVERT: M 94 LYS cc_start: 0.8226 (mtpt) cc_final: 0.7913 (mttp) REVERT: M 129 ARG cc_start: 0.8266 (ptm160) cc_final: 0.7777 (ptt-90) REVERT: M 290 LYS cc_start: 0.7313 (mttp) cc_final: 0.7000 (mmtt) REVERT: M 315 GLU cc_start: 0.7477 (mm-30) cc_final: 0.7025 (mp0) REVERT: N 170 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.6889 (mmt-90) REVERT: O 135 ARG cc_start: 0.8941 (mtt180) cc_final: 0.8712 (mtt180) REVERT: O 170 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.6998 (mmt-90) REVERT: P 170 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.6898 (mmt-90) outliers start: 57 outliers final: 44 residues processed: 387 average time/residue: 0.3953 time to fit residues: 221.7923 Evaluate side-chains 378 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 329 time to evaluate : 2.304 ------------------------------------------------------------------------------- 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 440 VAL Chi-restraints excluded: chain B residue 488 HIS Chi-restraints excluded: chain C residue 104 LYS 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 362 ILE Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 297 VAL 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 391 LEU 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 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 302 THR Chi-restraints excluded: chain J residue 101 CYS Chi-restraints excluded: chain J residue 170 ARG 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 170 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 15 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 264 optimal weight: 1.9990 chunk 267 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 209 optimal weight: 0.0970 chunk 87 optimal weight: 1.9990 chunk 168 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 236 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 293 GLN I 293 GLN M 293 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.132187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.096261 restraints weight = 25188.208| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 2.11 r_work: 0.2456 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22492 Z= 0.130 Angle : 0.514 6.630 30468 Z= 0.270 Chirality : 0.041 0.135 3380 Planarity : 0.004 0.044 3844 Dihedral : 8.917 85.612 3301 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.77 % Favored : 97.15 % Rotamer: Outliers : 2.91 % Allowed : 13.21 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.16), residues: 2704 helix: 2.24 (0.14), residues: 1568 sheet: 0.58 (0.35), residues: 188 loop : -1.66 (0.17), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 185 HIS 0.005 0.001 HIS G 135 PHE 0.017 0.001 PHE D 406 TYR 0.010 0.001 TYR O 187 ARG 0.003 0.000 ARG I 40 Details of bonding type rmsd hydrogen bonds : bond 0.04978 ( 1124) hydrogen bonds : angle 3.49876 ( 3228) SS BOND : bond 0.00341 ( 4) SS BOND : angle 0.45754 ( 8) covalent geometry : bond 0.00300 (22488) covalent geometry : angle 0.51416 (30460) *********************** 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 394 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 326 time to evaluate : 2.406 Fit side-chains REVERT: B 433 ASP cc_start: 0.9128 (t0) cc_final: 0.8749 (t0) REVERT: B 485 TYR cc_start: 0.8983 (t80) cc_final: 0.8716 (t80) REVERT: C 94 LYS cc_start: 0.8243 (mtpt) cc_final: 0.7870 (mttp) REVERT: C 129 ARG cc_start: 0.8337 (ptm160) cc_final: 0.7831 (ptt-90) REVERT: C 223 GLU cc_start: 0.8231 (tp30) cc_final: 0.7795 (tm-30) REVERT: C 290 LYS cc_start: 0.7493 (mtmt) cc_final: 0.7152 (mmtt) REVERT: G 94 LYS cc_start: 0.8201 (mtpt) cc_final: 0.7845 (mttp) REVERT: G 129 ARG cc_start: 0.8428 (ptm160) cc_final: 0.7967 (ptt-90) REVERT: G 315 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7122 (mp0) REVERT: H 485 TYR cc_start: 0.8967 (t80) cc_final: 0.8705 (t80) REVERT: I 94 LYS cc_start: 0.8231 (mtpt) cc_final: 0.7790 (mttp) REVERT: I 129 ARG cc_start: 0.8293 (ptm160) cc_final: 0.7787 (ptt-90) REVERT: I 290 LYS cc_start: 0.7639 (mtmt) cc_final: 0.7343 (mmtt) REVERT: J 170 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.6950 (mtt-85) REVERT: