Starting phenix.real_space_refine on Fri Mar 6 06:42:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v61_31732/03_2026/7v61_31732.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v61_31732/03_2026/7v61_31732.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/7v61_31732/03_2026/7v61_31732.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v61_31732/03_2026/7v61_31732.map" model { file = "/net/cci-nas-00/data/ceres_data/7v61_31732/03_2026/7v61_31732.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v61_31732/03_2026/7v61_31732.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= 0.000 sd= 0.004 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 Zn 2 6.06 5 S 152 5.16 5 C 18710 2.51 5 N 4696 2.21 5 O 5516 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29076 Number of models: 1 Model: "" Number of chains: 28 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: 6111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 6111 Classifications: {'peptide': 751} Link IDs: {'PTRANS': 35, 'TRANS': 715} Chain: "H" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1712 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 12, 'TRANS': 210} Chain: "K" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1652 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 11, 'TRANS': 202} Chain: "C" 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: "D" Number of atoms: 6111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 6111 Classifications: {'peptide': 751} Link IDs: {'PTRANS': 35, 'TRANS': 715} Chain: "I" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1712 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 12, 'TRANS': 210} Chain: "M" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1652 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 11, 'TRANS': 202} 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: "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: "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: "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: "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: "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: "U" 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: "V" 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' ZN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' ZN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 6.13, per 1000 atoms: 0.21 Number of scatterers: 29076 At special positions: 0 Unit cell: (194.937, 214.323, 200.322, 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) Zn 2 29.99 S 152 16.00 O 5516 8.00 N 4696 7.00 C 18710 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, 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=2.05 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 344 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 530 " - pdb=" SG CYS B 542 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 148 " - pdb=" SG CYS H 204 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 134 " - pdb=" SG CYS K 194 " distance=2.03 Simple disulfide: pdb=" SG CYS C 153 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 383 " distance=2.05 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.04 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 148 " - pdb=" SG CYS I 204 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 134 " - pdb=" SG CYS M 194 " 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 J 1 " - " NAG J 2 " " NAG L 1 " - " NAG L 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 U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " NAG-ASN " NAG A 701 " - " ASN A 158 " " NAG A 702 " - " ASN A 182 " " NAG A 703 " - " ASN A 354 " " NAG A 704 " - " ASN A 368 " " NAG B 901 " - " ASN B 322 " " NAG C 701 " - " ASN C 158 " " NAG C 702 " - " ASN C 182 " " NAG C 703 " - " ASN C 354 " " NAG C 704 " - " ASN C 368 " " NAG D 901 " - " ASN D 322 " " NAG E 1 " - " ASN A 258 " " NAG F 1 " - " ASN B 53 " " NAG G 1 " - " ASN B 90 " " NAG J 1 " - " ASN B 103 " " NAG L 1 " - " ASN B 432 " " NAG N 1 " - " ASN B 546 " " NAG O 1 " - " ASN B 690 " " NAG P 1 " - " ASN C 258 " " NAG Q 1 " - " ASN D 53 " " NAG R 1 " - " ASN D 90 " " NAG S 1 " - " ASN D 103 " " NAG T 1 " - " ASN D 432 " " NAG U 1 " - " ASN D 546 " " NAG V 1 " - " ASN D 690 " Time building additional restraints: 2.45 Conformation dependent library (CDL) restraints added in 1.2 seconds 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6716 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 34 sheets defined 50.6% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 removed outlier: 4.160A pdb=" N GLU A 25 " --> pdb=" O LEU A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 50 removed outlier: 3.683A pdb=" N THR A 44 " --> pdb=" O GLN A 40 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE A 48 " --> pdb=" O THR A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 65 removed outlier: 3.561A pdb=" N GLN A 63 " --> pdb=" O PRO A 59 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N HIS A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 79 Processing helix chain 'A' and resid 81 through 97 removed outlier: 3.548A pdb=" N ILE A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN A 94 " --> pdb=" O PHE A 90 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 105 removed outlier: 3.682A pdb=" N TRP A 104 " --> pdb=" O SER A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 142 removed outlier: 3.667A pdb=" N LEU A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR A 128 " --> pdb=" O MET A 124 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN A 130 " --> pdb=" O GLY A 126 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE A 133 " --> pdb=" O TYR A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 169 Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.515A pdb=" N TRP A 176 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 212 removed outlier: 3.767A pdb=" N CYS A 211 " --> pdb=" O VAL A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 242 Proline residue: A 230 - end of helix removed outlier: 3.621A pdb=" N ILE A 239 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG A 240 " --> pdb=" O ILE A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 removed outlier: 3.536A pdb=" N LEU A 254 " --> pdb=" O GLY A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 263 Processing helix chain 'A' and resid 266 through 279 removed outlier: 3.698A pdb=" N ASP A 270 " --> pdb=" O ASP A 266 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL A 275 " --> pdb=" O ALA A 271 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 291 Processing helix chain 'A' and resid 299 through 349 removed outlier: 3.601A pdb=" N SER A 303 " --> pdb=" O CYS A 299 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL A 304 " --> pdb=" O GLU A 300 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER A 314 " --> pdb=" O ASN A 310 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL A 315 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA A 318 " --> pdb=" O SER A 314 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL A 324 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N THR A 339 " --> pdb=" O ASP A 335 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU A 344 " --> pdb=" O ASN A 340 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP A 349 " --> pdb=" O ILE A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 371 removed outlier: 3.775A pdb=" N CYS A 367 " --> pdb=" O MET A 363 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN A 368 " --> pdb=" O GLN A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 401 Processing helix chain 'A' and resid 402 through 409 removed outlier: 3.553A pdb=" N ALA A 406 " --> pdb=" O VAL A 402 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 441 removed outlier: 4.224A pdb=" N VAL A 418 " --> pdb=" O PRO A 414 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET A 423 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 424 " --> pdb=" O PHE A 420 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL A 441 " --> pdb=" O GLU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 446 Processing helix chain 'A' and resid 454 through 470 removed outlier: 3.741A pdb=" N LEU A 458 " --> pdb=" O PRO A 454 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR A 459 " --> pdb=" O LYS A 455 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE A 467 " --> pdb=" O CYS A 463 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU A 468 " --> pdb=" O LEU A 464 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 475 Processing helix chain 'A' and resid 477 through 507 removed outlier: 3.539A pdb=" N TRP A 481 " --> pdb=" O SER A 477 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 485 " --> pdb=" O TRP A 481 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASP A 486 " --> pdb=" O LEU A 482 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N SER A 487 " --> pdb=" O SER A 483 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N TYR A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Proline residue: A 493 - end of helix removed outlier: 3.642A pdb=" N CYS A 500 " --> pdb=" O ILE A 496 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N MET A 502 " --> pdb=" O ALA A 498 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 505 " --> pdb=" O GLU A 501 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL A 506 " --> pdb=" O MET A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 523 removed outlier: 3.520A pdb=" N LYS A 516 " --> pdb=" O ASP A 512 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N MET A 521 " --> pdb=" O ASP A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 536 Processing helix chain 'A' and resid 536 through 553 removed outlier: 3.564A pdb=" N LEU A 543 " --> pdb=" O PRO A 539 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A 544 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE A 545 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE A 546 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N PHE A 550 " --> pdb=" O PHE A 546 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 551 " --> pdb=" O LEU A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 608 removed outlier: 4.117A pdb=" N VAL A 585 " --> pdb=" O TRP A 581 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL A 592 " --> pdb=" O ILE A 588 " (cutoff:3.500A) Proline residue: A 593 - end of helix removed outlier: 4.670A pdb=" N ILE A 597 " --> pdb=" O PRO A 593 " (cutoff:3.500A) Proline residue: A 598 - end of helix removed outlier: 3.952A pdb=" N ALA A 601 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A 605 " --> pdb=" O ALA A 601 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN A 608 " --> pdb=" O LYS A 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 53 removed outlier: 3.512A pdb=" N GLU B 35 " --> pdb=" O LYS B 31 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP B 38 " --> pdb=" O HIS B 34 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN B 42 " --> pdb=" O ASP B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 79 removed outlier: 3.688A pdb=" N MET B 62 " --> pdb=" O ASN B 58 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA B 65 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS B 74 " --> pdb=" O SER B 70 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR B 78 " --> pdb=" O LYS B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 83 removed outlier: 3.589A pdb=" N TYR B 83 " --> pdb=" O ALA B 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 80 through 83' Processing helix chain 'B' and resid 90 through 102 removed outlier: 3.505A pdb=" N GLN B 96 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA B 99 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN B 102 " --> pdb=" O GLN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.551A pdb=" N SER B 106 " --> pdb=" O ASN B 103 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL B 107 " --> pdb=" O GLY B 104 