Starting phenix.real_space_refine on Fri May 23 17:22:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jxe_36698/05_2025/8jxe_36698.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jxe_36698/05_2025/8jxe_36698.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jxe_36698/05_2025/8jxe_36698.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jxe_36698/05_2025/8jxe_36698.map" model { file = "/net/cci-nas-00/data/ceres_data/8jxe_36698/05_2025/8jxe_36698.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jxe_36698/05_2025/8jxe_36698.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 12 9.91 5 Ni 2 6.56 5 S 168 5.16 5 C 14962 2.51 5 N 4113 2.21 5 O 4720 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 23977 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 11477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1469, 11477 Classifications: {'peptide': 1469} Link IDs: {'PTRANS': 73, 'TRANS': 1395} Chain: "B" Number of atoms: 11468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1468, 11468 Classifications: {'peptide': 1468} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 73, 'TRANS': 1394} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 33 Classifications: {'peptide': 6} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 5} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'UNK:plan-1': 5} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 16 Classifications: {'peptide': 3} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'UNK:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "K" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 23 Classifications: {'peptide': 3} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UNK:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Classifications: {'peptide': 2} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'UNK:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 28 Classifications: {'peptide': 5} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'UNK:plan-1': 4} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 33 Classifications: {'peptide': 6} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 5} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'UNK:plan-1': 5} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 16 Classifications: {'peptide': 3} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'UNK:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "G" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 23 Classifications: {'peptide': 3} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UNK:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Classifications: {'peptide': 2} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'UNK:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 28 Classifications: {'peptide': 5} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'UNK:plan-1': 4} Unresolved non-hydrogen planarities: 4 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: "A" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 77 Unusual residues: {' CA': 6, ' NI': 1, 'A2G': 1, 'NAG': 4} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 77 Unusual residues: {' CA': 6, ' NI': 1, 'A2G': 1, 'NAG': 4} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 22989 SG CYS J 2 58.519 86.165 113.217 1.00 29.87 S ATOM 23099 SG CYS D 2 79.016 90.271 114.666 1.00 13.08 S Time building chain proxies: 14.76, per 1000 atoms: 0.62 Number of scatterers: 23977 At special positions: 0 Unit cell: (142.511, 174.964, 150.977, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ni 2 28.00 Ca 12 19.99 S 168 16.00 O 4720 8.00 N 4113 7.00 C 14962 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=55, symmetry=0 Simple disulfide: pdb=" SG CYS A1313 " - pdb=" SG CYS A1326 " distance=2.03 Simple disulfide: pdb=" SG CYS A1320 " - pdb=" SG CYS A1339 " distance=2.03 Simple disulfide: pdb=" SG CYS A1333 " - pdb=" SG CYS A1349 " distance=2.03 Simple disulfide: pdb=" SG CYS A1354 " - pdb=" SG CYS A1365 " distance=2.03 Simple disulfide: pdb=" SG CYS A1361 " - pdb=" SG CYS A1374 " distance=2.03 Simple disulfide: pdb=" SG CYS A1376 " - pdb=" SG CYS A1389 " distance=2.03 Simple disulfide: pdb=" SG CYS A1395 " - pdb=" SG CYS A1405 " distance=2.03 Simple disulfide: pdb=" SG CYS A1401 " - pdb=" SG CYS A1414 " distance=2.03 Simple disulfide: pdb=" SG CYS A1416 " - pdb=" SG CYS A1429 " distance=2.03 Simple disulfide: pdb=" SG CYS A1705 " - pdb=" SG CYS A1714 " distance=2.03 Simple disulfide: pdb=" SG CYS A1710 " - pdb=" SG CYS A1726 " distance=2.03 Simple disulfide: pdb=" SG CYS A1728 " - pdb=" SG CYS A1741 " distance=2.03 Simple disulfide: pdb=" SG CYS A2023 " - pdb=" SG CYS A2034 " distance=2.03 Simple disulfide: pdb=" SG CYS A2030 " - pdb=" SG CYS A2044 " distance=2.03 Simple disulfide: pdb=" SG CYS A2046 " - pdb=" SG CYS A2059 " distance=2.03 Simple disulfide: pdb=" SG CYS A2347 " - pdb=" SG CYS A2358 " distance=2.03 Simple disulfide: pdb=" SG CYS A2354 " - pdb=" SG CYS A2369 " distance=2.03 Simple disulfide: pdb=" SG CYS A2371 " - pdb=" SG CYS A2383 " distance=2.03 Simple disulfide: pdb=" SG CYS A2518 " - pdb=" SG CYS A2652 " distance=2.03 Simple disulfide: pdb=" SG CYS A2656 " - pdb=" SG CYS A2667 " distance=2.03 Simple disulfide: pdb=" SG CYS A2663 " - pdb=" SG CYS A2676 " distance=2.03 Simple disulfide: pdb=" SG CYS A2678 " - pdb=" SG CYS A2693 " distance=2.03 Simple disulfide: pdb=" SG CYS A2701 " - pdb=" SG CYS A2713 " distance=2.03 Simple disulfide: pdb=" SG CYS A2708 " - pdb=" SG CYS A2726 " distance=2.03 Simple disulfide: pdb=" SG CYS A2720 " - pdb=" SG CYS A2737 " distance=2.03 Simple disulfide: pdb=" SG CYS A2742 " - pdb=" SG CYS A2754 " distance=2.03 Simple disulfide: pdb=" SG CYS A2749 " - pdb=" SG CYS A2767 " distance=2.03 Simple disulfide: pdb=" SG CYS A2761 " - pdb=" SG CYS A2776 " distance=2.03 Simple disulfide: pdb=" SG CYS B1313 " - pdb=" SG CYS B1326 " distance=2.03 Simple disulfide: pdb=" SG CYS B1320 " - pdb=" SG CYS B1339 " distance=2.03 Simple disulfide: pdb=" SG CYS B1333 " - pdb=" SG CYS B1349 " distance=2.04 Simple disulfide: pdb=" SG CYS B1354 " - pdb=" SG CYS B1365 " distance=2.03 Simple disulfide: pdb=" SG CYS B1361 " - pdb=" SG CYS B1374 " distance=2.03 Simple disulfide: pdb=" SG CYS B1376 " - pdb=" SG CYS B1389 " distance=2.03 Simple disulfide: pdb=" SG CYS B1395 " - pdb=" SG CYS B1405 " distance=2.03 Simple disulfide: pdb=" SG CYS B1401 " - pdb=" SG CYS B1414 " distance=2.03 Simple disulfide: pdb=" SG CYS B1416 " - pdb=" SG CYS B1429 " distance=2.03 Simple disulfide: pdb=" SG CYS B1710 " - pdb=" SG CYS B1726 " distance=2.03 Simple disulfide: pdb=" SG CYS B1728 " - pdb=" SG CYS B1741 " distance=2.03 Simple disulfide: pdb=" SG CYS B2023 " - pdb=" SG CYS B2034 " distance=2.03 Simple disulfide: pdb=" SG CYS B2030 " - pdb=" SG CYS B2044 " distance=2.03 Simple disulfide: pdb=" SG CYS B2046 " - pdb=" SG CYS B2059 " distance=2.03 Simple disulfide: pdb=" SG CYS B2347 " - pdb=" SG CYS B2358 " distance=2.03 Simple disulfide: pdb=" SG CYS B2354 " - pdb=" SG CYS B2369 " distance=2.03 Simple disulfide: pdb=" SG CYS B2371 " - pdb=" SG CYS B2383 " distance=2.03 Simple disulfide: pdb=" SG CYS B2518 " - pdb=" SG CYS B2652 " distance=2.03 Simple disulfide: pdb=" SG CYS B2656 " - pdb=" SG CYS B2667 " distance=2.03 Simple disulfide: pdb=" SG CYS B2663 " - pdb=" SG CYS B2676 " distance=2.03 Simple disulfide: pdb=" SG CYS B2678 " - pdb=" SG CYS B2693 " distance=2.03 Simple disulfide: pdb=" SG CYS B2701 " - pdb=" SG CYS B2713 " distance=2.03 Simple disulfide: pdb=" SG CYS B2708 " - pdb=" SG CYS B2726 " distance=2.03 Simple disulfide: pdb=" SG CYS B2720 " - pdb=" SG CYS B2737 " distance=2.03 Simple disulfide: pdb=" SG CYS B2742 " - pdb=" SG CYS B2754 " distance=2.04 Simple disulfide: pdb=" SG CYS B2749 " - pdb=" SG CYS B2767 " distance=2.03 Simple disulfide: pdb=" SG CYS B2761 " - pdb=" SG CYS B2776 " 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=2, symmetry=0 Links applied ALPHA1-3 " BMA O 3 " - " MAN O 4 " " BMA Q 3 " - " MAN Q 4 " " BMA X 3 " - " MAN X 4 " " BMA Z 3 " - " MAN Z 4 " ALPHA1-6 " BMA O 3 " - " MAN O 5 " " BMA Q 3 " - " MAN Q 5 " " BMA X 3 " - " MAN X 5 " " BMA Z 3 " - " MAN Z 5 " BETA1-3 " NAG R 1 " - " NAG R 2 " " NAG Z 1 " - " NAG Z 2 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " NAG-ASN " NAG A4701 " - " ASN A1384 " " NAG A4702 " - " ASN A2134 " " NAG A4703 " - " ASN A2225 " " NAG A4704 " - " ASN A2488 " " NAG B4701 " - " ASN B1384 " " NAG B4702 " - " ASN B2134 " " NAG B4703 " - " ASN B2225 " " NAG B4704 " - " ASN B2488 " " NAG E 1 " - " ASN A1451 " " NAG F 1 " - " ASN A1497 " " NAG M 1 " - " ASN A1551 " " NAG N 1 " - " ASN A1676 " " NAG O 1 " - " ASN A1733 " " NAG P 1 " - " ASN A1811 " " NAG Q 1 " - " ASN A2178 " " NAG R 1 " - " ASN A2396 " " NAG S 1 " - " ASN A2548 " " NAG T 1 " - " ASN B1451 " " NAG U 1 " - " ASN B1497 " " NAG V 1 " - " ASN B1551 " " NAG W 1 " - " ASN B1676 " " NAG X 1 " - " ASN B1733 " " NAG Y 1 " - " ASN B1811 " " NAG Z 1 " - " ASN B2178 " " NAG a 1 " - " ASN B2396 " " NAG b 1 " - " ASN B2548 " TRANS " UNK G 4 " - " GLU G 3 " " UNK K 4 " - " GLU K 3 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.56 Conformation dependent library (CDL) restraints added in 2.9 seconds 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5486 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 78 sheets defined 4.4% alpha, 35.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.22 Creating SS restraints... Processing helix chain 'A' and resid 1328 through 1332 Processing helix chain 'A' and resid 1356 through 1360 Processing helix chain 'A' and resid 1694 through 1698 Processing helix chain 'A' and resid 1788 through 1790 No H-bonds generated for 'chain 'A' and resid 1788 through 1790' Processing helix chain 'A' and resid 2016 through 2020 removed outlier: 4.108A pdb=" N SER A2020 " --> pdb=" O ALA A2017 " (cutoff:3.500A) Processing helix chain 'A' and resid 2021 through 2026 Processing helix chain 'A' and resid 2119 through 2123 removed outlier: 3.562A pdb=" N SER A2122 " --> pdb=" O VAL A2119 " (cutoff:3.500A) Processing helix chain 'A' and resid 2345 through 2354 removed outlier: 4.401A pdb=" N SER A2350 " --> pdb=" O CYS A2347 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ASN A2351 " --> pdb=" O LEU A2348 " (cutoff:3.500A) Processing helix chain 'A' and resid 2654 through 2663 removed outlier: 4.674A pdb=" N PHE A2659 " --> pdb=" O CYS A2656 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ASN A2660 " --> pdb=" O ASP A2657 " (cutoff:3.500A) Processing helix chain 'A' and resid 2687 through 2691 Processing helix chain 'A' and resid 2717 through 2719 No H-bonds generated for 'chain 'A' and resid 2717 through 2719' Processing helix chain 'A' and resid 2729 through 2732 Processing helix chain 'A' and resid 2733 through 2738 removed outlier: 3.514A pdb=" N CYS A2737 " --> pdb=" O LEU A2733 " (cutoff:3.500A) Processing helix chain 'A' and resid 2756 through 2760 Processing helix chain 'B' and resid 1328 through 1332 removed outlier: 3.844A pdb=" N LEU B1332 " --> pdb=" O LEU B1329 " (cutoff:3.500A) Processing helix chain 'B' and resid 1357 through 1361 Processing helix chain 'B' and resid 1694 through 1698 Processing helix chain 'B' and resid 1788 through 1790 No H-bonds generated for 'chain 'B' and resid 1788 through 1790' Processing helix chain 'B' and resid 2021 through 2026 Processing helix chain 'B' and resid 2350 through 2354 Processing helix chain 'B' and resid 2654 through 2663 removed outlier: 3.935A pdb=" N GLN B2658 " --> pdb=" O PRO B2655 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N PHE B2659 " --> pdb=" O CYS B2656 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ASN B2660 " --> pdb=" O ASP B2657 " (cutoff:3.500A) Processing helix chain 'B' and resid 2717 through 2719 No H-bonds generated for 'chain 'B' and resid 2717 through 2719' Processing helix chain 'B' and resid 2733 through 2738 Processing helix chain 'B' and resid 2770 through 2774 Processing sheet with id=AA1, first strand: chain 'A' and resid 1318 through 1319 Processing sheet with id=AA2, first strand: chain 'A' and resid 1364 through 1366 removed outlier: 3.825A pdb=" N GLN A1364 " --> pdb=" O LEU A1375 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1380 through 1382 Processing sheet with id=AA4, first strand: chain 'A' and resid 1405 through 1407 Processing sheet with id=AA5, first strand: chain 'A' and resid 1420 through 1422 Processing sheet with id=AA6, first strand: chain 'A' and resid 1456 through 1461 removed outlier: 3.834A pdb=" N ASN A1458 " --> pdb=" O ASN A1451 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1469 through 1475 removed outlier: 4.179A pdb=" N ALA A1471 " --> pdb=" O SER A1484 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR A1491 " --> pdb=" O VAL A1504 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1512 through 1518 removed outlier: 3.897A pdb=" N MET A1514 " --> pdb=" O THR A1527 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE A1534 " --> pdb=" O LEU A1547 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1555 through 1561 removed outlier: 6.881A pdb=" N ILE A1580 " --> pdb=" O ILE A1593 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1601 through 1607 removed outlier: 5.060A pdb=" N GLY A1603 " --> pdb=" O MET A1616 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N MET A1616 " --> pdb=" O GLY A1603 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N PHE A1625 " --> pdb=" O GLN A1635 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N GLN A1635 " --> pdb=" O PHE A1625 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1646 through 1652 removed outlier: 6.676A pdb=" N THR A1659 " --> pdb=" O HIS A1647 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU A1649 " --> pdb=" O TYR A1657 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N TYR A1657 " --> pdb=" O LEU A1649 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N LEU A1651 " --> pdb=" O PHE A1655 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N PHE A1655 " --> pdb=" O LEU A1651 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL A1666 " --> pdb=" O VAL A1680 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1713 through 1716 Processing sheet with id=AB4, first strand: chain 'A' and resid 1732 through 1734 Processing sheet with id=AB5, first strand: chain 'A' and resid 1757 through 1761 removed outlier: 3.528A pdb=" N VAL A1752 " --> pdb=" O GLY A2007 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLY A2007 " --> pdb=" O VAL A1752 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1785 through 1787 removed outlier: 3.813A pdb=" N GLU A1801 " --> pdb=" O GLU A1797 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE A1802 " --> pdb=" O PHE A1815 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1827 through 1830 removed outlier: 6.682A pdb=" N VAL A1848 " --> pdb=" O THR A1860 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N THR A1860 " --> pdb=" O VAL A1848 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N THR A1850 " --> pdb=" O GLY A1858 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N GLY A1858 " --> pdb=" O THR A1850 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1873 through 1880 removed outlier: 6.135A pdb=" N HIS A1891 " --> pdb=" O PRO A1874 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY A1876 " --> pdb=" O SER A1889 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS A1885 " --> pdb=" O ASP A1880 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE A1901 " --> pdb=" O LEU A1914 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1922 through 1928 removed outlier: 5.366A pdb=" N VAL A1924 " --> pdb=" O ALA A1937 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA A1937 " --> pdb=" O VAL A1924 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ARG A1946 " --> pdb=" O ILE A1956 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N ILE A1956 " --> pdb=" O ARG A1946 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1964 through 1970 removed outlier: 6.654A pdb=" N ILE A1984 " --> pdb=" O LEU A1998 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 2033 