Starting phenix.real_space_refine on Fri Mar 6 19:06:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kj3_22892/03_2026/7kj3_22892_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kj3_22892/03_2026/7kj3_22892.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kj3_22892/03_2026/7kj3_22892.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kj3_22892/03_2026/7kj3_22892.map" model { file = "/net/cci-nas-00/data/ceres_data/7kj3_22892/03_2026/7kj3_22892_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kj3_22892/03_2026/7kj3_22892_neut.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 161 5.16 5 C 21421 2.51 5 N 5472 2.21 5 O 6589 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 221 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33643 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 7661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 981, 7661 Classifications: {'peptide': 981} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 48, 'TRANS': 932} Chain breaks: 10 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 7665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 981, 7665 Classifications: {'peptide': 981} Link IDs: {'PTRANS': 48, 'TRANS': 932} Chain breaks: 10 Chain: "C" Number of atoms: 7509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 961, 7509 Classifications: {'peptide': 961} Link IDs: {'PTRANS': 48, 'TRANS': 912} Chain breaks: 10 Chain: "D" Number of atoms: 4844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4844 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 27, 'TRANS': 565} Chain: "E" Number of atoms: 4844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4844 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 27, 'TRANS': 565} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "W" 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: "X" 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: "Y" 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: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.60, per 1000 atoms: 0.23 Number of scatterers: 33643 At special positions: 0 Unit cell: (134.475, 167.475, 234.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 161 16.00 O 6589 8.00 N 5472 7.00 C 21421 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.45 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.54 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.07 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.26 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.49 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.25 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.00 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.67 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.99 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.05 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.05 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.84 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.83 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.49 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.88 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.05 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.32 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.02 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.22 Simple disulfide: pdb=" SG CYS E 344 " - pdb=" SG CYS E 361 " distance=1.99 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.01 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 Atom "HETATM33403 O5 NAG B1310 .*. O " rejected from bonding due to valence issues. Atom "HETATM33165 O5 NAG A1306 .*. O " rejected from bonding due to valence issues. Atom "HETATM33277 O5 NAG B1301 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=2, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 343 " " NAG A1307 " - " ASN A 603 " " NAG A1308 " - " ASN A 616 " " NAG A1309 " - " ASN A 657 " " NAG A1310 " - " ASN A 709 " " NAG A1311 " - " ASN A 717 " " NAG A1312 " - " ASN A1074 " " NAG B1301 " - " ASN B 616 " " NAG B1302 " - " ASN B 657 " " NAG B1303 " - " ASN B 709 " " NAG B1304 " - " ASN B 717 " " NAG B1305 " - " ASN B1074 " " NAG B1307 " - " ASN B 61 " " NAG B1308 " - " ASN B 122 " " NAG B1309 " - " ASN B 234 " " NAG B1310 " - " ASN B 282 " " NAG B1311 " - " ASN B 331 " " NAG B1312 " - " ASN B 343 " " NAG B1313 " - " ASN B 603 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 603 " " NAG C1308 " - " ASN C 616 " " NAG C1309 " - " ASN C 657 " " NAG C1310 " - " ASN C 709 " " NAG C1311 " - " ASN C1074 " " NAG C1312 " - " ASN C 165 " " NAG D 701 " - " ASN D 322 " " NAG E 701 " - " ASN E 322 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 801 " " NAG J 1 " - " ASN B1098 " " NAG K 1 " - " ASN B1134 " " NAG L 1 " - " ASN C 717 " " NAG M 1 " - " ASN C 801 " " NAG N 1 " - " ASN C1098 " " NAG O 1 " - " ASN C1134 " " NAG P 1 " - " ASN D 53 " " NAG Q 1 " - " ASN D 90 " " NAG R 1 " - " ASN D 103 " " NAG S 1 " - " ASN D 432 " " NAG T 1 " - " ASN D 546 " " NAG U 1 " - " ASN E 53 " " NAG V 1 " - " ASN E 90 " " NAG W 1 " - " ASN E 103 " " NAG X 1 " - " ASN E 432 " " NAG Y 1 " - " ASN E 546 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.84 Conformation dependent library (CDL) restraints added in 1.1 seconds 8078 Ramachandran restraints generated. 4039 Oldfield, 0 Emsley, 4039 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7730 Finding SS restraints... Secondary structure from input PDB file: 141 helices and 49 sheets defined 40.0% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.248A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.740A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.727A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.555A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.583A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 4.850A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.221A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.168A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.562A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.832A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.732A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.153A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.683A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.200A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.593A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.602A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.757A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 341 Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.848A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.568A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 408 removed outlier: 3.654A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.596A pdb=" N GLU B 619 " --> pdb=" O ASN B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.819A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.204A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.075A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 removed outlier: 3.549A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 883 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.598A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.576A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.520A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.516A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.708A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.431A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.154A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 removed outlier: 3.635A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 4.070A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 Processing helix chain 'C' and resid 405 through 410 removed outlier: 5.076A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.676A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.948A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.736A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.160A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.752A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.537A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.649A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.765A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.507A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.062A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 