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU B 108 " --> pdb=" O SER B 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 108' Processing helix chain 'B' and resid 109 through 130 removed outlier: 3.533A pdb=" N ASN B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER B 128 " --> pdb=" O SER B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 155 removed outlier: 3.631A pdb=" N MET B 152 " --> pdb=" O LEU B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 193 Proline residue: B 178 - end of helix removed outlier: 3.884A pdb=" N GLU B 189 " --> pdb=" O VAL B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 204 Processing helix chain 'B' and resid 205 through 207 No H-bonds generated for 'chain 'B' and resid 205 through 207' Processing helix chain 'B' and resid 220 through 231 removed outlier: 3.704A pdb=" N GLU B 224 " --> pdb=" O GLY B 220 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU B 231 " --> pdb=" O GLU B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 249 removed outlier: 3.556A pdb=" N HIS B 239 " --> pdb=" O PRO B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 277 No H-bonds generated for 'chain 'B' and resid 275 through 277' Processing helix chain 'B' and resid 278 through 283 Processing helix chain 'B' and resid 295 through 300 Processing helix chain 'B' and resid 305 through 317 removed outlier: 3.519A pdb=" N PHE B 315 " --> pdb=" O ALA B 311 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER B 317 " --> pdb=" O LYS B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 383 removed outlier: 3.533A pdb=" N HIS B 373 " --> pdb=" O PHE B 369 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS B 378 " --> pdb=" O HIS B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 removed outlier: 4.551A pdb=" N ALA B 387 " --> pdb=" O ALA B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 393 Processing helix chain 'B' and resid 400 through 413 removed outlier: 3.632A pdb=" N GLY B 405 " --> pdb=" O HIS B 401 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU B 406 " --> pdb=" O GLU B 402 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N SER B 409 " --> pdb=" O GLY B 405 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER B 411 " --> pdb=" O ILE B 407 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA B 413 " --> pdb=" O SER B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 419 Processing helix chain 'B' and resid 433 through 444 removed outlier: 3.655A pdb=" N LYS B 441 " --> pdb=" O ASN B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 448 No H-bonds generated for 'chain 'B' and resid 446 through 448' Processing helix chain 'B' and resid 449 through 465 Processing helix chain 'B' and resid 472 through 484 removed outlier: 3.744A pdb=" N TRP B 478 " --> pdb=" O MET B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 502 removed outlier: 3.512A pdb=" N SER B 502 " --> pdb=" O ASP B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 508 Processing helix chain 'B' and resid 513 through 533 removed outlier: 3.647A pdb=" N THR B 519 " --> pdb=" O TYR B 515 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE B 523 " --> pdb=" O THR B 519 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA B 532 " --> pdb=" O ALA B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 542 removed outlier: 3.662A pdb=" N LYS B 541 " --> pdb=" O PRO B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 559 removed outlier: 3.854A pdb=" N LYS B 553 " --> pdb=" O GLU B 549 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N MET B 557 " --> pdb=" O LYS B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 572 removed outlier: 3.628A pdb=" N GLU B 571 " --> pdb=" O THR B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 588 Processing helix chain 'B' and resid 588 through 599 removed outlier: 3.643A pdb=" N TRP B 594 " --> pdb=" O PRO B 590 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP B 597 " --> pdb=" O THR B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 628 removed outlier: 3.824A pdb=" N ALA B 627 " --> pdb=" O SER B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 658 removed outlier: 3.510A pdb=" N MET B 640 " --> pdb=" O ASN B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 668 No H-bonds generated for 'chain 'B' and resid 666 through 668' Processing helix chain 'B' and resid 696 through 707 removed outlier: 3.506A pdb=" N LYS B 702 " --> pdb=" O THR B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 715 removed outlier: 3.678A pdb=" N ASP B 713 " --> pdb=" O SER B 709 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 714 " --> pdb=" O ARG B 710 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE B 715 " --> pdb=" O ILE B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 768 removed outlier: 3.553A pdb=" N VAL B 745 " --> pdb=" O ILE B 741 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL B 752 " --> pdb=" O VAL B 748 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL B 754 " --> pdb=" O MET B 750 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE B 759 " --> pdb=" O VAL B 755 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU B 760 " --> pdb=" O GLY B 756 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 56 removed outlier: 3.749A pdb=" N ASP H 56 " --> pdb=" O PRO H 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 53 through 56' Processing helix chain 'H' and resid 195 through 197 No H-bonds generated for 'chain 'H' and resid 195 through 197' Processing helix chain 'K' and resid 121 through 128 Processing helix chain 'K' and resid 183 through 187 Processing helix chain 'C' and resid 20 through 25 removed outlier: 4.160A pdb=" N GLU C 25 " --> pdb=" O LEU C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 50 removed outlier: 3.683A pdb=" N THR C 44 " --> pdb=" O GLN C 40 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE C 48 " --> pdb=" O THR C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 65 removed outlier: 3.561A pdb=" N GLN C 63 " --> pdb=" O PRO C 59 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N HIS C 65 " --> pdb=" O LEU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 79 Processing helix chain 'C' and resid 81 through 97 removed outlier: 3.548A pdb=" N ILE C 92 " --> pdb=" O LEU C 88 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY C 93 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN C 94 " --> pdb=" O PHE C 90 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG C 95 " --> pdb=" O ALA C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 105 removed outlier: 3.682A pdb=" N TRP C 104 " --> pdb=" O SER C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 142 removed outlier: 3.667A pdb=" N LEU C 116 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR C 128 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN C 130 " --> pdb=" O GLY C 126 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR C 131 " --> pdb=" O LEU C 127 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE C 133 " --> pdb=" O TYR C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 169 Processing helix chain 'C' and resid 170 through 178 removed outlier: 3.515A pdb=" N TRP C 176 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR C 177 " --> pdb=" O ASP C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 212 removed outlier: 3.767A pdb=" N CYS C 211 " --> pdb=" O VAL C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 242 Proline residue: C 230 - end of helix removed outlier: 3.621A pdb=" N ILE C 239 " --> pdb=" O THR C 235 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG C 240 " --> pdb=" O ILE C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 255 removed outlier: 3.536A pdb=" N LEU C 254 " --> pdb=" O GLY C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 263 Processing helix chain 'C' and resid 266 through 279 removed outlier: 3.698A pdb=" N ASP C 270 " --> pdb=" O ASP C 266 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL C 275 " --> pdb=" O ALA C 271 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE C 276 " --> pdb=" O GLY C 272 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE C 277 " --> pdb=" O ALA C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 291 Processing helix chain 'C' and resid 299 through 349 removed outlier: 3.601A pdb=" N SER C 303 " --> pdb=" O CYS C 299 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL C 304 " --> pdb=" O GLU C 300 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER C 314 " --> pdb=" O ASN C 310 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL C 315 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA C 318 " --> pdb=" O SER C 314 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL C 324 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N THR C 339 " --> pdb=" O ASP C 335 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU C 344 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP C 349 " --> pdb=" O ILE C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 371 removed outlier: 3.775A pdb=" N CYS C 367 " --> pdb=" O MET C 363 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN C 368 " --> pdb=" O GLN C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 401 Processing helix chain 'C' and resid 402 through 409 removed outlier: 3.553A pdb=" N ALA C 406 " --> pdb=" O VAL C 402 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR C 408 " --> pdb=" O THR C 404 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS C 409 " --> pdb=" O GLU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 441 removed outlier: 4.224A pdb=" N VAL C 418 " --> pdb=" O PRO C 414 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET C 423 " --> pdb=" O LEU C 419 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU C 424 " --> pdb=" O PHE C 420 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL C 441 " --> pdb=" O GLU C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 446 Processing helix chain 'C' and resid 454 through 470 removed outlier: 3.741A pdb=" N LEU C 458 " --> pdb=" O PRO C 454 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR C 459 " --> pdb=" O LYS C 455 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE C 467 " --> pdb=" O CYS C 463 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU C 468 " --> pdb=" O LEU C 464 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE C 469 " --> pdb=" O GLY C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 475 Processing helix chain 'C' and resid 477 through 507 removed outlier: 3.539A pdb=" N TRP C 481 " --> pdb=" O SER C 477 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU C 485 " --> pdb=" O TRP C 481 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASP C 486 " --> pdb=" O LEU C 482 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N SER C 487 " --> pdb=" O SER C 483 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N TYR C 488 " --> pdb=" O LEU C 484 " (cutoff:3.500A) Proline residue: C 493 - end of helix removed outlier: 3.642A pdb=" N CYS C 500 " --> pdb=" O ILE C 496 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N MET C 502 " --> pdb=" O ALA C 498 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL C 505 " --> pdb=" O GLU C 501 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL C 506 " --> pdb=" O MET C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 523 removed outlier: 3.520A pdb=" N LYS C 516 " --> pdb=" O ASP C 512 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N MET C 521 " --> pdb=" O ASP C 517 " (cutoff:3.500A) Processing helix chain 'C' and resid 527 through 536 Processing helix chain 'C' and resid 536 through 553 removed outlier: 3.564A pdb=" N LEU C 543 " --> pdb=" O PRO C 539 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE C 544 " --> pdb=" O LEU C 540 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE C 545 " --> pdb=" O LEU C 541 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE C 546 " --> pdb=" O MET C 542 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N PHE C 550 " --> pdb=" O