through 2037 Processing sheet with id=AC3, first strand: chain 'A' and resid 2050 through 2052 Processing sheet with id=AC4, first strand: chain 'A' and resid 2091 through 2092 Processing sheet with id=AC5, first strand: chain 'A' and resid 2098 through 2104 removed outlier: 4.351A pdb=" N HIS A2100 " --> pdb=" O CYS A2113 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY A2124 " --> pdb=" O ASP A2114 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE A2125 " --> pdb=" O VAL A2138 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS A2129 " --> pdb=" O ASN A2134 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ASN A2134 " --> pdb=" O LYS A2129 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 2146 through 2154 removed outlier: 6.481A pdb=" N ILE A2148 " --> pdb=" O ALA A2165 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ALA A2165 " --> pdb=" O ILE A2148 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY A2150 " --> pdb=" O THR A2163 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N THR A2170 " --> pdb=" O LYS A2187 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LYS A2187 " --> pdb=" O THR A2170 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE A2172 " --> pdb=" O LEU A2185 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 2196 through 2199 removed outlier: 6.693A pdb=" N ILE A2216 " --> pdb=" O LEU A2229 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 2237 through 2242 removed outlier: 4.344A pdb=" N GLY A2239 " --> pdb=" O VAL A2252 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE A2259 " --> pdb=" O VAL A2272 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 2281 through 2287 removed outlier: 4.094A pdb=" N GLY A2283 " --> pdb=" O VAL A2294 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL A2301 " --> pdb=" O ILE A2317 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 2357 through 2359 Processing sheet with id=AD2, first strand: chain 'A' and resid 2375 through 2376 Processing sheet with id=AD3, first strand: chain 'A' and resid 2416 through 2417 removed outlier: 3.665A pdb=" N SER A2394 " --> pdb=" O GLY A2640 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N GLY A2640 " --> pdb=" O SER A2394 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 2421 through 2428 removed outlier: 5.917A pdb=" N ALA A2422 " --> pdb=" O LYS A2439 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N LYS A2439 " --> pdb=" O ALA A2422 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ALA A2424 " --> pdb=" O THR A2437 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE A2447 " --> pdb=" O LEU A2462 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 2469 through 2475 removed outlier: 4.473A pdb=" N GLY A2471 " --> pdb=" O SER A2484 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG A2480 " --> pdb=" O ASP A2475 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE A2491 " --> pdb=" O ILE A2504 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 2510 through 2516 removed outlier: 5.154A pdb=" N ALA A2512 " --> pdb=" O THR A2525 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N THR A2525 " --> pdb=" O ALA A2512 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE A2533 " --> pdb=" O ILE A2546 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 2556 through 2560 removed outlier: 3.508A pdb=" N GLY A2556 " --> pdb=" O ALA A2569 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A2565 " --> pdb=" O ASP A2560 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS A2575 " --> pdb=" O ASP A2570 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE A2576 " --> pdb=" O VAL A2589 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 2596 through 2602 removed outlier: 4.047A pdb=" N GLY A2598 " --> pdb=" O THR A2609 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS A2615 " --> pdb=" O ASP A2610 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 2666 through 2669 Processing sheet with id=AE1, first strand: chain 'A' and resid 2684 through 2686 Processing sheet with id=AE2, first strand: chain 'A' and resid 2705 through 2707 Processing sheet with id=AE3, first strand: chain 'A' and resid 2747 through 2748 Processing sheet with id=AE4, first strand: chain 'B' and resid 1318 through 1319 Processing sheet with id=AE5, first strand: chain 'B' and resid 1365 through 1366 Processing sheet with id=AE6, first strand: chain 'B' and resid 1380 through 1382 Processing sheet with id=AE7, first strand: chain 'B' and resid 1405 through 1407 Processing sheet with id=AE8, first strand: chain 'B' and resid 1420 through 1422 Processing sheet with id=AE9, first strand: chain 'B' and resid 1459 through 1461 Processing sheet with id=AF1, first strand: chain 'B' and resid 1469 through 1475 removed outlier: 4.200A pdb=" N ALA B1471 " --> pdb=" O SER B1484 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER B1484 " --> pdb=" O ALA B1471 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N SER B1493 " --> pdb=" O VAL B1503 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N VAL B1503 " --> pdb=" O SER B1493 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 1512 through 1518 removed outlier: 4.132A pdb=" N MET B1514 " --> pdb=" O THR B1527 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE B1534 " --> pdb=" O LEU B1547 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 1555 through 1561 removed outlier: 5.773A pdb=" N SER B1572 " --> pdb=" O ARG B1556 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU B1558 " --> pdb=" O PHE B1570 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N PHE B1570 " --> pdb=" O LEU B1558 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N LEU B1560 " --> pdb=" O VAL B1568 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL B1568 " --> pdb=" O LEU B1560 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE B1580 " --> pdb=" O ILE B1593 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 1601 through 1607 removed outlier: 5.275A pdb=" N GLY B1603 " --> pdb=" O MET B1616 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N MET B1616 " --> pdb=" O GLY B1603 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR B1622 " --> pdb=" O ASP B1617 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE B1623 " --> pdb=" O VAL B1636 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 1646 through 1652 removed outlier: 3.793A pdb=" N ALA B1648 " --> pdb=" O THR B1659 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL B1666 " --> pdb=" O VAL B1680 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 1713 through 1716 Processing sheet with id=AF7, first strand: chain 'B' and resid 1732 through 1734 removed outlier: 3.579A pdb=" N VAL B1742 " --> pdb=" O ASN B1733 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B' and resid 1775 through 1776 removed outlier: 3.502A pdb=" N ILE B1756 " --> pdb=" O ARG B1753 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLY B2007 " --> pdb=" O VAL B1752 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'B' and resid 1785 through 1787 removed outlier: 3.916A pdb=" N GLU B1801 " --> pdb=" O GLU B1797 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE B1802 " --> pdb=" O PHE B1815 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'B' and resid 1826 through 1830 removed outlier: 3.591A pdb=" N GLY B1826 " --> pdb=" O THR B1839 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE B1846 " --> pdb=" O LEU B1861 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'B' and resid 1873 through 1880 removed outlier: 6.572A pdb=" N HIS B1891 " --> pdb=" O PRO B1874 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY B1876 " --> pdb=" O SER B1889 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE B1901 " --> pdb=" O LEU B1914 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 1922 through 1928 removed outlier: 5.222A pdb=" N VAL B1924 " --> pdb=" O ALA B1937 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA B1937 " --> pdb=" O VAL B1924 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE B1944 " --> pdb=" O LEU B1957 