982 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.190A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing helix chain 'D' and resid 22 through 52 removed outlier: 4.137A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N TYR D 41 " --> pdb=" O GLU D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 removed outlier: 3.629A pdb=" N GLU D 75 " --> pdb=" O ALA D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 83 No H-bonds generated for 'chain 'D' and resid 82 through 83' Processing helix chain 'D' and resid 84 through 88 Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.622A pdb=" N GLN D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 130 Processing helix chain 'D' and resid 147 through 155 removed outlier: 3.541A pdb=" N ILE D 151 " --> pdb=" O GLY D 147 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET D 152 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 172 removed outlier: 3.648A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 194 removed outlier: 3.641A pdb=" N LEU D 176 " --> pdb=" O VAL D 172 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 3.934A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.633A pdb=" N TYR D 202 " --> pdb=" O ASP D 198 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TRP D 203 " --> pdb=" O TYR D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 220 through 252 removed outlier: 3.618A pdb=" N GLU D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 4.059A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ASN D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' 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 293 through 300 Processing helix chain 'D' and resid 303 through 319 removed outlier: 3.544A pdb=" N PHE D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 331 Processing helix chain 'D' and resid 365 through 386 removed outlier: 3.602A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 388 No H-bonds generated for 'chain 'D' and resid 387 through 388' Processing helix chain 'D' and resid 389 through 393 removed outlier: 3.583A pdb=" N ARG D 393 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.589A pdb=" N ALA D 403 " --> pdb=" O GLY D 399 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE D 407 " --> pdb=" O ALA D 403 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 447 removed outlier: 4.010A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE D 436 " --> pdb=" O ASN D 432 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASN D 437 " --> pdb=" O GLU D 433 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 465 removed outlier: 3.819A pdb=" N GLU D 457 " --> pdb=" O THR D 453 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS D 465 " --> pdb=" O TRP D 461 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.703A pdb=" N ARG D 482 " --> pdb=" O TRP D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 533 removed outlier: 4.346A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 548 through 559 removed outlier: 3.739A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 574 removed outlier: 4.176A pdb=" N GLU D 571 " --> pdb=" O THR D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 598 removed outlier: 3.521A pdb=" N PHE D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) Proline residue: D 590 - end of helix removed outlier: 4.278A pdb=" N TRP D 594 " --> pdb=" O PRO D 590 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP D 597 " --> pdb=" O THR D 593 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 53 removed outlier: 4.384A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR E 41 " --> pdb=" O GLU E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 81 removed outlier: 4.359A pdb=" N LEU E 79 " --> pdb=" O GLU E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 83 No H-bonds generated for 'chain 'E' and resid 82 through 83' Processing helix chain 'E' and resid 84 through 88 Processing helix chain 'E' and resid 90 through 102 removed outlier: 3.541A pdb=" N GLN E 96 " --> pdb=" O THR E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 130 Processing helix chain 'E' and resid 147 through 155 removed outlier: 3.613A pdb=" N MET E 152 " --> pdb=" O LEU E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 172 Processing helix chain 'E' and resid 172 through 194 Proline residue: E 178 - end of helix removed outlier: 4.105A pdb=" N GLU E 182 " --> pdb=" O PRO E 178 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL E 185 " --> pdb=" O GLU E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 205 Processing helix chain 'E' and resid 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'E' and resid 220 through 252 removed outlier: 3.873A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU E 227 " --> pdb=" O ILE E 223 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLU E 232 " --> pdb=" O HIS E 228 " (cutoff:3.500A) Proline residue: E 235 - end of helix removed outlier: 4.187A pdb=" N ASN E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA E 251 " --> pdb=" O LYS E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 267 No H-bonds generated for 'chain 'E' and resid 265 through 267' Processing helix chain 'E' and resid 275 through 277 No H-bonds generated for 'chain 'E' and resid 275 through 277' Processing helix chain 'E' and resid 278 through 283 Processing helix chain 'E' and resid 293 through 300 Processing helix chain 'E' and resid 303 through 319 removed outlier: 3.980A pdb=" N PHE E 314 " --> pdb=" O GLU E 310 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N PHE E 315 " --> pdb=" O ALA E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 331 Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.775A pdb=" N HIS E 373 " --> pdb=" O PHE E 369 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N HIS E 378 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR E 381 " --> pdb=" O GLY E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 388 No H-bonds generated for 'chain 'E' and resid 386 through 388' Processing helix chain 'E' and resid 389 through 393 Processing helix chain 'E' and resid 399 through 414 removed outlier: 4.634A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER E 411 " --> pdb=" O ILE E 407 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR E 414 " --> pdb=" O LEU E 410 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 Processing helix chain 'E' and resid 431 through 447 removed outlier: 3.617A pdb=" N LYS E 441 " --> pdb=" O ASN E 437 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR E 445 " --> pdb=" O LYS E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 465 removed outlier: 4.231A pdb=" N GLU E 457 " --> pdb=" O THR E 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 484 Processing helix chain 'E' and resid 499 through 502 Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 512 through 533 removed outlier: 4.291A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA E 528 " --> pdb=" O GLN E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 Processing helix chain 'E' and resid 548 through 559 removed outlier: 4.088A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 574 removed outlier: 4.390A pdb=" N GLU E 571 " --> pdb=" O THR E 567 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN E 572 " --> pdb=" O LEU E 568 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 599 Proline residue: E 590 - end of helix removed outlier: 3.714A pdb=" N TRP E 594 " --> pdb=" O PRO E 590 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.627A pdb=" N THR A 29 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.414A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.671A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.855A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 52 removed outlier: 3.646A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 3.616A pdb=" N TYR A 313 