Starting phenix.real_space_refine on Sat Jul 4 16:29:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wbz_37428/07_2026/8wbz_37428_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wbz_37428/07_2026/8wbz_37428.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wbz_37428/07_2026/8wbz_37428.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wbz_37428/07_2026/8wbz_37428.map" model { file = "/net/cci-nas-00/data/ceres_data/8wbz_37428/07_2026/8wbz_37428_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wbz_37428/07_2026/8wbz_37428_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.085 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Br 2 7.06 5 S 128 5.16 5 C 14486 2.51 5 N 3564 2.21 5 O 4162 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22342 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 4794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4794 Classifications: {'peptide': 605} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 31, 'TRANS': 573} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 6 Chain: "B" Number of atoms: 6095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 6095 Classifications: {'peptide': 749} Link IDs: {'PTRANS': 35, 'TRANS': 713} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 6095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 6095 Classifications: {'peptide': 749} Link IDs: {'PTRANS': 35, 'TRANS': 713} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 4794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4794 Classifications: {'peptide': 605} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 31, 'TRANS': 573} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 6 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 44 Unusual residues: {'NAG': 2, 'XF0': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 44 Unusual residues: {'NAG': 2, 'XF0': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.15, per 1000 atoms: 0.23 Number of scatterers: 22342 At special positions: 0 Unit cell: (133.59, 111.69, 186.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Br 2 34.99 S 128 16.00 O 4162 8.00 N 3564 7.00 C 14486 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 153 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 383 " distance=2.03 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 141 " distance=2.05 Simple disulfide: pdb=" SG CYS B 344 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 530 " - pdb=" SG CYS B 542 " distance=2.04 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 141 " distance=2.05 Simple disulfide: pdb=" SG CYS C 344 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 530 " - pdb=" SG CYS C 542 " distance=2.03 Simple disulfide: pdb=" SG CYS D 153 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 383 " 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 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A 701 " - " ASN A 354 " " NAG A 702 " - " ASN A 182 " " NAG B 901 " - " ASN B 322 " " NAG C 901 " - " ASN C 322 " " NAG D 701 " - " ASN D 182 " " NAG D 702 " - " ASN D 354 " " NAG E 1 " - " ASN B 432 " " NAG F 1 " - " ASN B 103 " " NAG G 1 " - " ASN A 258 " " NAG H 1 " - " ASN C 690 " " NAG I 1 " - " ASN C 103 " " NAG J 1 " - " ASN C 90 " " NAG K 1 " - " ASN C 53 " " NAG L 1 " - " ASN C 546 " " NAG M 1 " - " ASN B 546 " " NAG N 1 " - " ASN D 258 " " NAG O 1 " - " ASN B 690 " " NAG P 1 " - " ASN B 90 " " NAG Q 1 " - " ASN A 368 " " NAG R 1 " - " ASN D 368 " " NAG S 1 " - " ASN C 432 " " NAG T 1 " - " ASN B 53 " Time building additional restraints: 2.19 Conformation dependent library (CDL) restraints added in 1.1 seconds 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5080 Finding SS restraints... Secondary structure from input PDB file: 131 helices and 10 sheets defined 67.6% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 17 through 26 removed outlier: 3.643A pdb=" N GLN A 26 " --> pdb=" O GLU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 54 removed outlier: 3.611A pdb=" N TYR A 41 " --> pdb=" O ASN A 37 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR A 44 " --> pdb=" O GLN A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 65 Processing helix chain 'A' and resid 70 through 93 removed outlier: 5.176A pdb=" N ILE A 83 " --> pdb=" O VAL A 79 " (cutoff:3.500A) Proline residue: A 84 - end of helix Processing helix chain 'A' and resid 99 through 107 removed outlier: 3.909A pdb=" N ILE A 107 " --> pdb=" O VAL A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 129 removed outlier: 3.961A pdb=" N LEU A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 142 Processing helix chain 'A' and resid 148 through 152 removed outlier: 3.900A pdb=" N ASP A 152 " --> pdb=" O PRO A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 169 Processing helix chain 'A' and resid 170 through 178 Processing helix chain 'A' and resid 194 through 212 Processing helix chain 'A' and resid 215 through 227 removed outlier: 4.630A pdb=" N LYS A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TYR A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ILE A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 242 removed outlier: 3.856A pdb=" N VAL A 232 " --> pdb=" O THR A 228 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N LEU A 234 " --> pdb=" O PRO A 230 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR A 235 " --> pdb=" O TYR A 231 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE A 236 " --> pdb=" O VAL A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 256 removed outlier: 3.533A pdb=" N PHE A 253 " --> pdb=" O ASN A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 264 removed outlier: 3.649A pdb=" N GLN A 264 " --> pdb=" O THR A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 279 removed outlier: 3.944A pdb=" N ALA A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 291 Processing helix chain 'A' and resid 298 through 349 removed outlier: 3.512A pdb=" N ASP A 302 " --> pdb=" O ASN A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 371 removed outlier: 3.744A pdb=" N MET A 363 " --> pdb=" O ASN A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 378 Processing helix chain 'A' and resid 396 through 401 removed outlier: 4.046A pdb=" N PHE A 400 " --> pdb=" O THR A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 410 removed outlier: 3.756A pdb=" N GLU A 405 " --> pdb=" O ILE A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 438 removed outlier: 3.719A pdb=" N TRP A 416 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY A 438 " --> pdb=" O GLY A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 446 Processing helix chain 'A' and resid 454 through 471 Processing helix chain 'A' and resid 472 through 475 Processing helix chain 'A' and resid 477 through 489 removed outlier: 3.629A pdb=" N TYR A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 507 Processing helix chain 'A' and resid 510 through 522 Processing helix chain 'A' and resid 527 through 536 removed outlier: 3.623A pdb=" N GLN A 531 " --> pdb=" O ASN A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 553 removed outlier: 3.589A pdb=" N LEU A 540 " --> pdb=" O VAL A 536 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A 545 " --> pdb=" O LEU A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 removed outlier: 4.055A pdb=" N VAL A 585 " --> pdb=" O TRP A 581 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL A 586 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL A 587 " --> pdb=" O TYR A 583 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE A 588 " --> pdb=" O VAL A 584 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 581 through 588' Processing helix chain 'A' and resid 592 through 594 No H-bonds generated for 'chain 'A' and resid 592 through 594' Processing helix chain 'A' and resid 595 through 608 removed outlier: 3.872A pdb=" N GLY A 599 " --> pdb=" O LEU A 595 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASN A 608 " --> pdb=" O LYS A 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 53 removed outlier: 4.240A pdb=" N ASP B 38 " --> pdb=" O HIS B 34 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LEU B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 77 removed outlier: 3.966A pdb=" N ALA B 65 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE B 72 " --> pdb=" O LYS B 68 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU B 73 " --> pdb=" O TRP B 69 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS B 74 " --> pdb=" O SER B 70 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 80 No H-bonds generated for 'chain 'B' and resid 78 through 80' Processing helix chain 'B' and resid 90 through 102 removed outlier: 4.155A pdb=" N GLN B 102 " --> pdb=" O GLN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 108 removed outlier: 4.350A pdb=" N VAL B 107 " --> pdb=" O GLY B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 129 Processing helix chain 'B' and resid 147 through 155 Processing helix chain 'B' and resid 157 through 193 Proline residue: B 178 - end of