PHE C 546 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL C 551 " --> pdb=" O LEU C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 608 removed outlier: 4.117A pdb=" N VAL C 585 " --> pdb=" O TRP C 581 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL C 592 " --> pdb=" O ILE C 588 " (cutoff:3.500A) Proline residue: C 593 - end of helix removed outlier: 4.670A pdb=" N ILE C 597 " --> pdb=" O PRO C 593 " (cutoff:3.500A) Proline residue: C 598 - end of helix removed outlier: 3.952A pdb=" N ALA C 601 " --> pdb=" O ILE C 597 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU C 605 " --> pdb=" O ALA C 601 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN C 608 " --> pdb=" O LYS C 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 53 removed outlier: 3.512A pdb=" N GLU D 35 " --> pdb=" O LYS D 31 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN D 42 " --> pdb=" O ASP D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 79 removed outlier: 3.688A pdb=" N MET D 62 " --> pdb=" O ASN D 58 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS D 74 " --> pdb=" O SER D 70 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR D 78 " --> pdb=" O LYS D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 83 removed outlier: 3.589A pdb=" N TYR D 83 " --> pdb=" O ALA D 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 80 through 83' Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.505A pdb=" N GLN D 96 " --> pdb=" O THR D 92 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.551A pdb=" N SER D 106 " --> pdb=" O ASN D 103 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU D 108 " --> pdb=" O SER D 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 108' Processing helix chain 'D' and resid 109 through 130 removed outlier: 3.533A pdb=" N ASN D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER D 128 " --> pdb=" O SER D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 155 removed outlier: 3.631A pdb=" N MET D 152 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 193 Proline residue: D 178 - end of helix removed outlier: 3.884A pdb=" N GLU D 189 " --> pdb=" O VAL D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 204 Processing helix chain 'D' and resid 205 through 207 No H-bonds generated for 'chain 'D' and resid 205 through 207' Processing helix chain 'D' and resid 220 through 231 removed outlier: 3.704A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 249 removed outlier: 3.556A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 277 No H-bonds generated for 'chain 'D' and resid 275 through 277' Processing helix chain 'D' and resid 278 through 283 Processing helix chain 'D' and resid 295 through 300 Processing helix chain 'D' and resid 305 through 317 removed outlier: 3.519A pdb=" N PHE D 315 " --> pdb=" O ALA D 311 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER D 317 " --> pdb=" O LYS D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 383 removed outlier: 3.533A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 388 removed outlier: 4.551A pdb=" N ALA D 387 " --> pdb=" O ALA D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 400 through 413 removed outlier: 3.632A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU D 406 " --> pdb=" O GLU D 402 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER D 411 " --> pdb=" O ILE D 407 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA D 413 " --> pdb=" O SER D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 419 Processing helix chain 'D' and resid 433 through 444 removed outlier: 3.655A pdb=" N LYS D 441 " --> pdb=" O ASN D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 448 No H-bonds generated for 'chain 'D' and resid 446 through 448' Processing helix chain 'D' and resid 449 through 465 Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.744A pdb=" N TRP D 478 " --> pdb=" O MET D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 502 removed outlier: 3.512A pdb=" N SER D 502 " --> pdb=" O ASP D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 533 removed outlier: 3.647A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA D 532 " --> pdb=" O ALA D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.662A pdb=" N LYS D 541 " --> pdb=" O PRO D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.854A pdb=" N LYS D 553 " --> pdb=" O GLU D 549 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 removed outlier: 3.628A pdb=" N GLU D 571 " --> pdb=" O THR D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 599 removed outlier: 3.643A pdb=" N TRP D 594 " --> pdb=" O PRO D 590 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP D 597 " --> pdb=" O THR D 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 623 through 628 removed outlier: 3.824A pdb=" N ALA D 627 " --> pdb=" O SER D 623 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 658 removed outlier: 3.510A pdb=" N MET D 640 " --> pdb=" O ASN D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 668 No H-bonds generated for 'chain 'D' and resid 666 through 668' Processing helix chain 'D' and resid 696 through 707 removed outlier: 3.506A pdb=" N LYS D 702 " --> pdb=" O THR D 698 " (cutoff:3.500A) Processing helix chain 'D' and resid 707 through 715 removed outlier: 3.678A pdb=" N ASP D 713 " --> pdb=" O SER D 709 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA D 714 " --> pdb=" O ARG D 710 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE D 715 " --> pdb=" O ILE D 711 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 768 removed outlier: 3.553A pdb=" N VAL D 745 " --> pdb=" O ILE D 741 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL D 752 " --> pdb=" O VAL D 748 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL D 754 " --> pdb=" O MET D 750 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE D 759 " --> pdb=" O VAL D 755 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU D 760 " --> pdb=" O GLY D 756 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 56 removed outlier: 3.749A pdb=" N ASP I 56 " --> pdb=" O PRO I 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 53 through 56' Processing helix chain 'I' and resid 195 through 197 No H-bonds generated for 'chain 'I' and resid 195 through 197' Processing helix chain 'M' and resid 121 through 128 Processing helix chain 'M' and resid 183 through 187 Processing sheet with id=AA1, first strand: chain 'B' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'B' and resid 262 through 263 removed outlier: 6.048A 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 350 Processing sheet with id=AA4, first strand: chain 'B' and resid 670 through 676 removed outlier: 3.944A pdb=" N LEU B 675 " --> pdb=" O SER B 680 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N SER B 680 " --> pdb=" O LEU B 675 " (cutoff:3.500A) removed outlier: 6.479A 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 676 removed outlier: 3.944A pdb=" N LEU B 675 " --> pdb=" O SER B 680 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N SER B 680 " --> pdb=" O LEU B 675 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AA7, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AA8, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.933A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N TYR H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N CYS H 96 " --> pdb=" O TRP H 111 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N TRP H 111 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ARG H 98 " --> pdb=" O ASP H 109 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.933A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N TYR H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 128 through 132 removed outlier: 5.008A pdb=" N ALA H 145 " --> pdb=" O VAL H 192 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL H 192 " --> pdb=" O ALA H 145 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLY H 147 " --> pdb=" O VAL H 190 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL H 190 " --> pdb=" O GLY H 147 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU H 149 " --> pdb=" O SER H 188 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER H 188 " --> pdb=" O LEU H 149 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS H 151 " --> pdb=" O LEU H 186 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU H 186 " --> pdb=" O LYS H 151 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 128 through 132 removed outlier: 5.008A pdb=" N ALA H 145 " --> pdb=" O VAL H 192 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL H 192 " --> pdb=" O ALA H 145 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLY H 147 " --> pdb=" O VAL H 190 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL H 190 " --> pdb=" O GLY H 147 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU H 149 " --> pdb=" O SER H 188 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER H 188 " --> pdb=" O LEU H 149 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS H 151 " --> pdb=" O LEU H 186 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU H 186 " --> pdb=" O LYS H 151 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 158 through 162 Processing sheet with id=AB4, first strand: chain 'K' and resid 5 through 6 removed outlier: 3.545A pdb=" N PHE K 71 " --> pdb=" O CYS K 23 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 10 through 11 Processing sheet with id=AB6, first strand: chain 'K' and resid 45 through 48 removed outlier: 6.367A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 114 through 118 Processing sheet with id=AB8, first strand: chain 'K' and resid 153 through 154 Processing sheet with id=AB9, first strand: chain 'D' and resid 131 through 133 Processing sheet with id=AC1, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.048A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 347 through 350 Processing sheet with id=AC3, first strand: chain 'D' and resid 670 through 676 removed outlier: 3.944A pdb=" N LEU D 675 " --> pdb=" O SER D 680 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N SER D 680 " --> pdb=" O LEU D 675 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ASP D 693 " --> pdb=" O ALA D 687 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 670 through 676 removed outlier: 3.944A pdb=" N LEU D 675 " --> pdb=" O SER D 680 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N SER D 680 " --> pdb=" O LEU D 675 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 3 through 5 Processing sheet with id=AC6, first strand: chain 'I' and resid 11 through 12 Processing sheet with id=AC7, first strand: chain 'I' and resid 58 through 60 removed outlier: 6.933A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N TYR I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE I 34 " --> pdb=" O TYR I 50 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N CYS I 96 " --> pdb=" O TRP I 111 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N TRP I 111 " --> pdb=" O CYS I 96 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ARG I 98 " --> pdb=" O ASP I 109 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 58 through 60 removed outlier: 6.933A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N TYR I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE I 34 " --> pdb=" O TYR I 50 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 128 through 132 removed outlier: 5.008A pdb=" N ALA I 145 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL I 192 " --> pdb=" O ALA I 145 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLY I 147 " --> pdb=" O VAL I 190 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL I 190 " --> pdb=" O GLY I 147 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU I 149 " --> pdb=" O SER I 188 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER I 188 " --> pdb=" O LEU I 149 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS I 151 " --> pdb=" O LEU I 186 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU I 186 " --> pdb=" O LYS I 151 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 128 through 132 removed outlier: 5.008A pdb=" N ALA I 145 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL I 192 " --> pdb=" O ALA I 145 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLY I 147 " --> pdb=" O VAL I 190 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL I 190 " --> pdb=" O GLY I 147 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU I 149 " --> pdb=" O SER I 188 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER I 188 " --> pdb=" O LEU I 149 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS I 151 " --> pdb=" O LEU I 186 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU I 186 " --> pdb=" O LYS I 151 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 158 through 162 Processing sheet with id=AD3, first strand: chain 'M' and resid 5 through 6 removed outlier: 3.545A pdb=" N PHE M 71 " --> pdb=" O CYS M 23 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 10 through 11 Processing sheet with id=AD5, first strand: chain 'M' and resid 45 through 48 removed outlier: 6.367A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 114 through 118 Processing sheet with id=AD7, first strand: chain 'M' and resid 153 through 154 1274 hydrogen bonds defined for protein. 