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.045A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.671A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.069A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.672A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB4, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.313A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.255A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.840A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.377A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.666A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.795A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.353A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 324 through 328 removed outlier: 7.271A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 324 through 328 removed outlier: 7.271A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.692A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.477A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 453 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.128A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.980A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.864A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.403A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD4, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.472A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.874A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.938A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 334 through 335 removed outlier: 6.524A pdb=" N ASN C 334 " --> pdb=" O VAL C 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.746A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.219A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.540A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.540A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.182A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 131 through 133 Processing sheet with id=AE9, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.108A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'D' and resid 347 through 350 Processing sheet with id=AF2, first strand: chain 'E' and resid 132 through 133 Processing sheet with id=AF3, first strand: chain 'E' and resid 262 through 263 removed outlier: 6.106A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'E' and resid 347 through 350 1492 hydrogen bonds defined for protein. 4158 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: 7.48 Time building geometry restraints manager: 3.71 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: 7041 1.33 - 1.45: 8181 1.45 - 1.58: 18932 1.58 - 1.70: 38 1.70 - 1.82: 227 Bond restraints: 34419 Sorted by residual: bond pdb=" C1 NAG B1311 " pdb=" C2 NAG B1311 " ideal model delta sigma weight residual 1.532 1.633 -0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" CA ASN B 282 " pdb=" CB ASN B 282 " ideal model delta sigma weight residual 1.527 1.584 -0.058 1.15e-02 7.56e+03 2.52e+01 bond pdb=" N CYS A 488 " pdb=" CA CYS A 488 " ideal model delta sigma weight residual 1.457 1.511 -0.054 1.24e-02 6.50e+03 1.93e+01 bond pdb=" C5 NAG B1309 " pdb=" O5 NAG B1309 " ideal model delta sigma weight residual 1.413 1.493 -0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" C5 NAG U 2 " pdb=" O5 NAG U 2 " ideal model delta sigma weight residual 1.413 1.490 -0.077 2.00e-02 2.50e+03 1.49e+01 ... (remaining 34414 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 39696 2.52 - 5.05: 6731 5.05 - 7.57: 339 7.57 - 10.09: 25 10.09 - 12.61: 5 Bond angle restraints: 46796 Sorted by residual: angle pdb=" CA PHE B 377 " pdb=" CB PHE B 377 " pdb=" CG PHE B 377 " ideal model delta sigma weight residual 113.80 121.24 -7.44 1.00e+00 1.00e+00 5.53e+01 angle pdb=" C ARG C 403 " pdb=" N GLY C 404 " pdb=" CA GLY C 404 " ideal model delta sigma weight residual 119.98 127.94 -7.96 1.11e+00 8.12e-01 5.15e+01 angle pdb=" CA PHE A 559 " pdb=" CB PHE A 559 " pdb=" CG PHE A 559 " ideal model delta sigma weight residual 113.80 120.95 -7.15 1.00e+00 1.00e+00 5.11e+01 angle pdb=" N ASN B 331 " pdb=" CA ASN B 331 " pdb=" C ASN B 331 " ideal model delta sigma weight residual 110.19 118.78 -8.59 1.24e+00 6.50e-01 4.80e+01 angle pdb=" N CYS C 361 " pdb=" CA CYS C 361 " pdb=" C CYS C 361 " ideal model delta sigma weight residual 108.38 117.24 -8.86 1.35e+00 5.49e-01 4.30e+01 ... (remaining 46791 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.09: 19754 18.09 - 36.19: 1318 36.19 - 54.28: 281 54.28 - 72.37: 101 72.37 - 90.47: 40 Dihedral angle restraints: 21494 sinusoidal: 9507 harmonic: 11987 Sorted by residual: dihedral pdb=" CB CYS E 344 " pdb=" SG CYS E 344 " pdb=" SG CYS E 361 " pdb=" CB CYS E 361 " ideal model delta sinusoidal sigma weight residual -86.00 -173.89 87.89 1 1.00e+01 1.00e-02 9.25e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual -86.00 -5.20 -80.80 1 1.00e+01 1.00e-02 8.07e+01 dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 13.44 79.56 1 1.00e+01 1.00e-02 7.86e+01 ... (remaining 21491 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.867: 5414 0.867 - 1.735: 14 1.735 - 2.602: 6 2.602 - 3.470: 1 3.470 - 4.337: 1 Chirality restraints: 5436 Sorted by residual: chirality pdb=" C1 NAG C1305 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG C1305 " pdb=" O5 NAG C1305 " both_signs ideal model delta sigma weight residual False -2.40 1.94 -4.34 2.00e-01 2.50e+01 4.70e+02 chirality pdb=" C1 NAG A1305 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1305 " pdb=" O5 NAG A1305 " both_signs ideal model delta sigma weight residual False -2.40 0.80 -3.20 2.00e-01 2.50e+01 2.56e+02 chirality pdb=" C1 NAG B1310 " pdb=" ND2 ASN B 282 " pdb=" C2 NAG B1310 " pdb=" O5 NAG B1310 " both_signs ideal model delta sigma weight residual False -2.40 -0.02 -2.38 2.00e-01 2.50e+01 1.42e+02 ... (remaining 5433 not shown) Planarity restraints: 6000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 2 " -0.354 2.00e-02 2.50e+03 3.05e-01 1.17e+03 pdb=" C7 NAG R 2 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG R 2 " -0.107 2.00e-02 2.50e+03 pdb=" N2 NAG R 2 " 0.543 2.00e-02 2.50e+03 pdb=" O7 NAG R 2 " -0.167 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG W 2 " -0.354 2.00e-02 2.50e+03 3.05e-01 1.16e+03 pdb=" C7 NAG W 2 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG W 2 " -0.107 2.00e-02 2.50e+03 pdb=" N2 NAG W 2 " 0.543 2.00e-02 2.50e+03 pdb=" O7 NAG W 2 " -0.167 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 546 " -0.189 2.00e-02 2.50e+03 3.03e-01 1.15e+03 pdb=" CG ASN E 546 " 0.067 2.00e-02 2.50e+03 pdb=" OD1 ASN E 546 " -0.037 2.00e-02 2.50e+03 pdb=" ND2 ASN E 546 " 0.530 2.00e-02 2.50e+03 pdb=" C1 NAG Y 1 " -0.371 2.00e-02 2.50e+03 ... (remaining 5997 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.13: 6 2.13 - 2.82: 7042 2.82 - 3.51: 46105 3.51 - 4.21: 80645 4.21 - 4.90: 138147 Nonbonded interactions: 271945 Sorted by model distance: nonbonded pdb=" ND2 ASN C 125 " pdb=" C8 NAG C1302 " model vdw 1.436 3.540 nonbonded pdb=" O GLY A 485 " pdb=" OH TYR A 489 " model vdw 1.934 3.040 nonbonded pdb=" OH TYR B 380 " pdb=" O ILE B 410 " model vdw 1.979 3.040 nonbonded pdb=" OD1 ASN C 282 " pdb=" C1 NAG C1304 " model vdw 2.067 2.776 nonbonded pdb=" OH TYR B 495 " pdb=" CD1 TYR B 505 " model vdw 2.068 3.340 ... (remaining 271940 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 140 or resid 165 through 263 or resid 265 throu \ gh 444 or resid 448 through 454 or resid 462 through 470 or resid 491 through 67 \ 6 or resid 690 through 827 or resid 856 through 1312)) selection = (chain 'B' and (resid 27 through 140 or resid 165 through 263 or resid 265 throu \ gh 308 or (resid 309 and (name N or name CA or name C or name O or name CB )) or \ resid 310 through 444 or resid 448 through 454 or resid 462 through 470 or resi \ d 491 through 676 or resid 690 through 827 or resid 856 through 1312)) selection = (chain 'C' and (resid 27 through 140 or resid 165 through 196 or resid 200 throu \ gh 211 or resid 215 through 308 or (resid 309 and (name N or name CA or name C o \ r name O or name CB )) or resid 310 through 515 or resid 522 through 1312)) } ncs_group { reference = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.800 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: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 29.920 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 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 : 0.020 0.963 34542 Z= 1.124 Angle : 2.154 57.008 47115 Z= 1.264 Chirality : 0.157 4.337 5436 Planarity : 0.014 0.305 5943 Dihedral : 13.634 90.465 13632 Min Nonbonded Distance : 1.436 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.69 % Allowed : 6.46 % Favored : 92.84 % Rotamer: Outliers : 1.58 % Allowed : 4.04 % Favored : 94.38 % Cbeta Deviations : 0.28 % 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: -2.24 (0.12), residues: 4039 helix: -2.04 (0.11), residues: 1366 sheet: 0.22 (0.21), residues: 503 loop : -1.50 (0.12), residues: 2170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 454 TYR 0.117 0.020 TYR B 453 PHE 0.095 0.014 PHE B 429 TRP 0.181 0.027 TRP E 48 HIS 0.012 0.004 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.01360 (34419) covalent geometry : angle 1.76805 (46796) SS BOND : bond 0.31778 ( 44) SS BOND : angle 12.73706 ( 88) hydrogen bonds : bond 0.17468 ( 1481) hydrogen bonds : angle 8.37923 ( 4158) Misc. bond : bond 0.54146 ( 2) link_BETA1-4 : bond 0.03418 ( 20) link_BETA1-4 : angle 3.95088 ( 60) link_NAG-ASN : bond 0.20291 ( 57) link_NAG-ASN : angle 18.28713 ( 171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8078 Ramachandran restraints generated. 