helix Processing helix chain 'B' and resid 198 through 205 Processing helix chain 'B' and resid 218 through 232 removed outlier: 3.727A pdb=" N LEU B 222 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ILE B 223 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU B 224 " --> pdb=" O GLY B 220 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU B 232 " --> pdb=" O HIS B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 252 removed outlier: 3.903A pdb=" N ASN B 250 " --> pdb=" O ALA B 246 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ALA B 251 " --> pdb=" O LYS B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 267 No H-bonds generated for 'chain 'B' and resid 265 through 267' Processing helix chain 'B' and resid 275 through 282 removed outlier: 4.224A pdb=" N SER B 280 " --> pdb=" O ASN B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 301 Processing helix chain 'B' and resid 305 through 318 removed outlier: 3.772A pdb=" N VAL B 318 " --> pdb=" O PHE B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 330 removed outlier: 4.117A pdb=" N TRP B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 385 removed outlier: 3.612A pdb=" N HIS B 373 " --> pdb=" O PHE B 369 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N TYR B 385 " --> pdb=" O TYR B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 413 removed outlier: 3.732A pdb=" N GLY B 405 " --> pdb=" O HIS B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 421 Processing helix chain 'B' and resid 431 through 447 removed outlier: 3.682A pdb=" N GLU B 435 " --> pdb=" O ASP B 431 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR B 445 " --> pdb=" O LYS B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 465 Processing helix chain 'B' and resid 472 through 484 Processing helix chain 'B' and resid 498 through 502 Processing helix chain 'B' and resid 503 through 508 Processing helix chain 'B' and resid 513 through 533 removed outlier: 3.668A pdb=" N THR B 519 " --> pdb=" O TYR B 515 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N PHE B 523 " --> pdb=" O THR B 519 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N CYS B 530 " --> pdb=" O GLN B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 542 Processing helix chain 'B' and resid 547 through 559 removed outlier: 3.824A pdb=" N MET B 557 " --> pdb=" O LYS B 553 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG B 559 " --> pdb=" O PHE B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 575 removed outlier: 3.576A pdb=" N ALA B 569 " --> pdb=" O PRO B 565 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL B 573 " --> pdb=" O ALA B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 588 Processing helix chain 'B' and resid 588 through 599 Processing helix chain 'B' and resid 623 through 629 removed outlier: 3.586A pdb=" N ALA B 627 " --> pdb=" O SER B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 658 Processing helix chain 'B' and resid 696 through 715 removed outlier: 5.567A pdb=" N SER B 709 " --> pdb=" O ARG B 705 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ARG B 710 " --> pdb=" O MET B 706 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N PHE B 715 " --> pdb=" O ILE B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 766 removed outlier: 3.881A pdb=" N ILE B 744 " --> pdb=" O SER B 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 53 removed outlier: 4.224A pdb=" N ASP C 38 " --> pdb=" O HIS C 34 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEU C 39 " --> pdb=" O GLU C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 80 removed outlier: 3.872A pdb=" N ASN C 63 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ASN C 64 " --> pdb=" O GLN C 60 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ALA C 65 " --> pdb=" O ASN C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 102 removed outlier: 3.637A pdb=" N GLN C 96 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLN C 102 " --> pdb=" O GLN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 108 removed outlier: 4.189A pdb=" N VAL C 107 " --> pdb=" O GLY C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 130 Processing helix chain 'C' and resid 147 through 155 Processing helix chain 'C' and resid 157 through 194 Proline residue: C 178 - end of helix Processing helix chain 'C' and resid 198 through 205 Processing helix chain 'C' and resid 218 through 232 removed outlier: 3.795A pdb=" N LEU C 222 " --> pdb=" O SER C 218 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE C 223 " --> pdb=" O ARG C 219 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU C 224 " --> pdb=" O GLY C 220 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU C 232 " --> pdb=" O HIS C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 252 removed outlier: 3.719A pdb=" N ASN C 250 " --> pdb=" O ALA C 246 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA C 251 " --> pdb=" O LYS C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 267 No H-bonds generated for 'chain 'C' and resid 265 through 267' Processing helix chain 'C' and resid 275 through 282 removed outlier: 3.844A pdb=" N TYR C 279 " --> pdb=" O THR C 276 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N SER C 280 " --> pdb=" O ASN C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 300 Processing helix chain 'C' and resid 305 through 317 Processing helix chain 'C' and resid 324 through 330 removed outlier: 3.859A pdb=" N TRP C 328 " --> pdb=" O THR C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 384 Processing helix chain 'C' and resid 399 through 413 removed outlier: 3.776A pdb=" N GLY C 405 " --> pdb=" O HIS C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 421 Processing helix chain 'C' and resid 431 through 447 removed outlier: 3.618A pdb=" N GLU C 435 " --> pdb=" O ASP C 431 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR C 445 " --> pdb=" O LYS C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 465 Processing helix chain 'C' and resid 472 through 484 Processing helix chain 'C' and resid 498 through 502 Processing helix chain 'C' and resid 503 through 508 Processing helix chain 'C' and resid 513 through 533 removed outlier: 3.547A pdb=" N THR C 517 " --> pdb=" O ILE C 513 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR C 519 " --> pdb=" O TYR C 515 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE C 523 " --> pdb=" O THR C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 559 removed outlier: 3.775A pdb=" N MET C 557 " --> pdb=" O LYS C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 575 removed outlier: 3.540A pdb=" N ALA C 569 " --> pdb=" O PRO C 565 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL C 573 " --> pdb=" O ALA C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 588 Processing helix chain 'C' and resid 588 through 599 Processing helix chain 'C' and resid 623 through 628 removed outlier: 3.761A pdb=" N ALA C 627 " --> pdb=" O SER C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 658 Processing helix chain 'C' and resid 696 through 715 removed outlier: 5.568A pdb=" N SER C 709 " --> pdb=" O ARG C 705 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ARG C 710 " --> pdb=" O MET C 706 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE C 715 " --> pdb=" O ILE C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 767 removed outlier: 4.084A pdb=" N ILE C 744 " --> pdb=" O SER C 740 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 26 Processing helix chain 'D' and resid 37 through 54 removed outlier: 3.732A pdb=" N GLY D 53 " --> pdb=" O CYS D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 65 removed outlier: 3.546A pdb=" N GLN D 63 " --> pdb=" O PRO D 59 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS D 65 " --> pdb=" O LEU D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 93 removed outlier: 5.175A pdb=" N ILE D 83 " --> pdb=" O VAL D 79 " (cutoff:3.500A) Proline residue: D 84 - end of helix Processing helix chain 'D' and resid 99 through 108 removed outlier: 3.870A pdb=" N HIS D 108 " --> pdb=" O TRP D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 129 removed outlier: 4.412A pdb=" N LEU D 116 " --> pdb=" O LYS D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 142 Processing helix chain 'D' and resid 163 through 169 Processing helix chain 'D' and resid 170 through 178 Processing helix chain 'D' and resid 194 through 212 removed outlier: 3.512A pdb=" N CYS D 200 " --> pdb=" O TRP D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 227 removed outlier: 3.784A pdb=" N THR D 218 " --> pdb=" O ARG D 214 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N LYS D 221 " --> pdb=" O GLU D 217 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE D 225 " --> pdb=" O LYS D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 243 removed outlier: 3.840A pdb=" N VAL D 232 " --> pdb=" O THR D 228 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N LEU D 234 " --> pdb=" O PRO D 230 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N THR D 243 " --> pdb=" O ILE D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 256 removed outlier: 3.515A pdb=" N PHE D 253 " --> pdb=" O ASN D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 264 removed outlier: 3.624A pdb=" N LEU D 262 " --> pdb=" O ASN D 258 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA D 263 " --> pdb=" O VAL D 259 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN D 264 " --> pdb=" O THR D 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 258 through 264' Processing helix chain 'D' and resid 265 through 279 Processing helix chain 'D' and resid 285 through 291 Processing helix chain 'D' and resid 298 through 349 removed outlier: 3.826A pdb=" N ASP D 302 " --> pdb=" O ASN D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 371 removed outlier: 3.545A pdb=" N MET D 363 " --> pdb=" O ASN D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 401 removed outlier: 3.792A pdb=" N PHE D 400 " --> pdb=" O THR D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 410 removed outlier: 4.040A pdb=" N GLU D 405 " --> pdb=" O ILE D 401 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 439 removed outlier: 3.612A pdb=" N TRP D 416 " --> pdb=" O LEU D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 446 Processing helix chain 'D' and resid 454 through 471 removed outlier: 3.838A pdb=" N LEU D 458 " --> pdb=" O PRO D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 475 Processing helix chain 'D' and resid 477 through 489 removed outlier: 3.501A pdb=" N SER D 487 " --> pdb=" O SER D 483 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR D 488 " --> pdb=" O LEU D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 491 through 507 Processing helix chain 'D' and resid 510 through 522 Processing helix chain 'D' and resid 527 through 536 Processing helix chain 'D' and resid 536 through 553 Processing helix chain 'D' and resid 581 through 591 removed outlier: 4.172A pdb=" N VAL D 585 " --> pdb=" O TRP D 581 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N VAL D 587 " --> pdb=" O TYR D 583 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE D 588 " --> pdb=" O VAL D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 591 through 609 removed outlier: 3.788A pdb=" N ILE D 597 " --> pdb=" O PRO D 593 " (cutoff:3.500A) Proline residue: D 598 - end of helix removed outlier: 4.106A pdb=" N ALA D 601 " --> pdb=" O ILE D 597 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 132 through 133 Processing sheet with id=AA2, first strand: chain 'B' and resid 262 through 263 removed outlier: 6.160A pdb=" N LEU B 262 " --> pdb=" O VAL B 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 347 through 352 removed outlier: 6.439A pdb=" N ASP B 355 " --> pdb=" O LEU B 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 670 through 673 removed outlier: 6.311A pdb=" N ASP B 693 " --> pdb=" O ALA B 687 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 670 through 673 Processing sheet with id=AA6, first strand: chain 'C' and resid 132 through 133 Processing sheet with id=AA7, first strand: chain 'C' and resid 262 through 263 removed outlier: 6.115A pdb=" N LEU C 262 " --> pdb=" O VAL C 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 347 through 352 removed outlier: 6.212A pdb=" N ASP C 355 " --> pdb=" O LEU C 351 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 670 through 673 removed outlier: 6.490A pdb=" N ASP C 693 " --> pdb=" O ALA C 687 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 670 through 673 1220 hydrogen bonds defined for protein. 3576 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.22 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 5563 1.33 - 1.49: 7843 1.49 - 1.65: 9330 1.65 - 1.81: 176 1.81 - 1.96: 36 Bond restraints: 22948 Sorted by residual: bond pdb=" C5 NAG T 1 " pdb=" O5 NAG T 1 " ideal model delta sigma weight residual 1.413 1.551 -0.138 2.00e-02 2.50e+03 4.74e+01 bond pdb=" C5 NAG K 1 " pdb=" O5 NAG K 1 " ideal model delta sigma weight residual 1.413 1.550 -0.137 2.00e-02 2.50e+03 4.69e+01 bond pdb=" C5 NAG K 2 " pdb=" O5 NAG K 2 " ideal model delta sigma weight residual 1.413 1.550 -0.137 2.00e-02 2.50e+03 4.66e+01 bond pdb=" C5 NAG S 2 " pdb=" O5 NAG S 2 " ideal model delta sigma weight residual 1.413 1.548 -0.135 2.00e-02 2.50e+03 4.58e+01 bond pdb=" C5 NAG C 901 " pdb=" O5 NAG C 901 " ideal model delta sigma weight residual 1.413 1.545 -0.132 2.00e-02 2.50e+03 4.34e+01 ... (remaining 22943 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 30413 2.19 - 4.37: 655 4.37 - 6.56: 134 6.56 - 8.74: 22 8.74 - 10.93: 10 Bond angle restraints: 31234 Sorted by residual: angle pdb=" C HIS D 108 " pdb=" N PRO D 109 " pdb=" CA PRO D 109 " ideal model delta sigma weight residual 121.00 115.14 5.86 1.16e+00 7.43e-01 2.55e+01 angle pdb=" N ILE D 132 " pdb=" CA ILE D 132 " pdb=" C ILE D 132 " ideal model delta sigma weight residual 110.72 106.12 4.60 1.01e+00 9.80e-01 2.08e+01 angle pdb=" CA GLU D 569 " pdb=" CB GLU D 569 " pdb=" CG GLU D 569 " ideal model delta sigma weight residual 114.10 122.96 -8.86 2.00e+00 2.50e-01 1.96e+01 angle pdb=" N LEU C 45 " pdb=" CA LEU C 45 " pdb=" C LEU C 45 " ideal model delta sigma weight residual 111.07 106.37 4.70 1.07e+00 8.73e-01 1.93e+01 angle pdb=" C PHE A 400 " pdb=" N ILE A 401 " pdb=" CA ILE A 401 " ideal model delta sigma weight residual 122.77 118.62 4.15 1.05e+00 9.07e-01 1.56e+01 ... (remaining 31229 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.16: 12440 25.16 - 50.31: 1246 50.31 - 75.46: 156 75.46 - 100.62: 46 100.62 - 125.77: 44 Dihedral angle restraints: 13932 sinusoidal: 6030 harmonic: 7902 Sorted by residual: dihedral pdb=" CB CYS C 530 " pdb=" SG CYS C 530 " pdb=" SG CYS C 542 " pdb=" CB CYS C 542 " ideal model delta sinusoidal sigma weight residual -86.00 -151.32 65.32 1 1.00e+01 1.00e-02 5.59e+01 dihedral pdb=" CB CYS C 344 " pdb=" SG CYS C 344 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual -86.00 -24.89 -61.11 1 1.00e+01 1.00e-02 4.96e+01 dihedral pdb=" CB CYS B 530 " pdb=" SG CYS B 530 " pdb=" SG CYS B 542 " pdb=" CB CYS B 542 " ideal model delta sinusoidal sigma weight residual -86.00 -144.97 58.97 1 1.00e+01 1.00e-02 4.65e+01 ... (remaining 13929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.403: 3513 0.403 - 0.806: 5 0.806 - 1.209: 3 1.209 - 1.612: 2 1.612 - 2.015: 1 Chirality restraints: 3524 Sorted by residual: chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-02 2.50e+03 7.78e+02 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-02 2.50e+03 6.37e+02 chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-02 2.50e+03 2.47e+02 ... (remaining 3521 not shown) Planarity restraints: 3934 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 1 " -0.362 2.00e-02 2.50e+03 3.11e-01 1.21e+03 pdb=" C7 NAG R 1 " 0.087 2.00e-02 2.50e+03 pdb=" C8 NAG R 1 " -0.126 2.00e-02 2.50e+03 pdb=" N2 NAG R 1 " 0.553 2.00e-02 2.50e+03 pdb=" O7 NAG R 1 " -0.152 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG Q 1 " 0.362 2.00e-02 2.50e+03 3.11e-01 1.21e+03 pdb=" C7 NAG Q 1 " -0.087 2.00e-02 2.50e+03 pdb=" C8 NAG Q 1 " 0.126 2.00e-02 2.50e+03 pdb=" N2 NAG Q 1 " -0.553 2.00e-02 2.50e+03 pdb=" O7 NAG Q 1 " 0.152 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 2 " -0.360 2.00e-02 2.50e+03 3.05e-01 1.16e+03 pdb=" C7 NAG I 2 " 0.095 2.00e-02 2.50e+03 pdb=" C8 NAG I 2 " -0.179 2.00e-02 2.50e+03 pdb=" N2 NAG I 2 " 0.534 2.00e-02 2.50e+03 pdb=" O7 NAG I 2 " -0.089 2.00e-02 2.50e+03 ... (remaining 3931 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1823 2.74 - 3.28: 23220 3.28 - 3.82: 37429 3.82 - 4.36: 41724 4.36 - 4.90: 72715 Nonbonded interactions: 176911 Sorted by model distance: nonbonded pdb=" NE2 GLN A 364 " pdb=" OH TYR A 375 " model vdw 2.196 3.120 nonbonded pdb=" OH TYR A 231 " pdb=" OG1 THR A 313 " model vdw 2.199 3.040 nonbonded pdb=" O GLU B 75 " pdb=" OG1 THR B 78 " model vdw 2.203 3.040 nonbonded pdb=" ND2 ASN B 690 " pdb=" N2 NAG O 1 " model vdw 2.220 2.560 nonbonded pdb=" O TYR C 41 " pdb=" OG SER C 44 " model vdw 2.236 3.040 ... (remaining 176906 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.390 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.217 22996 Z= 0.424 Angle : 1.065 39.874 31368 Z= 0.438 Chirality : 0.079 2.015 3524 Planarity : 0.018 0.311 3912 Dihedral : 20.366 125.775 8822 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 0.25 % Allowed : 29.06 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.16), residues: 2700 helix: 0.89 (0.13), residues: 1631 sheet: -1.17 (0.70), residues: 42 loop : -1.95 (0.19), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 192 TYR 0.016 0.001 TYR A 41 PHE 0.031 0.001 PHE A 503 TRP 0.032 0.001 TRP A 534 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00799 / 0.40 (22948) covalent geometry : angle 0.76762 / 0.36 (31234) SS BOND : bond 0.00920 / 0.35 ( 10) SS BOND : angle 1.39627 / 0.67 ( 20) hydrogen bonds : bond 0.14750 / 9.66 ( 1212) hydrogen bonds : angle 5.93706 / 4.30 ( 3576) link_BETA1-4 : bond 0.07345 / 4.63 ( 16) link_BETA1-4 : angle 9.38998 / 5.39 ( 48) link_NAG-ASN : bond 0.07515 / 4.29 ( 22) link_NAG-ASN : angle 13.99965 / 11.17 ( 66) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 283 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 42 MET cc_start: 0.7411 (mmp) cc_final: 0.7196 (mmt) outliers start: 6 outliers final: 0 residues processed: 288 average time/residue: 0.1397 time to fit residues: 65.6868 Evaluate side-chains 266 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.0870 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 9.9990 overall best weight: 1.2560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 GLN B 159 ASN C 98 GLN C 159 ASN D 194 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.201349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.156650 restraints weight = 27936.712| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 2.68 r_work: 0.3274 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.0839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22996 Z= 0.158 Angle : 0.756 19.290 31368 Z= 0.349 Chirality : 0.049 0.564 3524 Planarity : 0.004 0.044 3912 Dihedral : 14.505 109.436 3728 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.93 % Favored : 92.96 % Rotamer: Outliers : 2.90 % Allowed : 27.38 % Favored : 69.