Starting phenix.real_space_refine on Fri Mar 6 12:54:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7czy_30521/03_2026/7czy_30521.cif Found real_map, /net/cci-nas-00/data/ceres_data/7czy_30521/03_2026/7czy_30521.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7czy_30521/03_2026/7czy_30521.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7czy_30521/03_2026/7czy_30521.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7czy_30521/03_2026/7czy_30521.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7czy_30521/03_2026/7czy_30521.map" } resolution = 3.3 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= 0.005 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 135 5.16 5 C 19777 2.51 5 N 5088 2.21 5 O 6186 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 81 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: 31186 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 7863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7863 Classifications: {'peptide': 1006} Link IDs: {'PTRANS': 50, 'TRANS': 955} Chain breaks: 8 Chain: "B" Number of atoms: 7696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 982, 7696 Classifications: {'peptide': 982} Link IDs: {'PTRANS': 47, 'TRANS': 934} Chain breaks: 11 Chain: "C" Number of atoms: 7853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1004, 7853 Classifications: {'peptide': 1004} Link IDs: {'PTRANS': 49, 'TRANS': 954} Chain breaks: 8 Chain: "H" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1670 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 13, 'TRANS': 210} Chain: "K" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1685 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 208} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1670 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 13, 'TRANS': 210} Chain: "N" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1685 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 208} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" 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: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "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: "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: "Z" 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: 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: "b" 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: "c" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 6.33, per 1000 atoms: 0.20 Number of scatterers: 31186 At special positions: 0 Unit cell: (134.788, 173.92, 245.662, 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 135 16.00 O 6186 8.00 N 5088 7.00 C 19777 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.28 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.15 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.05 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.05 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.26 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.15 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.17 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=1.98 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 149 " - pdb=" SG CYS H 205 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 94 " distance=2.80 Simple disulfide: pdb=" SG CYS K 140 " - pdb=" SG CYS K 200 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 149 " - pdb=" SG CYS J 205 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 94 " distance=2.80 Simple disulfide: pdb=" SG CYS N 140 " - pdb=" SG CYS N 200 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B1410 " - " NAG B1411 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 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 Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " NAG c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " NAG d 3 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 165 " " NAG A1404 " - " ASN A 234 " " NAG A1405 " - " ASN A 282 " " NAG A1406 " - " ASN A 603 " " NAG A1407 " - " ASN A 616 " " NAG A1408 " - " ASN A 657 " " NAG A1409 " - " ASN A 709 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 122 " " NAG B1403 " - " ASN B 165 " " NAG B1404 " - " ASN B 234 " " NAG B1405 " - " ASN B 282 " " NAG B1406 " - " ASN B 343 " " NAG B1407 " - " ASN B 603 " " NAG B1408 " - " ASN B 616 " " NAG B1409 " - " ASN B 657 " " NAG B1410 " - " ASN B1074 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 122 " " NAG C1403 " - " ASN C 165 " " NAG C1404 " - " ASN C 234 " " NAG C1405 " - " ASN C 282 " " NAG C1406 " - " ASN C 603 " " NAG C1407 " - " ASN C 616 " " NAG C1408 " - " ASN C 657 " " NAG D 1 " - " ASN A 331 " " NAG E 1 " - " ASN A 343 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG I 1 " - " ASN A1074 " " NAG L 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG O 1 " - " ASN B 331 " " NAG P 1 " - " ASN B 709 " " NAG Q 1 " - " ASN B 717 " " NAG R 1 " - " ASN B 801 " " NAG S 1 " - " ASN B1098 " " NAG T 1 " - " ASN B1134 " " NAG U 1 " - " ASN C 331 " " NAG V 1 " - " ASN C 343 " " NAG W 1 " - " ASN C 709 " " NAG X 1 " - " ASN C 717 " " NAG Y 1 " - " ASN C 801 " " NAG Z 1 " - " ASN C1074 " " NAG a 1 " - " ASN C1098 " " NAG b 1 " - " ASN C1134 " " NAG c 1 " - " ASN H 73 " " NAG d 1 " - " ASN J 73 " Time building additional restraints: 2.81 Conformation dependent library (CDL) restraints added in 1.3 seconds 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7260 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 62 sheets defined 19.1% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.074A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.256A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.626A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.739A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.631A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (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: 3.771A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 removed outlier: 3.634A pdb=" N LYS A 814 " --> pdb=" O LYS A 811 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG A 815 " --> pdb=" O PRO A 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 811 through 815' Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.646A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.574A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 3.994A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.625A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.878A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 981 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.632A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.647A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.640A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 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: 3.965A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.543A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.603A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.011A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.372A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.074A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.256A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.626A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.738A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.581A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.717A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (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: 3.561A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.604A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.636A 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 897 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.591A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.356A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR C 961 " --> pdb=" O GLN C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 977 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.220A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 