4039 Oldfield, 0 Emsley, 4039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8078 Ramachandran restraints generated. 4039 Oldfield, 0 Emsley, 4039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 825 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 768 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.6321 (t80) cc_final: 0.6039 (t80) REVERT: A 584 ILE cc_start: 0.8602 (mm) cc_final: 0.8370 (mt) REVERT: A 881 THR cc_start: 0.8499 (m) cc_final: 0.8267 (m) REVERT: A 973 ILE cc_start: 0.9035 (OUTLIER) cc_final: 0.8678 (tp) REVERT: B 333 THR cc_start: 0.5776 (OUTLIER) cc_final: 0.5550 (m) REVERT: B 973 ILE cc_start: 0.6991 (pp) cc_final: 0.6779 (tt) REVERT: C 875 SER cc_start: 0.9080 (t) cc_final: 0.8846 (m) REVERT: C 965 GLN cc_start: 0.8027 (mm110) cc_final: 0.7815 (mm-40) REVERT: C 984 LEU cc_start: 0.6633 (mt) cc_final: 0.6245 (mp) REVERT: C 1135 ASN cc_start: 0.7850 (t0) cc_final: 0.7581 (t0) REVERT: D 249 MET cc_start: 0.2927 (mtp) cc_final: 0.2703 (ptp) REVERT: D 376 MET cc_start: 0.5006 (ttm) cc_final: 0.4638 (ttm) REVERT: D 549 GLU cc_start: 0.7057 (tp30) cc_final: 0.6169 (mp0) REVERT: D 585 LEU cc_start: 0.3498 (mt) cc_final: 0.3010 (mt) REVERT: E 210 ASN cc_start: 0.4760 (OUTLIER) cc_final: 0.2574 (p0) REVERT: E 221 GLN cc_start: 0.3606 (tt0) cc_final: 0.2669 (mm-40) REVERT: E 297 MET cc_start: 0.0483 (mtp) cc_final: 0.0187 (ttm) REVERT: E 369 PHE cc_start: 0.1988 (t80) cc_final: 0.1743 (t80) REVERT: E 579 MET cc_start: 0.4489 (ptt) cc_final: 0.2998 (ttp) outliers start: 57 outliers final: 12 residues processed: 812 average time/residue: 0.2212 time to fit residues: 282.6143 Evaluate side-chains 383 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 368 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 210 ASN Chi-restraints excluded: chain E residue 371 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 197 optimal weight: 0.6980 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 164 ASN A 207 HIS A 218 GLN A 448 ASN A 564 GLN A1048 HIS ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 ASN B 450 ASN B 493 GLN B 901 GLN B 935 GLN B 949 GLN B 965 GLN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN C 394 ASN C 762 GLN C 787 GLN C 804 GLN C 960 ASN C1048 HIS D 58 ASN D 81 GLN D 117 ASN D 175 GLN D 330 ASN D 417 HIS D 505 HIS D 572 ASN D 599 ASN E 63 ASN E 117 ASN E 175 GLN E 508 ASN ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 552 GLN E 572 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.167172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.146563 restraints weight = 78786.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.143172 restraints weight = 139545.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.140349 restraints weight = 131087.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.140005 restraints weight = 124498.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.139161 restraints weight = 100042.917| |-----------------------------------------------------------------------------| r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 34542 Z= 0.172 Angle : 0.799 17.644 47115 Z= 0.399 Chirality : 0.051 0.618 5436 Planarity : 0.006 0.277 5943 Dihedral : 7.658 59.397 6090 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.64 % Favored : 96.26 % Rotamer: Outliers : 1.94 % Allowed : 10.50 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.05 % 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: -0.95 (0.12), residues: 4039 helix: -0.12 (0.13), residues: 1383 sheet: 0.17 (0.18), residues: 636 loop : -1.23 (0.13), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 518 TYR 0.055 0.002 TYR B 904 PHE 0.030 0.002 PHE C 392 TRP 0.031 0.002 TRP B1102 HIS 0.010 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00363 (34419) covalent geometry : angle 0.73706 (46796) SS BOND : bond 0.00921 ( 44) SS BOND : angle 2.34570 ( 88) hydrogen bonds : bond 0.05058 ( 1481) hydrogen bonds : angle 5.97611 ( 4158) Misc. bond : bond 0.00811 ( 2) link_BETA1-4 : bond 0.00704 ( 20) link_BETA1-4 : angle 2.15561 ( 60) link_NAG-ASN : bond 0.00724 ( 57) link_NAG-ASN : angle 4.75898 ( 171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8078 Ramachandran restraints generated. 4039 Oldfield, 0 Emsley, 4039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8078 Ramachandran restraints generated. 4039 Oldfield, 0 Emsley, 4039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 442 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 333 THR cc_start: 0.5841 (OUTLIER) cc_final: 0.5559 (m) REVERT: C 559 PHE cc_start: 0.5758 (m-80) cc_final: 0.5492 (m-80) REVERT: D 34 HIS cc_start: 0.6499 (m-70) cc_final: 0.6196 (m170) REVERT: D 332 MET cc_start: 0.1361 (ttt) cc_final: 0.1135 (tmm) REVERT: D 480 MET cc_start: 0.5851 (ttm) cc_final: 0.4789 (mtt) REVERT: D 567 THR cc_start: 0.4840 (p) cc_final: 0.4191 (p) REVERT: D 578 ASN cc_start: 0.1678 (OUTLIER) cc_final: 0.1131 (t0) REVERT: D 585 LEU cc_start: 0.2794 (mt) cc_final: 0.2345 (mt) REVERT: E 152 MET cc_start: -0.2010 (mmm) cc_final: -0.2318 (mmp) REVERT: E 210 ASN cc_start: 0.5033 (OUTLIER) cc_final: 0.2920 (p0) REVERT: E 297 MET cc_start: 0.1778 (mtp) cc_final: 0.1523 (ttm) REVERT: E 338 ASN cc_start: 0.2586 (t0) cc_final: 0.1612 (t0) REVERT: E 474 MET cc_start: 0.2914 (tpp) cc_final: -0.0053 (ttt) REVERT: E 579 MET cc_start: 0.4779 (ptt) cc_final: 0.3182 (ttp) outliers start: 70 outliers final: 35 residues processed: 488 average time/residue: 0.2105 time to fit residues: 166.7471 Evaluate side-chains 348 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 310 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain D residue 589 GLU Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 210 ASN Chi-restraints excluded: chain E residue 271 TRP Chi-restraints excluded: chain E residue 366 MET Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 554 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 28 optimal weight: 1.9990 chunk 218 optimal weight: 5.9990 chunk 393 optimal weight: 8.9990 chunk 295 optimal weight: 6.9990 chunk 170 optimal weight: 5.9990 chunk 221 optimal weight: 0.4980 chunk 145 optimal weight: 5.9990 chunk 390 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 176 optimal weight: 1.9990 chunk 397 optimal weight: 30.0000 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 HIS ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN D 60 GLN D 373 HIS ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.163137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.141982 restraints weight = 78328.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.139525 restraints weight = 140009.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.137458 restraints weight = 111358.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.135970 restraints weight = 111538.