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.16), residues: 2700 helix: 1.14 (0.13), residues: 1669 sheet: -1.16 (0.70), residues: 42 loop : -1.92 (0.19), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 192 TYR 0.017 0.001 TYR D 128 PHE 0.018 0.001 PHE A 400 TRP 0.018 0.001 TRP D 196 HIS 0.005 0.001 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (22948) covalent geometry : angle 0.71471 / 0.34 (31234) SS BOND : bond 0.00306 / 0.15 ( 10) SS BOND : angle 1.23511 / 0.58 ( 20) hydrogen bonds : bond 0.05335 / 3.54 ( 1212) hydrogen bonds : angle 4.57864 / 3.33 ( 3576) link_BETA1-4 : bond 0.00457 / 0.26 ( 16) link_BETA1-4 : angle 3.12489 / 2.62 ( 48) link_NAG-ASN : bond 0.00877 / 0.52 ( 22) link_NAG-ASN : angle 4.70004 / 3.82 ( 66) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 293 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 PHE cc_start: 0.8202 (OUTLIER) cc_final: 0.7243 (t80) REVERT: A 530 TRP cc_start: 0.6515 (m-90) cc_final: 0.5962 (m-90) REVERT: A 576 ILE cc_start: 0.8087 (OUTLIER) cc_final: 0.7740 (pp) REVERT: B 323 MET cc_start: 0.6492 (OUTLIER) cc_final: 0.6167 (tpp) REVERT: B 406 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7731 (mm-30) REVERT: B 481 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8473 (tptm) REVERT: B 718 ASN cc_start: 0.8433 (p0) cc_final: 0.8012 (p0) REVERT: C 232 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.6606 (mp0) REVERT: C 288 LYS cc_start: 0.8364 (pttp) cc_final: 0.7980 (pttp) REVERT: C 582 ARG cc_start: 0.8310 (mmm160) cc_final: 0.8023 (mmm160) REVERT: C 719 ASP cc_start: 0.8308 (t0) cc_final: 0.8104 (t0) REVERT: C 725 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8891 (mp) REVERT: D 436 MET cc_start: 0.7598 (tpp) cc_final: 0.7397 (tpp) outliers start: 69 outliers final: 32 residues processed: 344 average time/residue: 0.1282 time to fit residues: 73.1473 Evaluate side-chains 304 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 266 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 237 PHE Chi-restraints excluded: chain A residue 316 TYR Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain B residue 494 ASP Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 553 LYS Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 183 TYR Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 417 HIS Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 725 LEU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 354 ASN Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 463 CYS Chi-restraints excluded: chain D residue 588 ILE Chi-restraints excluded: chain D residue 595 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 93 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 chunk 168 optimal weight: 8.9990 chunk 29 optimal weight: 10.0000 chunk 111 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 50 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 238 optimal weight: 0.7980 chunk 135 optimal weight: 2.9990 chunk 246 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.200714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.156033 restraints weight = 27949.648| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 2.80 r_work: 0.3200 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22996 Z= 0.162 Angle : 0.710 15.993 31368 Z= 0.332 Chirality : 0.047 0.537 3524 Planarity : 0.004 0.045 3912 Dihedral : 13.016 107.655 3728 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.81 % Favored : 93.04 % Rotamer: Outliers : 3.36 % Allowed : 26.83 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.16), residues: 2700 helix: 1.19 (0.13), residues: 1674 sheet: -1.11 (0.70), residues: 42 loop : -1.94 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 214 TYR 0.017 0.001 TYR D 128 PHE 0.018 0.001 PHE A 400 TRP 0.020 0.001 TRP D 196 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (22948) covalent geometry : angle 0.68061 / 0.33 (31234) SS BOND : bond 0.00614 / 0.26 ( 10) SS BOND : angle 1.23213 / 0.58 ( 20) hydrogen bonds : bond 0.05299 / 3.50 ( 1212) hydrogen bonds : angle 4.44491 / 3.23 ( 3576) link_BETA1-4 : bond 0.00730 / 0.47 ( 16) link_BETA1-4 : angle 2.56826 / 2.22 ( 48) link_NAG-ASN : bond 0.00856 / 0.46 ( 22) link_NAG-ASN : angle 3.89303 / 2.72 ( 66) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 285 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.7681 (tmm) cc_final: 0.7306 (tmm) REVERT: A 237 PHE cc_start: 0.8222 (OUTLIER) cc_final: 0.7253 (t80) REVERT: A 302 ASP cc_start: 0.6944 (t70) cc_final: 0.6420 (m-30) REVERT: A 530 TRP cc_start: 0.6576 (m-90) cc_final: 0.6017 (m-90) REVERT: A 576 ILE cc_start: 0.8172 (OUTLIER) cc_final: 0.7840 (pp) REVERT: B 140 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.6896 (pm20) REVERT: B 323 MET cc_start: 0.6493 (OUTLIER) cc_final: 0.6220 (tpp) REVERT: B 406 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7886 (mm-30) REVERT: B 718 ASN cc_start: 0.8390 (p0) cc_final: 0.7955 (p0) REVERT: C 98 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8333 (pp30) REVERT: C 232 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.6857 (mp0) REVERT: C 288 LYS cc_start: 0.8421 (pttp) cc_final: 0.7967 (pttp) REVERT: C 582 ARG cc_start: 0.8417 (mmm160) cc_final: 0.7982 (mmm160) REVERT: C 718 ASN cc_start: 0.8292 (p0) cc_final: 0.7852 (p0) REVERT: C 719 ASP cc_start: 0.8394 (t0) cc_final: 0.8121 (t0) REVERT: C 725 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8949 (mp) REVERT: D 199 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7785 (mp) REVERT: D 210 MET cc_start: 0.7594 (tmm) cc_final: 0.7231 (tmm) REVERT: D 363 MET cc_start: 0.7901 (tpp) cc_final: 0.7217 (mpp) REVERT: D 423 MET cc_start: 0.7895 (ttm) cc_final: 0.7693 (ttt) outliers start: 80 outliers final: 50 residues processed: 345 average time/residue: 0.1318 time to fit residues: 75.7090 Evaluate side-chains 328 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 270 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 237 PHE Chi-restraints excluded: chain A residue 316 TYR Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 494 ASP Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 183 TYR Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 723 GLU Chi-restraints excluded: chain C residue 725 LEU Chi-restraints excluded: chain C residue 741 ILE Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 354 ASN Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 463 CYS Chi-restraints excluded: chain D residue 504 SER Chi-restraints excluded: chain D residue 588 ILE Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 595 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 251 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 221 optimal weight: 1.9990 chunk 244 optimal weight: 0.9980 chunk 169 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 208 optimal weight: 30.0000 chunk 44 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.200742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.129745 restraints weight = 27352.562| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.37 r_work: 0.3197 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22996 Z= 0.131 Angle : 0.668 14.127 31368 Z= 0.311 Chirality : 0.045 0.485 3524 Planarity : 0.004 0.044 3912 Dihedral : 11.548 107.332 3728 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.89 % Favored : 93.00 % Rotamer: Outliers : 3.24 % Allowed : 26.91 % Favored : 69.