Processing helix chain 'H' and resid 196 through 198 No H-bonds generated for 'chain 'H' and resid 196 through 198' Processing helix chain 'K' and resid 127 through 134 Processing helix chain 'K' and resid 189 through 193 Processing helix chain 'J' and resid 196 through 198 No H-bonds generated for 'chain 'J' and resid 196 through 198' Processing helix chain 'N' and resid 127 through 134 Processing helix chain 'N' and resid 189 through 193 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.060A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.569A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 116 through 121 removed outlier: 3.730A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN A 134 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 309 through 319 removed outlier: 6.679A pdb=" N GLU A 309 " --> pdb=" O GLY A 601 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N GLY A 601 " --> pdb=" O GLU A 309 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.542A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 448 through 454 removed outlier: 5.864A pdb=" N TYR A 449 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE A 497 " --> pdb=" O TYR A 449 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 539 through 543 removed outlier: 5.338A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.257A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.588A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.588A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.504A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.713A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.539A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.441A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 10.074A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.650A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.779A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.572A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.673A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC7, first strand: chain 'B' and resid 539 through 543 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.220A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.542A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.542A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.577A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 31 removed outlier: 8.151A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 10.527A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.758A pdb=" N THR C 274 " --> pdb=" O CYS C 291 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N CYS C 291 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 128 through 131 removed outlier: 4.247A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.666A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.543A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 448 through 454 removed outlier: 5.865A pdb=" N TYR C 449 " --> pdb=" O PHE C 497 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N PHE C 497 " --> pdb=" O TYR C 449 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE3, first strand: chain 'C' and resid 538 through 543 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.230A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.592A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.592A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.568A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE9, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.995A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER H 7 " --> pdb=" O SER H 21 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N SER H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.575A pdb=" N TYR H 94 " --> pdb=" O THR H 116 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 129 through 133 removed outlier: 5.008A pdb=" N ALA H 146 " --> pdb=" O VAL H 193 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL H 193 " --> pdb=" O ALA H 146 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY H 148 " --> pdb=" O VAL H 191 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL H 191 " --> pdb=" O GLY H 148 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU H 150 " --> pdb=" O SER H 189 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER H 189 " --> pdb=" O LEU H 150 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS H 152 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU H 187 " --> pdb=" O LYS H 152 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 129 through 133 removed outlier: 5.008A pdb=" N ALA H 146 " --> pdb=" O VAL H 193 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL H 193 " --> pdb=" O ALA H 146 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY H 148 " --> pdb=" O VAL H 191 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL H 191 " --> pdb=" O GLY H 148 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU H 150 " --> pdb=" O SER H 189 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER H 189 " --> pdb=" O LEU H 150 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS H 152 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU H 187 " --> pdb=" O LYS H 152 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 159 through 163 Processing sheet with id=AF5, first strand: chain 'K' and resid 5 through 6 removed outlier: 3.914A pdb=" N THR K 5 " --> pdb=" O LYS K 24 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS K 24 " --> pdb=" O THR K 5 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N CYS K 23 " --> pdb=" O PHE K 77 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE K 77 " --> pdb=" O CYS K 23 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 42 through 44 Processing sheet with id=AF7, first strand: chain 'K' and resid 120 through 124 Processing sheet with id=AF8, first strand: chain 'K' and resid 159 through 160 Processing sheet with id=AF9, first strand: chain 'J' and resid 3 through 7 removed outlier: 3.995A pdb=" N GLN J 3 " --> pdb=" O SER J 25 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER J 25 " --> pdb=" O GLN J 3 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER J 7 " --> pdb=" O SER J 21 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N SER J 21 " --> pdb=" O SER J 7 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.576A pdb=" N TYR J 94 " --> pdb=" O THR J 116 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 129 through 133 removed outlier: 5.008A pdb=" N ALA J 146 " --> pdb=" O VAL J 193 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL J 193 " --> pdb=" O ALA J 146 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLY J 148 " --> pdb=" O VAL J 191 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL J 191 " --> pdb=" O GLY J 148 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU J 150 " --> pdb=" O SER J 189 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER J 189 " --> pdb=" O LEU J 150 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS J 152 " --> pdb=" O LEU J 187 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU J 187 " --> pdb=" O LYS J 152 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 129 through 133 removed outlier: 5.008A pdb=" N ALA J 146 " --> pdb=" O VAL J 193 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL J 193 " --> pdb=" O ALA J 146 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLY J 148 " --> pdb=" O VAL J 191 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL J 191 " --> pdb=" O GLY J 148 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU J 150 " --> pdb=" O SER J 189 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER J 189 " --> pdb=" O LEU J 150 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS J 152 " --> pdb=" O LEU J 187 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU J 187 " --> pdb=" O LYS J 152 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'J' and resid 159 through 163 Processing sheet with id=AG5, first strand: chain 'N' and resid 5 through 6 removed outlier: 3.914A pdb=" N THR N 5 " --> pdb=" O LYS N 24 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS N 24 " --> pdb=" O THR N 5 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N CYS N 23 " --> pdb=" O PHE N 77 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE N 77 " --> pdb=" O CYS N 23 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'N' and resid 42 through 44 Processing sheet with id=AG7, first strand: chain 'N' and resid 120 through 124 Processing sheet with id=AG8, first strand: chain 'N' and resid 159 through 160 1091 hydrogen bonds defined for protein. 