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.134744 restraints weight = 105530.156| |-----------------------------------------------------------------------------| r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 34542 Z= 0.258 Angle : 0.786 19.119 47115 Z= 0.392 Chirality : 0.051 0.584 5436 Planarity : 0.006 0.235 5943 Dihedral : 7.676 104.295 6077 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.95 % Favored : 94.97 % Rotamer: Outliers : 3.13 % Allowed : 11.82 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -0.86 (0.12), residues: 4039 helix: 0.21 (0.13), residues: 1377 sheet: -0.17 (0.18), residues: 636 loop : -1.24 (0.13), residues: 2026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 237 TYR 0.026 0.002 TYR B1067 PHE 0.023 0.002 PHE B 58 TRP 0.030 0.002 TRP A 353 HIS 0.014 0.002 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00599 (34419) covalent geometry : angle 0.73947 (46796) SS BOND : bond 0.00511 ( 44) SS BOND : angle 2.28742 ( 88) hydrogen bonds : bond 0.04681 ( 1481) hydrogen bonds : angle 5.82368 ( 4158) Misc. bond : bond 0.00275 ( 2) link_BETA1-4 : bond 0.00639 ( 20) link_BETA1-4 : angle 1.97829 ( 60) link_NAG-ASN : bond 0.00811 ( 57) link_NAG-ASN : angle 4.06116 ( 171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8078 Ramachandran restraints generated. 4039 Oldfield, 0 Emsley, 4039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8078 Ramachandran restraints generated. 4039 Oldfield, 0 Emsley, 4039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 335 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 HIS cc_start: 0.6507 (OUTLIER) cc_final: 0.6272 (p90) REVERT: B 1067 TYR cc_start: 0.9008 (OUTLIER) cc_final: 0.8726 (t80) REVERT: C 436 TRP cc_start: 0.5104 (p90) cc_final: 0.4751 (p90) REVERT: C 732 THR cc_start: 0.9151 (OUTLIER) cc_final: 0.8746 (p) REVERT: C 1041 ASP cc_start: 0.7911 (m-30) cc_final: 0.7677 (m-30) REVERT: D 34 HIS cc_start: 0.6529 (m-70) cc_final: 0.6222 (m-70) REVERT: D 332 MET cc_start: 0.1432 (ttt) cc_final: 0.1174 (tmm) REVERT: D 455 MET cc_start: 0.4849 (ptm) cc_final: 0.4269 (ptm) REVERT: E 210 ASN cc_start: 0.5181 (OUTLIER) cc_final: 0.2931 (p0) REVERT: E 297 MET cc_start: 0.1668 (mtp) cc_final: 0.1376 (ttm) REVERT: E 338 ASN cc_start: 0.2568 (t0) cc_final: 0.1823 (t0) REVERT: E 579 MET cc_start: 0.4865 (ptt) cc_final: 0.3326 (ttp) outliers start: 113 outliers final: 74 residues processed: 416 average time/residue: 0.2010 time to fit residues: 138.8770 Evaluate side-chains 369 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 291 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain D residue 60 GLN Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 504 PHE Chi-restraints excluded: chain D residue 589 GLU Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 210 ASN Chi-restraints excluded: chain E residue 271 TRP Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 497 TYR Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain E residue 571 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 281 optimal weight: 7.9990 chunk 388 optimal weight: 30.0000 chunk 296 optimal weight: 20.0000 chunk 12 optimal weight: 7.9990 chunk 148 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 366 optimal weight: 3.9990 chunk 210 optimal weight: 0.9990 chunk 318 optimal weight: 0.0470 chunk 112 optimal weight: 3.9990 chunk 204 optimal weight: 5.9990 overall best weight: 2.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 519 HIS C 935 GLN D 60 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.163290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.142930 restraints weight = 77769.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.140543 restraints weight = 129905.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.136613 restraints weight = 109286.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.135189 restraints weight = 128269.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.134217 restraints weight = 110587.338| |-----------------------------------------------------------------------------| r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 34542 Z= 0.202 Angle : 0.722 19.980 47115 Z= 0.358 Chirality : 0.049 0.784 5436 Planarity : 0.005 0.203 5943 Dihedral : 7.494 109.639 6073 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.51 % Favored : 95.42 % Rotamer: Outliers : 2.94 % Allowed : 13.49 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -0.71 (0.13), residues: 4039 helix: 0.44 (0.13), residues: 1388 sheet: -0.22 (0.18), residues: 617 loop : -1.17 (0.13), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1107 TYR 0.022 0.002 TYR B1067 PHE 0.019 0.002 PHE C 400 TRP 0.037 0.002 TRP B 353 HIS 0.005 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00463 (34419) covalent geometry : angle 0.67606 (46796) SS BOND : bond 0.00556 ( 44) SS BOND : angle 2.75765 ( 88) hydrogen bonds : bond 0.04227 ( 1481) hydrogen bonds : angle 5.64262 ( 4158) Misc. bond : bond 0.00314 ( 2) link_BETA1-4 : bond 0.00612 ( 20) link_BETA1-4 : angle 1.85527 ( 60) link_NAG-ASN : bond 0.00653 ( 57) link_NAG-ASN : angle 3.66057 ( 171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8078 Ramachandran restraints generated. 4039 Oldfield, 0 Emsley, 4039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8078 Ramachandran restraints generated. 4039 Oldfield, 0 Emsley, 4039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 327 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 HIS cc_start: 0.6551 (OUTLIER) cc_final: 0.6277 (p90) REVERT: A 822 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8168 (mm) REVERT: B 474 GLN cc_start: 0.5194 (OUTLIER) cc_final: 0.3961 (pp30) REVERT: B 1067 TYR cc_start: 0.8998 (OUTLIER) cc_final: 0.8654 (t80) REVERT: C 436 TRP cc_start: 0.5222 (p90) cc_final: 0.4831 (p90) REVERT: C 519 HIS cc_start: 0.4766 (OUTLIER) cc_final: 0.2848 (t-170) REVERT: C 734 THR cc_start: 0.9324 (m) cc_final: 0.9079 (p) REVERT: C 1027 THR cc_start: 0.9575 (m) cc_final: 0.9147 (p) REVERT: D 34 HIS cc_start: 0.6705 (m-70) cc_final: 0.6421 (m-70) REVERT: D 332 MET cc_start: 0.1392 (ttt) cc_final: 0.1183 (tmm) REVERT: D 455 MET cc_start: 0.4858 (ptm) cc_final: 0.4640 (ptm) REVERT: D 518 ARG cc_start: 0.6677 (OUTLIER) cc_final: 0.6457 (ptm160) REVERT: E 210 ASN cc_start: 0.5018 (OUTLIER) cc_final: 0.2674 (p0) REVERT: E 297 MET cc_start: 0.1741 (mtp) cc_final: 0.1530 (ttm) REVERT: E 338 ASN cc_start: 0.2487 (t0) cc_final: 0.1395 (t0) REVERT: E 574 VAL cc_start: 0.1138 (OUTLIER) cc_final: 0.0697 (p) REVERT: E 579 MET cc_start: 0.4845 (ptt) cc_final: 0.3259 (ttp) outliers start: 106 outliers final: 73 residues processed: 401 average time/residue: 0.2053 time to fit residues: 135.1898 Evaluate side-chains 369 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 288 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1146 ASP Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 504 PHE Chi-restraints excluded: chain D residue 518 ARG Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 589 GLU Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain E residue 34 HIS Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 210 ASN Chi-restraints excluded: chain E residue 271 TRP Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 497 TYR Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain E residue 574 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 87 optimal weight: 0.7980 chunk 199 optimal weight: 0.3980 chunk 394 optimal weight: 40.0000 chunk 193 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 161 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 374 optimal weight: 0.3980 chunk 222 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 935 GLN C 207 HIS C 394 ASN ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 ASN E 505 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.165078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.144952 restraints weight = 78353.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.142482 restraints weight = 131323.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.140313 restraints weight = 109783.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.139596 restraints weight = 110139.