3618 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: 5.58 Time building geometry restraints manager: 3.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8406 1.33 - 1.46: 8202 1.46 - 1.59: 12996 1.59 - 1.72: 0 1.72 - 1.85: 240 Bond restraints: 29844 Sorted by residual: bond pdb=" C ILE A 492 " pdb=" N PRO A 493 " ideal model delta sigma weight residual 1.335 1.401 -0.066 1.38e-02 5.25e+03 2.29e+01 bond pdb=" C ILE C 492 " pdb=" N PRO C 493 " ideal model delta sigma weight residual 1.335 1.401 -0.066 1.38e-02 5.25e+03 2.29e+01 bond pdb=" N PRO C 493 " pdb=" CD PRO C 493 " ideal model delta sigma weight residual 1.473 1.539 -0.066 1.40e-02 5.10e+03 2.19e+01 bond pdb=" N PRO A 493 " pdb=" CD PRO A 493 " ideal model delta sigma weight residual 1.473 1.539 -0.066 1.40e-02 5.10e+03 2.19e+01 bond pdb=" C SER A 170 " pdb=" N PRO A 171 " ideal model delta sigma weight residual 1.336 1.392 -0.056 1.23e-02 6.61e+03 2.10e+01 ... (remaining 29839 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 39648 2.67 - 5.35: 836 5.35 - 8.02: 104 8.02 - 10.70: 18 10.70 - 13.37: 10 Bond angle restraints: 40616 Sorted by residual: angle pdb=" N LEU A 485 " pdb=" CA LEU A 485 " pdb=" C LEU A 485 " ideal model delta sigma weight residual 111.28 121.07 -9.79 1.09e+00 8.42e-01 8.07e+01 angle pdb=" N LEU C 485 " pdb=" CA LEU C 485 " pdb=" C LEU C 485 " ideal model delta sigma weight residual 111.28 121.07 -9.79 1.09e+00 8.42e-01 8.07e+01 angle pdb=" C ILE A 492 " pdb=" N PRO A 493 " pdb=" CA PRO A 493 " ideal model delta sigma weight residual 119.24 112.45 6.79 1.04e+00 9.25e-01 4.26e+01 angle pdb=" C ILE C 492 " pdb=" N PRO C 493 " pdb=" CA PRO C 493 " ideal model delta sigma weight residual 119.24 112.45 6.79 1.04e+00 9.25e-01 4.26e+01 angle pdb=" N MET C 71 " pdb=" CA MET C 71 " pdb=" C MET C 71 " ideal model delta sigma weight residual 111.07 104.39 6.68 1.07e+00 8.73e-01 3.90e+01 ... (remaining 40611 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 16062 17.97 - 35.95: 1466 35.95 - 53.92: 404 53.92 - 71.89: 92 71.89 - 89.87: 36 Dihedral angle restraints: 18060 sinusoidal: 7600 harmonic: 10460 Sorted by residual: dihedral pdb=" CB CYS B 344 " pdb=" SG CYS B 344 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual 93.00 135.97 -42.97 1 1.00e+01 1.00e-02 2.58e+01 dihedral pdb=" CB CYS D 344 " pdb=" SG CYS D 344 " pdb=" SG CYS D 361 " pdb=" CB CYS D 361 " ideal model delta sinusoidal sigma weight residual 93.00 135.97 -42.97 1 1.00e+01 1.00e-02 2.58e+01 dihedral pdb=" CA ILE C 576 " pdb=" C ILE C 576 " pdb=" N SER C 577 " pdb=" CA SER C 577 " ideal model delta harmonic sigma weight residual 180.00 154.71 25.29 0 5.00e+00 4.00e-02 2.56e+01 ... (remaining 18057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.197: 4518 0.197 - 0.394: 34 0.394 - 0.591: 8 0.591 - 0.788: 0 0.788 - 0.986: 4 Chirality restraints: 4564 Sorted by residual: chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.45 -0.95 2.00e-02 2.50e+03 2.24e+03 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.45 -0.95 2.00e-02 2.50e+03 2.24e+03 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 6.91e+01 ... (remaining 4561 not shown) Planarity restraints: 5138 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 103 " -0.041 2.00e-02 2.50e+03 4.79e-02 2.87e+01 pdb=" CG ASN B 103 " 0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN B 103 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN B 103 " 0.078 2.00e-02 2.50e+03 pdb=" C1 NAG J 1 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 103 " -0.041 2.00e-02 2.50e+03 4.79e-02 2.87e+01 pdb=" CG ASN D 103 " 0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN D 103 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN D 103 " 0.078 2.00e-02 2.50e+03 pdb=" C1 NAG S 1 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 492 " -0.068 5.00e-02 4.00e+02 9.96e-02 1.59e+01 pdb=" N PRO A 493 " 0.172 5.00e-02 4.00e+02 pdb=" CA PRO A 493 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 493 " -0.059 5.00e-02 4.00e+02 ... (remaining 5135 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 294 2.57 - 3.15: 22710 3.15 - 3.73: 44541 3.73 - 4.32: 63463 4.32 - 4.90: 104591 Nonbonded interactions: 235599 Sorted by model distance: nonbonded pdb=" O ASN H 31 " pdb=" ND1 HIS H 32 " model vdw 1.986 3.120 nonbonded pdb=" O ASN I 31 " pdb=" ND1 HIS I 32 " model vdw 1.986 3.120 nonbonded pdb=" O ASN K 137 " pdb=" O ASN K 138 " model vdw 2.038 3.040 nonbonded pdb=" O ASN M 137 " pdb=" O ASN M 138 " model vdw 2.038 3.040 nonbonded pdb=" O GLN D 18 " pdb=" OG SER D 19 " model vdw 2.117 3.040 ... (remaining 235594 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } ncs_group { reference = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'K' selection = chain 'M' } 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: 0.010 Normalize map: mean=0, sd=1: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 25.360 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 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 : 0.007 0.154 29900 Z= 0.348 Angle : 1.119 52.439 40766 Z= 0.601 Chirality : 0.068 0.986 4564 Planarity : 0.007 0.100 5114 Dihedral : 15.530 89.865 11290 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 21.49 Ramachandran Plot: Outliers : 1.90 % Allowed : 9.30 % Favored : 88.80 % Rotamer: Outliers : 5.08 % Allowed : 8.89 % Favored : 86.02 % Cbeta Deviations : 0.06 % 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: -5.19 (0.11), residues: 3570 helix: -4.31 (0.06), residues: 1606 sheet: -1.35 (0.22), residues: 454 loop : -2.92 (0.14), residues: 1510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 366 TYR 0.022 0.002 TYR C 560 PHE 0.015 0.002 PHE B 683 TRP 0.048 0.002 TRP H 99 HIS 0.006 0.001 HIS H 208 Details of bonding type rmsd covalent geometry : bond 0.00668 (29844) covalent geometry : angle 0.97169 (40616) SS BOND : bond 0.00601 ( 18) SS BOND : angle 1.23391 ( 36) hydrogen bonds : bond 0.29371 ( 1228) hydrogen bonds : angle 9.83915 ( 3618) link_BETA1-4 : bond 0.01976 ( 14) link_BETA1-4 : angle 16.07942 ( 42) link_NAG-ASN : bond 0.04798 ( 24) link_NAG-ASN : angle 4.98102 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 539 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6053 (tp30) REVERT: A 386 ASN cc_start: 0.6477 (m110) cc_final: 0.6133 (t0) REVERT: A 430 SER cc_start: 0.6194 (OUTLIER) cc_final: 0.5958 (m) REVERT: B 171 GLU cc_start: 0.5068 (OUTLIER) cc_final: 0.4532 (mt-10) REVERT: B 175 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7418 (mm-40) REVERT: B 678 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.5412 (tpt170) REVERT: H 31 ASN cc_start: 0.8328 (t0) cc_final: 0.7884 (t0) REVERT: H 64 PHE cc_start: 0.6345 (m-80) cc_final: 0.5783 (m-10) REVERT: H 152 ASP cc_start: 0.7694 (m-30) cc_final: 0.7445 (p0) REVERT: H 163 ASN cc_start: 0.5792 (m-40) cc_final: 0.5391 (t0) REVERT: H 164 SER cc_start: 0.6974 (OUTLIER) cc_final: 0.6408 (p) REVERT: H 174 PHE cc_start: -0.0343 (m-80) cc_final: -0.0756 (m-80) REVERT: H 222 LYS cc_start: -0.1379 (OUTLIER) cc_final: -0.2080 (mtmm) REVERT: K 70 ASP cc_start: 0.6493 (m-30) cc_final: 0.6231 (p0) REVERT: K 98 PHE cc_start: 0.6008 (m-80) cc_final: 0.5685 (m-10) REVERT: C 352 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6052 (tp30) REVERT: C 386 ASN cc_start: 0.6479 (m110) cc_final: 0.6136 (t0) REVERT: C 430 SER cc_start: 0.6198 (OUTLIER) cc_final: 0.5961 (m) REVERT: D 171 GLU cc_start: 0.5070 (OUTLIER) cc_final: 0.4535 (mt-10) REVERT: D 175 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7418 (mm-40) REVERT: D 678 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.5410 (tpt170) REVERT: I 31 ASN cc_start: 0.8329 (t0) cc_final: 0.7885 (t0) REVERT: I 64 PHE cc_start: 0.6339 (m-80) cc_final: 0.5774 (m-10) REVERT: I 152 ASP cc_start: 0.7690 (m-30) cc_final: 0.7439 (p0) REVERT: I 163 ASN cc_start: 0.5795 (m-40) cc_final: 0.5395 (t0) REVERT: I 164 SER cc_start: 0.6976 (OUTLIER) cc_final: 0.6413 (p) REVERT: I 174 PHE cc_start: -0.0348 (m-80) cc_final: -0.0758 (m-80) REVERT: I 222 LYS cc_start: -0.1384 (OUTLIER) cc_final: -0.2083 (mtmm) REVERT: M 70 ASP cc_start: 0.6499 (m-30) cc_final: 0.6237 (p0) REVERT: M 98 PHE cc_start: 0.6008 (m-80) cc_final: 0.5688 (m-10) outliers start: 160 outliers final: 26 residues processed: 667 average time/residue: 0.1897 time to fit residues: 201.0890 Evaluate side-chains 319 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 279 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 678 ARG Chi-restraints excluded: chain B residue 758 VAL Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 763 THR Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain H residue 211 SER Chi-restraints excluded: chain H residue 222 LYS Chi-restraints excluded: chain H residue 223 SER Chi-restraints excluded: chain K residue 142 ARG Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 175 GLN Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 678 ARG Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 759 ILE Chi-restraints excluded: chain D residue 763 THR Chi-restraints excluded: chain I residue 103 ASP Chi-restraints excluded: chain I residue 106 TRP Chi-restraints excluded: chain I residue 146 LEU Chi-restraints excluded: chain I residue 164 SER Chi-restraints excluded: chain I residue 211 SER Chi-restraints excluded: chain I residue 222 LYS Chi-restraints excluded: chain I residue 223 SER Chi-restraints excluded: chain M residue 142 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.0870 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 3.9990 overall best weight: 3.