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.16), residues: 2700 helix: 1.30 (0.13), residues: 1680 sheet: -1.10 (0.68), residues: 42 loop : -1.84 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 192 TYR 0.021 0.001 TYR A 41 PHE 0.019 0.001 PHE C 72 TRP 0.022 0.001 TRP A 416 HIS 0.005 0.001 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (22948) covalent geometry : angle 0.63969 / 0.30 (31234) SS BOND : bond 0.00436 / 0.18 ( 10) SS BOND : angle 1.11545 / 0.53 ( 20) hydrogen bonds : bond 0.04551 / 3.00 ( 1212) hydrogen bonds : angle 4.28180 / 3.11 ( 3576) link_BETA1-4 : bond 0.00587 / 0.32 ( 16) link_BETA1-4 : angle 2.80422 / 2.36 ( 48) link_NAG-ASN : bond 0.00589 / 0.38 ( 22) link_NAG-ASN : angle 3.46898 / 2.40 ( 66) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 292 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.7558 (tmm) cc_final: 0.7123 (tmm) REVERT: A 237 PHE cc_start: 0.8056 (OUTLIER) cc_final: 0.7140 (t80) REVERT: A 302 ASP cc_start: 0.6916 (OUTLIER) cc_final: 0.6359 (m-30) REVERT: A 363 MET cc_start: 0.7511 (tpp) cc_final: 0.7148 (mpp) REVERT: A 436 MET cc_start: 0.7403 (tpp) cc_final: 0.7010 (tpp) REVERT: A 486 ASP cc_start: 0.7931 (OUTLIER) cc_final: 0.7625 (t0) REVERT: A 530 TRP cc_start: 0.6476 (m-90) cc_final: 0.5827 (m-90) REVERT: A 546 PHE cc_start: 0.7911 (t80) cc_final: 0.7409 (t80) REVERT: A 576 ILE cc_start: 0.8192 (OUTLIER) cc_final: 0.7899 (pp) REVERT: B 140 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6770 (pm20) REVERT: B 323 MET cc_start: 0.6406 (ttm) cc_final: 0.6119 (tpp) REVERT: B 406 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7896 (mm-30) REVERT: B 718 ASN cc_start: 0.8337 (p0) cc_final: 0.7940 (p0) REVERT: C 232 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.6876 (mp0) REVERT: C 288 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.7963 (pttp) REVERT: C 562 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8018 (ttmm) REVERT: C 582 ARG cc_start: 0.8402 (mmm160) cc_final: 0.7837 (mmm160) REVERT: C 718 ASN cc_start: 0.8237 (p0) cc_final: 0.7818 (p0) REVERT: C 719 ASP cc_start: 0.8401 (t0) cc_final: 0.8098 (t0) REVERT: C 725 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8979 (mp) REVERT: D 199 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7668 (mt) REVERT: D 210 MET cc_start: 0.7516 (tmm) cc_final: 0.7065 (tmm) REVERT: D 363 MET cc_start: 0.7846 (tpp) cc_final: 0.7178 (mpp) REVERT: D 436 MET cc_start: 0.7497 (tpp) cc_final: 0.7205 (tpp) outliers start: 77 outliers final: 54 residues processed: 350 average time/residue: 0.1429 time to fit residues: 83.4300 Evaluate side-chains 334 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 270 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 196 TRP Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 237 PHE Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 316 TYR Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 435 ASN Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 494 ASP Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 518 ARG Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 579 MET Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 183 TYR Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 261 CYS Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 494 ASP Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 562 LYS Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 723 GLU Chi-restraints excluded: chain C residue 725 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 354 ASN Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 477 SER Chi-restraints excluded: chain D residue 588 ILE Chi-restraints excluded: chain D residue 595 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 114 optimal weight: 5.9990 chunk 212 optimal weight: 3.9990 chunk 165 optimal weight: 0.9990 chunk 153 optimal weight: 7.9990 chunk 179 optimal weight: 0.6980 chunk 84 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 157 optimal weight: 0.6980 chunk 239 optimal weight: 0.9980 chunk 90 optimal weight: 9.9990 chunk 184 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.202096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.157145 restraints weight = 27929.505| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 2.69 r_work: 0.3254 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22996 Z= 0.127 Angle : 0.666 13.405 31368 Z= 0.311 Chirality : 0.045 0.467 3524 Planarity : 0.004 0.045 3912 Dihedral : 10.980 109.500 3728 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.63 % Favored : 93.26 % Rotamer: Outliers : 3.78 % Allowed : 26.91 % Favored : 69.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.17), residues: 2700 helix: 1.38 (0.13), residues: 1669 sheet: -1.14 (0.67), residues: 42 loop : -1.82 (0.19), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 192 TYR 0.018 0.001 TYR D 87 PHE 0.020 0.001 PHE C 72 TRP 0.022 0.001 TRP A 416 HIS 0.006 0.001 HIS B 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (22948) covalent geometry : angle 0.63810 / 0.30 (31234) SS BOND : bond 0.00489 / 0.19 ( 10) SS BOND : angle 1.32794 / 0.66 ( 20) hydrogen bonds : bond 0.04476 / 2.95 ( 1212) hydrogen bonds : angle 4.22076 / 3.07 ( 3576) link_BETA1-4 : bond 0.00589 / 0.33 ( 16) link_BETA1-4 : angle 2.92014 / 2.43 ( 48) link_NAG-ASN : bond 0.00576 / 0.37 ( 22) link_NAG-ASN : angle 3.38636 / 2.41 ( 66) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 282 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 PRO cc_start: 0.7698 (Cg_endo) cc_final: 0.7479 (Cg_exo) REVERT: A 199 LEU cc_start: 0.7915 (mp) cc_final: 0.7691 (mp) REVERT: A 210 MET cc_start: 0.7693 (tmm) cc_final: 0.7264 (tmm) REVERT: A 237 PHE cc_start: 0.8172 (OUTLIER) cc_final: 0.7161 (t80) REVERT: A 302 ASP cc_start: 0.6814 (OUTLIER) cc_final: 0.6342 (m-30) REVERT: A 363 MET cc_start: 0.7645 (tpp) cc_final: 0.7335 (mpp) REVERT: A 432 MET cc_start: 0.7990 (tpt) cc_final: 0.7580 (tpt) REVERT: A 436 MET cc_start: 0.7491 (tpp) cc_final: 0.7143 (tpp) REVERT: A 530 TRP cc_start: 0.6606 (m-90) cc_final: 0.5977 (m-90) REVERT: A 543 LEU cc_start: 0.8239 (tp) cc_final: 0.7985 (mp) REVERT: A 546 PHE cc_start: 0.7972 (t80) cc_final: 0.7337 (t80) REVERT: A 576 ILE cc_start: 0.8175 (OUTLIER) cc_final: 0.7879 (pp) REVERT: B 140 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.6745 (pm20) REVERT: B 323 MET cc_start: 0.6381 (ttm) cc_final: 0.6096 (tpp) REVERT: B 718 ASN cc_start: 0.8262 (p0) cc_final: 0.7883 (p0) REVERT: C 232 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.6867 (mp0) REVERT: C 288 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7933 (pttp) REVERT: C 350 ASP cc_start: 0.7013 (t70) cc_final: 0.5842 (t70) REVERT: C 562 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8167 (ttmm) REVERT: C 582 ARG cc_start: 0.8450 (mmm160) cc_final: 0.7880 (mmm160) REVERT: C 718 ASN cc_start: 0.8141 (p0) cc_final: 0.7743 (p0) REVERT: C 719 ASP cc_start: 0.8314 (t0) cc_final: 0.8008 (t0) REVERT: C 725 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8993 (mp) REVERT: D 210 MET cc_start: 0.7669 (tmm) cc_final: 0.7189 (tmm) REVERT: D 302 ASP cc_start: 0.7455 (OUTLIER) cc_final: 0.6869 (t0) REVERT: D 363 MET cc_start: 0.7956 (tpp) cc_final: 0.7300 (mpp) REVERT: D 432 MET cc_start: 0.7848 (tpt) cc_final: 0.7616 (tpt) outliers start: 90 outliers final: 64 residues processed: 344 average time/residue: 0.1413 time to fit residues: 80.8363 Evaluate side-chains 346 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 273 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 196 TRP Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 237 PHE Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 316 TYR Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 435 ASN Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 494 ASP Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 518 ARG Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 579 MET Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 183 TYR Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 261 CYS Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 494 ASP Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 531 GLN Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 562 LYS Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 723 GLU Chi-restraints excluded: chain C residue 725 LEU Chi-restraints excluded: chain C residue 743 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 354 ASN Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 477 SER Chi-restraints excluded: chain D residue 595 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 132 optimal weight: 6.9990 chunk 202 optimal weight: 3.9990 chunk 247 optimal weight: 1.9990 chunk 217 optimal weight: 9.9990 chunk 252 optimal weight: 0.8980 chunk 246 optimal weight: 1.9990 chunk 197 optimal weight: 0.9980 chunk 136 optimal weight: 9.9990 chunk 192 optimal weight: 0.0970 chunk 156 optimal weight: 3.9990 chunk 133 optimal weight: 0.