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.138490 restraints weight = 93119.381| |-----------------------------------------------------------------------------| r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 34542 Z= 0.127 Angle : 0.647 19.671 47115 Z= 0.319 Chirality : 0.048 1.277 5436 Planarity : 0.004 0.174 5943 Dihedral : 6.948 112.776 6073 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.99 % Favored : 95.91 % Rotamer: Outliers : 2.63 % Allowed : 14.37 % Favored : 83.00 % 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: -0.43 (0.13), residues: 4039 helix: 0.72 (0.14), residues: 1396 sheet: -0.11 (0.19), residues: 633 loop : -1.05 (0.14), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1107 TYR 0.029 0.002 TYR C1110 PHE 0.030 0.001 PHE C 817 TRP 0.046 0.001 TRP B 353 HIS 0.022 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00275 (34419) covalent geometry : angle 0.60941 (46796) SS BOND : bond 0.00385 ( 44) SS BOND : angle 1.58925 ( 88) hydrogen bonds : bond 0.03740 ( 1481) hydrogen bonds : angle 5.38442 ( 4158) Misc. bond : bond 0.00296 ( 2) link_BETA1-4 : bond 0.00537 ( 20) link_BETA1-4 : angle 1.78399 ( 60) link_NAG-ASN : bond 0.00480 ( 57) link_NAG-ASN : angle 3.33619 ( 171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8078 Ramachandran restraints generated. 4039 Oldfield, 0 Emsley, 4039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8078 Ramachandran restraints generated. 4039 Oldfield, 0 Emsley, 4039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 349 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 584 ILE cc_start: 0.8177 (mm) cc_final: 0.7935 (mt) REVERT: A 822 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8084 (mm) REVERT: B 474 GLN cc_start: 0.5302 (OUTLIER) cc_final: 0.4067 (pp30) REVERT: B 1067 TYR cc_start: 0.8959 (OUTLIER) cc_final: 0.8730 (t80) REVERT: C 221 SER cc_start: 0.8474 (t) cc_final: 0.8185 (p) REVERT: C 732 THR cc_start: 0.9048 (OUTLIER) cc_final: 0.8615 (p) REVERT: C 1027 THR cc_start: 0.9615 (m) cc_final: 0.9209 (p) REVERT: D 34 HIS cc_start: 0.6500 (m-70) cc_final: 0.6210 (m170) REVERT: D 152 MET cc_start: 0.3881 (mmm) cc_final: 0.3537 (mmt) REVERT: D 518 ARG cc_start: 0.6492 (OUTLIER) cc_final: 0.6285 (ptm160) REVERT: E 210 ASN cc_start: 0.4692 (OUTLIER) cc_final: 0.2501 (p0) REVERT: E 338 ASN cc_start: 0.2574 (t0) cc_final: 0.1402 (t0) REVERT: E 574 VAL cc_start: 0.1039 (OUTLIER) cc_final: 0.0641 (p) REVERT: E 579 MET cc_start: 0.4731 (ptt) cc_final: 0.3296 (ttp) outliers start: 95 outliers final: 54 residues processed: 418 average time/residue: 0.2043 time to fit residues: 142.0337 Evaluate side-chains 360 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 299 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 518 ARG Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain E residue 34 HIS Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 210 ASN Chi-restraints excluded: chain E residue 271 TRP Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 438 PHE Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain E residue 574 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 288 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 316 optimal weight: 30.0000 chunk 128 optimal weight: 7.9990 chunk 367 optimal weight: 6.9990 chunk 174 optimal weight: 5.9990 chunk 205 optimal weight: 7.9990 chunk 132 optimal weight: 10.0000 chunk 112 optimal weight: 0.0370 chunk 313 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 overall best weight: 3.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 519 HIS C 901 GLN C1048 HIS ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 ASN ** D 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 GLN E 540 HIS E 599 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.162019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.140882 restraints weight = 77550.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.137997 restraints weight = 144593.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.135579 restraints weight = 128224.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.134701 restraints weight = 122932.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.133206 restraints weight = 110010.700| |-----------------------------------------------------------------------------| r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.4572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 34542 Z= 0.236 Angle : 0.736 19.701 47115 Z= 0.365 Chirality : 0.050 0.872 5436 Planarity : 0.005 0.204 5943 Dihedral : 7.242 111.276 6072 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.88 % Favored : 95.02 % Rotamer: Outliers : 3.27 % Allowed : 14.73 % Favored : 82.00 % 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: -0.62 (0.13), residues: 4039 helix: 0.53 (0.14), residues: 1397 sheet: -0.27 (0.19), residues: 628 loop : -1.10 (0.14), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 169 TYR 0.026 0.002 TYR C1110 PHE 0.019 0.002 PHE C 275 TRP 0.044 0.002 TRP D 275 HIS 0.007 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00547 (34419) covalent geometry : angle 0.69443 (46796) SS BOND : bond 0.00513 ( 44) SS BOND : angle 2.39772 ( 88) hydrogen bonds : bond 0.04112 ( 1481) hydrogen bonds : angle 5.57068 ( 4158) Misc. bond : bond 0.00307 ( 2) link_BETA1-4 : bond 0.00573 ( 20) link_BETA1-4 : angle 1.77721 ( 60) link_NAG-ASN : bond 0.00491 ( 57) link_NAG-ASN : angle 3.65784 ( 171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8078 Ramachandran restraints generated. 4039 Oldfield, 0 Emsley, 4039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8078 Ramachandran restraints generated. 4039 Oldfield, 0 Emsley, 4039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 300 time to evaluate : 1.221 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 584 ILE cc_start: 0.8279 (mm) cc_final: 0.8049 (mt) REVERT: A 592 PHE cc_start: 0.6726 (p90) cc_final: 0.6475 (p90) REVERT: A 822 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8169 (mm) REVERT: A 1005 GLN cc_start: 0.7941 (mm-40) cc_final: 0.7406 (mt0) REVERT: B 1067 TYR cc_start: 0.8986 (OUTLIER) cc_final: 0.8754 (t80) REVERT: C 190 ARG cc_start: 0.5762 (mtt180) cc_final: 0.4969 (mtt180) REVERT: C 221 SER cc_start: 0.8540 (t) cc_final: 0.8272 (p) REVERT: C 519 HIS cc_start: 0.5042 (OUTLIER) cc_final: 0.2604 (t-90) REVERT: C 732 THR cc_start: 0.9127 (OUTLIER) cc_final: 0.8672 (p) REVERT: C 1027 THR cc_start: 0.9572 (m) cc_final: 0.9174 (p) REVERT: D 34 HIS cc_start: 0.6758 (m-70) cc_final: 0.6479 (m-70) REVERT: D 57 GLU cc_start: 0.4746 (OUTLIER) cc_final: 0.4244 (pm20) REVERT: D 111 ASP cc_start: 0.5400 (t0) cc_final: 0.5198 (t0) REVERT: D 360 MET cc_start: 0.5323 (tmm) cc_final: 0.4997 (tpt) REVERT: E 338 ASN cc_start: 0.2912 (t0) cc_final: 0.1671 (t0) REVERT: E 574 VAL cc_start: 0.1529 (OUTLIER) cc_final: 0.1031 (p) REVERT: E 579 MET cc_start: 0.4869 (ptt) cc_final: 0.3328 (ttp) outliers start: 118 outliers final: 87 residues processed: 395 average time/residue: 0.1892 time to fit residues: 125.8001 Evaluate side-chains 368 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 275 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1146 ASP Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 504 PHE Chi-restraints excluded: chain E residue 34 HIS Chi-restraints excluded: chain E residue 40 PHE Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 271 TRP Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 574 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 130 optimal weight: 5.9990 chunk 281 optimal weight: 0.9990 chunk 376 optimal weight: 9.9990 chunk 373 optimal weight: 10.0000 chunk 68 optimal weight: 0.8980 chunk 248 optimal weight: 2.9990 chunk 223 optimal weight: 5.9990 chunk 364 optimal weight: 20.0000 chunk 251 optimal weight: 0.8980 chunk 225 optimal weight: 1.9990 chunk 145 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 935 GLN C1135 ASN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 378 HIS E 34 HIS E 210 ASN E 374 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.163987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.143314 restraints weight = 77522.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.140445 restraints weight = 140673.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.138110 restraints weight = 117086.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.137240 restraints weight = 118034.