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'B' and resid 1964 through 1970 removed outlier: 3.614A pdb=" N GLY B1966 " --> pdb=" O SER B1977 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE B1984 " --> pdb=" O LEU B1998 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'B' and resid 2033 through 2037 removed outlier: 3.670A pdb=" N MET B2041 " --> pdb=" O VAL B2037 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'B' and resid 2050 through 2052 Processing sheet with id=AG7, first strand: chain 'B' and resid 2086 through 2091 removed outlier: 7.809A pdb=" N ALA B2087 " --> pdb=" O SER B2078 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N SER B2078 " --> pdb=" O ALA B2087 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL B2089 " --> pdb=" O GLY B2076 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLY B2076 " --> pdb=" O VAL B2089 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'B' and resid 2100 through 2104 removed outlier: 4.285A pdb=" N HIS B2100 " --> pdb=" O CYS B2113 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ILE B2125 " --> pdb=" O VAL B2138 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'B' and resid 2147 through 2154 removed outlier: 5.707A pdb=" N ILE B2148 " --> pdb=" O ALA B2165 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA B2165 " --> pdb=" O ILE B2148 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLY B2150 " --> pdb=" O THR B2163 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N THR B2170 " --> pdb=" O LYS B2187 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LYS B2187 " --> pdb=" O THR B2170 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE B2172 " --> pdb=" O LEU B2185 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'B' and resid 2193 through 2199 removed outlier: 3.682A pdb=" N HIS B2195 " --> pdb=" O ALA B2208 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE B2216 " --> pdb=" O LEU B2229 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'B' and resid 2237 through 2242 removed outlier: 4.129A pdb=" N GLY B2239 " --> pdb=" O VAL B2252 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ARG B2261 " --> pdb=" O VAL B2271 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N VAL B2271 " --> pdb=" O ARG B2261 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'B' and resid 2281 through 2287 removed outlier: 4.178A pdb=" N GLY B2283 " --> pdb=" O VAL B2294 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS B2300 " --> pdb=" O ASP B2295 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL B2301 " --> pdb=" O ILE B2317 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'B' and resid 2357 through 2359 Processing sheet with id=AH5, first strand: chain 'B' and resid 2375 through 2376 Processing sheet with id=AH6, first strand: chain 'B' and resid 2416 through 2417 removed outlier: 5.062A pdb=" N GLY B2640 " --> pdb=" O SER B2394 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'B' and resid 2421 through 2428 removed outlier: 6.529A pdb=" N THR B2437 " --> pdb=" O ILE B2423 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LEU B2425 " --> pdb=" O PHE B2435 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N PHE B2435 " --> pdb=" O LEU B2425 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N TYR B2427 " --> pdb=" O ARG B2433 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ARG B2433 " --> pdb=" O TYR B2427 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N GLY B2445 " --> pdb=" O SER B2464 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N SER B2464 " --> pdb=" O GLY B2445 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE B2447 " --> pdb=" O LEU B2462 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'B' and resid 2473 through 2475 removed outlier: 6.439A pdb=" N ILE B2491 " --> pdb=" O ILE B2504 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'B' and resid 2510 through 2516 removed outlier: 4.240A pdb=" N ALA B2512 " --> pdb=" O THR B2525 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ARG B2535 " --> pdb=" O PRO B2545 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'B' and resid 2554 through 2560 removed outlier: 6.759A pdb=" N ILE B2576 " --> pdb=" O VAL B2589 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'B' and resid 2596 through 2602 removed outlier: 4.352A pdb=" N GLY B2598 " --> pdb=" O THR B2609 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'B' and resid 2666 through 2669 removed outlier: 3.547A pdb=" N ILE B2666 " --> pdb=" O GLN B2677 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'B' and resid 2684 through 2687 Processing sheet with id=AI5, first strand: chain 'B' and resid 2705 through 2707 Processing sheet with id=AI6, first strand: chain 'B' and resid 2747 through 2748 736 hydrogen bonds defined for protein. 1719 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: 13.68 Time building geometry restraints manager: 8.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7875 1.34 - 1.46: 5813 1.46 - 1.58: 10629 1.58 - 1.70: 0 1.70 - 1.83: 214 Bond restraints: 24531 Sorted by residual: bond pdb=" N VAL B1494 " pdb=" CA VAL B1494 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.08e-02 8.57e+03 9.43e+00 bond pdb=" N THR A2224 " pdb=" CA THR A2224 " ideal model delta sigma weight residual 1.452 1.489 -0.037 1.22e-02 6.72e+03 9.01e+00 bond pdb=" N THR B2699 " pdb=" CA THR B2699 " ideal model delta sigma weight residual 1.453 1.489 -0.036 1.31e-02 5.83e+03 7.50e+00 bond pdb=" N ARG B2743 " pdb=" CA ARG B2743 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.31e+00 bond pdb=" N HIS B2740 " pdb=" CA HIS B2740 " ideal model delta sigma weight residual 1.458 1.490 -0.033 1.24e-02 6.50e+03 6.96e+00 ... (remaining 24526 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 32138 1.76 - 3.52: 1075 3.52 - 5.29: 155 5.29 - 7.05: 19 7.05 - 8.81: 10 Bond angle restraints: 33397 Sorted by residual: angle pdb=" C SER A2454 " pdb=" CA SER A2454 " pdb=" CB SER A2454 " ideal model delta sigma weight residual 117.23 110.84 6.39 1.36e+00 5.41e-01 2.21e+01 angle pdb=" C THR B2224 " pdb=" N ASN B2225 " pdb=" CA ASN B2225 " ideal model delta sigma weight residual 123.24 116.76 6.48 1.54e+00 4.22e-01 1.77e+01 angle pdb=" CA TYR A2210 " pdb=" CB TYR A2210 " pdb=" CG TYR A2210 " ideal model delta sigma weight residual 113.90 121.17 -7.27 1.80e+00 3.09e-01 1.63e+01 angle pdb=" CA VAL B1494 " pdb=" C VAL B1494 " pdb=" O VAL B1494 " ideal model delta sigma weight residual 121.45 117.52 3.93 1.00e+00 1.00e+00 1.55e+01 angle pdb=" CA CYS B2223 " pdb=" C CYS B2223 " pdb=" O CYS B2223 " ideal model delta sigma weight residual 122.14 117.43 4.71 1.24e+00 6.50e-01 1.44e+01 ... (remaining 33392 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.99: 14178 21.99 - 43.97: 958 43.97 - 65.96: 154 65.96 - 87.95: 69 87.95 - 109.93: 25 Dihedral angle restraints: 15384 sinusoidal: 6809 harmonic: 8575 Sorted by residual: dihedral pdb=" CB CYS B2371 " pdb=" SG CYS B2371 " pdb=" SG CYS B2383 " pdb=" CB CYS B2383 " ideal model delta sinusoidal sigma weight residual 93.00 179.80 -86.80 1 1.00e+01 1.00e-02 9.06e+01 dihedral pdb=" CB CYS A2656 " pdb=" SG CYS A2656 " pdb=" SG CYS A2667 " pdb=" CB CYS A2667 " ideal model delta sinusoidal sigma weight residual 93.00 179.14 -86.14 1 1.00e+01 1.00e-02 8.95e+01 dihedral pdb=" CB CYS A1354 " pdb=" SG CYS A1354 " pdb=" SG CYS A1365 " pdb=" CB CYS A1365 " ideal model delta sinusoidal sigma weight residual 93.00 178.64 -85.64 1 1.00e+01 1.00e-02 8.87e+01 ... (remaining 15381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 3683 0.114 - 0.228: 136 0.228 - 0.342: 4 0.342 - 0.456: 0 0.456 - 0.570: 2 Chirality restraints: 3825 Sorted by residual: chirality pdb=" C1 NAG Z 2 " pdb=" O3 NAG Z 1 " pdb=" C2 NAG Z 2 " pdb=" O5 NAG Z 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-02 2.50e+03 5.90e+02 chirality pdb=" C1 NAG R 2 " pdb=" O3 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 7.76e+01 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 -2.24 -0.16 2.00e-02 2.50e+03 6.56e+01 ... (remaining 3822 not shown) Planarity