M 94 LYS cc_start: 0.8220 (mtpt) cc_final: 0.7862 (mttp) REVERT: M 105 LYS cc_start: 0.8340 (tttt) cc_final: 0.8083 (tttm) REVERT: M 129 ARG cc_start: 0.8417 (ptm160) cc_final: 0.7853 (ptt-90) REVERT: M 290 LYS cc_start: 0.7427 (mttp) cc_final: 0.7110 (mmtt) REVERT: M 315 GLU cc_start: 0.7523 (mm-30) cc_final: 0.7049 (mp0) REVERT: N 170 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.6922 (mmt-90) REVERT: O 105 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.7252 (mtm180) REVERT: O 170 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7075 (mmt-90) REVERT: P 170 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.6952 (mtt-85) outliers start: 68 outliers final: 55 residues processed: 377 average time/residue: 0.3957 time to fit residues: 216.5000 Evaluate side-chains 382 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 322 time to evaluate : 2.465 ------------------------------------------------------------------------------- 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 362 ILE Chi-restraints excluded: chain B residue 414 SER Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 104 LYS 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 362 ILE Chi-restraints excluded: chain D residue 440 VAL 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 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 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 G residue 354 ILE Chi-restraints excluded: chain H residue 303 ILE 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 471 THR Chi-restraints excluded: chain H residue 488 HIS Chi-restraints excluded: chain I residue 58 VAL 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 145 GLU Chi-restraints excluded: chain M residue 223 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 M residue 353 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 105 ARG 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 122 optimal weight: 3.9990 chunk 173 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 71 optimal weight: 0.0270 chunk 186 optimal weight: 0.0030 chunk 110 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 242 optimal weight: 1.9990 overall best weight: 1.1652 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 293 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.130798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.096663 restraints weight = 25217.605| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 2.37 r_work: 0.2476 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22492 Z= 0.144 Angle : 0.535 5.632 30468 Z= 0.281 Chirality : 0.042 0.138 3380 Planarity : 0.004 0.045 3844 Dihedral : 9.445 83.715 3301 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.18 % Favored : 96.71 % Rotamer: Outliers : 3.33 % Allowed : 13.08 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.16), residues: 2704 helix: 2.17 (0.14), residues: 1568 sheet: 0.09 (0.38), residues: 148 loop : -1.57 (0.17), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 185 HIS 0.005 0.001 HIS M 135 PHE 0.017 0.001 PHE D 406 TYR 0.011 0.001 TYR J 187 ARG 0.004 0.000 ARG G 40 Details of bonding type rmsd hydrogen bonds : bond 0.05431 ( 1124) hydrogen bonds : angle 3.59389 ( 3228) SS BOND : bond 0.00319 ( 4) SS BOND : angle 0.49932 ( 8) covalent geometry : bond 0.00340 (22488) covalent geometry : angle 0.53478 (30460) *********************** 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 410 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 332 time to evaluate : 2.361 Fit side-chains REVERT: B 433 ASP cc_start: 0.9089 (t0) cc_final: 0.8677 (t0) REVERT: B 485 TYR cc_start: 0.8967 (t80) cc_final: 0.8676 (t80) REVERT: C 94 LYS cc_start: 0.8253 (mtpt) cc_final: 0.7891 (mttp) REVERT: C 129 ARG cc_start: 0.8279 (ptm160) cc_final: 0.7829 (ptt-90) REVERT: C 223 GLU cc_start: 0.8253 (tp30) cc_final: 0.7809 (tm-30) REVERT: C 290 LYS cc_start: 0.7392 (mtmt) cc_final: 0.7060 (mmtt) REVERT: G 94 LYS cc_start: 0.8195 (mtpt) cc_final: 0.7849 (mttp) REVERT: G 129 ARG cc_start: 0.8360 (ptm160) cc_final: 0.7944 (ptt-90) REVERT: H 485 TYR cc_start: 0.8970 (t80) cc_final: 0.8686 (t80) REVERT: I 94 LYS cc_start: 