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.136145 restraints weight = 104752.862| |-----------------------------------------------------------------------------| r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 0.4741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 34542 Z= 0.137 Angle : 0.649 12.259 47115 Z= 0.323 Chirality : 0.046 0.501 5436 Planarity : 0.005 0.193 5943 Dihedral : 6.807 115.155 6068 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.91 % Favored : 95.99 % Rotamer: Outliers : 2.58 % Allowed : 15.67 % Favored : 81.75 % 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: -0.43 (0.13), residues: 4039 helix: 0.81 (0.14), residues: 1396 sheet: -0.32 (0.18), residues: 641 loop : -1.04 (0.14), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A1107 TYR 0.036 0.002 TYR B 904 PHE 0.017 0.001 PHE B 92 TRP 0.030 0.001 TRP B 353 HIS 0.012 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00309 (34419) covalent geometry : angle 0.61485 (46796) SS BOND : bond 0.00361 ( 44) SS BOND : angle 2.06199 ( 88) hydrogen bonds : bond 0.03671 ( 1481) hydrogen bonds : angle 5.34746 ( 4158) Misc. bond : bond 0.00389 ( 2) link_BETA1-4 : bond 0.00528 ( 20) link_BETA1-4 : angle 1.69640 ( 60) link_NAG-ASN : bond 0.00417 ( 57) link_NAG-ASN : angle 3.07335 ( 171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8078 Ramachandran restraints generated. 4039 Oldfield, 0 Emsley, 4039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8078 Ramachandran restraints generated. 4039 Oldfield, 0 Emsley, 4039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 308 time to evaluate : 1.266 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: A 592 PHE cc_start: 0.6657 (p90) cc_final: 0.6391 (p90) REVERT: A 822 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8072 (mm) REVERT: A 1005 GLN cc_start: 0.7900 (mm-40) cc_final: 0.7334 (tt0) REVERT: B 1067 TYR cc_start: 0.8990 (OUTLIER) cc_final: 0.8772 (t80) REVERT: C 221 SER cc_start: 0.8438 (t) cc_final: 0.8208 (p) REVERT: C 732 THR cc_start: 0.9028 (OUTLIER) cc_final: 0.8578 (p) REVERT: C 1027 THR cc_start: 0.9574 (m) cc_final: 0.9189 (p) REVERT: D 34 HIS cc_start: 0.6680 (m-70) cc_final: 0.6472 (m170) REVERT: D 480 MET cc_start: 0.4691 (ttm) cc_final: 0.3788 (mtt) REVERT: D 518 ARG cc_start: 0.6574 (OUTLIER) cc_final: 0.6308 (ptm160) REVERT: E 152 MET cc_start: -0.1769 (mmm) cc_final: -0.3519 (mmp) REVERT: E 338 ASN cc_start: 0.3039 (t0) cc_final: 0.1827 (m-40) REVERT: E 574 VAL cc_start: 0.1856 (OUTLIER) cc_final: 0.1317 (p) REVERT: E 579 MET cc_start: 0.4773 (ptt) cc_final: 0.3220 (ttp) outliers start: 93 outliers final: 63 residues processed: 380 average time/residue: 0.1980 time to fit residues: 125.5599 Evaluate side-chains 342 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 274 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 504 PHE Chi-restraints excluded: chain D residue 518 ARG Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain E residue 34 HIS Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 271 TRP Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain E residue 574 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 204 optimal weight: 2.9990 chunk 307 optimal weight: 10.0000 chunk 253 optimal weight: 0.2980 chunk 114 optimal weight: 0.6980 chunk 292 optimal weight: 0.9980 chunk 143 optimal weight: 0.1980 chunk 252 optimal weight: 0.9990 chunk 233 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 20 optimal weight: 0.1980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN C 641 ASN C 901 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.165259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.145086 restraints weight = 77472.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.142382 restraints weight = 129879.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.139923 restraints weight = 108990.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.138075 restraints weight = 110503.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.136892 restraints weight = 108841.615| |-----------------------------------------------------------------------------| r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.4892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 34542 Z= 0.118 Angle : 0.623 11.885 47115 Z= 0.311 Chirality : 0.045 0.468 5436 Planarity : 0.006 0.392 5943 Dihedral : 6.482 115.436 6068 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.71 % Favored : 96.19 % Rotamer: Outliers : 2.22 % Allowed : 16.20 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.13), residues: 4039 helix: 1.04 (0.14), residues: 1392 sheet: -0.07 (0.19), residues: 628 loop : -1.00 (0.14), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 509 TYR 0.064 0.001 TYR B 904 PHE 0.019 0.001 PHE B 565 TRP 0.026 0.001 TRP B 353 HIS 0.024 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00257 (34419) covalent geometry : angle 0.59342 (46796) SS BOND : bond 0.00284 ( 44) SS BOND : angle 1.79164 ( 88) hydrogen bonds : bond 0.03522 ( 1481) hydrogen bonds : angle 5.23178 ( 4158) Misc. bond : bond 0.00670 ( 2) link_BETA1-4 : bond 0.00481 ( 20) link_BETA1-4 : angle 1.65557 ( 60) link_NAG-ASN : bond 0.00428 ( 57) link_NAG-ASN : angle 2.80217 ( 171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8078 Ramachandran restraints generated. 4039 Oldfield, 0 Emsley, 4039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8078 Ramachandran restraints generated. 4039 Oldfield, 0 Emsley, 4039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 308 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 822 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8042 (mm) REVERT: A 1005 GLN cc_start: 0.7723 (mm-40) cc_final: 0.7181 (tt0) REVERT: C 732 THR cc_start: 0.9251 (OUTLIER) cc_final: 0.8853 (p) REVERT: C 1027 THR cc_start: 0.9565 (m) cc_final: 0.9181 (p) REVERT: D 34 HIS cc_start: 0.6814 (m-70) cc_final: 0.6587 (m170) REVERT: D 190 MET cc_start: 0.4850 (mmt) cc_final: 0.4228 (mtp) REVERT: D 480 MET cc_start: 0.4924 (ttm) cc_final: 0.4011 (mtt) REVERT: D 518 ARG cc_start: 0.6578 (OUTLIER) cc_final: 0.6357 (ptm160) REVERT: E 338 ASN cc_start: 0.3129 (t0) cc_final: 0.1947 (m-40) REVERT: E 579 MET cc_start: 0.4806 (ptt) cc_final: 0.3101 (ttp) outliers start: 80 outliers final: 61 residues processed: 367 average time/residue: 0.2005 time to fit residues: 122.2198 Evaluate side-chains 338 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 274 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 504 PHE Chi-restraints excluded: chain D residue 518 ARG Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain E residue 34 HIS Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 271 TRP Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 438 PHE Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 574 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 273 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 297 optimal weight: 8.9990 chunk 200 optimal weight: 0.2980 chunk 163 optimal weight: 4.9990 chunk 57 optimal weight: 0.0040 chunk 282 optimal weight: 1.9990 chunk 223 optimal weight: 10.0000 chunk 182 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 overall best weight: 0.8594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 641 ASN C 901 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.165069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.145320 restraints weight = 77064.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.142714 restraints weight = 128439.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.139126 restraints weight = 109477.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.137837 restraints weight = 120823.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.137014 restraints weight = 103139.447| |-----------------------------------------------------------------------------| r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.5021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 34542 Z= 0.129 Angle : 0.636 14.553 47115 Z= 0.317 Chirality : 0.045 0.449 5436 Planarity : 0.006 0.358 5943 Dihedral : 6.330 113.885 6068 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.84 % Favored : 96.06 % Rotamer: Outliers : 2.19 % Allowed : 16.92 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.15 (0.13), residues: 4039 helix: 1.12 (0.14), residues: 1386 sheet: 0.00 (0.18), residues: 632 loop : -1.00 (0.14), residues: 2021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1107 TYR 0.044 0.001 TYR B 904 PHE 0.025 0.001 PHE B 565 TRP 0.029 0.001 TRP D 69 HIS 0.006 0.001 HIS E 378 Details of bonding type rmsd covalent geometry : bond 0.00291 (34419) covalent geometry : angle 0.60890 (46796) SS BOND : bond 0.00514 ( 44) SS BOND : angle 1.87722 ( 88) hydrogen bonds : bond 0.03486 ( 1481) hydrogen bonds : angle 5.19566 ( 4158) Misc. bond : bond 0.00590 ( 2) link_BETA1-4 : bond 0.00493 ( 20) link_BETA1-4 : angle 1.62174 ( 60) link_NAG-ASN : bond 0.00410 ( 57) link_NAG-ASN : angle 2.70546 ( 171) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8078 Ramachandran restraints generated. 