2961 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: 7.53 Time building geometry restraints manager: 3.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9691 1.34 - 1.46: 8286 1.46 - 1.59: 13710 1.59 - 1.72: 0 1.72 - 1.85: 172 Bond restraints: 31859 Sorted by residual: bond pdb=" C THR C 478 " pdb=" N PRO C 479 " ideal model delta sigma weight residual 1.330 1.390 -0.060 1.19e-02 7.06e+03 2.53e+01 bond pdb=" C THR A 478 " pdb=" N PRO A 479 " ideal model delta sigma weight residual 1.330 1.390 -0.059 1.19e-02 7.06e+03 2.49e+01 bond pdb=" N PRO K 147 " pdb=" CD PRO K 147 " ideal model delta sigma weight residual 1.473 1.534 -0.061 1.40e-02 5.10e+03 1.87e+01 bond pdb=" N PRO N 147 " pdb=" CD PRO N 147 " ideal model delta sigma weight residual 1.473 1.533 -0.060 1.40e-02 5.10e+03 1.86e+01 bond pdb=" N PRO A 479 " pdb=" CD PRO A 479 " ideal model delta sigma weight residual 1.473 1.532 -0.059 1.40e-02 5.10e+03 1.79e+01 ... (remaining 31854 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 42226 2.70 - 5.40: 1017 5.40 - 8.10: 81 8.10 - 10.80: 7 10.80 - 13.50: 7 Bond angle restraints: 43338 Sorted by residual: angle pdb=" C PHE A 86 " pdb=" N ASN A 87 " pdb=" CA ASN A 87 " ideal model delta sigma weight residual 121.54 132.82 -11.28 1.91e+00 2.74e-01 3.49e+01 angle pdb=" N GLU C 156 " pdb=" CA GLU C 156 " pdb=" C GLU C 156 " ideal model delta sigma weight residual 108.45 115.86 -7.41 1.26e+00 6.30e-01 3.46e+01 angle pdb=" C THR C 588 " pdb=" N PRO C 589 " pdb=" CA PRO C 589 " ideal model delta sigma weight residual 119.78 114.05 5.73 1.03e+00 9.43e-01 3.10e+01 angle pdb=" C THR A 478 " pdb=" N PRO A 479 " pdb=" CA PRO A 479 " ideal model delta sigma weight residual 119.93 114.02 5.91 1.07e+00 8.73e-01 3.05e+01 angle pdb=" C THR C 478 " pdb=" N PRO C 479 " pdb=" CA PRO C 479 " ideal model delta sigma weight residual 119.93 114.03 5.90 1.07e+00 8.73e-01 3.04e+01 ... (remaining 43333 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 17204 17.91 - 35.82: 1940 35.82 - 53.72: 602 53.72 - 71.63: 197 71.63 - 89.54: 55 Dihedral angle restraints: 19998 sinusoidal: 8717 harmonic: 11281 Sorted by residual: dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual 93.00 12.17 80.83 1 1.00e+01 1.00e-02 8.07e+01 dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual 93.00 19.58 73.42 1 1.00e+01 1.00e-02 6.86e+01 dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.13 71.87 1 1.00e+01 1.00e-02 6.61e+01 ... (remaining 19995 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.329: 5142 0.329 - 0.657: 3 0.657 - 0.986: 4 0.986 - 1.314: 1 1.314 - 1.643: 1 Chirality restraints: 5151 Sorted by residual: chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.54 -0.86 2.00e-02 2.50e+03 1.84e+03 chirality pdb=" C1 NAG B1411 " pdb=" O4 NAG B1410 " pdb=" C2 NAG B1411 " pdb=" O5 NAG B1411 " both_signs ideal model delta sigma weight residual False -2.40 -3.08 0.68 2.00e-02 2.50e+03 1.14e+03 chirality pdb=" C1 NAG c 3 " pdb=" O4 NAG c 2 " pdb=" C2 NAG c 3 " pdb=" O5 NAG c 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-02 2.50e+03 1.43e+02 ... (remaining 5148 not shown) Planarity restraints: 5538 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG d 2 " 0.295 2.00e-02 2.50e+03 2.48e-01 7.69e+02 pdb=" C7 NAG d 2 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG d 2 " 0.188 2.00e-02 2.50e+03 pdb=" N2 NAG d 2 " -0.423 2.00e-02 2.50e+03 pdb=" O7 NAG d 2 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG c 2 " -0.295 2.00e-02 2.50e+03 2.48e-01 7.68e+02 pdb=" C7 NAG c 2 " 0.077 2.00e-02 2.50e+03 pdb=" C8 NAG c 2 " -0.188 2.00e-02 2.50e+03 pdb=" N2 NAG c 2 " 0.423 2.00e-02 2.50e+03 pdb=" O7 NAG c 2 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG U 2 " -0.239 2.00e-02 2.50e+03 1.99e-01 4.94e+02 pdb=" C7 NAG U 2 " 0.065 2.00e-02 2.50e+03 pdb=" C8 NAG U 2 " -0.167 2.00e-02 2.50e+03 pdb=" N2 NAG U 2 " 0.329 2.00e-02 2.50e+03 pdb=" O7 NAG U 2 " 0.012 2.00e-02 2.50e+03 ... (remaining 5535 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 240 2.47 - 3.08: 21254 3.08 - 3.69: 44888 3.69 - 4.29: 68035 4.29 - 4.90: 113052 Nonbonded interactions: 247469 Sorted by model distance: nonbonded pdb=" O ALA K 86 " pdb=" OE1 GLU K 87 " model vdw 1.865 3.040 nonbonded pdb=" O ALA N 86 " pdb=" OE1 GLU N 87 " model vdw 1.865 3.040 nonbonded pdb=" NH1 ARG A 346 " pdb=" O PHE A 347 " model vdw 1.981 3.120 nonbonded pdb=" NH1 ARG C 346 " pdb=" O PHE C 347 " model vdw 1.981 3.120 nonbonded pdb=" O ALA N 86 " pdb=" CD GLU N 87 " model vdw 2.019 3.270 ... (remaining 247464 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 441 or resid 451 through 475 or resid 487 throu \ gh 497 or resid 503 through 620 or resid 641 through 939 or resid 944 through 14 \ 08)) selection = (chain 'B' and (resid 27 through 620 or resid 641 through 826 or resid 855 throu \ gh 1408)) selection = (chain 'C' and (resid 27 through 441 or resid 451 through 475 or resid 487 throu \ gh 497 or resid 503 through 826 or resid 855 through 1408)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'L' selection = chain 'M' 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' selection = chain 'Z' selection = chain 'a' selection = chain 'b' } ncs_group { reference = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'N' } ncs_group { reference = chain 'c' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.060 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: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 28.510 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 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 : 0.013 0.771 31981 Z= 0.582 Angle : 1.294 48.937 43658 Z= 0.658 Chirality : 0.072 1.643 5151 Planarity : 0.009 0.248 5488 Dihedral : 17.632 89.540 12600 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 25.79 Ramachandran Plot: Outliers : 2.65 % Allowed : 10.31 % Favored : 87.04 % Rotamer: Outliers : 12.01 % Allowed : 18.70 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.80 (0.11), residues: 3812 helix: -2.15 (0.16), residues: 661 sheet: -1.57 (0.15), residues: 1013 loop : -3.26 (0.11), residues: 2138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG J 98 TYR 0.026 0.003 TYR B1067 PHE 0.026 0.003 PHE A 898 TRP 0.035 0.003 TRP N 56 HIS 0.009 0.002 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.01077 (31859) covalent geometry : angle 1.02480 (43338) SS BOND : bond 0.17142 ( 46) SS BOND : angle 9.48914 ( 92) hydrogen bonds : bond 0.19081 ( 1037) hydrogen bonds : angle 7.67920 ( 2961) link_BETA1-4 : bond 0.05416 ( 26) link_BETA1-4 : angle 11.28909 ( 78) link_NAG-ASN : bond 0.02516 ( 50) link_NAG-ASN : angle 7.89532 ( 150) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 866 residues out of total 3386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 406 poor density : 460 time to evaluate : 1.204 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 787 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.7349 (mm110) REVERT: A 960 ASN cc_start: 0.8139 (OUTLIER) cc_final: 0.7867 (m110) REVERT: A 976 VAL cc_start: 0.8548 (OUTLIER) cc_final: 0.8344 (t) REVERT: B 214 ARG cc_start: -0.0367 (OUTLIER) cc_final: -0.0954 (mtt180) REVERT: B 421 TYR cc_start: 0.5183 (m-10) cc_final: 0.4959 (m-10) REVERT: B 441 LEU cc_start: 0.5283 (OUTLIER) cc_final: 0.5072 (mt) REVERT: B 462 LYS cc_start: 0.6176 (OUTLIER) cc_final: 0.5648 (pttm) REVERT: B 676 THR cc_start: 0.5930 (OUTLIER) cc_final: 0.5725 (m) REVERT: B 787 GLN cc_start: 0.7788 (OUTLIER) cc_final: 0.7491 (mt0) REVERT: B 1030 SER cc_start: 0.9510 (OUTLIER) cc_final: 0.9088 (m) REVERT: C 200 TYR cc_start: 0.5631 (m-80) cc_final: 0.5230 (m-80) REVERT: C 216 LEU cc_start: 0.2143 (OUTLIER) cc_final: 0.1744 (tp) REVERT: C 389 ASP cc_start: 0.5044 (OUTLIER) cc_final: 0.3230 (t0) REVERT: C 878 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8447 (mt) REVERT: H 30 THR cc_start: -0.1589 (OUTLIER) cc_final: -0.1822 (p) REVERT: K 20 THR cc_start: 0.0155 (m) cc_final: -0.0169 (p) REVERT: K 39 LEU cc_start: 0.1695 (OUTLIER) cc_final: 0.0176 (tt) REVERT: K 59 THR cc_start: 0.3407 (OUTLIER) cc_final: 0.3140 (p) REVERT: J 2 VAL cc_start: -0.0577 (OUTLIER) cc_final: -0.0802 (t) REVERT: J 126 LYS cc_start: 0.1380 (OUTLIER) cc_final: 0.0391 (mmmt) REVERT: N 182 SER cc_start: 0.1741 (OUTLIER) cc_final: 0.1010 (p) outliers start: 406 outliers final: 89 residues processed: 793 average time/residue: 0.1832 time to fit residues: 236.9722 Evaluate side-chains 322 residues out of total 3386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 215 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain K residue 38 TYR Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 99 SER Chi-restraints excluded: chain K residue 100 THR Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 50 TRP Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 107 LYS Chi-restraints excluded: chain J residue 126 LYS Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 38 TYR Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 97 TYR Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain N residue 103 THR Chi-restraints excluded: chain N residue 182 SER Chi-restraints excluded: chain N residue 208 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 GLN A 137 ASN A 188 ASN A 422 ASN A 440 ASN A 481 ASN A 498 GLN A 644 GLN A 658 ASN A 690 GLN A 703 ASN A 787 GLN A 856 ASN A 901 GLN A 914 ASN A 919 ASN A 926 GLN A 955 ASN A 992 GLN A1010 GLN A1054 GLN B 115 GLN B 188 ASN B 409 GLN B 414 GLN B 422 ASN B 487 ASN B 540 ASN B 563 GLN B 703 ASN B 901 GLN B 914 ASN B 919 ASN B 920 GLN B 926 GLN B 992 GLN B1010 GLN B1054 GLN C 30 ASN C 134 GLN C 188 ASN C 280 ASN C 321 GLN C 422 ASN C 440 ASN C 481 ASN C 498 GLN C 536 ASN C 606 ASN C 641 ASN C 690 GLN C 703 ASN C 751 ASN C 784 GLN C 901 GLN C 914 ASN C 926 GLN C 935 GLN C 957 GLN C 969 ASN C 992 GLN C1071 GLN C1101 HIS H 6 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 180 GLN K 43 GLN ** K 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 GLN ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 43 GLN ** N 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 69 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.216138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.172672 restraints weight = 55689.859| |-----------------------------------------------------------------------------| r_work (start): 0.4063 rms_B_bonded: 2.93 r_work: 0.3514 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 31981 Z= 0.173 Angle : 0.869 23.743 43658 Z= 0.421 Chirality : 0.052 0.499 5151 Planarity : 0.005 0.077 5488 Dihedral : 10.220 66.174 5908 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.66 % Allowed : 8.26 % Favored : 91.08 % Rotamer: Outliers : 5.62 % Allowed : 19.56 % Favored : 74.82 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.61 (0.12), residues: 3812 helix: -0.20 (0.20), residues: 683 sheet: -0.95 (0.15), residues: 1037 loop : -2.80 (0.12), residues: 2092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 567 TYR 0.017 0.002 TYR N 93 PHE 0.031 0.002 PHE B 168 TRP 0.025 0.002 TRP N 56 HIS 0.004 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00377 (31859) covalent geometry : angle 0.80020 (43338) SS BOND : bond 0.00705 ( 46) SS BOND : angle 2.58663 ( 92) hydrogen bonds : bond 0.04896 ( 1037) hydrogen bonds : angle 5.82558 ( 2961) link_BETA1-4 : bond 0.00752 ( 26) link_BETA1-4 : angle 3.12052 ( 78) link_NAG-ASN : bond 0.00792 ( 50) link_NAG-ASN : angle 5.08685 ( 150) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 3386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 252 time to evaluate : 1.087 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 81 ASN cc_start: 0.4364 (OUTLIER) cc_final: 0.3920 (t0) REVERT: A 729 VAL cc_start: 0.9036 (OUTLIER) cc_final: 0.8808 (t) REVERT: A 988 GLU cc_start: 0.7240 (mm-30) cc_final: 0.6942 (tp30) REVERT: B 97 LYS cc_start: 0.4236 (OUTLIER) cc_final: 0.3531 (pttt) REVERT: B 129 LYS cc_start: 0.7452 (mtmm) cc_final: 0.7068 (ttmt) REVERT: B 191 GLU cc_start: 0.7234 (mt-10) cc_final: 0.6598 (mp0) REVERT: B 616 ASN cc_start: 0.7591 (OUTLIER) cc_final: 0.7011 (t0) REVERT: B 988 GLU cc_start: 0.8134 (mp0) cc_final: 0.7919 (pm20) REVERT: C 64 TRP cc_start: 0.6004 (t60) cc_final: 0.5736 (t60) REVERT: C 102 ARG cc_start: 0.5194 (tpp-160) cc_final: 0.4848 (tpp-160) REVERT: C 200 TYR cc_start: 0.6447 (m-80) cc_final: 0.5934 (m-80) REVERT: C 237 ARG cc_start: 0.6440 (mtm180) cc_final: 0.5044 (mmt90) REVERT: C 239 GLN cc_start: 0.7192 (mp10) cc_final: 0.6909 (mp10) REVERT: C 389 ASP cc_start: 0.5138 (OUTLIER) cc_final: 0.4102 (t0) REVERT: C 486 PHE cc_start: 0.1900 (OUTLIER) cc_final: 0.0999 (m-80) REVERT: C 586 ASP cc_start: 0.5984 (OUTLIER) cc_final: 0.5517 (m-30) REVERT: C 823 PHE cc_start: 0.8132 (OUTLIER) cc_final: 0.7458 (t80) REVERT: C 878 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8411 (mt) REVERT: C 975 SER cc_start: 0.8550 (OUTLIER) cc_final: 0.8316 (t) REVERT: H 81 MET cc_start: -0.1506 (tmm) cc_final: -0.2038 (mmm) REVERT: K 20 THR cc_start: 0.0544 (m) cc_final: 0.0113 (p) REVERT: K 59 THR cc_start: 0.3029 (OUTLIER) cc_final: 0.2630 (p) REVERT: J 51 MET cc_start: 0.1968 (ptp) cc_final: 0.0030 (mmm) REVERT: J 126 LYS cc_start: 0.1857 (OUTLIER) cc_final: 0.0896 (mmmt) outliers start: 190 outliers final: 92 residues processed: 426 average time/residue: 0.1806 time to fit residues: 128.2992 Evaluate side-chains 292 residues out of total 3386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 188 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain K residue 38 TYR Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 126 LYS Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain N residue 38 TYR Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain N residue 103 THR Chi-restraints excluded: chain N residue 122 PHE Chi-restraints excluded: chain N residue 177 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 300 optimal weight: 6.9990 chunk 301 optimal weight: 20.0000 chunk 268 optimal weight: 0.0000 chunk 197 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 353 optimal weight: 7.9990 chunk 91 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 373 optimal weight: 40.0000 chunk 25 optimal weight: 9.9990 chunk 118 optimal weight: 8.9990 overall best weight: 2.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 658 ASN A 824 ASN A 856 ASN A 955 ASN A1002 GLN B 474 GLN B 913 GLN C 271 GLN C 450 ASN C 658 ASN C 957 GLN C1002 GLN ** K 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 143 ASN J 39 GLN J 180 GLN ** N 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.210700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.169221 restraints weight = 54871.511| |-----------------------------------------------------------------------------| r_work (start): 0.4043 rms_B_bonded: 2.82 r_work: 0.3493 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 31981 Z= 0.207 Angle : 0.840 19.685 43658 Z= 0.401 Chirality : 0.053 0.618 5151 Planarity : 0.005 0.078 5488 Dihedral : 9.143 59.995 5818 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.26 % Favored : 91.42 % Rotamer: Outliers : 5.80 % Allowed : 19.64 % Favored : 74.56 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.02 (0.13), residues: 3812 helix: 0.39 (0.20), residues: 687 sheet: -0.58 (0.15), residues: 1075 loop : -2.48 (0.12), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 34 TYR 0.027 0.002 TYR B 453 PHE 0.025 0.002 PHE B 168 TRP 0.025 0.002 TRP N 56 HIS 0.007 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00484 (31859) covalent