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 HIS C 63 ASN C 98 GLN ** D 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.201169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 124)---------------| | r_work = 0.3584 r_free = 0.3584 target = 0.134679 restraints weight = 27420.307| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.54 r_work: 0.3299 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22996 Z= 0.131 Angle : 0.663 12.699 31368 Z= 0.309 Chirality : 0.045 0.462 3524 Planarity : 0.004 0.044 3912 Dihedral : 10.425 112.981 3728 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.93 % Favored : 92.96 % Rotamer: Outliers : 4.21 % Allowed : 26.41 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.17), residues: 2700 helix: 1.35 (0.13), residues: 1677 sheet: -1.10 (0.68), residues: 42 loop : -1.81 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 192 TYR 0.017 0.001 TYR D 128 PHE 0.022 0.001 PHE C 72 TRP 0.022 0.001 TRP A 416 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (22948) covalent geometry : angle 0.63567 / 0.30 (31234) SS BOND : bond 0.00453 / 0.18 ( 10) SS BOND : angle 1.31546 / 0.65 ( 20) hydrogen bonds : bond 0.04498 / 2.96 ( 1212) hydrogen bonds : angle 4.18023 / 3.04 ( 3576) link_BETA1-4 : bond 0.00566 / 0.31 ( 16) link_BETA1-4 : angle 3.04346 / 2.52 ( 48) link_NAG-ASN : bond 0.00544 / 0.35 ( 22) link_NAG-ASN : angle 3.25600 / 2.32 ( 66) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 281 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.7552 (tmm) cc_final: 0.7118 (tmm) REVERT: A 237 PHE cc_start: 0.8094 (OUTLIER) cc_final: 0.7174 (t80) REVERT: A 363 MET cc_start: 0.7638 (tpp) cc_final: 0.7319 (mpp) REVERT: A 436 MET cc_start: 0.7499 (tpp) cc_final: 0.7092 (tpp) REVERT: A 530 TRP cc_start: 0.6691 (m-90) cc_final: 0.6113 (m-90) REVERT: A 543 LEU cc_start: 0.8237 (tp) cc_final: 0.7962 (mp) REVERT: A 546 PHE cc_start: 0.7982 (t80) cc_final: 0.7407 (t80) REVERT: A 576 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.7997 (pp) REVERT: B 140 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.6937 (pm20) REVERT: B 406 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7877 (mm-30) REVERT: B 481 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8449 (mmmm) REVERT: B 718 ASN cc_start: 0.8414 (p0) cc_final: 0.8025 (p0) REVERT: C 232 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.6883 (mp0) REVERT: C 288 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.7970 (pttp) REVERT: C 371 THR cc_start: 0.8853 (m) cc_final: 0.8652 (p) REVERT: C 562 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8050 (ttmm) REVERT: C 582 ARG cc_start: 0.8476 (mmm160) cc_final: 0.7987 (mmm160) REVERT: C 718 ASN cc_start: 0.8299 (p0) cc_final: 0.7887 (p0) REVERT: C 719 ASP cc_start: 0.8387 (t0) cc_final: 0.8130 (t0) REVERT: C 725 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.8995 (mp) REVERT: D 210 MET cc_start: 0.7540 (tmm) cc_final: 0.7121 (tmm) REVERT: D 292 TYR cc_start: 0.7741 (OUTLIER) cc_final: 0.7411 (m-80) REVERT: D 302 ASP cc_start: 0.7428 (OUTLIER) cc_final: 0.6851 (t70) REVERT: D 363 MET cc_start: 0.7925 (tpp) cc_final: 0.7235 (mpp) REVERT: D 436 MET cc_start: 0.7529 (tpp) cc_final: 0.6461 (ttm) REVERT: D 488 TYR cc_start: 0.8173 (m-80) cc_final: 0.7946 (m-80) outliers start: 100 outliers final: 73 residues processed: 356 average time/residue: 0.1443 time to fit residues: 85.0809 Evaluate side-chains 356 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 273 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 196 TRP Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 237 PHE Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 316 TYR Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 435 ASN Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain B residue 76 GLN Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 481 LYS Chi-restraints excluded: chain B residue 494 ASP Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 518 ARG Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 579 MET Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 183 TYR Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 261 CYS Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 494 ASP Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 531 GLN Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 562 LYS Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 723 GLU Chi-restraints excluded: chain C residue 725 LEU Chi-restraints excluded: chain C residue 743 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 292 TYR Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 354 ASN Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 477 SER Chi-restraints excluded: chain D residue 595 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 266 optimal weight: 3.9990 chunk 221 optimal weight: 5.9990 chunk 195 optimal weight: 0.9990 chunk 166 optimal weight: 10.0000 chunk 133 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 239 optimal weight: 0.8980 chunk 161 optimal weight: 8.9990 chunk 64 optimal weight: 7.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 HIS B 98 GLN C 98 GLN ** D 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.199309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.155116 restraints weight = 27662.008| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 2.75 r_work: 0.3190 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22996 Z= 0.184 Angle : 0.703 12.387 31368 Z= 0.333 Chirality : 0.046 0.440 3524 Planarity : 0.004 0.045 3912 Dihedral : 10.214 115.731 3728 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.44 % Favored : 92.41 % Rotamer: Outliers : 4.50 % Allowed : 26.32 % Favored : 69.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.16), residues: 2700 helix: 1.20 (0.13), residues: 1684 sheet: -1.04 (0.70), residues: 42 loop : -1.89 (0.19), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 192 TYR 0.019 0.002 TYR D 87 PHE 0.022 0.002 PHE C 72 TRP 0.026 0.002 TRP D 453 HIS 0.005 0.001 HIS B 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.18 (22948) covalent geometry : angle 0.67656 / 0.33 (31234) SS BOND : bond 0.00750 / 0.29 ( 10) SS BOND : angle 1.53275 / 0.75 ( 20) hydrogen bonds : bond 0.05399 / 3.55 ( 1212) hydrogen bonds : angle 4.27485 / 3.10 ( 3576) link_BETA1-4 : bond 0.00532 / 0.29 ( 16) link_BETA1-4 : angle 3.14472 / 2.56 ( 48) link_NAG-ASN : bond 0.00535 / 0.35 ( 22) link_NAG-ASN : angle 3.24220 / 2.33 ( 66) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 276 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 LEU cc_start: 0.7914 (mp) cc_final: 0.7703 (mp) REVERT: A 210 MET cc_start: 0.7691 (tmm) cc_final: 0.7229 (tmm) REVERT: A 223 VAL cc_start: 0.7866 (m) cc_final: 0.7587 (p) REVERT: A 363 MET cc_start: 0.7836 (tpp) cc_final: 0.7537 (mpp) REVERT: A 436 MET cc_start: 0.7556 (tpp) cc_final: 0.7223 (tpp) REVERT: A 530 TRP cc_start: 0.6948 (m-90) cc_final: 0.6637 (m-90) REVERT: A 543 LEU cc_start: 0.8263 (tp) cc_final: 0.8008 (mp) REVERT: A 546 PHE cc_start: 0.7967 (t80) cc_final: 0.7674 (t80) REVERT: A 549 PHE cc_start: 0.7341 (t80) cc_final: 0.7045 (t80) REVERT: A 576 ILE cc_start: 0.8239 (OUTLIER) cc_final: 0.7978 (pp) REVERT: B 140 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.6974 (pm20) REVERT: B 215 TYR cc_start: 0.8214 (m-10) cc_final: 0.7934 (m-10) REVERT: B 406 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7832 (mm-30) REVERT: B 651 MET cc_start: 0.9325 (mmm) cc_final: 0.9120 (mmm) REVERT: B 718 ASN cc_start: 0.8555 (p0) cc_final: 0.8122 (p0) REVERT: B 725 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8865 (mp) REVERT: C 232 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.6954 (mp0) REVERT: C 288 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.7902 (pttp) REVERT: C 562 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8464 (mtpp) REVERT: C 582 ARG cc_start: 0.8473 (mmm160) cc_final: 0.8043 (mmm160) REVERT: C 651 MET cc_start: 0.9303 (mmm) cc_final: 0.9089 (mmm) REVERT: C 718 ASN cc_start: 0.8423 (p0) cc_final: 0.8017 (p0) REVERT: C 719 ASP cc_start: 0.8349 (t0) cc_final: 0.8028 (t0) REVERT: C 725 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.8961 (mp) REVERT: D 210 MET cc_start: 0.7690 (tmm) cc_final: 0.7217 (tmm) REVERT: D 363 MET cc_start: 0.8120 (tpp) cc_final: 0.7449 (mpp) outliers start: 107 outliers final: 82 residues processed: 353 average time/residue: 0.1394 time to fit residues: 81.6103 Evaluate side-chains 356 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 267 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 196 TRP Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 237 PHE Chi-restraints excluded: chain A residue 316 TYR Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 435 ASN Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain B residue 76 GLN Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 102 GLN Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 494 ASP Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 518 ARG Chi-restraints excluded: chain B residue 579 MET Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 689 LYS Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 183 TYR Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 261 CYS Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 494 ASP Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 531 GLN Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 562 LYS Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 723 GLU Chi-restraints