4039 Oldfield, 0 Emsley, 4039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8078 Ramachandran restraints generated. 4039 Oldfield, 0 Emsley, 4039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 287 time to evaluate : 0.990 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 822 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.7955 (mm) REVERT: A 1005 GLN cc_start: 0.7956 (mm-40) cc_final: 0.7396 (tt0) REVERT: B 131 CYS cc_start: 0.5370 (OUTLIER) cc_final: 0.4511 (m) REVERT: C 732 THR cc_start: 0.9018 (OUTLIER) cc_final: 0.8640 (p) REVERT: C 1027 THR cc_start: 0.9557 (m) cc_final: 0.9219 (p) REVERT: D 34 HIS cc_start: 0.6767 (m-70) cc_final: 0.6519 (m170) REVERT: D 455 MET cc_start: 0.4976 (ttt) cc_final: 0.4553 (ttt) REVERT: D 462 MET cc_start: 0.5162 (mmp) cc_final: 0.4864 (mmp) REVERT: D 480 MET cc_start: 0.5045 (ttm) cc_final: 0.4226 (mtt) REVERT: E 338 ASN cc_start: 0.2958 (t0) cc_final: 0.1911 (m-40) REVERT: E 579 MET cc_start: 0.4826 (ptt) cc_final: 0.3206 (ttp) outliers start: 79 outliers final: 59 residues processed: 346 average time/residue: 0.1942 time to fit residues: 112.6945 Evaluate side-chains 330 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 268 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 504 PHE Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 271 TRP Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 438 PHE Chi-restraints excluded: chain E residue 485 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 161 optimal weight: 3.9990 chunk 310 optimal weight: 30.0000 chunk 83 optimal weight: 0.9990 chunk 264 optimal weight: 0.5980 chunk 259 optimal weight: 3.9990 chunk 203 optimal weight: 8.9990 chunk 355 optimal weight: 9.9990 chunk 191 optimal weight: 0.0470 chunk 127 optimal weight: 7.9990 chunk 327 optimal weight: 40.0000 chunk 336 optimal weight: 0.9980 overall best weight: 1.3282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 907 ASN C1113 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.164508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.143830 restraints weight = 77568.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.141353 restraints weight = 137690.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.139313 restraints weight = 103232.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.137581 restraints weight = 106905.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.136471 restraints weight = 103245.251| |-----------------------------------------------------------------------------| r_work (final): 0.3955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.5136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 34542 Z= 0.144 Angle : 0.644 11.675 47115 Z= 0.321 Chirality : 0.045 0.438 5436 Planarity : 0.006 0.393 5943 Dihedral : 6.310 112.697 6068 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.13 % Favored : 95.77 % Rotamer: Outliers : 1.86 % Allowed : 17.31 % Favored : 80.84 % 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: -0.17 (0.13), residues: 4039 helix: 1.10 (0.14), residues: 1389 sheet: -0.00 (0.19), residues: 633 loop : -1.00 (0.14), residues: 2017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A1107 TYR 0.092 0.002 TYR B 904 PHE 0.026 0.001 PHE B 565 TRP 0.028 0.002 TRP D 69 HIS 0.009 0.001 HIS E 378 Details of bonding type rmsd covalent geometry : bond 0.00328 (34419) covalent geometry : angle 0.61851 (46796) SS BOND : bond 0.00390 ( 44) SS BOND : angle 1.69196 ( 88) hydrogen bonds : bond 0.03560 ( 1481) hydrogen bonds : angle 5.19294 ( 4158) Misc. bond : bond 0.00770 ( 2) link_BETA1-4 : bond 0.00488 ( 20) link_BETA1-4 : angle 1.60839 ( 60) link_NAG-ASN : bond 0.00411 ( 57) link_NAG-ASN : angle 2.65886 ( 171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8078 Ramachandran restraints generated. 4039 Oldfield, 0 Emsley, 4039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8078 Ramachandran restraints generated. 4039 Oldfield, 0 Emsley, 4039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 288 time to evaluate : 1.505 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 822 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8082 (mm) REVERT: A 964 LYS cc_start: 0.8183 (mttt) cc_final: 0.7864 (ttmt) REVERT: B 131 CYS cc_start: 0.5493 (OUTLIER) cc_final: 0.4650 (m) REVERT: C 732 THR cc_start: 0.9138 (OUTLIER) cc_final: 0.8734 (p) REVERT: C 1027 THR cc_start: 0.9525 (m) cc_final: 0.9089 (p) REVERT: D 34 HIS cc_start: 0.6712 (m-70) cc_final: 0.6490 (m170) REVERT: D 455 MET cc_start: 0.4931 (ttt) cc_final: 0.4442 (ttt) REVERT: D 480 MET cc_start: 0.4995 (ttm) cc_final: 0.4144 (mtt) REVERT: E 338 ASN cc_start: 0.2937 (t0) cc_final: 0.1961 (m-40) REVERT: E 433 GLU cc_start: 0.3396 (mm-30) cc_final: 0.3102 (mt-10) REVERT: E 579 MET cc_start: 0.4776 (ptt) cc_final: 0.3174 (ttp) outliers start: 67 outliers final: 55 residues processed: 340 average time/residue: 0.1915 time to fit residues: 109.2387 Evaluate side-chains 328 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 270 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 504 PHE Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 271 TRP Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 485 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 302 optimal weight: 6.9990 chunk 367 optimal weight: 30.0000 chunk 127 optimal weight: 6.9990 chunk 363 optimal weight: 20.0000 chunk 246 optimal weight: 0.8980 chunk 384 optimal weight: 20.0000 chunk 144 optimal weight: 10.0000 chunk 397 optimal weight: 7.9990 chunk 62 optimal weight: 0.6980 chunk 295 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 overall best weight: 4.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 414 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 34 HIS E 51 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.160416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.139012 restraints weight = 77366.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.136117 restraints weight = 142204.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.133314 restraints weight = 125574.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.132811 restraints weight = 125383.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.131860 restraints weight = 99641.822| |-----------------------------------------------------------------------------| r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.5268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.096 34542 Z= 0.323 Angle : 0.815 23.823 47115 Z= 0.404 Chirality : 0.051 0.543 5436 Planarity : 0.007 0.414 5943 Dihedral : 7.350 113.138 6068 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.50 % Favored : 94.40 % Rotamer: Outliers : 2.30 % Allowed : 17.23 % Favored : 80.48 % 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: -0.70 (0.13), residues: 4039 helix: 0.52 (0.14), residues: 1418 sheet: -0.31 (0.19), residues: 600 loop : -1.21 (0.14), residues: 2021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG A1107 TYR 0.087 0.003 TYR B 904 PHE 0.032 0.003 PHE B 565 TRP 0.024 0.002 TRP A 353 HIS 0.012 0.002 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00748 (34419) covalent geometry : angle 0.78010 (46796) SS BOND : bond 0.00659 ( 44) SS BOND : angle 2.33700 ( 88) hydrogen bonds : bond 0.04277 ( 1481) hydrogen bonds : angle 5.63230 ( 4158) Misc. bond : bond 0.00598 ( 2) link_BETA1-4 : bond 0.00517 ( 20) link_BETA1-4 : angle 1.75202 ( 60) link_NAG-ASN : bond 0.00442 ( 57) link_NAG-ASN : angle 3.54051 ( 171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5362.29 seconds wall clock time: 93 minutes 51.04 seconds (5631.04 seconds total)