geometry : angle 0.78180 (43338) SS BOND : bond 0.00663 ( 46) SS BOND : angle 2.15264 ( 92) hydrogen bonds : bond 0.04921 ( 1037) hydrogen bonds : angle 5.49489 ( 2961) link_BETA1-4 : bond 0.00724 ( 26) link_BETA1-4 : angle 2.76991 ( 78) link_NAG-ASN : bond 0.00881 ( 50) link_NAG-ASN : angle 4.70127 ( 150) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 3386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 202 time to evaluate : 0.748 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 407 VAL cc_start: 0.2628 (OUTLIER) cc_final: 0.2413 (p) REVERT: A 960 ASN cc_start: 0.8528 (OUTLIER) cc_final: 0.8295 (m110) REVERT: B 129 LYS cc_start: 0.7574 (mtmm) cc_final: 0.7222 (ttmt) REVERT: B 191 GLU cc_start: 0.7291 (mt-10) cc_final: 0.6976 (mp0) REVERT: B 214 ARG cc_start: 0.1612 (OUTLIER) cc_final: 0.0720 (mtt180) REVERT: B 341 VAL cc_start: 0.7157 (OUTLIER) cc_final: 0.6780 (p) REVERT: B 981 LEU cc_start: 0.7607 (mt) cc_final: 0.7376 (mt) REVERT: C 102 ARG cc_start: 0.5589 (tpp-160) cc_final: 0.5283 (tpp-160) REVERT: C 200 TYR cc_start: 0.6696 (m-80) cc_final: 0.6223 (m-80) REVERT: C 239 GLN cc_start: 0.7658 (mp10) cc_final: 0.7298 (mp10) REVERT: C 241 LEU cc_start: 0.4713 (OUTLIER) cc_final: 0.4475 (mt) REVERT: C 546 LEU cc_start: 0.5085 (OUTLIER) cc_final: 0.4271 (tt) REVERT: H 81 MET cc_start: -0.1321 (tmm) cc_final: -0.1827 (mmm) REVERT: K 20 THR cc_start: 0.0917 (m) cc_final: 0.0544 (p) REVERT: K 59 THR cc_start: 0.2930 (OUTLIER) cc_final: 0.2524 (p) REVERT: J 70 MET cc_start: 0.1733 (mmp) cc_final: 0.0973 (mpp) REVERT: J 126 LYS cc_start: 0.1779 (OUTLIER) cc_final: 0.0995 (mmmt) outliers start: 196 outliers final: 116 residues processed: 385 average time/residue: 0.1656 time to fit residues: 108.3858 Evaluate side-chains 299 residues out of total 3386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 175 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 177 SER Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 50 TRP Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 126 LYS Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 188 SER Chi-restraints excluded: chain J residue 204 ILE Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 38 TYR Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain N residue 103 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 257 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 218 optimal weight: 9.9990 chunk 109 optimal weight: 10.0000 chunk 201 optimal weight: 8.9990 chunk 348 optimal weight: 30.0000 chunk 153 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 112 optimal weight: 9.9990 chunk 231 optimal weight: 40.0000 chunk 276 optimal weight: 0.8980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN A1101 HIS B 360 ASN C1002 GLN ** K 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 166 GLN ** N 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 166 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.209996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.165732 restraints weight = 53990.708| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 2.79 r_work: 0.3421 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.4515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 31981 Z= 0.180 Angle : 0.775 20.155 43658 Z= 0.370 Chirality : 0.050 0.479 5151 Planarity : 0.005 0.068 5488 Dihedral : 8.867 107.394 5798 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.53 % Favored : 92.13 % Rotamer: Outliers : 5.00 % Allowed : 20.80 % Favored : 74.20 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.13), residues: 3812 helix: 0.85 (0.21), residues: 676 sheet: -0.34 (0.15), residues: 1080 loop : -2.30 (0.12), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 34 TYR 0.022 0.002 TYR A1067 PHE 0.025 0.002 PHE B 168 TRP 0.014 0.001 TRP K 56 HIS 0.006 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00415 (31859) covalent geometry : angle 0.72882 (43338) SS BOND : bond 0.00547 ( 46) SS BOND : angle 1.86810 ( 92) hydrogen bonds : bond 0.04395 ( 1037) hydrogen bonds : angle 5.31646 ( 2961) link_BETA1-4 : bond 0.00613 ( 26) link_BETA1-4 : angle 2.44078 ( 78) link_NAG-ASN : bond 0.00878 ( 50) link_NAG-ASN : angle 4.00848 ( 150) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 3386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 209 time to evaluate : 1.074 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: A 407 VAL cc_start: 0.2971 (OUTLIER) cc_final: 0.2769 (p) REVERT: A 603 ASN cc_start: 0.6804 (OUTLIER) cc_final: 0.5940 (p0) REVERT: A 787 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8101 (mt0) REVERT: A 988 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7386 (tp30) REVERT: B 97 LYS cc_start: 0.3837 (OUTLIER) cc_final: 0.3541 (pttt) REVERT: B 129 LYS cc_start: 0.7646 (mtmm) cc_final: 0.7126 (ttmt) REVERT: B 191 GLU cc_start: 0.7321 (mt-10) cc_final: 0.6939 (mp0) REVERT: B 214 ARG cc_start: 0.2026 (OUTLIER) cc_final: 0.1538 (mmt90) REVERT: B 460 ASN cc_start: 0.6213 (m-40) cc_final: 0.5863 (p0) REVERT: B 969 ASN cc_start: 0.8856 (OUTLIER) cc_final: 0.8652 (m110) REVERT: C 102 ARG cc_start: 0.5881 (tpp-160) cc_final: 0.5461 (tpp-160) REVERT: C 200 TYR cc_start: 0.6687 (m-80) cc_final: 0.6372 (m-80) REVERT: C 229 LEU cc_start: 0.7059 (tt) cc_final: 0.6839 (tt) REVERT: C 239 GLN cc_start: 0.7755 (mp10) cc_final: 0.7245 (mp10) REVERT: C 486 PHE cc_start: 0.2389 (OUTLIER) cc_final: 0.1966 (m-80) REVERT: C 546 LEU cc_start: 0.5701 (OUTLIER) cc_final: 0.5088 (tt) REVERT: H 74 THR cc_start: 0.2148 (OUTLIER) cc_final: 0.1773 (t) REVERT: H 81 MET cc_start: -0.1401 (tmm) cc_final: -0.1706 (mmm) REVERT: K 20 THR cc_start: 0.0840 (m) cc_final: 0.0536 (p) REVERT: K 59 THR cc_start: 0.2999 (OUTLIER) cc_final: 0.2738 (p) REVERT: J 70 MET cc_start: 0.1895 (mmp) cc_final: -0.1628 (ttt) outliers start: 169 outliers final: 102 residues processed: 366 average time/residue: 0.1616 time to fit residues: 101.6597 Evaluate side-chains 295 residues out of total 3386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 183 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 50 TRP Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 121 SER Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 188 SER Chi-restraints excluded: chain J residue 204 ILE Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 103 THR Chi-restraints excluded: chain N residue 127 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 381 optimal weight: 20.0000 chunk 198 optimal weight: 20.0000 chunk 209 optimal weight: 8.9990 chunk 354 optimal weight: 7.9990 chunk 362 optimal weight: 30.0000 chunk 88 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 302 optimal weight: 0.2980 chunk 234 optimal weight: 20.0000 chunk 77 optimal weight: 0.9990 chunk 28 optimal weight: 20.0000 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 856 ASN B 360 ASN B1010 GLN C 66 HIS ** K 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.207928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.163996 restraints weight = 54231.409| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 2.79 r_work: 0.3395 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.4962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 31981 Z= 0.187 Angle : 0.757 20.079 43658 Z= 0.362 Chirality : 0.050 0.443 5151 Planarity : 0.005 0.069 5488 Dihedral : 8.076 59.736 5774 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.74 % Favored : 91.92 % Rotamer: Outliers : 5.27 % Allowed : 20.56 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.13), residues: 3812 helix: 1.04 (0.21), residues: 670 sheet: -0.22 (0.15), residues: 1088 loop : -2.21 (0.12), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 158 TYR 0.050 0.002 TYR N 38 PHE 0.020 0.002 PHE C 58 TRP 0.013 0.001 TRP N 56 HIS 0.009 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00442 (31859) covalent geometry : angle 0.70871 (43338) SS BOND : bond 0.00492 ( 46) SS BOND : angle 1.92783 ( 92) hydrogen bonds : bond 0.04486 ( 1037) hydrogen bonds : angle 5.26924 ( 2961) link_BETA1-4 : bond 0.00593 ( 