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 94 GLN A 293 ASN A 297 ASN A 340 ASN A 357 GLN A 364 GLN A 574 GLN B 24 GLN B 33 ASN B 61 ASN B 101 GLN B 117 ASN B 139 GLN B 175 GLN B 194 ASN B 239 HIS B 250 ASN B 277 ASN B 373 HIS B 505 HIS B 586 ASN B 599 ASN ** H 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 ASN ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 GLN C 94 GLN C 293 ASN C 297 ASN C 340 ASN C 357 GLN C 364 GLN C 574 GLN D 24 GLN D 33 ASN D 61 ASN D 101 GLN D 117 ASN D 139 GLN D 175 GLN D 194 ASN D 239 HIS D 250 ASN D 277 ASN D 373 HIS D 505 HIS D 586 ASN D 599 ASN ** I 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 35 ASN ** M 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.147896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.099017 restraints weight = 64644.528| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 3.37 r_work: 0.2992 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 29900 Z= 0.260 Angle : 0.819 11.406 40766 Z= 0.414 Chirality : 0.050 0.468 4564 Planarity : 0.006 0.051 5114 Dihedral : 8.314 72.034 4744 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.01 % Favored : 91.60 % Rotamer: Outliers : 3.62 % Allowed : 13.79 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.28 (0.12), residues: 3570 helix: -2.08 (0.11), residues: 1680 sheet: -0.60 (0.22), residues: 480 loop : -2.73 (0.15), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 169 TYR 0.020 0.002 TYR B 385 PHE 0.019 0.002 PHE I 29 TRP 0.030 0.002 TRP I 99 HIS 0.007 0.002 HIS I 32 Details of bonding type rmsd covalent geometry : bond 0.00608 (29844) covalent geometry : angle 0.79924 (40616) SS BOND : bond 0.00509 ( 18) SS BOND : angle 1.10348 ( 36) hydrogen bonds : bond 0.06559 ( 1228) hydrogen bonds : angle 5.33984 ( 3618) link_BETA1-4 : bond 0.00617 ( 14) link_BETA1-4 : angle 3.31718 ( 42) link_NAG-ASN : bond 0.00608 ( 24) link_NAG-ASN : angle 3.49430 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 292 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.6966 (pt) REVERT: A 119 MET cc_start: 0.7041 (ttt) cc_final: 0.6557 (mtm) REVERT: A 279 PHE cc_start: 0.6701 (m-10) cc_final: 0.6445 (m-10) REVERT: A 331 GLN cc_start: 0.8028 (tp40) cc_final: 0.7741 (tm-30) REVERT: A 403 PHE cc_start: 0.8304 (OUTLIER) cc_final: 0.7997 (m-80) REVERT: A 543 LEU cc_start: 0.7590 (pp) cc_final: 0.7297 (mt) REVERT: B 171 GLU cc_start: 0.6736 (OUTLIER) cc_final: 0.6432 (mm-30) REVERT: B 325 GLN cc_start: 0.8491 (tm-30) cc_final: 0.8191 (tm-30) REVERT: H 31 ASN cc_start: 0.8085 (t0) cc_final: 0.7669 (t0) REVERT: H 37 MET cc_start: 0.7977 (mpp) cc_final: 0.7707 (mpp) REVERT: H 74 ARG cc_start: 0.6605 (ttm110) cc_final: 0.6049 (mtm180) REVERT: H 163 ASN cc_start: 0.6738 (m-40) cc_final: 0.6505 (t0) REVERT: H 174 PHE cc_start: -0.0471 (m-80) cc_final: -0.0809 (m-80) REVERT: H 202 TYR cc_start: 0.1286 (m-80) cc_final: 0.0991 (m-80) REVERT: K 70 ASP cc_start: 0.6989 (m-30) cc_final: 0.6303 (p0) REVERT: K 98 PHE cc_start: 0.6272 (m-80) cc_final: 0.5563 (m-80) REVERT: K 110 VAL cc_start: 0.5768 (OUTLIER) cc_final: 0.5414 (t) REVERT: K 198 HIS cc_start: 0.3990 (t-90) cc_final: 0.3496 (t70) REVERT: C 101 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.6964 (pt) REVERT: C 119 MET cc_start: 0.7037 (ttt) cc_final: 0.6555 (mtm) REVERT: C 279 PHE cc_start: 0.6704 (m-10) cc_final: 0.6449 (m-10) REVERT: C 331 GLN cc_start: 0.8031 (tp40) cc_final: 0.7742 (tm-30) REVERT: C 403 PHE cc_start: 0.8298 (OUTLIER) cc_final: 0.7993 (m-80) REVERT: C 543 LEU cc_start: 0.7592 (pp) cc_final: 0.7300 (mt) REVERT: D 171 GLU cc_start: 0.6727 (OUTLIER) cc_final: 0.6418 (mm-30) REVERT: D 325 GLN cc_start: 0.8484 (tm-30) cc_final: 0.8183 (tm-30) REVERT: I 31 ASN cc_start: 0.8089 (t0) cc_final: 0.7670 (t0) REVERT: I 37 MET cc_start: 0.7975 (mpp) cc_final: 0.7705 (mpp) REVERT: I 74 ARG cc_start: 0.6605 (ttm110) cc_final: 0.6046 (mtm180) REVERT: I 163 ASN cc_start: 0.6740 (m-40) cc_final: 0.6515 (t0) REVERT: I 174 PHE cc_start: -0.0453 (m-80) cc_final: -0.0802 (m-80) REVERT: I 202 TYR cc_start: 0.1302 (m-80) cc_final: 0.1003 (m-80) REVERT: M 70 ASP cc_start: 0.6984 (m-30) cc_final: 0.6301 (p0) REVERT: M 98 PHE cc_start: 0.6266 (m-80) cc_final: 0.5555 (m-80) REVERT: M 110 VAL cc_start: 0.5759 (OUTLIER) cc_final: 0.5403 (t) REVERT: M 198 HIS cc_start: 0.3998 (t-90) cc_final: 0.3503 (t70) outliers start: 114 outliers final: 61 residues processed: 386 average time/residue: 0.1931 time to fit residues: 120.9403 Evaluate side-chains 309 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 240 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 692 SER Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 762 PHE Chi-restraints excluded: chain H residue 5 GLU Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain H residue 135 SER Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 223 SER Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain K residue 110 VAL Chi-restraints excluded: chain K residue 142 ARG Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 403 PHE Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 175 GLN Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 692 SER Chi-restraints excluded: chain D residue 759 ILE Chi-restraints excluded: chain D residue 762 PHE Chi-restraints excluded: chain I residue 5 GLU Chi-restraints excluded: chain I residue 100 ARG Chi-restraints excluded: chain I residue 103 ASP Chi-restraints excluded: chain I residue 106 TRP Chi-restraints excluded: chain I residue 135 SER Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 146 LEU Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 223 SER Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 142 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 308 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 307 optimal weight: 0.8980 chunk 272 optimal weight: 1.9990 chunk 265 optimal weight: 1.9990 chunk 319 optimal weight: 9.9990 chunk 251 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 61 ASN ** H 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 166 GLN ** 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 = 0.148378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.096683 restraints weight = 64773.849| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 3.17 r_work: 0.3017 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 29900 Z= 0.158 Angle : 0.709 13.077 40766 Z= 0.351 Chirality : 0.045 0.401 4564 Planarity : 0.004 0.054 5114 Dihedral : 7.164 71.149 4708 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.95 % Favored : 92.72 % Rotamer: Outliers : 2.99 % Allowed : 14.77 % Favored : 82.24 % 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: -2.11 (0.13), residues: 3570 helix: -0.82 (0.12), residues: 1662 sheet: -0.41 (0.22), residues: 504 loop : -2.42 (0.15), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 513 TYR 0.033 0.001 TYR C 578 PHE 0.022 0.002 PHE I 154 TRP 0.019 0.001 TRP I 99 HIS 0.005 0.001 HIS I 172 Details of bonding type rmsd covalent geometry : bond 0.00355 (29844) covalent geometry : angle 0.68847 (40616) SS BOND : bond 0.00719 ( 18) SS BOND : angle 0.91035 ( 36) hydrogen bonds : bond 0.05087 ( 1228) hydrogen bonds : angle 4.79610 ( 3618) link_BETA1-4 : bond 0.00250 ( 14) link_BETA1-4 : angle 3.47803 ( 42) link_NAG-ASN : bond 0.00564 ( 24) link_NAG-ASN : angle 3.12693 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 273 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.8423 (ptp) cc_final: 0.8077 (ptm) REVERT: A 331 GLN cc_start: 0.8039 (tp40) cc_final: 0.7748 (tm-30) REVERT: A 403 PHE cc_start: 0.8272 (OUTLIER) cc_final: 0.8014 (m-80) REVERT: A 542 MET cc_start: 0.5022 (ttp) cc_final: 0.4754 (ttp) REVERT: A 543 LEU cc_start: 0.7870 (pp) cc_final: 0.7662 (mt) REVERT: B 662 MET cc_start: 0.8265 (tmm) cc_final: 0.8054 (tmm) REVERT: H 31 ASN cc_start: 0.8191 (t0) cc_final: 0.7793 (t0) REVERT: H 154 PHE cc_start: 0.6617 (t80) cc_final: 0.6253 (t80) REVERT: H 163 ASN cc_start: 0.7003 (m-40) cc_final: 0.6761 (t0) REVERT: H 174 PHE cc_start: -0.0884 (m-80) cc_final: -0.1136 (m-80) REVERT: H 202 TYR cc_start: 0.1304 (m-80) cc_final: 0.1006 (m-80) REVERT: K 70 ASP cc_start: 0.6942 (m-30) cc_final: 0.6477 (p0) REVERT: C 137 MET cc_start: 0.8426 (ptp) cc_final: 0.8080 (ptm) REVERT: C 331 GLN cc_start: 0.8041 (tp40) cc_final: 0.7753 (tm-30) REVERT: C 403 PHE cc_start: 0.8277 (OUTLIER) cc_final: 0.8020 (m-80) REVERT: C 542 MET cc_start: 0.5025 (ttp) cc_final: 0.4757 (ttp) REVERT: C 543 LEU cc_start: 0.7869 (pp) cc_final: 0.7664 (mt) REVERT: D 61 ASN cc_start: 0.8870 (t0) cc_final: 0.8668 (t0) REVERT: D 662 MET cc_start: 0.8256 (tmm) cc_final: 0.8047 (tmm) REVERT: I 31 ASN cc_start: 0.8187 (t0) cc_final: 0.7783 (t0) REVERT: I 154 PHE cc_start: 0.6612 (t80) cc_final: 0.6251 (t80) REVERT: I 163 ASN cc_start: 0.7015 (m-40) cc_final: 0.6775 (t0) REVERT: I 174 PHE cc_start: -0.0885 (m-80) cc_final: -0.1140 (m-80) REVERT: I 202 TYR cc_start: 0.1303 (m-80) cc_final: 0.1007 (m-80) REVERT: M 70 ASP cc_start: 0.6935 (m-30) cc_final: 0.6474 (p0) outliers start: 94 outliers final: 56 residues processed: 347 average time/residue: 0.1977 time to fit residues: 109.8623 Evaluate side-chains 304 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 246 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 692 SER Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 762 PHE Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 99 TRP Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain H residue 135 SER Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain K residue 61 ARG Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain K residue 142 ARG Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 403 PHE Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain D residue 175 GLN Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 692 SER Chi-restraints excluded: chain D residue 759 ILE Chi-restraints excluded: chain D residue 762 PHE Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 99 TRP Chi-restraints excluded: chain I residue 100 ARG Chi-restraints excluded: chain I residue 106 TRP Chi-restraints excluded: chain I residue 135 SER Chi-restraints excluded: chain I residue 146 LEU Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain M residue 142 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 115 optimal weight: 1.9990 chunk 334 optimal weight: 30.0000 chunk 20 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 200 optimal weight: 0.9980 chunk 91 optimal weight: 0.0060 chunk 199 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 139 optimal weight: 8.9990 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 179 GLN ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 198 HIS ** 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 = 0.4268 r_free = 0.4268 target = 0.148245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.096360 restraints weight = 64186.431| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 3.32 r_work: 0.3034 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29900 Z= 0.131 Angle : 0.648 11.759 40766 Z= 0.323 Chirality : 0.044 0.381 4564 Planarity : 0.004 0.051 5114 Dihedral : 6.643 68.960 4696 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.28 % Favored : 92.44 % Rotamer: Outliers : 3.24 % Allowed : 15.06 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.14), residues: 3570 helix: -0.10 (0.13), residues: 1648 sheet: -0.14 (0.22), residues: 510 loop : -2.15 (0.16), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 13 TYR 0.014 0.001 TYR A 567 PHE 0.013 0.001 PHE I 29 TRP 0.017 0.001 TRP I 99 HIS 0.010 0.001 HIS A 108 Details of bonding type rmsd covalent geometry : bond 0.00291 (29844) covalent geometry : angle 0.62946 (40616) SS BOND : bond 0.00310 ( 18) SS BOND : angle 1.04720 ( 36) hydrogen bonds : bond 0.04337 ( 1228) hydrogen bonds : angle 4.49883 ( 3618) link_BETA1-4 : bond 0.00276 ( 14) link_BETA1-4 : angle 3.07801 ( 42) link_NAG-ASN : bond 0.00542 ( 24) link_NAG-ASN : angle 2.86455 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 254 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.6778 (mtp) cc_final: 0.6523 (mtp) REVERT: A 137 MET cc_start: 0.8416 (ptp) cc_final: 0.8067 (ptm) REVERT: A 237 PHE cc_start: 0.6694 (OUTLIER) cc_final: 0.6135 (t80) REVERT: A 279 PHE cc_start: 0.6373 (m-10) cc_final: 0.6107 (m-10) REVERT: A 331 GLN cc_start: 0.8009 (tp40) cc_final: 0.7756 (tm-30) REVERT: A 446 LEU cc_start: 0.6822 (OUTLIER) cc_final: 0.6599 (tt) REVERT: B 37 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.7881 (tm-30) REVERT: B 61 ASN cc_start: 0.8888 (t0) cc_final: 0.8676 (t0) REVERT: B 175 GLN cc_start: 0.9043 (OUTLIER) cc_final: 0.8723 (mt0) REVERT: B 662 MET cc_start: 0.8344 (tmm) cc_final: 0.8045 (tmm) REVERT: H 31 ASN cc_start: 0.8152 (t0) cc_final: 0.7738 (t0) REVERT: H 154 PHE cc_start: 0.6836 (t80) cc_final: 0.6586 (t80) REVERT: H 163 ASN cc_start: 0.7026 (m-40) cc_final: 0.6803 (t0) REVERT: H 174 PHE cc_start: -0.0894 (m-80) cc_final: -0.1187 (m-80) REVERT: K 33 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7617 (tt) REVERT: K 45 ARG cc_start: 