0.8255 (mtpt) cc_final: 0.7876 (mttp) REVERT: I 129 ARG cc_start: 0.8253 (ptm160) cc_final: 0.7800 (ptt-90) REVERT: I 290 LYS cc_start: 0.7641 (mtmt) cc_final: 0.7338 (mmtt) REVERT: J 170 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.6866 (mtt-85) REVERT: M 94 LYS cc_start: 0.8238 (mtpt) cc_final: 0.7890 (mttp) REVERT: M 129 ARG cc_start: 0.8328 (ptm160) cc_final: 0.7843 (ptt-90) REVERT: M 290 LYS cc_start: 0.7413 (mttp) cc_final: 0.7089 (mmtt) REVERT: N 170 ARG cc_start: 0.7764 (OUTLIER) cc_final: 0.6848 (mmt-90) REVERT: O 105 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7214 (mtm180) REVERT: O 170 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.6997 (mmt-90) REVERT: P 170 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.6883 (mtt-85) outliers start: 78 outliers final: 67 residues processed: 389 average time/residue: 0.3955 time to fit residues: 224.0172 Evaluate side-chains 397 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 325 time to evaluate : 2.394 ------------------------------------------------------------------------------- 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 362 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 58 VAL Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain D residue 291 PHE 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 471 THR 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 414 SER Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 471 THR 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 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 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 471 THR Chi-restraints excluded: chain H residue 488 HIS Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 145 GLU 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 M residue 58 VAL Chi-restraints excluded: chain M residue 127 THR Chi-restraints excluded: chain M residue 145 GLU Chi-restraints excluded: chain M residue 223 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 M residue 353 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 105 ARG 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 123 optimal weight: 2.9990 chunk 231 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 236 optimal weight: 0.0170 chunk 93 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 257 optimal weight: 0.9980 chunk 265 optimal weight: 0.9980 chunk 222 optimal weight: 2.9990 chunk 259 optimal weight: 0.8980 overall best weight: 0.7418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 293 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 = 0.3321 r_free = 0.3321 target = 0.132522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.098185 restraints weight = 25122.892| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 2.18 r_work: 0.2455 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22492 Z= 0.116 Angle : 0.505 7.944 30468 Z= 0.265 Chirality : 0.040 0.135 3380 Planarity : 0.004 0.044 3844 Dihedral : 8.968 83.408 3301 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.66 % Favored : 97.23 % Rotamer: Outliers : 3.33 % Allowed : 13.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.16), residues: 2704 helix: 2.25 (0.14), residues: 1568 sheet: 0.22 (0.37), residues: 152 loop : -1.55 (0.17), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 185 HIS 0.005 0.001 HIS G 135 PHE 0.016 0.001 PHE D 406 TYR 0.009 0.001 TYR F 487 ARG 0.004 0.000 ARG M 40 Details of bonding type rmsd hydrogen bonds : bond 0.04703 ( 1124) hydrogen bonds : angle 3.48797 ( 3228) SS BOND : bond 0.00294 ( 4) SS BOND : angle 0.48511 ( 8) covalent geometry : bond 0.00256 (22488) covalent geometry : angle 0.50515 (30460) *********************** 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 404 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 326 time to evaluate : 2.569 Fit side-chains REVERT: B 433 ASP cc_start: 0.9155 (t0) cc_final: 0.8770 (t0) REVERT: B 485 TYR cc_start: 0.9016 (t80) cc_final: 0.8734 (t80) REVERT: C 94 LYS cc_start: 0.8291 (mtpt) cc_final: 0.7936 (mttp) REVERT: C 129 ARG cc_start: 0.8343 (ptm160) cc_final: 0.7883 (ptt-90) REVERT: C 223 GLU cc_start: 0.8343 (tp30) cc_final: 