26) link_BETA1-4 : angle 2.36507 ( 78) link_NAG-ASN : bond 0.00685 ( 50) link_NAG-ASN : angle 4.05422 ( 150) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 191 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.4491 (p90) cc_final: 0.4247 (p90) REVERT: A 277 LEU cc_start: 0.7519 (OUTLIER) cc_final: 0.7260 (mp) REVERT: A 517 LEU cc_start: 0.1487 (OUTLIER) cc_final: 0.1015 (pt) REVERT: A 603 ASN cc_start: 0.7002 (OUTLIER) cc_final: 0.6298 (p0) REVERT: A 787 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.8207 (mt0) REVERT: A 988 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7470 (tp30) REVERT: A 1106 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8725 (pt0) REVERT: B 129 LYS cc_start: 0.7616 (mtmm) cc_final: 0.7067 (ttmt) REVERT: B 191 GLU cc_start: 0.7424 (mt-10) cc_final: 0.7165 (mp0) REVERT: B 214 ARG cc_start: 0.2289 (OUTLIER) cc_final: 0.1784 (mtt180) REVERT: B 233 ILE cc_start: 0.6555 (OUTLIER) cc_final: 0.6193 (tp) REVERT: B 341 VAL cc_start: 0.7022 (OUTLIER) cc_final: 0.6593 (p) REVERT: B 460 ASN cc_start: 0.6303 (m-40) cc_final: 0.5778 (p0) REVERT: C 200 TYR cc_start: 0.6741 (m-80) cc_final: 0.6409 (m-80) REVERT: C 239 GLN cc_start: 0.7880 (mp10) cc_final: 0.7421 (mp10) REVERT: C 486 PHE cc_start: 0.2386 (OUTLIER) cc_final: 0.1366 (t80) REVERT: C 546 LEU cc_start: 0.6131 (OUTLIER) cc_final: 0.5570 (tt) REVERT: H 74 THR cc_start: 0.2237 (OUTLIER) cc_final: 0.1996 (t) REVERT: H 81 MET cc_start: -0.1264 (tmm) cc_final: -0.1613 (mmm) REVERT: K 20 THR cc_start: 0.0701 (m) cc_final: 0.0419 (p) REVERT: J 48 MET cc_start: 0.0764 (ttp) cc_final: 0.0513 (ttp) REVERT: J 70 MET cc_start: 0.1868 (mmp) cc_final: -0.1608 (ttt) REVERT: N 4 MET cc_start: 0.1022 (OUTLIER) cc_final: 0.0355 (pmm) outliers start: 178 outliers final: 127 residues processed: 354 average time/residue: 0.1532 time to fit residues: 95.5695 Evaluate side-chains 309 residues out of total 3386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 170 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 201 GLN Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain K residue 38 TYR Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 177 SER Chi-restraints excluded: chain J residue 50 TRP Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 121 SER Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 188 SER Chi-restraints excluded: chain J residue 204 ILE Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 127 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 120 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 chunk 324 optimal weight: 5.9990 chunk 298 optimal weight: 20.0000 chunk 241 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 chunk 11 optimal weight: 20.0000 chunk 234 optimal weight: 20.0000 chunk 1 optimal weight: 6.9990 chunk 291 optimal weight: 3.9990 chunk 40 optimal weight: 0.0050 overall best weight: 3.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN A 856 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN C 762 GLN C1002 GLN H 52 ASN ** K 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.205271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.159367 restraints weight = 53472.951| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 2.71 r_work: 0.3366 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.5524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 31981 Z= 0.230 Angle : 0.805 20.513 43658 Z= 0.384 Chirality : 0.051 0.391 5151 Planarity : 0.005 0.067 5488 Dihedral : 8.175 59.833 5770 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.39 % Favored : 91.29 % Rotamer: Outliers : 5.38 % Allowed : 21.04 % Favored : 73.58 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.13), residues: 3812 helix: 0.93 (0.21), residues: 675 sheet: -0.27 (0.15), residues: 1071 loop : -2.25 (0.12), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 357 TYR 0.030 0.002 TYR K 38 PHE 0.028 0.002 PHE C 400 TRP 0.015 0.002 TRP C 64 HIS 0.006 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00548 (31859) covalent geometry : angle 0.75385 (43338) SS BOND : bond 0.00570 ( 46) SS BOND : angle 1.97326 ( 92) hydrogen bonds : bond 0.04907 ( 1037) hydrogen bonds : angle 5.37038 ( 2961) link_BETA1-4 : bond 0.00768 ( 26) link_BETA1-4 : angle 2.34922 ( 78) link_NAG-ASN : bond 0.01037 ( 50) link_NAG-ASN : angle 4.40103 ( 150) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 187 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.5088 (p90) cc_final: 0.4873 (p90) REVERT: A 343 ASN cc_start: 0.2968 (OUTLIER) cc_final: 0.2761 (t0) REVERT: A 392 PHE cc_start: 0.6502 (OUTLIER) cc_final: 0.5009 (m-80) REVERT: A 525 CYS cc_start: 0.4403 (OUTLIER) cc_final: 0.4146 (m) REVERT: A 762 GLN cc_start: 0.8580 (mm-40) cc_final: 0.8362 (mm110) REVERT: A 1106 GLN cc_start: 0.9102 (OUTLIER) cc_final: 0.8799 (pt0) REVERT: A 1139 ASP cc_start: 0.8645 (t0) cc_final: 0.7970 (p0) REVERT: B 129 LYS cc_start: 0.7432 (mtmm) cc_final: 0.7231 (ttmt) REVERT: B 191 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7521 (mp0) REVERT: B 200 TYR cc_start: 0.7032 (m-80) cc_final: 0.6754 (m-80) REVERT: B 211 ASN cc_start: 0.5761 (OUTLIER) cc_final: 0.5237 (p0) REVERT: B 341 VAL cc_start: 0.6904 (OUTLIER) cc_final: 0.6422 (p) REVERT: B 460 ASN cc_start: 0.6293 (m-40) cc_final: 0.5694 (p0) REVERT: C 200 TYR cc_start: 0.6866 (m-80) cc_final: 0.6656 (m-80) REVERT: C 239 GLN cc_start: 0.8119 (mp10) cc_final: 0.7708 (mp10) REVERT: C 486 PHE cc_start: 0.2684 (OUTLIER) cc_final: 0.1055 (t80) REVERT: H 81 MET cc_start: -0.1138 (tmm) cc_final: -0.1366 (mmt) REVERT: K 20 THR cc_start: 0.0473 (m) cc_final: 0.0240 (p) REVERT: J 70 MET cc_start: 0.2049 (mmp) cc_final: -0.1277 (ttt) REVERT: N 4 MET cc_start: 0.1217 (OUTLIER) cc_final: 0.0425 (pmm) outliers start: 182 outliers final: 124 residues processed: 356 average time/residue: 0.1619 time to fit residues: 99.4695 Evaluate side-chains 295 residues out of total 3386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 163 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 201 GLN Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 177 SER Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 50 TRP Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 121 SER Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 182 SER Chi-restraints excluded: chain J residue 204 ILE Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 127 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 47 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 158 optimal weight: 0.8980 chunk 350 optimal weight: 50.0000 chunk 198 optimal weight: 20.0000 chunk 259 optimal weight: 0.8980 chunk 68 optimal weight: 0.4980 chunk 384 optimal weight: 1.9990 chunk 226 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 277 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN B 414 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN ** K 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 130 GLN ** 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 = 0.4486 r_free = 0.4486 target = 0.207083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.162286 restraints weight = 53512.493| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 2.69 r_work: 0.3405 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.5678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 31981 Z= 0.134 Angle : 0.715 19.983 43658 Z= 0.339 Chirality : 0.048 0.391 5151 Planarity : 0.004 0.069 5488 Dihedral : 7.533 59.894 5762 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.42 % Favored : 92.26 % Rotamer: Outliers : 4.02 % Allowed : 22.34 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.13), residues: 3812 helix: 1.27 (0.21), residues: 669 sheet: -0.09 (0.15), residues: 1075 loop : -2.14 (0.12), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 355 TYR 0.024 0.001 TYR N 38 PHE 0.020 0.001 PHE C 58 TRP 0.015 0.001 TRP H 47 HIS 0.003 0.001 HIS H 209 Details of bonding type rmsd covalent geometry : bond 0.00304 (31859) covalent geometry : angle 0.67004 (43338) SS BOND : bond 0.00399 ( 46) SS BOND : angle 1.71771 ( 92) hydrogen bonds : bond 0.03951 ( 1037) hydrogen bonds : angle 5.12125 ( 2961) link_BETA1-4 : bond 0.00614 ( 26) link_BETA1-4 : angle 2.21092 ( 78) link_NAG-ASN : bond 0.00729 ( 50) link_NAG-ASN : angle 3.84172 ( 150) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 3386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 184 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 PHE cc_start: 0.8069 (m-10) cc_final: 0.7820 (m-10) REVERT: A 517 LEU cc_start: 0.1199 (OUTLIER) cc_final: 0.0827 (pt) REVERT: A 525 CYS cc_start: 0.4445 (OUTLIER) cc_final: 0.4209 (m) REVERT: A 722 VAL cc_start: 0.9433 (OUTLIER) cc_final: 0.9190 (t) REVERT: A 787 GLN cc_start: 0.9024 (OUTLIER) cc_final: 0.8361 (mt0) REVERT: A 988 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7495 (tp30) REVERT: A 1106 GLN cc_start: 0.8978 (OUTLIER) cc_final: 0.8630 (pt0) REVERT: A 1139 ASP cc_start: 0.8638 (t0) cc_final: 0.8006 (p0) REVERT: B 129 LYS cc_start: 0.7443 (mtmm) cc_final: 0.7200 (ttmt) REVERT: B 200 TYR cc_start: 0.7049 (m-80) cc_final: 0.6709 (m-80) REVERT: B 214 ARG cc_start: 0.2142 (OUTLIER) cc_final: 0.0752 (mtm-85) REVERT: B 341 VAL cc_start: 0.6813 (OUTLIER) cc_final: 0.6354 (p) REVERT: B 460 ASN cc_start: 0.6302 (m-40) cc_final: 0.5660 (p0) REVERT: C 239 GLN cc_start: 0.8019 (mp10) cc_final: 0.7616 (mp10) REVERT: C 486 PHE cc_start: 0.2605 (OUTLIER) cc_final: 0.1076 (t80) REVERT: C 811 LYS cc_start: 0.6560 (OUTLIER) cc_final: 0.5940 (ptmt) REVERT: C 904 TYR cc_start: 0.8586 (m-10) cc_final: 0.8382 (m-10) REVERT: J 70 MET cc_start: 0.1864 (mmp) cc_final: -0.1430 (ttt) REVERT: N 4 MET cc_start: 0.0894 (OUTLIER) cc_final: 0.0364 (pmm) outliers start: 136 outliers final: 109 residues processed: 308 average time/residue: 0.1693 time to fit residues: 90.0301 Evaluate side-chains 287 residues out of total 3386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 168 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 811 LYS Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 201 GLN Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 38 TYR Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 50 TRP Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 121 SER Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 204 ILE Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 61 GLU Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 87 GLU Chi-restraints excluded: chain N residue 127 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 64 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 306 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 202 optimal weight: 0.0770 chunk 349 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 chunk 216 optimal weight: 9.9990 chunk 204 optimal weight: 7.9990 chunk 363 optimal weight: 7.9990 chunk 346 optimal weight: 9.9990 overall best weight: 5.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN B 360 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B 913 GLN B1010 GLN C 751 ASN ** K 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.202660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.155553 restraints weight = 53507.812| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 2.69 r_work: 0.3324 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.6148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.101 31981 Z= 0.295 Angle : 0.861 21.088 43658 Z= 0.411 Chirality : 0.054 0.413 5151 Planarity : 0.005 0.073 5488 Dihedral : 8.723 88.935 5762 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.10 % Favored : 90.61 % Rotamer: Outliers : 4.79 % Allowed : 22.16 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.13), residues: 3812 helix: 0.77 (0.20), residues: 674 sheet: -0.29 (0.15), residues: 1089 loop : -2.36 (0.12), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 454 TYR 0.021 0.002 TYR A1067 PHE 0.026 0.002 PHE A 86 TRP 0.013 0.002 TRP C 104 HIS 0.008 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00710 (31859) covalent geometry : angle 0.81278 (43338) SS BOND : bond 0.00577 ( 46) SS BOND : angle 2.26961 ( 92) hydrogen bonds : bond 0.05568 ( 1037) hydrogen bonds : angle 5.56096 ( 2961) link_BETA1-4 : bond 0.00586 ( 26) link_BETA1-4 : angle 2.52520 ( 78) link_NAG-ASN : bond 0.00766 ( 50) link_NAG-ASN : angle 4.29235 ( 150) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 172 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 PHE cc_start: 0.6488 (OUTLIER) cc_final: 0.4930 (m-80) REVERT: A 525 CYS cc_start: 0.4482 (OUTLIER) cc_final: 0.4225 (m) REVERT: A 722 VAL cc_start: 0.9505 (OUTLIER) cc_final: 0.9156 (t) REVERT: A 787 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.8277 (mt0) REVERT: A 988 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7608 (tp30) REVERT: A 1106 GLN cc_start: 0.9123 (OUTLIER) cc_final: 0.8841 (pt0) REVERT: A 1139 ASP cc_start: 0.8450 (t0) cc_final: 0.7992 (p0) REVERT: B 129 LYS cc_start: 0.7281 (mtmm) cc_final: 0.7038 (ttmt) REVERT: B 200 TYR cc_start: 0.7270 (m-80) cc_final: 0.6856 (m-80) REVERT: B 245 HIS cc_start: 0.4522 (OUTLIER) cc_final: 0.4317 (m170) REVERT: B 341 VAL cc_start: 0.7035 (OUTLIER) cc_final: 0.6505 (p) REVERT: B 460 ASN cc_start: 0.6308 (m-40) cc_final: 0.5748 (p0) REVERT: C 40 ASP cc_start: 0.7089 (m-30) cc_final: 0.6688 (m-30) REVERT: C 239 GLN cc_start: 0.8180 (mp10) cc_final: 0.7809 (mp10) REVERT: J 70 MET cc_start: 0.1629 (mmp) cc_final: -0.1715 (ttt) REVERT: J 81 MET cc_start: 0.0514 (tpt) cc_final: 0.0218 (tpt) REVERT: N 4 MET cc_start: 0.0913 (OUTLIER) cc_final: 0.0382 (mtm) REVERT: N 114 ARG cc_start: 0.2536 (OUTLIER) cc_final: 0.1840 (mmp80) outliers start: 162 outliers final: 130 residues processed: 317 average time/residue: 0.1617 time to fit residues: 89.1344 Evaluate side-chains 301 residues out of total 3386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 162 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 811 LYS Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 50 TRP Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 201 GLN Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 38 TYR Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 177 SER Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 50 TRP Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 121 SER Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 182 SER Chi-restraints excluded: chain J residue 204 ILE Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 61 GLU Chi-restraints excluded: chain N residue 87 GLU Chi-restraints excluded: chain N residue 114 ARG Chi-restraints excluded: chain N residue 127 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 19 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 166 optimal weight: 0.7980 chunk 110 optimal weight: 0.8980 chunk 189 optimal weight: 0.6980 chunk 227 optimal weight: 7.9990 chunk 107 optimal weight: 30.0000 chunk 259 optimal weight: 0.9990 chunk 171 optimal weight: 0.7980 chunk 262 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN B1010 GLN ** K 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN ** N 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.207036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.162481 restraints weight = 53165.866| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 2.67 r_work: 0.3418 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.6214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31981 Z= 0.120 Angle : 0.711 19.745 43658 Z= 0.337 Chirality : 0.048 0.388 5151 Planarity : 0.004 0.074 5488 Dihedral : 7.970 109.691 5762 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.56 % Favored : 93.15 % Rotamer: Outliers : 2.69 % Allowed : 24.38 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.13), residues: 3812 helix: 1.26 (0.21), residues: 675 sheet: -0.12 (0.15), residues: 1088 loop : -2.14 (0.12), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 319 TYR 0.022 0.001 TYR N 38 PHE 0.018 0.001 PHE C 133 TRP 0.017 0.001 TRP C 104 HIS 0.003 0.000 HIS H 209 Details of bonding type rmsd covalent geometry : bond 0.00255 (31859) covalent geometry : angle 