0.8330 (mmm160) cc_final: 0.8092 (mmm160) REVERT: K 70 ASP cc_start: 0.6933 (m-30) cc_final: 0.6390 (p0) REVERT: K 198 HIS cc_start: 0.3485 (t70) cc_final: 0.2644 (t70) REVERT: C 119 MET cc_start: 0.6777 (mtp) cc_final: 0.6523 (mtp) REVERT: C 137 MET cc_start: 0.8415 (ptp) cc_final: 0.8069 (ptm) REVERT: C 237 PHE cc_start: 0.6702 (OUTLIER) cc_final: 0.6141 (t80) REVERT: C 279 PHE cc_start: 0.6384 (m-10) cc_final: 0.6122 (m-10) REVERT: C 331 GLN cc_start: 0.8016 (tp40) cc_final: 0.7761 (tm-30) REVERT: C 446 LEU cc_start: 0.6821 (OUTLIER) cc_final: 0.6599 (tt) REVERT: D 37 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.7875 (tm-30) REVERT: D 61 ASN cc_start: 0.8895 (t0) cc_final: 0.8661 (t0) REVERT: D 175 GLN cc_start: 0.9041 (OUTLIER) cc_final: 0.8723 (mt0) REVERT: D 662 MET cc_start: 0.8336 (tmm) cc_final: 0.8040 (tmm) REVERT: I 31 ASN cc_start: 0.8153 (t0) cc_final: 0.7737 (t0) REVERT: I 154 PHE cc_start: 0.6836 (t80) cc_final: 0.6585 (t80) REVERT: I 163 ASN cc_start: 0.7033 (m-40) cc_final: 0.6811 (t0) REVERT: I 174 PHE cc_start: -0.0893 (m-80) cc_final: -0.1186 (m-80) REVERT: M 33 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7616 (tt) REVERT: M 45 ARG cc_start: 0.8349 (mmm160) cc_final: 0.8106 (mmm160) REVERT: M 70 ASP cc_start: 0.6923 (m-30) cc_final: 0.6386 (p0) REVERT: M 198 HIS cc_start: 0.3486 (t70) cc_final: 0.2647 (t70) outliers start: 102 outliers final: 62 residues processed: 346 average time/residue: 0.1915 time to fit residues: 107.8101 Evaluate side-chains 292 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 220 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 237 PHE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 501 GLU Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 692 SER Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 762 PHE Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 99 TRP Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain H residue 135 SER Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 61 ARG Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain K residue 142 ARG Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 237 PHE Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 385 ILE Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 501 GLU Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 175 GLN Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 692 SER Chi-restraints excluded: chain D residue 759 ILE Chi-restraints excluded: chain D residue 762 PHE Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 99 TRP Chi-restraints excluded: chain I residue 106 TRP Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 135 SER Chi-restraints excluded: chain I residue 146 LEU Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain M residue 32 TYR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain M residue 142 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 56 optimal weight: 0.2980 chunk 238 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 138 optimal weight: 20.0000 chunk 113 optimal weight: 0.5980 chunk 135 optimal weight: 7.9990 chunk 303 optimal weight: 1.9990 chunk 150 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 318 optimal weight: 4.9990 chunk 347 optimal weight: 8.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 179 GLN ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 198 HIS ** 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 = 0.4247 r_free = 0.4247 target = 0.146706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.094976 restraints weight = 64139.692| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 3.28 r_work: 0.3000 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 29900 Z= 0.162 Angle : 0.662 11.326 40766 Z= 0.329 Chirality : 0.044 0.371 4564 Planarity : 0.004 0.056 5114 Dihedral : 6.341 61.323 4696 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.28 % Favored : 92.49 % Rotamer: Outliers : 3.18 % Allowed : 16.26 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.14), residues: 3570 helix: 0.16 (0.13), residues: 1652 sheet: -0.02 (0.22), residues: 512 loop : -2.05 (0.16), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 13 TYR 0.024 0.001 TYR A 567 PHE 0.012 0.001 PHE B 684 TRP 0.019 0.001 TRP I 99 HIS 0.011 0.001 HIS A 108 Details of bonding type rmsd covalent geometry : bond 0.00374 (29844) covalent geometry : angle 0.64438 (40616) SS BOND : bond 0.00432 ( 18) SS BOND : angle 1.30400 ( 36) hydrogen bonds : bond 0.04390 ( 1228) hydrogen bonds : angle 4.44738 ( 3618) link_BETA1-4 : bond 0.00214 ( 14) link_BETA1-4 : angle 2.96242 ( 42) link_NAG-ASN : bond 0.00530 ( 24) link_NAG-ASN : angle 2.75951 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 240 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.8461 (ptp) cc_final: 0.8104 (ptm) REVERT: A 237 PHE cc_start: 0.6540 (OUTLIER) cc_final: 0.6166 (t80) REVERT: A 398 LEU cc_start: 0.9159 (tp) cc_final: 0.8759 (tt) REVERT: A 487 SER cc_start: 0.1945 (OUTLIER) cc_final: 0.1596 (p) REVERT: B 37 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8171 (tp30) REVERT: B 61 ASN cc_start: 0.8951 (t0) cc_final: 0.8676 (t0) REVERT: H 31 ASN cc_start: 0.8211 (t0) cc_final: 0.7799 (t0) REVERT: H 163 ASN cc_start: 0.6964 (m-40) cc_final: 0.6555 (t0) REVERT: H 174 PHE cc_start: -0.0844 (m-80) cc_final: -0.1070 (m-80) REVERT: K 33 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7622 (tt) REVERT: K 45 ARG cc_start: 0.8332 (mmm160) cc_final: 0.8111 (mmm160) REVERT: K 61 ARG cc_start: 0.6405 (OUTLIER) cc_final: 0.6026 (ptp90) REVERT: K 70 ASP cc_start: 0.6983 (m-30) cc_final: 0.6363 (p0) REVERT: K 82 ASP cc_start: 0.5130 (m-30) cc_final: 0.4837 (m-30) REVERT: C 137 MET cc_start: 0.8463 (ptp) cc_final: 0.8110 (ptm) REVERT: C 237 PHE cc_start: 0.6541 (OUTLIER) cc_final: 0.6170 (t80) REVERT: C 398 LEU cc_start: 0.9156 (tp) cc_final: 0.8739 (tt) REVERT: C 487 SER cc_start: 0.1944 (OUTLIER) cc_final: 0.1594 (p) REVERT: D 37 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8175 (tp30) REVERT: D 61 ASN cc_start: 0.8963 (t0) cc_final: 0.8663 (t0) REVERT: I 31 ASN cc_start: 0.8214 (t0) cc_final: 0.7800 (t0) REVERT: I 163 ASN cc_start: 0.6964 (m-40) cc_final: 0.6554 (t0) REVERT: I 174 PHE cc_start: -0.0860 (m-80) cc_final: -0.1076 (m-80) REVERT: M 33 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7624 (tt) REVERT: M 45 ARG cc_start: 0.8340 (mmm160) cc_final: 0.8116 (mmm160) REVERT: M 61 ARG cc_start: 0.6410 (OUTLIER) cc_final: 0.6031 (ptp90) REVERT: M 70 ASP cc_start: 0.6972 (m-30) cc_final: 0.6357 (p0) REVERT: M 82 ASP cc_start: 0.5121 (m-30) cc_final: 0.4829 (m-30) outliers start: 100 outliers final: 70 residues processed: 326 average time/residue: 0.1885 time to fit residues: 101.0293 Evaluate side-chains 296 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 216 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 237 PHE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 501 GLU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 578 TYR Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 692 SER Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 762 PHE Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 99 TRP Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain H residue 135 SER Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 61 ARG Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 237 PHE Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 501 GLU Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 578 TYR Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 692 SER Chi-restraints excluded: chain D residue 759 ILE Chi-restraints excluded: chain D residue 762 PHE Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 99 TRP Chi-restraints excluded: chain I residue 106 TRP Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 135 SER Chi-restraints excluded: chain I residue 146 LEU Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain M residue 32 TYR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 106 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 8 optimal weight: 10.0000 chunk 334 optimal weight: 20.0000 chunk 267 optimal weight: 0.4980 chunk 111 optimal weight: 5.9990 chunk 86 optimal weight: 0.3980 chunk 300 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 257 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 335 optimal weight: 30.0000 chunk 134 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 GLN H 32 HIS ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 GLN I 32 HIS ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.148068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.096889 restraints weight = 64446.549| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 3.42 r_work: 0.3027 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 29900 Z= 0.115 Angle : 0.628 11.084 40766 Z= 0.311 Chirality : 0.043 0.357 4564 Planarity : 0.004 0.054 5114 Dihedral : 5.648 58.224 4682 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.03 % Favored : 92.86 % Rotamer: Outliers : 2.86 % Allowed : 17.09 % Favored : 80.05 % 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: -0.82 (0.14), residues: 3570 helix: 0.39 (0.13), residues: 1652 sheet: 0.14 (0.22), residues: 504 loop : -1.93 (0.17), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 332 TYR 0.018 0.001 TYR A 578 PHE 0.011 0.001 PHE D 762 TRP 0.017 0.001 TRP I 99 HIS 0.010 0.001 HIS A 108 Details of bonding type rmsd covalent geometry : bond 0.00246 (29844) covalent geometry : angle 0.61173 (40616) SS BOND : bond 0.00342 ( 18) SS BOND : angle 0.75744 ( 36) hydrogen bonds : bond 0.03986 ( 1228) hydrogen bonds : angle 4.36289 ( 3618) link_BETA1-4 : bond 0.00279 ( 14) link_BETA1-4 : angle 2.84007 ( 42) link_NAG-ASN : bond 0.00533 ( 24) link_NAG-ASN : angle 2.62485 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 240 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.8467 (ptp) cc_final: 0.8117 (ptm) REVERT: A 237 PHE cc_start: 0.6366 (OUTLIER) cc_final: 0.6094 (t80) REVERT: A 398 LEU cc_start: 0.9104 (tp) cc_final: 0.8700 (tt) REVERT: A 487 SER cc_start: 0.1956 (OUTLIER) cc_final: 0.1621 (p) REVERT: B 37 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8191 (tp30) REVERT: B 61 ASN cc_start: 0.9024 (t0) cc_final: 0.8736 (t0) REVERT: H 163 ASN cc_start: 0.7132 (m-40) cc_final: 0.6864 (t0) REVERT: H 174 PHE cc_start: -0.0877 (m-80) cc_final: -0.1081 (m-80) REVERT: K 33 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7504 (tt) REVERT: K 45 ARG cc_start: 0.8336 (mmm160) cc_final: 0.8068 (mmm160) REVERT: K 142 ARG cc_start: 0.4611 (OUTLIER) cc_final: 0.3996 (tpp-160) REVERT: K 198 HIS cc_start: 0.3599 (t70) cc_final: 0.2775 (t70) REVERT: C 137 MET cc_start: 0.8461 (ptp) cc_final: 0.8112 (ptm) REVERT: C 237 PHE cc_start: 0.6366 (OUTLIER) cc_final: 0.6092 (t80) REVERT: C 398 LEU cc_start: 0.9103 (tp) cc_final: 0.8701 (tt) REVERT: C 487 SER cc_start: 0.1955 (OUTLIER) cc_final: 0.1619 (p) REVERT: D 37 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8193 (tp30) REVERT: D 61 ASN cc_start: 0.8991 (t0) cc_final: 0.8685 (t0) REVERT: I 163 ASN cc_start: 0.7134 (m-40) cc_final: 0.6865 (t0) REVERT: I 174 PHE cc_start: -0.0876 (m-80) cc_final: -0.1086 (m-80) REVERT: M 33 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7506 (tt) REVERT: M 45 ARG cc_start: 0.8346 (mmm160) cc_final: 0.8075 (mmm160) REVERT: M 142 ARG cc_start: 0.4604 (OUTLIER) cc_final: 0.3988 (tpp-160) REVERT: M 198 HIS cc_start: 0.3585 (t70) cc_final: 0.2763 (t70) outliers start: 90 outliers final: 70 residues processed: 322 average time/residue: 0.1884 time to fit residues: 99.6618 Evaluate side-chains 294 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 214 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 237 PHE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 501 GLU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 578 TYR Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 692 SER Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 762 PHE Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 99 TRP Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain H residue 135 SER Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 61 ARG Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain K residue 142 ARG Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 237 PHE Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 385 ILE Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 501 GLU Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 578 TYR Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 692 SER Chi-restraints excluded: chain D residue 743 LEU Chi-restraints excluded: chain D residue 759 ILE Chi-restraints excluded: chain D residue 762 PHE Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 99 TRP Chi-restraints excluded: chain I residue 103 ASP Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 135 SER Chi-restraints excluded: chain I residue 146 LEU Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain M residue 32 TYR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain M residue 142 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 118 optimal weight: 0.0980 chunk 231 optimal weight: 6.9990 chunk 155 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 311 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 251 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 257 optimal weight: 6.9990 chunk 26 optimal weight: 8.