0.7922 (tm-30) REVERT: C 290 LYS cc_start: 0.7466 (mtmt) cc_final: 0.7147 (mmtt) REVERT: F 367 ARG cc_start: 0.8506 (ttt-90) cc_final: 0.8202 (ttt-90) REVERT: F 392 LYS cc_start: 0.8751 (tttm) cc_final: 0.8509 (tptm) REVERT: G 94 LYS cc_start: 0.8246 (mtpt) cc_final: 0.7904 (mttp) REVERT: G 105 LYS cc_start: 0.8449 (tttt) cc_final: 0.8191 (tttm) REVERT: G 129 ARG cc_start: 0.8436 (ptm160) cc_final: 0.8012 (ptt-90) REVERT: H 485 TYR cc_start: 0.9029 (t80) cc_final: 0.8754 (t80) REVERT: I 94 LYS cc_start: 0.8262 (mtpt) cc_final: 0.7957 (mttp) REVERT: I 129 ARG cc_start: 0.8321 (ptm160) cc_final: 0.7841 (ptt-90) REVERT: I 290 LYS cc_start: 0.7728 (mtmt) cc_final: 0.7437 (mmtt) REVERT: J 170 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.6974 (mtt-85) REVERT: M 94 LYS cc_start: 0.8276 (mtpt) cc_final: 0.7942 (mttp) REVERT: M 129 ARG cc_start: 0.8406 (ptm160) cc_final: 0.7885 (ptt-90) REVERT: M 290 LYS cc_start: 0.7520 (mttp) cc_final: 0.7193 (mmtt) REVERT: N 170 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.6942 (mmt-90) REVERT: O 105 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.7291 (mtm180) REVERT: O 170 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7116 (mmt-90) REVERT: P 170 ARG cc_start: 0.7805 (OUTLIER) cc_final: 0.6987 (mtt-85) outliers start: 78 outliers final: 64 residues processed: 388 average time/residue: 0.3852 time to fit residues: 220.0497 Evaluate side-chains 393 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 324 time to evaluate : 2.471 ------------------------------------------------------------------------------- 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 362 ILE Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 488 HIS Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 104 LYS 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 471 THR 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 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 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 471 THR Chi-restraints excluded: chain H residue 488 HIS Chi-restraints excluded: chain I residue 58 VAL 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 58 VAL 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 M residue 353 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 105 ARG 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 Chi-restraints excluded: chain P residue 174 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 192 optimal weight: 4.9990 chunk 170 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 149 optimal weight: 0.5980 chunk 173 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 249 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 293 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.132419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.098466 restraints weight = 25274.423| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 2.46 r_work: 0.2499 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2831 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= 0.118 Angle : 0.507 5.564 30468 Z= 0.265 Chirality : 0.041 0.140 3380 Planarity : 0.004 0.044 3844 Dihedral : 8.899 82.470 3301 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.00 % Favored : 96.89 % Rotamer: Outliers : 3.03 % Allowed : 13.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.16), residues: 2704 helix: 2.27 (0.14), residues: 1568 sheet: 0.09 (0.38), residues: 148 loop : -1.54 (0.17), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 185 HIS 0.005 0.001 HIS G 135 PHE 0.016 0.001 PHE D 406 TYR 0.009 0.001 TYR H 487 ARG 0.004 0.000 ARG G 40 Details of bonding type rmsd hydrogen bonds : bond 0.04735 ( 1124) hydrogen bonds : angle 3.47660 ( 3228) SS BOND : bond 0.00311 ( 4) SS BOND : angle 0.46965 ( 8) covalent geometry : bond 0.00265 (22488) covalent geometry : angle 0.50657 (30460) ********************** 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 398 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 327 time to evaluate : 2.982 Fit side-chains REVERT: B 433 ASP cc_start: 0.9066 (t0) cc_final: 0.8643 (t0) REVERT: B 485 TYR cc_start: 0.8965 (t80) cc_final: 0.8684 (t80) REVERT: C 94 LYS cc_start: 0.8210 (mtpt) cc_final: 0.7858 (mttp) REVERT: C 129 ARG cc_start: 0.8228 (ptm160) cc_final: 0.7786 (ptt-90) REVERT: C 223 GLU cc_start: 0.8225 (tp30) cc_final: 0.7801 (tm-30) REVERT: C 290 LYS cc_start: 0.7343 (mtmt) cc_final: 0.7034 (mmtt) REVERT: F 367 ARG cc_start: 0.8449 (ttt-90) cc_final: 0.8152 (ttt-90) REVERT: F 392 LYS cc_start: 0.8709 (tttm) cc_final: 0.8481 (tptm) REVERT: G 94 LYS cc_start: 0.8171 (mtpt) cc_final: 0.7833 (mttp) REVERT: G 105 LYS cc_start: 0.8353 (tttt) cc_final: 0.8084 (tttm) REVERT: G 129 ARG cc_start: 0.8318 (ptm160) cc_final: 0.7907 (ptt-90) REVERT: H 485 TYR cc_start: 0.8970 (t80) cc_final: 0.8683 (t80) REVERT: I 94 LYS cc_start: 0.8163 (mtpt) cc_final: 0.7854 (mttp) REVERT: I 129 ARG cc_start: 0.8211 (ptm160) cc_final: 0.7744 (ptt-90) REVERT: I 290 LYS cc_start: 0.7616 (mtmt) cc_final: 0.7327 (mmtt) REVERT: J 170 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.6862 (mtt-85) REVERT: M 94 LYS cc_start: 0.8172 (mtpt) cc_final: 0.7826 (mttp) REVERT: M 129 ARG cc_start: 0.8283 (ptm160) cc_final: 0.7784 (ptt-90) REVERT: M 290 LYS cc_start: 0.7378 (mttp) cc_final: 0.7058 (mmtt) REVERT: N 170 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.6833 (mmt-90) REVERT: O 105 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7177 (mtm180) REVERT: O 170 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.6997 (mmt-90) REVERT: P 170 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.6870 (mtt-85) outliers start: 71 outliers final: 65 residues processed: 382 average time/residue: 0.4131 time to fit residues: 233.8389 Evaluate side-chains 393 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 323 time to evaluate : 2.625 ------------------------------------------------------------------------------- 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 362 ILE Chi-restraints excluded: chain B residue 384 LEU 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 58 VAL Chi-restraints excluded: chain C residue 104 LYS 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 471 THR 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 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 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 58 VAL 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 58 VAL 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 M residue 353 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 105 ARG 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 Chi-restraints excluded: chain P residue 174 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 157 optimal weight: 0.1980 chunk 33 optimal weight: 0.9980 chunk 244 optimal weight: 2.9990 chunk 209 optimal weight: 2.9990 chunk 251 optimal weight: 0.5980 chunk 149 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 227 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 293 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.133280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.099195 restraints weight = 25079.383| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 2.24 r_work: 0.2486 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2896 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= 0.109 Angle : 0.496 7.451 30468 Z= 0.259 Chirality : 0.040 0.132 3380 Planarity : 0.004 0.043 3844 Dihedral : 8.630 81.729 3301 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.63 % Favored : 97.26 % Rotamer: Outliers : 2.99 % Allowed : 13.42 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.16), residues: 2704 helix: 2.38 (0.14), residues: 1556 sheet: 0.21 (0.37), residues: 152 loop : -1.54 (0.17), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 185 HIS 0.004 0.001 HIS G 135 PHE 0.016 0.001 PHE D 406 TYR 0.008 0.001 TYR F 487 ARG 0.003 0.000 ARG G 40 Details of bonding type rmsd hydrogen bonds : bond 0.04402 ( 1124) hydrogen bonds : angle 3.42113 ( 3228) SS BOND : bond 0.00294 ( 4) SS BOND : angle 0.45002 ( 8) covalent geometry : bond 0.00238 (22488) covalent geometry : angle 0.49562 (30460) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11941.99 seconds wall clock time: 209 minutes 25.34 seconds (12565.34 seconds total)