restraints: 4319 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG W 1 " 0.341 2.00e-02 2.50e+03 2.95e-01 1.09e+03 pdb=" C7 NAG W 1 " -0.081 2.00e-02 2.50e+03 pdb=" C8 NAG W 1 " 0.131 2.00e-02 2.50e+03 pdb=" N2 NAG W 1 " -0.526 2.00e-02 2.50e+03 pdb=" O7 NAG W 1 " 0.135 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 A2G A4705 " -0.326 2.00e-02 2.50e+03 2.78e-01 9.64e+02 pdb=" C7 A2G A4705 " 0.085 2.00e-02 2.50e+03 pdb=" C8 A2G A4705 " -0.177 2.00e-02 2.50e+03 pdb=" N2 A2G A4705 " 0.486 2.00e-02 2.50e+03 pdb=" O7 A2G A4705 " -0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG Z 1 " -0.311 2.00e-02 2.50e+03 2.65e-01 8.78e+02 pdb=" C7 NAG Z 1 " 0.077 2.00e-02 2.50e+03 pdb=" C8 NAG Z 1 " -0.178 2.00e-02 2.50e+03 pdb=" N2 NAG Z 1 " 0.463 2.00e-02 2.50e+03 pdb=" O7 NAG Z 1 " -0.051 2.00e-02 2.50e+03 ... (remaining 4316 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 300 2.63 - 3.20: 21364 3.20 - 3.76: 36342 3.76 - 4.33: 53369 4.33 - 4.90: 88599 Nonbonded interactions: 199974 Sorted by model distance: nonbonded pdb=" OE2 GLU A1923 " pdb="NI NI A4712 " model vdw 2.059 2.180 nonbonded pdb=" NE2 HIS B1963 " pdb="NI NI B4712 " model vdw 2.075 2.260 nonbonded pdb=" OD1 ASP B2721 " pdb="CA CA B4709 " model vdw 2.148 2.510 nonbonded pdb=" NE2 HIS B1921 " pdb="NI NI B4712 " model vdw 2.163 2.260 nonbonded pdb=" OD2 ASP B2731 " pdb="CA CA B4709 " model vdw 2.171 2.510 ... (remaining 199969 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 1309 through 2693 or (resid 2694 and (name N or name CA or \ name C or name O or name CB )) or resid 2695 through 2776 or resid 4701 through \ 4712)) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'a' selection = chain 'b' } ncs_group { reference = chain 'F' selection = chain 'U' } ncs_group { reference = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'O' selection = chain 'Q' selection = chain 'X' selection = chain 'Z' } 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: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.840 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 63.070 Find NCS groups from input model: 1.530 Set up NCS constraints: 0.190 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:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 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 : 0.004 0.038 24648 Z= 0.230 Angle : 0.754 12.879 33687 Z= 0.397 Chirality : 0.052 0.570 3825 Planarity : 0.013 0.295 4291 Dihedral : 15.764 109.934 9727 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.64 % Favored : 95.29 % Rotamer: Outliers : 1.88 % Allowed : 13.18 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.16), residues: 2933 helix: -3.29 (0.48), residues: 56 sheet: -0.46 (0.15), residues: 1078 loop : -0.52 (0.15), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B2684 HIS 0.004 0.001 HIS B1891 PHE 0.024 0.001 PHE A2706 TYR 0.021 0.001 TYR B2210 ARG 0.014 0.000 ARG B2506 Details of bonding type rmsd link_TRANS : bond 0.00647 ( 2) link_TRANS : angle 1.43617 ( 6) link_NAG-ASN : bond 0.00845 ( 26) link_NAG-ASN : angle 2.76880 ( 78) link_ALPHA1-6 : bond 0.00273 ( 4) link_ALPHA1-6 : angle 1.01114 ( 12) link_BETA1-4 : bond 0.00585 ( 22) link_BETA1-4 : angle 2.20592 ( 66) link_ALPHA1-3 : bond 0.00317 ( 4) link_ALPHA1-3 : angle 1.17455 ( 12) hydrogen bonds : bond 0.23666 ( 736) hydrogen bonds : angle 10.10203 ( 1719) SS BOND : bond 0.00192 ( 55) SS BOND : angle 0.97574 ( 110) link_BETA1-3 : bond 0.01587 ( 2) link_BETA1-3 : angle 6.39221 ( 6) covalent geometry : bond 0.00426 (24531) covalent geometry : angle 0.73129 (33397) Misc. bond : bond 0.02517 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 180 time to evaluate : 2.675 Fit side-chains revert: symmetry clash REVERT: A 1500 ASP cc_start: 0.7928 (t70) cc_final: 0.7711 (t0) REVERT: A 2565 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8948 (mp) REVERT: B 1808 ASP cc_start: 0.8278 (m-30) cc_final: 0.7911 (m-30) REVERT: B 2650 GLN cc_start: 0.8141 (mm-40) cc_final: 0.7661 (mm-40) outliers start: 48 outliers final: 43 residues processed: 224 average time/residue: 0.4183 time to fit residues: 140.6412 Evaluate side-chains 210 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 166 time to evaluate : 2.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1343 THR Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain A residue 1503 VAL Chi-restraints excluded: chain A residue 1594 VAL Chi-restraints excluded: chain A residue 1636 VAL Chi-restraints excluded: chain A residue 1656 VAL Chi-restraints excluded: chain A residue 1728 CYS Chi-restraints excluded: chain A residue 1925 VAL Chi-restraints excluded: chain A residue 1969 VAL Chi-restraints excluded: chain A residue 2002 VAL Chi-restraints excluded: chain A residue 2070 MET Chi-restraints excluded: chain A residue 2170 THR Chi-restraints excluded: chain A residue 2174 VAL Chi-restraints excluded: chain A residue 2189 SER Chi-restraints excluded: chain A residue 2210 TYR Chi-restraints excluded: chain A residue 2230 VAL Chi-restraints excluded: chain A residue 2338 SER Chi-restraints excluded: chain A residue 2394 SER Chi-restraints excluded: chain A residue 2507 VAL Chi-restraints excluded: chain A residue 2565 LEU Chi-restraints excluded: chain A residue 2600 THR Chi-restraints excluded: chain A residue 2601 VAL Chi-restraints excluded: chain A residue 2636 THR Chi-restraints excluded: chain A residue 2645 VAL Chi-restraints excluded: chain A residue 2657 ASP Chi-restraints excluded: chain A residue 2773 GLU Chi-restraints excluded: chain B residue 1388 THR Chi-restraints excluded: chain B residue 1397 ILE Chi-restraints excluded: chain B residue 1449 VAL Chi-restraints excluded: chain B residue 1504 VAL Chi-restraints excluded: chain B residue 1517 VAL Chi-restraints excluded: chain B residue 1636 VAL Chi-restraints excluded: chain B residue 1666 VAL Chi-restraints excluded: chain B residue 1728 CYS Chi-restraints excluded: chain B residue 1734 LEU Chi-restraints excluded: chain B residue 1854 ASP Chi-restraints excluded: chain B residue 2002 VAL Chi-restraints excluded: chain B residue 2110 ILE Chi-restraints excluded: chain B residue 2174 VAL Chi-restraints excluded: chain B residue 2191 ASP Chi-restraints excluded: chain B residue 2323 LEU Chi-restraints excluded: chain B residue 2366 THR Chi-restraints excluded: chain B residue 2759 TYR Chi-restraints excluded: chain G residue 3 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 246 optimal weight: 0.9980 chunk 221 optimal weight: 0.9990 chunk 122 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 chunk 118 optimal weight: 8.9990 chunk 228 optimal weight: 0.7980 chunk 88 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 265 optimal weight: 7.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1393 ASN A1963 HIS A2333 HIS A2595 HIS ** A2651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2703 GLN ** A2722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1769 ASN B1891 HIS B1980 GLN B2012 HIS B2297 ASN B2378 ASN B2500 ASN B2665 HIS B2710 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.122723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.086126 restraints weight = 33890.260| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 2.11 r_work: 0.2789 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 24648 Z= 0.228 Angle : 0.718 15.339 33687 Z= 0.358 Chirality : 0.052 0.300 3825 Planarity : 0.004 0.052 4291 Dihedral : 10.604 76.605 4547 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.33 % Allowed : 12.60 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.15), residues: 2933 helix: -3.07 (0.51), residues: 62 sheet: -0.59 (0.15), residues: 1079 loop : -0.58 (0.15), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B1492 HIS 0.007 0.001 HIS B2665 PHE 0.018 0.002 PHE B2413 TYR 0.032 0.002 TYR A2210 ARG 0.006 0.001 ARG A2519 Details of bonding type rmsd link_TRANS : bond 0.00240 ( 2) link_TRANS : angle 0.74324 ( 6) link_NAG-ASN : bond 0.00539 ( 26) link_NAG-ASN : angle 2.69834 ( 78) link_ALPHA1-6 : bond 0.00381 ( 