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 24 GLN H 39 GLN K 38 GLN ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN I 39 GLN M 38 GLN ** M 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.146826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.095421 restraints weight = 64251.583| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 3.44 r_work: 0.2991 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.4476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29900 Z= 0.147 Angle : 0.648 10.377 40766 Z= 0.321 Chirality : 0.044 0.360 4564 Planarity : 0.004 0.057 5114 Dihedral : 5.223 47.823 4678 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.56 % Favored : 92.32 % Rotamer: Outliers : 3.49 % Allowed : 16.99 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.73 (0.14), residues: 3570 helix: 0.42 (0.13), residues: 1648 sheet: 0.41 (0.23), residues: 482 loop : -1.87 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 100 TYR 0.017 0.001 TYR A 578 PHE 0.013 0.001 PHE B 684 TRP 0.017 0.001 TRP H 99 HIS 0.011 0.001 HIS A 108 Details of bonding type rmsd covalent geometry : bond 0.00340 (29844) covalent geometry : angle 0.63275 (40616) SS BOND : bond 0.00312 ( 18) SS BOND : angle 1.43540 ( 36) hydrogen bonds : bond 0.04194 ( 1228) hydrogen bonds : angle 4.34066 ( 3618) link_BETA1-4 : bond 0.00281 ( 14) link_BETA1-4 : angle 2.71734 ( 42) link_NAG-ASN : bond 0.00524 ( 24) link_NAG-ASN : angle 2.58385 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 240 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.8568 (ptp) cc_final: 0.8199 (ptm) REVERT: A 237 PHE cc_start: 0.6440 (OUTLIER) cc_final: 0.6117 (t80) REVERT: A 302 ASP cc_start: 0.4660 (m-30) cc_final: 0.4031 (t0) REVERT: A 335 ASP cc_start: 0.8344 (m-30) cc_final: 0.8126 (t0) REVERT: A 398 LEU cc_start: 0.9132 (tp) cc_final: 0.8816 (tt) REVERT: A 487 SER cc_start: 0.2055 (OUTLIER) cc_final: 0.1715 (p) REVERT: B 37 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8253 (tp30) REVERT: B 61 ASN cc_start: 0.9028 (t0) cc_final: 0.8724 (t0) REVERT: H 106 TRP cc_start: 0.6739 (OUTLIER) cc_final: 0.5542 (m-90) REVERT: H 163 ASN cc_start: 0.7079 (m-40) cc_final: 0.6781 (t0) REVERT: K 33 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7551 (tt) REVERT: K 70 ASP cc_start: 0.6779 (m-30) cc_final: 0.6033 (p0) REVERT: K 142 ARG cc_start: 0.4476 (OUTLIER) cc_final: 0.4045 (tpp-160) REVERT: C 137 MET cc_start: 0.8572 (ptp) cc_final: 0.8203 (ptm) REVERT: C 237 PHE cc_start: 0.6440 (OUTLIER) cc_final: 0.6111 (t80) REVERT: C 302 ASP cc_start: 0.4660 (m-30) cc_final: 0.4025 (t0) REVERT: C 335 ASP cc_start: 0.8341 (m-30) cc_final: 0.8121 (t0) REVERT: C 398 LEU cc_start: 0.9128 (tp) cc_final: 0.8813 (tt) REVERT: C 487 SER cc_start: 0.2052 (OUTLIER) cc_final: 0.1711 (p) REVERT: D 37 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8263 (tp30) REVERT: D 61 ASN cc_start: 0.9052 (t0) cc_final: 0.8752 (t0) REVERT: I 106 TRP cc_start: 0.6740 (OUTLIER) cc_final: 0.5539 (m-90) REVERT: I 163 ASN cc_start: 0.7093 (m-40) cc_final: 0.6798 (t0) REVERT: M 33 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7554 (tt) REVERT: M 70 ASP cc_start: 0.6775 (m-30) cc_final: 0.6032 (p0) REVERT: M 142 ARG cc_start: 0.4471 (OUTLIER) cc_final: 0.4039 (tpp-160) outliers start: 110 outliers final: 74 residues processed: 336 average time/residue: 0.1785 time to fit residues: 98.4777 Evaluate side-chains 308 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 222 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 237 PHE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 578 TYR Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 680 SER Chi-restraints excluded: chain B residue 692 SER Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 762 PHE Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 99 TRP Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain H residue 135 SER Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 61 ARG Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain K residue 142 ARG Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 237 PHE Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 542 MET Chi-restraints excluded: chain C residue 578 TYR Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 680 SER Chi-restraints excluded: chain D residue 692 SER Chi-restraints excluded: chain D residue 743 LEU Chi-restraints excluded: chain D residue 762 PHE Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 99 TRP Chi-restraints excluded: chain I residue 103 ASP Chi-restraints excluded: chain I residue 106 TRP Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 135 SER Chi-restraints excluded: chain I residue 146 LEU Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain M residue 32 TYR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain M residue 142 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 50 optimal weight: 8.9990 chunk 226 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 168 optimal weight: 0.9990 chunk 100 optimal weight: 0.0030 chunk 328 optimal weight: 40.0000 chunk 350 optimal weight: 9.9990 chunk 342 optimal weight: 10.0000 chunk 164 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 137 optimal weight: 20.0000 overall best weight: 0.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 ASN ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 198 HIS ** 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 = 0.147569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.096781 restraints weight = 63837.946| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 3.49 r_work: 0.3011 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.4651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 29900 Z= 0.118 Angle : 0.627 9.833 40766 Z= 0.309 Chirality : 0.043 0.346 4564 Planarity : 0.004 0.054 5114 Dihedral : 4.975 47.590 4674 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.00 % Favored : 92.89 % Rotamer: Outliers : 2.99 % Allowed : 17.76 % Favored : 79.26 % 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: -0.50 (0.14), residues: 3570 helix: 0.60 (0.13), residues: 1658 sheet: 0.72 (0.24), residues: 438 loop : -1.77 (0.16), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 13 TYR 0.016 0.001 TYR A 578 PHE 0.012 0.001 PHE D 762 TRP 0.013 0.001 TRP H 99 HIS 0.011 0.001 HIS C 108 Details of bonding type rmsd covalent geometry : bond 0.00264 (29844) covalent geometry : angle 0.61406 (40616) SS BOND : bond 0.00323 ( 18) SS BOND : angle 0.67893 ( 36) hydrogen bonds : bond 0.03839 ( 1228) hydrogen bonds : angle 4.26332 ( 3618) link_BETA1-4 : bond 0.00269 ( 14) link_BETA1-4 : angle 2.53776 ( 42) link_NAG-ASN : bond 0.00517 ( 24) link_NAG-ASN : angle 2.48612 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 226 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.8539 (ptp) cc_final: 0.8183 (ptm) REVERT: A 237 PHE cc_start: 0.6366 (OUTLIER) cc_final: 0.6117 (t80) REVERT: A 302 ASP cc_start: 0.4851 (m-30) cc_final: 0.4190 (t0) REVERT: A 335 ASP cc_start: 0.8314 (m-30) cc_final: 0.8086 (t0) REVERT: A 398 LEU cc_start: 0.9069 (tp) cc_final: 0.8749 (tt) REVERT: A 487 SER cc_start: 0.2657 (OUTLIER) cc_final: 0.2359 (p) REVERT: A 578 TYR cc_start: 0.4956 (OUTLIER) cc_final: 0.4747 (m-80) REVERT: B 37 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.7988 (tm-30) REVERT: B 61 ASN cc_start: 0.9025 (t0) cc_final: 0.8726 (t0) REVERT: H 31 ASN cc_start: 0.8319 (t0) cc_final: 0.7869 (t0) REVERT: H 106 TRP cc_start: 0.6696 (OUTLIER) cc_final: 0.5516 (m-90) REVERT: H 163 ASN cc_start: 0.7131 (m-40) cc_final: 0.6872 (t0) REVERT: K 33 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7555 (tt) REVERT: K 70 ASP cc_start: 0.6844 (m-30) cc_final: 0.6037 (p0) REVERT: K 198 HIS cc_start: 0.3734 (t70) cc_final: 0.2909 (t70) REVERT: C 137 MET cc_start: 0.8541 (ptp) cc_final: 0.8186 (ptm) REVERT: C 237 PHE cc_start: 0.6362 (OUTLIER) cc_final: 0.6116 (t80) REVERT: C 302 ASP cc_start: 0.4853 (m-30) cc_final: 0.4187 (t0) REVERT: C 335 ASP cc_start: 0.8312 (m-30) cc_final: 0.8081 (t0) REVERT: C 398 LEU cc_start: 0.9073 (tp) cc_final: 0.8754 (tt) REVERT: C 487 SER cc_start: 0.2653 (OUTLIER) cc_final: 0.2356 (p) REVERT: C 578 TYR cc_start: 0.4954 (OUTLIER) cc_final: 0.4745 (m-80) REVERT: D 37 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.7994 (tm-30) REVERT: D 61 ASN cc_start: 0.9036 (t0) cc_final: 0.8730 (t0) REVERT: I 31 ASN cc_start: 0.8318 (t0) cc_final: 0.7867 (t0) REVERT: I 106 TRP cc_start: 0.6692 (OUTLIER) cc_final: 0.5508 (m-90) REVERT: I 163 ASN cc_start: 0.7139 (m-40) cc_final: 0.6880 (t0) REVERT: M 33 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7557 (tt) REVERT: M 70 ASP cc_start: 0.6843 (m-30) cc_final: 0.6037 (p0) REVERT: M 198 HIS cc_start: 0.3725 (t70) cc_final: 0.2895 (t70) outliers start: 94 outliers final: 62 residues processed: 310 average time/residue: 0.1749 time to fit residues: 90.1906 Evaluate side-chains 294 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 220 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 PHE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 578 TYR Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 692 SER Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 762 PHE Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 99 TRP Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain H residue 135 SER Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 61 ARG Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain C residue 237 PHE Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 542 MET Chi-restraints excluded: chain C residue 578 TYR Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 692 SER Chi-restraints excluded: chain D residue 743 LEU Chi-restraints excluded: chain D residue 762 PHE Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 99 TRP Chi-restraints excluded: chain I residue 106 TRP Chi-restraints excluded: chain I residue 135 SER Chi-restraints excluded: chain I residue 146 LEU Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain M residue 32 TYR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 106 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 251 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 265 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 290 optimal weight: 0.9980 chunk 187 optimal weight: 9.9990 chunk 308 optimal weight: 3.9990 chunk 156 optimal weight: 50.0000 chunk 339 optimal weight: 2.9990 chunk 109 optimal weight: 0.3980 chunk 73 optimal weight: 4.