0.66756 (43338) SS BOND : bond 0.00357 ( 46) SS BOND : angle 1.47919 ( 92) hydrogen bonds : bond 0.03696 ( 1037) hydrogen bonds : angle 5.07596 ( 2961) link_BETA1-4 : bond 0.00662 ( 26) link_BETA1-4 : angle 2.17729 ( 78) link_NAG-ASN : bond 0.00776 ( 50) link_NAG-ASN : angle 3.81231 ( 150) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 186 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 517 LEU cc_start: 0.0669 (OUTLIER) cc_final: 0.0375 (pt) REVERT: A 525 CYS cc_start: 0.4506 (OUTLIER) cc_final: 0.4289 (m) REVERT: A 787 GLN cc_start: 0.9037 (OUTLIER) cc_final: 0.8381 (mt0) REVERT: A 988 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7604 (tp30) REVERT: A 1106 GLN cc_start: 0.8917 (OUTLIER) cc_final: 0.8541 (pt0) REVERT: A 1139 ASP cc_start: 0.8667 (t0) cc_final: 0.8093 (p0) REVERT: B 129 LYS cc_start: 0.7399 (mtmm) cc_final: 0.7175 (ttmt) REVERT: B 200 TYR cc_start: 0.7227 (m-80) cc_final: 0.6614 (m-80) REVERT: B 269 TYR cc_start: 0.8263 (m-80) cc_final: 0.7870 (m-80) REVERT: B 460 ASN cc_start: 0.6272 (m-40) cc_final: 0.5667 (p0) REVERT: B 675 GLN cc_start: 0.6910 (mm110) cc_final: 0.6502 (mt0) REVERT: C 40 ASP cc_start: 0.7323 (m-30) cc_final: 0.6756 (m-30) REVERT: C 239 GLN cc_start: 0.8053 (mp10) cc_final: 0.7630 (mp10) REVERT: C 811 LYS cc_start: 0.6590 (OUTLIER) cc_final: 0.6149 (ptmt) REVERT: C 904 TYR cc_start: 0.8537 (m-10) cc_final: 0.8331 (m-10) REVERT: J 70 MET cc_start: 0.1352 (mmp) cc_final: -0.1806 (ttt) REVERT: N 4 MET cc_start: 0.1112 (OUTLIER) cc_final: 0.0350 (pmm) outliers start: 91 outliers final: 63 residues processed: 267 average time/residue: 0.1699 time to fit residues: 77.5724 Evaluate side-chains 242 residues out of total 3386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 173 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 811 LYS Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 50 TRP Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 38 TYR Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain J residue 50 TRP Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 121 SER Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 204 ILE Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 87 GLU Chi-restraints excluded: chain N residue 127 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 1 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 312 optimal weight: 7.9990 chunk 184 optimal weight: 0.0970 chunk 321 optimal weight: 30.0000 chunk 178 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 296 optimal weight: 0.7980 chunk 187 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 246 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN B 360 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN C 907 ASN ** K 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.207021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.162009 restraints weight = 53124.290| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 2.69 r_work: 0.3415 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.6307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31981 Z= 0.120 Angle : 0.708 19.731 43658 Z= 0.334 Chirality : 0.052 1.232 5151 Planarity : 0.004 0.071 5488 Dihedral : 7.612 105.344 5758 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.53 % Favored : 92.18 % Rotamer: Outliers : 1.98 % Allowed : 25.15 % Favored : 72.87 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.13), residues: 3812 helix: 1.44 (0.21), residues: 681 sheet: 0.09 (0.15), residues: 1077 loop : -2.09 (0.13), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 319 TYR 0.021 0.001 TYR B 369 PHE 0.026 0.001 PHE B 168 TRP 0.012 0.001 TRP C 104 HIS 0.003 0.000 HIS H 209 Details of bonding type rmsd covalent geometry : bond 0.00257 (31859) covalent geometry : angle 0.66640 (43338) SS BOND : bond 0.00362 ( 46) SS BOND : angle 1.45818 ( 92) hydrogen bonds : bond 0.03561 ( 1037) hydrogen bonds : angle 4.93476 ( 2961) link_BETA1-4 : bond 0.00552 ( 26) link_BETA1-4 : angle 2.07749 ( 78) link_NAG-ASN : bond 0.00997 ( 50) link_NAG-ASN : angle 3.72528 ( 150) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 3386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 179 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.7794 (tt) cc_final: 0.7211 (mp) REVERT: A 190 ARG cc_start: 0.6504 (ptp-170) cc_final: 0.6063 (ptp90) REVERT: A 306 PHE cc_start: 0.8157 (m-10) cc_final: 0.7925 (m-10) REVERT: A 517 LEU cc_start: 0.0647 (OUTLIER) cc_final: 0.0339 (pt) REVERT: A 787 GLN cc_start: 0.9031 (OUTLIER) cc_final: 0.8372 (mt0) REVERT: A 988 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7446 (tp30) REVERT: A 1139 ASP cc_start: 0.8659 (t0) cc_final: 0.8077 (p0) REVERT: B 129 LYS cc_start: 0.7432 (mtmm) cc_final: 0.7170 (ttmt) REVERT: B 200 TYR cc_start: 0.7255 (m-80) cc_final: 0.6576 (m-80) REVERT: B 214 ARG cc_start: 0.1830 (OUTLIER) cc_final: 0.0836 (mpp-170) REVERT: B 228 ASP cc_start: 0.7366 (t70) cc_final: 0.6874 (p0) REVERT: B 269 TYR cc_start: 0.8233 (m-80) cc_final: 0.7858 (m-80) REVERT: B 460 ASN cc_start: 0.6202 (m-40) cc_final: 0.5534 (p0) REVERT: B 675 GLN cc_start: 0.6933 (mm110) cc_final: 0.6542 (mt0) REVERT: C 40 ASP cc_start: 0.7180 (m-30) cc_final: 0.6624 (m-30) REVERT: C 239 GLN cc_start: 0.8033 (mp10) cc_final: 0.7599 (mp10) REVERT: C 269 TYR cc_start: 0.5067 (m-10) cc_final: 0.4852 (m-10) REVERT: C 811 LYS cc_start: 0.6522 (OUTLIER) cc_final: 0.6018 (ptmt) REVERT: J 70 MET cc_start: 0.1139 (mmp) cc_final: -0.1551 (ttt) REVERT: N 4 MET cc_start: 0.1089 (OUTLIER) cc_final: 0.0732 (mtm) outliers start: 67 outliers final: 55 residues processed: 239 average time/residue: 0.1707 time to fit residues: 69.7309 Evaluate side-chains 229 residues out of total 3386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 169 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 811 LYS Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 38 TYR Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain J residue 50 TRP Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 121 SER Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 204 ILE Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 53 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 93 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 125 optimal weight: 4.9990 chunk 364 optimal weight: 0.3980 chunk 261 optimal weight: 0.9980 chunk 63 optimal weight: 0.0970 chunk 26 optimal weight: 10.0000 chunk 176 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 25 optimal weight: 20.0000 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN B 360 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN H 52 ASN ** K 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.206869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.161874 restraints weight = 53291.286| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 2.71 r_work: 0.3408 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.6406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 31981 Z= 0.124 Angle : 0.698 19.824 43658 Z= 0.329 Chirality : 0.048 0.772 5151 Planarity : 0.004 0.068 5488 Dihedral : 7.477 103.812 5755 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.21 % Favored : 92.50 % Rotamer: Outliers : 2.22 % Allowed : 24.85 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.13), residues: 3812 helix: 1.50 (0.21), residues: 681 sheet: 0.19 (0.15), residues: 1057 loop : -2.05 (0.13), residues: 2074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 319 TYR 0.021 0.001 TYR B 369 PHE 0.024 0.001 PHE A 306 TRP 0.011 0.001 TRP J 50 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00278 (31859) covalent geometry : angle 0.65687 (43338) SS BOND : bond 0.00372 ( 46) SS BOND : angle 1.51334 ( 92) hydrogen bonds : bond 0.03659 ( 1037) hydrogen bonds : angle 4.91208 ( 2961) link_BETA1-4 : bond 0.00551 ( 26) link_BETA1-4 : angle 2.04642 ( 78) link_NAG-ASN : bond 0.00745 ( 50) link_NAG-ASN : angle 3.67913 ( 150) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8793.27 seconds wall clock time: 150 minutes 51.57 seconds (9051.57 seconds total)