4) link_ALPHA1-6 : angle 1.87251 ( 12) link_BETA1-4 : bond 0.00630 ( 22) link_BETA1-4 : angle 2.90631 ( 66) link_ALPHA1-3 : bond 0.00758 ( 4) link_ALPHA1-3 : angle 1.61359 ( 12) hydrogen bonds : bond 0.04771 ( 736) hydrogen bonds : angle 7.26120 ( 1719) SS BOND : bond 0.00325 ( 55) SS BOND : angle 1.08018 ( 110) link_BETA1-3 : bond 0.03372 ( 2) link_BETA1-3 : angle 7.20539 ( 6) covalent geometry : bond 0.00537 (24531) covalent geometry : angle 0.68638 (33397) Misc. bond : bond 0.00086 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 176 time to evaluate : 2.677 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1500 ASP cc_start: 0.8243 (t70) cc_final: 0.7972 (t0) REVERT: A 1745 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.7864 (m-30) REVERT: A 2254 ASP cc_start: 0.8999 (p0) cc_final: 0.8788 (p0) REVERT: A 2429 ARG cc_start: 0.8186 (ttp80) cc_final: 0.7815 (ttt-90) REVERT: A 2519 ARG cc_start: 0.8635 (mtm-85) cc_final: 0.8431 (mtm-85) REVERT: A 2578 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7546 (ptm-80) REVERT: A 2665 HIS cc_start: 0.7606 (m-70) cc_final: 0.7392 (m-70) REVERT: A 2684 TRP cc_start: 0.7736 (m100) cc_final: 0.7466 (m100) REVERT: B 1808 ASP cc_start: 0.8530 (OUTLIER) cc_final: 0.8146 (m-30) REVERT: B 2013 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7365 (ttp80) REVERT: B 2258 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8624 (pt) REVERT: B 2690 ASN cc_start: 0.7939 (m-40) cc_final: 0.7664 (m110) outliers start: 85 outliers final: 54 residues processed: 239 average time/residue: 0.4025 time to fit residues: 146.8210 Evaluate side-chains 225 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 166 time to evaluate : 3.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1343 THR Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain A residue 1469 VAL Chi-restraints excluded: chain A residue 1503 VAL Chi-restraints excluded: chain A residue 1549 SER Chi-restraints excluded: chain A residue 1569 MET Chi-restraints excluded: chain A residue 1594 VAL Chi-restraints excluded: chain A residue 1598 ILE Chi-restraints excluded: chain A residue 1636 VAL Chi-restraints excluded: chain A residue 1745 ASP Chi-restraints excluded: chain A residue 1752 VAL Chi-restraints excluded: chain A residue 1886 LEU Chi-restraints excluded: chain A residue 1897 VAL Chi-restraints excluded: chain A residue 1969 VAL Chi-restraints excluded: chain A residue 1985 GLU Chi-restraints excluded: chain A residue 2002 VAL Chi-restraints excluded: chain A residue 2037 VAL Chi-restraints excluded: chain A residue 2070 MET Chi-restraints excluded: chain A residue 2170 THR Chi-restraints excluded: chain A residue 2174 VAL Chi-restraints excluded: chain A residue 2230 VAL Chi-restraints excluded: chain A residue 2285 THR Chi-restraints excluded: chain A residue 2394 SER Chi-restraints excluded: chain A residue 2507 VAL Chi-restraints excluded: chain A residue 2578 ARG Chi-restraints excluded: chain A residue 2601 VAL Chi-restraints excluded: chain A residue 2636 THR Chi-restraints excluded: chain A residue 2649 ARG Chi-restraints excluded: chain A residue 2657 ASP Chi-restraints excluded: chain A residue 2741 THR Chi-restraints excluded: chain B residue 1409 ARG Chi-restraints excluded: chain B residue 1445 ASP Chi-restraints excluded: chain B residue 1449 VAL Chi-restraints excluded: chain B residue 1463 VAL Chi-restraints excluded: chain B residue 1469 VAL Chi-restraints excluded: chain B residue 1504 VAL Chi-restraints excluded: chain B residue 1517 VAL Chi-restraints excluded: chain B residue 1589 MET Chi-restraints excluded: chain B residue 1636 VAL Chi-restraints excluded: chain B residue 1666 VAL Chi-restraints excluded: chain B residue 1808 ASP Chi-restraints excluded: chain B residue 1829 LEU Chi-restraints excluded: chain B residue 1845 SER Chi-restraints excluded: chain B residue 1911 LEU Chi-restraints excluded: chain B residue 1936 TRP Chi-restraints excluded: chain B residue 1967 LEU Chi-restraints excluded: chain B residue 2002 VAL Chi-restraints excluded: chain B residue 2013 ARG Chi-restraints excluded: chain B residue 2081 LEU Chi-restraints excluded: chain B residue 2174 VAL Chi-restraints excluded: chain B residue 2258 LEU Chi-restraints excluded: chain B residue 2323 LEU Chi-restraints excluded: chain B residue 2366 THR Chi-restraints excluded: chain B residue 2522 MET Chi-restraints excluded: chain B residue 2706 PHE Chi-restraints excluded: chain B residue 2736 VAL Chi-restraints excluded: chain B residue 2749 CYS Chi-restraints excluded: chain B residue 2759 TYR Chi-restraints excluded: chain G residue 3 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 289 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 218 optimal weight: 3.9990 chunk 173 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 147 optimal weight: 0.7980 chunk 241 optimal weight: 0.5980 chunk 193 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1891 HIS A2195 HIS A2530 ASN ** A2651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2722 ASN B2244 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.124669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.087065 restraints weight = 33610.010| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 1.90 r_work: 0.2809 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 24648 Z= 0.133 Angle : 0.652 16.313 33687 Z= 0.319 Chirality : 0.049 0.470 3825 Planarity : 0.004 0.048 4291 Dihedral : 9.285 72.088 4521 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.01 % Allowed : 13.22 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.15), residues: 2933 helix: -2.78 (0.54), residues: 56 sheet: -0.57 (0.15), residues: 1061 loop : -0.55 (0.15), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B1492 HIS 0.004 0.001 HIS A1891 PHE 0.013 0.001 PHE B2413 TYR 0.027 0.001 TYR A2210 ARG 0.005 0.000 ARG A1702 Details of bonding type rmsd link_TRANS : bond 0.00137 ( 2) link_TRANS : angle 0.64727 ( 6) link_NAG-ASN : bond 0.00686 ( 26) link_NAG-ASN : angle 3.49061 ( 78) link_ALPHA1-6 : bond 0.00507 ( 4) link_ALPHA1-6 : angle 1.93675 ( 12) link_BETA1-4 : bond 0.00591 ( 22) link_BETA1-4 : angle 2.63368 ( 66) link_ALPHA1-3 : bond 0.00999 ( 4) link_ALPHA1-3 : angle 1.31029 ( 12) hydrogen bonds : bond 0.03856 ( 736) hydrogen bonds : angle 6.82239 ( 1719) SS BOND : bond 0.00252 ( 55) SS BOND : angle 1.18471 ( 110) link_BETA1-3 : bond 0.02835 ( 2) link_BETA1-3 : angle 6.78027 ( 6) covalent geometry : bond 0.00297 (24531) covalent geometry : angle 0.60961 (33397) Misc. bond : bond 0.00168 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 191 time to evaluate : 2.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1745 ASP cc_start: 0.8111 (OUTLIER) cc_final: 0.7797 (m-30) REVERT: A 1877 ILE cc_start: 0.9377 (OUTLIER) cc_final: 0.9128 (mt) REVERT: A 2429 ARG cc_start: 0.8091 (ttp80) cc_final: 0.7821 (ttt-90) REVERT: A 2519 ARG cc_start: 0.8490 (mtm-85) cc_final: 0.8251 (mtm-85) REVERT: A 2578 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7525 (ptm-80) REVERT: B 1745 ASP cc_start: 0.7573 (m-30) cc_final: 0.7362 (m-30) REVERT: B 1798 ASN cc_start: 0.8267 (t0) cc_final: 0.7776 (t0) REVERT: B 1808 ASP cc_start: 0.8531 (OUTLIER) cc_final: 0.8127 (m-30) REVERT: B 2258 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8682 (pt) REVERT: B 2690 ASN cc_start: 0.7691 (m-40) cc_final: 0.7350 (m110) REVERT: C 3 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7935 (tt) outliers start: 77 outliers final: 52 residues processed: 248 average time/residue: 0.3844 time to fit residues: 144.9132 Evaluate side-chains 228 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 170 time to evaluate : 2.