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 63 ASN ** M 198 HIS ** 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 = 0.4253 r_free = 0.4253 target = 0.147108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.096530 restraints weight = 63873.910| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 3.40 r_work: 0.3004 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.4748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29900 Z= 0.128 Angle : 0.628 9.209 40766 Z= 0.311 Chirality : 0.043 0.346 4564 Planarity : 0.004 0.056 5114 Dihedral : 4.935 47.283 4674 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.34 % Favored : 92.55 % Rotamer: Outliers : 2.73 % Allowed : 17.92 % Favored : 79.35 % 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: -0.46 (0.14), residues: 3570 helix: 0.62 (0.13), residues: 1656 sheet: 0.74 (0.23), residues: 436 loop : -1.72 (0.16), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 142 TYR 0.018 0.001 TYR B 41 PHE 0.019 0.001 PHE I 174 TRP 0.014 0.001 TRP I 99 HIS 0.011 0.001 HIS C 108 Details of bonding type rmsd covalent geometry : bond 0.00292 (29844) covalent geometry : angle 0.61466 (40616) SS BOND : bond 0.00278 ( 18) SS BOND : angle 1.14449 ( 36) hydrogen bonds : bond 0.03870 ( 1228) hydrogen bonds : angle 4.24191 ( 3618) link_BETA1-4 : bond 0.00306 ( 14) link_BETA1-4 : angle 2.43714 ( 42) link_NAG-ASN : bond 0.00509 ( 24) link_NAG-ASN : angle 2.47021 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 230 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.8577 (ptp) cc_final: 0.8209 (ptm) REVERT: A 237 PHE cc_start: 0.6424 (OUTLIER) cc_final: 0.6144 (t80) REVERT: A 302 ASP cc_start: 0.4862 (m-30) cc_final: 0.4314 (t0) REVERT: A 398 LEU cc_start: 0.9064 (tp) cc_final: 0.8775 (tt) REVERT: A 487 SER cc_start: 0.2848 (OUTLIER) cc_final: 0.2579 (p) REVERT: A 578 TYR cc_start: 0.4883 (OUTLIER) cc_final: 0.4623 (m-80) REVERT: B 37 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8000 (tm-30) REVERT: B 61 ASN cc_start: 0.9052 (t0) cc_final: 0.8743 (t0) REVERT: H 31 ASN cc_start: 0.8328 (t0) cc_final: 0.7886 (t0) REVERT: H 106 TRP cc_start: 0.6768 (OUTLIER) cc_final: 0.5534 (m-90) REVERT: H 163 ASN cc_start: 0.7140 (m-40) cc_final: 0.6892 (t0) REVERT: H 202 TYR cc_start: 0.1317 (m-80) cc_final: 0.0991 (m-80) REVERT: K 33 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7557 (tt) REVERT: K 70 ASP cc_start: 0.6499 (m-30) cc_final: 0.5653 (p0) REVERT: K 198 HIS cc_start: 0.3852 (t70) cc_final: 0.3012 (t70) REVERT: C 137 MET cc_start: 0.8581 (ptp) cc_final: 0.8211 (ptm) REVERT: C 237 PHE cc_start: 0.6424 (OUTLIER) cc_final: 0.6146 (t80) REVERT: C 302 ASP cc_start: 0.4867 (m-30) cc_final: 0.4314 (t0) REVERT: C 398 LEU cc_start: 0.9064 (tp) cc_final: 0.8777 (tt) REVERT: C 487 SER cc_start: 0.2849 (OUTLIER) cc_final: 0.2579 (p) REVERT: C 578 TYR cc_start: 0.4882 (OUTLIER) cc_final: 0.4627 (m-80) REVERT: C 592 VAL cc_start: 0.2926 (OUTLIER) cc_final: 0.2667 (p) REVERT: D 37 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8003 (tm-30) REVERT: D 61 ASN cc_start: 0.9036 (t0) cc_final: 0.8719 (t0) REVERT: I 31 ASN cc_start: 0.8327 (t0) cc_final: 0.7882 (t0) REVERT: I 106 TRP cc_start: 0.6767 (OUTLIER) cc_final: 0.5530 (m-90) REVERT: I 163 ASN cc_start: 0.7149 (m-40) cc_final: 0.6903 (t0) REVERT: I 202 TYR cc_start: 0.1323 (m-80) cc_final: 0.0998 (m-80) REVERT: M 33 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7561 (tt) REVERT: M 70 ASP cc_start: 0.6492 (m-30) cc_final: 0.5649 (p0) REVERT: M 198 HIS cc_start: 0.3820 (t70) cc_final: 0.2976 (t70) outliers start: 86 outliers final: 65 residues processed: 304 average time/residue: 0.1793 time to fit residues: 90.8580 Evaluate side-chains 292 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 214 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 237 PHE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 578 TYR Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 692 SER Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 762 PHE Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 99 TRP Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain H residue 135 SER Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 61 ARG Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 237 PHE Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 578 TYR Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 692 SER Chi-restraints excluded: chain D residue 743 LEU Chi-restraints excluded: chain D residue 762 PHE Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 99 TRP Chi-restraints excluded: chain I residue 106 TRP Chi-restraints excluded: chain I residue 135 SER Chi-restraints excluded: chain I residue 146 LEU Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain M residue 32 TYR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 212 optimal weight: 2.9990 chunk 305 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 226 optimal weight: 1.9990 chunk 286 optimal weight: 3.9990 chunk 283 optimal weight: 0.8980 chunk 271 optimal weight: 8.9990 chunk 156 optimal weight: 0.9980 chunk 257 optimal weight: 0.7980 chunk 216 optimal weight: 10.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 63 ASN ** K 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 198 HIS ** 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 = 0.4256 r_free = 0.4256 target = 0.147329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.096734 restraints weight = 63614.439| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 3.30 r_work: 0.3021 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.4861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 29900 Z= 0.124 Angle : 0.627 8.960 40766 Z= 0.311 Chirality : 0.043 0.342 4564 Planarity : 0.004 0.054 5114 Dihedral : 4.867 46.664 4674 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.06 % Favored : 92.83 % Rotamer: Outliers : 2.70 % Allowed : 18.20 % Favored : 79.10 % 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: -0.37 (0.14), residues: 3570 helix: 0.70 (0.13), residues: 1662 sheet: 0.63 (0.23), residues: 448 loop : -1.67 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 142 TYR 0.020 0.001 TYR D 41 PHE 0.012 0.001 PHE B 762 TRP 0.014 0.001 TRP I 36 HIS 0.006 0.001 HIS K 198 Details of bonding type rmsd covalent geometry : bond 0.00280 (29844) covalent geometry : angle 0.61519 (40616) SS BOND : bond 0.00312 ( 18) SS BOND : angle 0.65931 ( 36) hydrogen bonds : bond 0.03803 ( 1228) hydrogen bonds : angle 4.23356 ( 3618) link_BETA1-4 : bond 0.00281 ( 14) link_BETA1-4 : angle 2.32752 ( 42) link_NAG-ASN : bond 0.00505 ( 24) link_NAG-ASN : angle 2.45049 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 220 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.8549 (ptp) cc_final: 0.8215 (ptm) REVERT: A 237 PHE cc_start: 0.6383 (OUTLIER) cc_final: 0.6151 (t80) REVERT: A 302 ASP cc_start: 0.4950 (m-30) cc_final: 0.4269 (t0) REVERT: A 398 LEU cc_start: 0.9070 (tp) cc_final: 0.8789 (tt) REVERT: A 574 GLN cc_start: 0.5424 (OUTLIER) cc_final: 0.5120 (mt0) REVERT: A 578 TYR cc_start: 0.4911 (OUTLIER) cc_final: 0.4646 (m-80) REVERT: A 592 VAL cc_start: 0.2798 (OUTLIER) cc_final: 0.2530 (p) REVERT: B 37 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.7982 (tm-30) REVERT: B 61 ASN cc_start: 0.9024 (t0) cc_final: 0.8699 (t0) REVERT: H 31 ASN cc_start: 0.8342 (t0) cc_final: 0.7862 (t0) REVERT: H 106 TRP cc_start: 0.6717 (OUTLIER) cc_final: 0.5410 (m-90) REVERT: H 163 ASN cc_start: 0.7079 (m-40) cc_final: 0.6735 (t0) REVERT: H 202 TYR cc_start: 0.1140 (m-80) cc_final: 0.0844 (m-80) REVERT: K 33 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7561 (tt) REVERT: K 70 ASP cc_start: 0.6436 (m-30) cc_final: 0.5644 (p0) REVERT: K 198 HIS cc_start: 0.3422 (t70) cc_final: 0.2497 (t70) REVERT: C 137 MET cc_start: 0.8548 (ptp) cc_final: 0.8215 (ptm) REVERT: C 237 PHE cc_start: 0.6376 (OUTLIER) cc_final: 0.6145 (t80) REVERT: C 302 ASP cc_start: 0.4946 (m-30) cc_final: 0.4263 (t0) REVERT: C 398 LEU cc_start: 0.9070 (tp) cc_final: 0.8791 (tt) REVERT: C 574 GLN cc_start: 0.5413 (OUTLIER) cc_final: 0.5114 (mt0) REVERT: C 578 TYR cc_start: 0.4913 (OUTLIER) cc_final: 0.4646 (m-80) REVERT: C 592 VAL cc_start: 0.2802 (OUTLIER) cc_final: 0.2533 (p) REVERT: D 37 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.7988 (tm-30) REVERT: D 61 ASN cc_start: 0.8998 (t0) cc_final: 0.8677 (t0) REVERT: I 31 ASN cc_start: 0.8345 (t0) cc_final: 0.7865 (t0) REVERT: I 106 TRP cc_start: 0.6712 (OUTLIER) cc_final: 0.5401 (m-90) REVERT: I 163 ASN cc_start: 0.7085 (m-40) cc_final: 0.6741 (t0) REVERT: I 202 TYR cc_start: 0.1153 (m-80) cc_final: 0.0856 (m-80) REVERT: M 33 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7562 (tt) REVERT: M 70 ASP cc_start: 0.6432 (m-30) cc_final: 0.5642 (p0) REVERT: M 198 HIS cc_start: 0.3415 (t70) cc_final: 0.2495 (t70) outliers start: 85 outliers final: 65 residues processed: 297 average time/residue: 0.1861 time to fit residues: 90.9736 Evaluate side-chains 289 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 210 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 237 PHE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 574 GLN Chi-restraints excluded: chain A residue 578 TYR Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 692 SER Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 762 PHE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 99 TRP Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain H residue 135 SER Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 61 ARG Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 237 PHE Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 574 GLN Chi-restraints excluded: chain C residue 578 TYR Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 692 SER Chi-restraints excluded: chain D residue 743 LEU Chi-restraints excluded: chain D residue 762 PHE Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 99 TRP Chi-restraints excluded: chain I residue 106 TRP Chi-restraints excluded: chain I residue 135 SER Chi-restraints excluded: chain I residue 146 LEU Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain M residue 32 TYR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 31 optimal weight: 2.9990 chunk 119 optimal weight: 0.1980 chunk 315 optimal weight: 20.0000 chunk 343 optimal weight: 9.9990 chunk 209 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 88 optimal weight: 9.9990 chunk 243 optimal weight: 7.9990 chunk 189 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 61 ASN K 147 GLN ** K 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 147 GLN ** M 198 HIS ** 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 = 0.4241 r_free = 0.4241 target = 0.146401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.095839 restraints weight = 64063.726| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 3.40 r_work: 0.2988 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.4992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 29900 Z= 0.148 Angle : 0.640 8.947 40766 Z= 0.318 Chirality : 0.043 0.344 4564 Planarity : 0.004 0.055 5114 Dihedral : 4.920 45.874 4672 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.39 % Favored : 92.55 % Rotamer: Outliers : 2.67 % Allowed : 18.27 % Favored : 79.07 % 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: -0.37 (0.14), residues: 3570 helix: 0.75 (0.13), residues: 1638 sheet: 0.64 (0.23), residues: 448 loop : -1.68 (0.16), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 142 TYR 0.020 0.001 TYR D 41 PHE 0.012 0.001 PHE D 684 TRP 0.016 0.001 TRP I 99 HIS 0.005 0.001 HIS K 198 Details of bonding type rmsd covalent geometry : bond 0.00342 (29844) covalent geometry : angle 0.62810 (40616) SS BOND : bond 0.00336 ( 18) SS BOND : angle 0.90361 ( 36) hydrogen bonds : bond 0.04046 ( 1228) hydrogen bonds : angle 4.28667 ( 3618) link_BETA1-4 : bond 0.00300 ( 14) link_BETA1-4 : angle 2.19761 ( 42) link_NAG-ASN : bond 0.00512 ( 24) link_NAG-ASN : angle 2.49297 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14645.06 seconds wall clock time: 248 minutes 56.42 seconds (14936.42 seconds total)