excluded: chain C residue 725 LEU Chi-restraints excluded: chain C residue 741 ILE Chi-restraints excluded: chain C residue 743 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 196 TRP Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 354 ASN Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 463 CYS Chi-restraints excluded: chain D residue 477 SER Chi-restraints excluded: chain D residue 504 SER Chi-restraints excluded: chain D residue 588 ILE Chi-restraints excluded: chain D residue 595 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 16 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 267 optimal weight: 10.0000 chunk 125 optimal weight: 1.9990 chunk 139 optimal weight: 8.9990 chunk 243 optimal weight: 3.9990 chunk 237 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 99 optimal weight: 8.9990 chunk 193 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 HIS ** D 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.199427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.155326 restraints weight = 27777.482| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.76 r_work: 0.3190 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22996 Z= 0.171 Angle : 0.693 11.981 31368 Z= 0.328 Chirality : 0.046 0.439 3524 Planarity : 0.004 0.043 3912 Dihedral : 9.899 118.600 3728 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.78 % Favored : 93.04 % Rotamer: Outliers : 4.12 % Allowed : 26.58 % Favored : 69.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.16), residues: 2700 helix: 1.19 (0.13), residues: 1684 sheet: -0.98 (0.70), residues: 42 loop : -1.91 (0.19), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 192 TYR 0.019 0.001 TYR D 87 PHE 0.025 0.001 PHE C 72 TRP 0.030 0.002 TRP A 416 HIS 0.004 0.001 HIS B 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 (22948) covalent geometry : angle 0.66553 / 0.32 (31234) SS BOND : bond 0.00562 / 0.24 ( 10) SS BOND : angle 1.54232 / 0.75 ( 20) hydrogen bonds : bond 0.05201 / 3.42 ( 1212) hydrogen bonds : angle 4.23784 / 3.07 ( 3576) link_BETA1-4 : bond 0.00518 / 0.28 ( 16) link_BETA1-4 : angle 3.26469 / 2.68 ( 48) link_NAG-ASN : bond 0.00529 / 0.35 ( 22) link_NAG-ASN : angle 3.18974 / 2.31 ( 66) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 276 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.7689 (tmm) cc_final: 0.7390 (tmm) REVERT: A 223 VAL cc_start: 0.7871 (m) cc_final: 0.7588 (p) REVERT: A 363 MET cc_start: 0.7812 (tpp) cc_final: 0.7505 (mpp) REVERT: A 432 MET cc_start: 0.8052 (tpt) cc_final: 0.7680 (tpt) REVERT: A 436 MET cc_start: 0.7512 (tpp) cc_final: 0.7136 (tpp) REVERT: A 530 TRP cc_start: 0.6962 (m-90) cc_final: 0.6654 (m-90) REVERT: A 546 PHE cc_start: 0.7939 (t80) cc_final: 0.7700 (t80) REVERT: A 549 PHE cc_start: 0.7378 (t80) cc_final: 0.7133 (t80) REVERT: A 576 ILE cc_start: 0.8241 (OUTLIER) cc_final: 0.7980 (pp) REVERT: B 140 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.7063 (pm20) REVERT: B 215 TYR cc_start: 0.8253 (m-10) cc_final: 0.7979 (m-10) REVERT: B 406 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7841 (mm-30) REVERT: B 651 MET cc_start: 0.9313 (mmm) cc_final: 0.9107 (mmm) REVERT: B 718 ASN cc_start: 0.8509 (p0) cc_final: 0.8104 (p0) REVERT: B 725 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8891 (mp) REVERT: C 232 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.6972 (mp0) REVERT: C 288 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.7928 (pttp) REVERT: C 562 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8425 (mtpp) REVERT: C 582 ARG cc_start: 0.8480 (mmm160) cc_final: 0.8060 (mmm160) REVERT: C 651 MET cc_start: 0.9304 (mmm) cc_final: 0.9087 (mmm) REVERT: C 718 ASN cc_start: 0.8345 (p0) cc_final: 0.8006 (p0) REVERT: C 719 ASP cc_start: 0.8352 (t0) cc_final: 0.8131 (t0) REVERT: C 725 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.8985 (mp) REVERT: D 210 MET cc_start: 0.7622 (tmm) cc_final: 0.7164 (tmm) REVERT: D 352 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7564 (tp30) REVERT: D 363 MET cc_start: 0.8116 (tpp) cc_final: 0.7445 (mpp) REVERT: D 436 MET cc_start: 0.7408 (tpp) cc_final: 0.6487 (ttm) REVERT: D 488 TYR cc_start: 0.8173 (m-80) cc_final: 0.7960 (m-80) outliers start: 98 outliers final: 82 residues processed: 347 average time/residue: 0.1387 time to fit residues: 80.1031 Evaluate side-chains 360 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 270 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 196 TRP Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 237 PHE Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 316 TYR Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 435 ASN Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain B residue 76 GLN Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 102 GLN Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 494 ASP Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 518 ARG Chi-restraints excluded: chain B residue 579 MET Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 709 SER Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 261 CYS Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 494 ASP Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 531 GLN Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 562 LYS Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 723 GLU Chi-restraints excluded: chain C residue 725 LEU Chi-restraints excluded: chain C residue 741 ILE Chi-restraints excluded: chain C residue 743 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 196 TRP Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 352 GLU Chi-restraints excluded: chain D residue 354 ASN Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 463 CYS Chi-restraints excluded: chain D residue 477 SER Chi-restraints excluded: chain D residue 588 ILE Chi-restraints excluded: chain D residue 595 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 43 optimal weight: 0.9980 chunk 223 optimal weight: 6.9990 chunk 173 optimal weight: 6.9990 chunk 169 optimal weight: 9.9990 chunk 267 optimal weight: 8.9990 chunk 25 optimal weight: 0.9980 chunk 182 optimal weight: 0.6980 chunk 133 optimal weight: 5.9990 chunk 129 optimal weight: 0.9990 chunk 131 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 GLN ** D 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.200491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.156786 restraints weight = 27924.387| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 2.77 r_work: 0.3217 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22996 Z= 0.138 Angle : 0.673 11.648 31368 Z= 0.316 Chirality : 0.045 0.435 3524 Planarity : 0.004 0.044 3912 Dihedral : 9.574 116.712 3728 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.78 % Favored : 93.04 % Rotamer: Outliers : 3.95 % Allowed : 26.58 % Favored : 69.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.17), residues: 2700 helix: 1.26 (0.13), residues: 1685 sheet: -0.95 (0.70), residues: 42 loop : -1.88 (0.19), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 192 TYR 0.020 0.001 TYR D 87 PHE 0.027 0.001 PHE C 72 TRP 0.023 0.001 TRP A 416 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (22948) covalent geometry : angle 0.64561 / 0.31 (31234) SS BOND : bond 0.00469 / 0.20 ( 10) SS BOND : angle 1.25781 / 0.61 ( 20) hydrogen bonds : bond 0.04717 / 3.10 ( 1212) hydrogen bonds : angle 4.19809 / 3.06 ( 3576) link_BETA1-4 : bond 0.00522 / 0.27 ( 16) link_BETA1-4 : angle 3.33605 / 2.76 ( 48) link_NAG-ASN : bond 0.00529 / 0.34 ( 22) link_NAG-ASN : angle 3.11918 / 2.26 ( 66) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 271 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7791 (mp) REVERT: A 210 MET cc_start: 0.7688 (tmm) cc_final: 0.7394 (tmm) REVERT: A 223 VAL cc_start: 0.7859 (m) cc_final: 0.7576 (p) REVERT: A 363 MET cc_start: 0.7646 (tpp) cc_final: 0.7334 (mpp) REVERT: A 432 MET cc_start: 0.8029 (tpt) cc_final: 0.7672 (tpt) REVERT: A 530 TRP cc_start: 0.7004 (m-90) cc_final: 0.6635 (m-90) REVERT: A 543 LEU cc_start: 0.8326 (tp) cc_final: 0.8040 (mp) REVERT: A 546 PHE cc_start: 0.7934 (t80) cc_final: 0.7609 (t80) REVERT: A 576 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7938 (pp) REVERT: B 140 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6967 (pm20) REVERT: B 215 TYR cc_start: 0.8200 (m-10) cc_final: 0.7975 (m-10) REVERT: B 406 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7816 (mm-30) REVERT: B 651 MET cc_start: 0.9302 (mmm) cc_final: 0.9093 (mmm) REVERT: B 718 ASN cc_start: 0.8378 (p0) cc_final: 0.7989 (p0) REVERT: C 232 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.6925 (mp0) REVERT: C 288 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.7926 (pttp) REVERT: C 562 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8423 (mtpp) REVERT: C 582 ARG cc_start: 0.8499 (mmm160) cc_final: 0.8118 (mmm160) REVERT: C 651 MET cc_start: 0.9296 (mmm) cc_final: 0.9070 (mmm) REVERT: C 718 ASN cc_start: 0.8243 (p0) cc_final: 0.7933 (p0) REVERT: C 719 ASP cc_start: 0.8297 (t0) cc_final: 0.8086 (t0) REVERT: C 725 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.9004 (mp) REVERT: D 210 MET cc_start: 0.7625 (tmm) cc_final: 0.7215 (tmm) REVERT: D 352 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7505 (tp30) REVERT: D 363 MET cc_start: 0.8072 (tpp) cc_final: 0.7414 (mpp) outliers start: 94 outliers final: 79 residues processed: 340 average time/residue: 0.1398 time to fit residues: 78.7009 Evaluate side-chains 352 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 265 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 196 TRP Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 237 PHE Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 435 ASN Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain B residue 76 GLN Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 102 GLN Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 494 ASP Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 518 ARG Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 579 MET Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 261 CYS Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 494 ASP Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 531 GLN Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 562 LYS Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 709 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 723 GLU Chi-restraints excluded: chain C residue 725 LEU Chi-restraints excluded: chain C residue 741 ILE Chi-restraints excluded: chain C residue 743 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 196 TRP Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 352 GLU Chi-restraints excluded: chain D residue 354 ASN Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 463 CYS Chi-restraints excluded: chain D residue 477 SER Chi-restraints excluded: chain D residue 588 ILE Chi-restraints excluded: chain D residue 595 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 18 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 chunk 83 optimal weight: 0.7980 chunk 56 optimal weight: 6.9990 chunk 155 optimal weight: 0.8980 chunk 169 optimal weight: 10.0000 chunk 205 optimal weight: 0.6980 chunk 63 optimal weight: 8.9990 chunk 131 optimal weight: 0.0000 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 HIS ** D 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.201359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.158061 restraints weight = 28317.668| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 2.79 r_work: 0.3217 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22996 Z= 0.128 Angle : 0.669 11.453 31368 Z= 0.312 Chirality : 0.044 0.427 3524 Planarity : 0.004 0.043 3912 Dihedral : 9.313 115.037 3728 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.59 % Favored : 93.26 % Rotamer: Outliers : 3.78 % Allowed : 26.83 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.17), residues: 2700 helix: 1.33 (0.13), residues: 1683 sheet: -0.94 (0.69), residues: 42 loop : -1.82 (0.19), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 192 TYR 0.020 0.001 TYR D 87 PHE 0.029 0.001 PHE C 72 TRP 0.022 0.001 TRP A 416 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (22948) covalent geometry : angle 0.64185 / 0.31 (31234) SS BOND : bond 0.00415 / 0.17 ( 10) SS BOND : angle 1.17469 / 0.57 ( 20) hydrogen bonds : bond 0.04411 / 2.90 ( 1212) hydrogen bonds : angle 4.14159 / 3.01 ( 3576) link_BETA1-4 : bond 0.00530 / 0.28 ( 16) link_BETA1-4 : angle 3.32396 / 2.76 ( 48) link_NAG-ASN : bond 0.00515 / 0.34 ( 22) link_NAG-ASN : angle 3.06999 / 2.23 ( 66) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5400 Ramachandran restraints generated. 2700 Oldfield, 0 Emsley, 2700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 271 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.7616 (tmm) cc_final: 0.7161 (tmm) REVERT: A 214 ARG cc_start: 0.7374 (ttm-80) cc_final: 0.7166 (ttm-80) REVERT: A 223 VAL cc_start: 0.7815 (m) cc_final: 0.7526 (p) REVERT: A 304 VAL cc_start: 0.7932 (p) cc_final: 0.7706 (m) REVERT: A 363 MET cc_start: 0.7614 (tpp) cc_final: 0.7330 (mpp) REVERT: A 432 MET cc_start: 0.7991 (tpt) cc_final: 0.7596 (tpt) REVERT: A 530 TRP cc_start: 0.6962 (m-90) cc_final: 0.6535 (m-90) REVERT: A 546 PHE cc_start: 0.7987 (t80) cc_final: 0.7733 (t80) REVERT: A 576 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7959 (pp) REVERT: B 140 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6888 (pm20) REVERT: B 406 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7796 (mm-30) REVERT: B 718 ASN cc_start: 0.8356 (p0) cc_final: 0.7965 (p0) REVERT: B 725 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8947 (mp) REVERT: C 232 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.6922 (mp0) REVERT: C 288 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.7918 (pttp) REVERT: C 297 MET cc_start: 0.5776 (tpt) cc_final: 0.5508 (tpp) REVERT: C 481 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8566 (mmmm) REVERT: C 562 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8369 (mtpp) REVERT: C 582 ARG cc_start: 0.8514 (mmm160) cc_final: 0.8129 (mmm160) REVERT: C 718 ASN cc_start: 0.8284 (p0) cc_final: 0.7945 (p0) REVERT: C 719 ASP cc_start: 0.8270 (t0) cc_final: 0.8053 (t0) REVERT: C 725 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.9007 (mp) REVERT: D 210 MET cc_start: 0.7624 (tmm) cc_final: 0.7181 (tmm) REVERT: D 302 ASP cc_start: 0.7262 (OUTLIER) cc_final: 0.6157 (t0) REVERT: D 352 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7501 (tp30) REVERT: D 363 MET cc_start: 0.8048 (tpp) cc_final: 0.7417 (mpp) outliers start: 90 outliers final: 75 residues processed: 336 average time/residue: 0.1409 time to fit residues: 78.5073 Evaluate side-chains 346 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 261 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 196 TRP Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 237 PHE Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 316 TYR Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain B residue 76 GLN Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 102 GLN Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 494 ASP Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 518 ARG Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 579 MET Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 183 TYR Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 261 CYS Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 481 LYS Chi-restraints excluded: chain C residue 494 ASP Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 512 PHE Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 531 GLN Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 562 LYS Chi-restraints excluded: chain C residue 579 MET Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 723 GLU Chi-restraints excluded: chain C residue 725 LEU Chi-restraints excluded: chain C residue 741 ILE Chi-restraints excluded: chain C residue 743 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 196 TRP Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 352 GLU Chi-restraints excluded: chain D residue 354 ASN Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 477 SER Chi-restraints excluded: chain D residue 595 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 43 optimal weight: 7.9990 chunk 249 optimal weight: 0.9990 chunk 85 optimal weight: 0.0030 chunk 68 optimal weight: 10.0000 chunk 116 optimal weight: 0.5980 chunk 231 optimal weight: 5.9990 chunk 239 optimal weight: 0.6980 chunk 8 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 chunk 107 optimal weight: 0.1980 chunk 88 optimal weight: 8.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.202854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.159949 restraints weight = 28262.134| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 2.75 r_work: 0.3265 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 22996 Z= 0.115 Angle : 0.661 11.084 31368 Z= 0.306 Chirality : 0.044 0.425 3524 Planarity : 0.004 0.044 3912 Dihedral : 9.061 112.605 3728 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.44 % Favored : 93.41 % Rotamer: Outliers : 3.24 % Allowed : 27.42 % Favored : 69.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.17), residues: 2700 helix: 1.41 (0.13), residues: 1674 sheet: -1.02 (0.68), residues: 42 loop : -1.76 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 192 TYR 0.020 0.001 TYR D 87 PHE 0.018 0.001 PHE D 520 TRP 0.022 0.001 TRP A 416 HIS 0.005 0.001 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (22948) covalent geometry : angle 0.63441 / 0.30 (31234) SS BOND : bond 0.00383 / 0.15 ( 10) SS BOND : angle 1.00443 / 0.48 ( 20) hydrogen bonds : bond 0.03936 / 2.59 ( 1212) hydrogen bonds : angle 4.09896 / 2.98 ( 3576) link_BETA1-4 : bond 0.00523 / 0.27 ( 16) link_BETA1-4 : angle 3.25125 / 2.69 ( 48) link_NAG-ASN : bond 0.00524 / 0.34 ( 22) link_NAG-ASN : angle 3.00748 / 2.20 ( 66) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5794.14 seconds wall clock time: 100 minutes 13.27 seconds (6013.27 seconds total)