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1343 THR Chi-restraints excluded: chain A residue 1450 ASP Chi-restraints excluded: chain A residue 1466 VAL Chi-restraints excluded: chain A residue 1469 VAL Chi-restraints excluded: chain A residue 1539 ILE Chi-restraints excluded: chain A residue 1549 SER Chi-restraints excluded: chain A residue 1569 MET Chi-restraints excluded: chain A residue 1585 MET Chi-restraints excluded: chain A residue 1594 VAL Chi-restraints excluded: chain A residue 1598 ILE Chi-restraints excluded: chain A residue 1636 VAL Chi-restraints excluded: chain A residue 1728 CYS Chi-restraints excluded: chain A residue 1745 ASP Chi-restraints excluded: chain A residue 1877 ILE Chi-restraints excluded: chain A residue 1886 LEU Chi-restraints excluded: chain A residue 1897 VAL Chi-restraints excluded: chain A residue 1925 VAL Chi-restraints excluded: chain A residue 1969 VAL Chi-restraints excluded: chain A residue 1985 GLU Chi-restraints excluded: chain A residue 2002 VAL Chi-restraints excluded: chain A residue 2070 MET Chi-restraints excluded: chain A residue 2088 MET Chi-restraints excluded: chain A residue 2174 VAL Chi-restraints excluded: chain A residue 2230 VAL Chi-restraints excluded: chain A residue 2285 THR Chi-restraints excluded: chain A residue 2394 SER Chi-restraints excluded: chain A residue 2578 ARG Chi-restraints excluded: chain A residue 2601 VAL Chi-restraints excluded: chain A residue 2636 THR Chi-restraints excluded: chain A residue 2657 ASP Chi-restraints excluded: chain A residue 2741 THR Chi-restraints excluded: chain A residue 2773 GLU Chi-restraints excluded: chain B residue 1445 ASP Chi-restraints excluded: chain B residue 1449 VAL Chi-restraints excluded: chain B residue 1463 VAL Chi-restraints excluded: chain B residue 1504 VAL Chi-restraints excluded: chain B residue 1517 VAL Chi-restraints excluded: chain B residue 1589 MET Chi-restraints excluded: chain B residue 1636 VAL Chi-restraints excluded: chain B residue 1666 VAL Chi-restraints excluded: chain B residue 1789 SER Chi-restraints excluded: chain B residue 1808 ASP Chi-restraints excluded: chain B residue 1936 TRP Chi-restraints excluded: chain B residue 2002 VAL Chi-restraints excluded: chain B residue 2081 LEU Chi-restraints excluded: chain B residue 2174 VAL Chi-restraints excluded: chain B residue 2224 THR Chi-restraints excluded: chain B residue 2258 LEU Chi-restraints excluded: chain B residue 2366 THR Chi-restraints excluded: chain B residue 2415 VAL Chi-restraints excluded: chain B residue 2522 MET Chi-restraints excluded: chain B residue 2563 THR Chi-restraints excluded: chain B residue 2706 PHE Chi-restraints excluded: chain B residue 2736 VAL Chi-restraints excluded: chain B residue 2749 CYS Chi-restraints excluded: chain B residue 2759 TYR Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain G residue 3 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 247 optimal weight: 3.9990 chunk 236 optimal weight: 3.9990 chunk 289 optimal weight: 6.9990 chunk 123 optimal weight: 7.9990 chunk 192 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 90 optimal weight: 0.4980 chunk 43 optimal weight: 3.9990 chunk 152 optimal weight: 0.6980 chunk 190 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2530 ASN ** A2651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2244 HIS B2677 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.124016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.087926 restraints weight = 33964.250| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 2.19 r_work: 0.2804 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 24648 Z= 0.150 Angle : 0.646 15.988 33687 Z= 0.317 Chirality : 0.049 0.395 3825 Planarity : 0.004 0.047 4291 Dihedral : 8.509 71.757 4515 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.68 % Allowed : 12.95 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.15), residues: 2933 helix: -2.67 (0.56), residues: 56 sheet: -0.52 (0.15), residues: 1070 loop : -0.57 (0.15), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B1492 HIS 0.006 0.001 HIS A2665 PHE 0.014 0.001 PHE B2413 TYR 0.026 0.001 TYR A2210 ARG 0.005 0.000 ARG A1702 Details of bonding type rmsd link_TRANS : bond 0.00140 ( 2) link_TRANS : angle 0.54251 ( 6) link_NAG-ASN : bond 0.00767 ( 26) link_NAG-ASN : angle 3.36477 ( 78) link_ALPHA1-6 : bond 0.00568 ( 4) link_ALPHA1-6 : angle 2.03859 ( 12) link_BETA1-4 : bond 0.00555 ( 22) link_BETA1-4 : angle 2.50061 ( 66) link_ALPHA1-3 : bond 0.01078 ( 4) link_ALPHA1-3 : angle 1.42670 ( 12) hydrogen bonds : bond 0.03554 ( 736) hydrogen bonds : angle 6.53923 ( 1719) SS BOND : bond 0.00296 ( 55) SS BOND : angle 1.32807 ( 110) link_BETA1-3 : bond 0.02767 ( 2) link_BETA1-3 : angle 6.70566 ( 6) covalent geometry : bond 0.00346 (24531) covalent geometry : angle 0.60479 (33397) Misc. bond : bond 0.00151 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 175 time to evaluate : 2.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1444 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.8158 (ttm170) REVERT: A 1539 ILE cc_start: 0.9231 (OUTLIER) cc_final: 0.8906 (tp) REVERT: A 1745 ASP cc_start: 0.8147 (OUTLIER) cc_final: 0.7830 (m-30) REVERT: A 1847 GLU cc_start: 0.8763 (pm20) cc_final: 0.8314 (pm20) REVERT: A 1979 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7919 (tt0) REVERT: A 2578 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7541 (ptm-80) REVERT: A 2690 ASN cc_start: 0.7583 (m-40) cc_final: 0.7362 (m-40) REVERT: B 1798 ASN cc_start: 0.8358 (t0) cc_final: 0.7884 (t0) REVERT: B 1808 ASP cc_start: 0.8589 (OUTLIER) cc_final: 0.8174 (m-30) REVERT: B 2258 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8687 (pt) REVERT: B 2592 THR cc_start: 0.8667 (OUTLIER) cc_final: 0.8218 (m) REVERT: B 2690 ASN cc_start: 0.7681 (m-40) cc_final: 0.7312 (m110) REVERT: B 2705 GLN cc_start: 0.6402 (OUTLIER) cc_final: 0.6071 (mt0) REVERT: C 3 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.7979 (tt) outliers start: 94 outliers final: 66 residues processed: 247 average time/residue: 0.4008 time to fit residues: 150.3791 Evaluate side-chains 245 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 169 time to evaluate : 2.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1343 THR Chi-restraints excluded: chain A residue 1444 ARG Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain A residue 1466 VAL Chi-restraints excluded: chain A residue 1469 VAL Chi-restraints excluded: chain A residue 1539 ILE Chi-restraints excluded: chain A residue 1549 SER Chi-restraints excluded: chain A residue 1569 MET Chi-restraints excluded: chain A residue 1585 MET Chi-restraints excluded: chain A residue 1594 VAL Chi-restraints excluded: chain A residue 1598 ILE Chi-restraints excluded: chain A residue 1636 VAL Chi-restraints excluded: chain A residue 1656 VAL Chi-restraints excluded: chain A residue 1667 MET Chi-restraints excluded: chain A residue 1728 CYS Chi-restraints excluded: chain A residue 1745 ASP Chi-restraints excluded: chain A residue 1752 VAL Chi-restraints excluded: chain A residue 1886 LEU Chi-restraints excluded: chain A residue 1897 VAL Chi-restraints excluded: chain A residue 1925 VAL Chi-restraints excluded: chain A residue 1969 VAL Chi-restraints excluded: chain A residue 1979 GLU Chi-restraints excluded: chain A residue 1985 GLU Chi-restraints excluded: chain A residue 2002 VAL Chi-restraints excluded: chain A residue 2037 VAL Chi-restraints excluded: chain A residue 2070 MET Chi-restraints excluded: chain A residue 2170 THR Chi-restraints excluded: chain A residue 2174 VAL Chi-restraints excluded: chain A residue 2230 VAL Chi-restraints excluded: chain A residue 2285 THR Chi-restraints excluded: chain A residue 2394 SER Chi-restraints excluded: chain A residue 2472 ILE Chi-restraints excluded: chain A residue 2507 VAL Chi-restraints excluded: chain A residue 2578 ARG Chi-restraints excluded: chain A residue 2601 VAL Chi-restraints excluded: chain A residue 2636 THR Chi-restraints excluded: chain A residue 2649 ARG Chi-restraints excluded: chain A residue 2657 ASP Chi-restraints excluded: chain A residue 2741 THR Chi-restraints excluded: chain A residue 2773 GLU Chi-restraints excluded: chain B residue 1397 ILE Chi-restraints excluded: chain B residue 1445 ASP Chi-restraints excluded: chain B residue 1449 VAL Chi-restraints excluded: chain B residue 1463 VAL Chi-restraints excluded: chain B residue 1469 VAL Chi-restraints excluded: chain B residue 1504 VAL Chi-restraints excluded: chain B residue 1517 VAL Chi-restraints excluded: chain B residue 1589 MET Chi-restraints excluded: chain B residue 1636 VAL Chi-restraints excluded: chain B residue 1650 THR Chi-restraints excluded: chain B residue 1666 VAL Chi-restraints excluded: chain B residue 1728 CYS Chi-restraints excluded: chain B residue 1789 SER Chi-restraints excluded: chain B residue 1808 ASP Chi-restraints excluded: chain B residue 1829 LEU Chi-restraints excluded: chain B residue 1911 LEU Chi-restraints excluded: chain B residue 1936 TRP Chi-restraints excluded: chain B residue 2002 VAL Chi-restraints excluded: chain B residue 2081 LEU Chi-restraints excluded: chain B residue 2224 THR Chi-restraints excluded: chain B residue 2258 LEU Chi-restraints excluded: chain B residue 2323 LEU Chi-restraints excluded: chain B residue 2366 THR Chi-restraints excluded: chain B residue 2522 MET Chi-restraints excluded: chain B residue 2533 ILE Chi-restraints excluded: chain B residue 2563 THR Chi-restraints excluded: chain B residue 2592 THR Chi-restraints excluded: chain B residue 2677 GLN Chi-restraints excluded: chain B residue 2678 CYS Chi-restraints excluded: chain B residue 2705 GLN Chi-restraints excluded: chain B residue 2706 PHE Chi-restraints excluded: chain B residue 2736 VAL Chi-restraints excluded: chain B residue 2749 CYS Chi-restraints excluded: chain B residue 2759 TYR Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain G residue 3 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 254 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 233 optimal weight: 4.9990 chunk 205 optimal weight: 0.9990 chunk 192 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 73 optimal weight: 0.5980 chunk 248 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2530 ASN ** A2651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2244 HIS B2677 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.123403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.086831 restraints weight = 33933.829| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 2.09 r_work: 0.2809 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.134 24648 Z= 0.180 Angle : 0.653 16.287 33687 Z= 0.322 Chirality : 0.050 0.386 3825 Planarity : 0.004 0.047 4291 Dihedral : 8.345 69.156 4514 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.60 % Allowed : 13.46 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.15), residues: 2933 helix: -2.65 (0.57), residues: 56 sheet: -0.58 (0.15), residues: 1077 loop : -0.58 (0.15), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B1492 HIS 0.005 0.001 HIS A2665 PHE 0.016 0.001 PHE B2413 TYR 0.029 0.002 TYR A2210 ARG 0.005 0.000 ARG A1702 Details of bonding type rmsd link_TRANS : bond 0.00149 ( 2) link_TRANS : angle 0.51628 ( 6) link_NAG-ASN : bond 0.00703 ( 26) link_NAG-ASN : angle 3.32749 ( 78) link_ALPHA1-6 : bond 0.00551 ( 4) link_ALPHA1-6 : angle 2.05242 ( 12) link_BETA1-4 : bond 0.00560 ( 22) link_BETA1-4 : angle 2.41146 ( 66) link_ALPHA1-3 : bond 0.01076 ( 4) link_ALPHA1-3 : angle 1.43023 ( 12) hydrogen bonds : bond 0.03604 ( 736) hydrogen bonds : angle 6.49172 ( 1719) SS BOND : bond 0.00278 ( 55) SS BOND : angle 1.09557 ( 110) link_BETA1-3 : bond 0.02852 ( 2) link_BETA1-3 : angle 6.84643 ( 6) covalent geometry : bond 0.00426 (24531) covalent geometry : angle 0.61486 (33397) Misc. bond : bond 0.00159 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 174 time to evaluate : 2.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1339 CYS cc_start: 0.5112 (OUTLIER) cc_final: 0.4535 (t) REVERT: A 1413 ARG cc_start: 0.7920 (mtm110) cc_final: 0.7274 (mtm-85) REVERT: A 1444 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.8123 (ttm170) REVERT: A 1539 ILE cc_start: 0.9237 (OUTLIER) cc_final: 0.8913 (tp) REVERT: A 1745 ASP cc_start: 0.8153 (OUTLIER) cc_final: 0.7834 (m-30) REVERT: A 1847 GLU cc_start: 0.8781 (pm20) cc_final: 0.8386 (pm20) REVERT: A 1979 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7927 (tt0) REVERT: A 2578 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7447 (ptm-80) REVERT: A 2690 ASN cc_start: 0.7592 (m-40) cc_final: 0.7353 (m-40) REVERT: B 1798 ASN cc_start: 0.8372 (t0) cc_final: 0.7902 (t0) REVERT: B 1808 ASP cc_start: 0.8610 (OUTLIER) cc_final: 0.8201 (m-30) REVERT: B 2013 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7464 (ttp80) REVERT: B 2066 MET cc_start: 0.9108 (OUTLIER) cc_final: 0.8857 (ptm) REVERT: B 2258 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8690 (pt) REVERT: B 2592 THR cc_start: 0.8697 (OUTLIER) cc_final: 0.8284 (m) REVERT: B 2677 GLN cc_start: 0.7799 (OUTLIER) cc_final: 0.7546 (mp10) REVERT: B 2690 ASN cc_start: 0.7805 (m-40) cc_final: 0.7500 (m110) REVERT: B 2705 GLN cc_start: 0.6374 (OUTLIER) cc_final: 0.6034 (mt0) REVERT: C 3 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7932 (tt) outliers start: 92 outliers final: 68 residues processed: 242 average time/residue: 0.3973 time to fit residues: 147.1268 Evaluate side-chains 252 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 170 time to evaluate : 2.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1339 CYS Chi-restraints excluded: chain A residue 1343 THR Chi-restraints excluded: chain A residue 1444 ARG Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain A residue 1450 ASP Chi-restraints excluded: chain A residue 1466 VAL Chi-restraints excluded: chain A residue 1469 VAL Chi-restraints excluded: chain A residue 1539 ILE Chi-restraints excluded: chain A residue 1569 MET Chi-restraints excluded: chain A residue 1585 MET Chi-restraints excluded: chain A residue 1594 VAL Chi-restraints excluded: chain A residue 1598 ILE Chi-restraints excluded: chain A residue 1636 VAL Chi-restraints excluded: chain A residue 1650 THR Chi-restraints excluded: chain A residue 1656 VAL Chi-restraints excluded: chain A residue 1667 MET Chi-restraints excluded: chain A residue 1728 CYS Chi-restraints excluded: chain A residue 1745 ASP Chi-restraints excluded: chain A residue 1752 VAL Chi-restraints excluded: chain A residue 1886 LEU Chi-restraints excluded: chain A residue 1897 VAL Chi-restraints excluded: chain A residue 1925 VAL Chi-restraints excluded: chain A residue 1969 VAL Chi-restraints excluded: chain A residue 1979 GLU Chi-restraints excluded: chain A residue 1985 GLU Chi-restraints excluded: chain A residue 2002 VAL Chi-restraints excluded: chain A residue 2070 MET Chi-restraints excluded: chain A residue 2170 THR Chi-restraints excluded: chain A residue 2174 VAL Chi-restraints excluded: chain A residue 2230 VAL Chi-restraints excluded: chain A residue 2285 THR Chi-restraints excluded: chain A residue 2394 SER Chi-restraints excluded: chain A residue 2472 ILE Chi-restraints excluded: chain A residue 2497 ASP Chi-restraints excluded: chain A residue 2507 VAL Chi-restraints excluded: chain A residue 2578 ARG Chi-restraints excluded: chain A residue 2601 VAL Chi-restraints excluded: chain A residue 2636 THR Chi-restraints excluded: chain A residue 2649 ARG Chi-restraints excluded: chain A residue 2657 ASP Chi-restraints excluded: chain A residue 2741 THR Chi-restraints excluded: chain A residue 2773 GLU Chi-restraints excluded: chain B residue 1397 ILE Chi-restraints excluded: chain B residue 1409 ARG Chi-restraints excluded: chain B residue 1445 ASP Chi-restraints excluded: chain B residue 1449 VAL Chi-restraints excluded: chain B residue 1463 VAL Chi-restraints excluded: chain B residue 1469 VAL Chi-restraints excluded: chain B residue 1504 VAL Chi-restraints excluded: chain B residue 1517 VAL Chi-restraints excluded: chain B residue 1589 MET Chi-restraints excluded: chain B residue 1636 VAL Chi-restraints excluded: chain B residue 1650 THR Chi-restraints excluded: chain B residue 1666 VAL Chi-restraints excluded: chain B residue 1667 MET Chi-restraints excluded: chain B residue 1726 CYS Chi-restraints excluded: chain B residue 1789 SER Chi-restraints excluded: chain B residue 1808 ASP Chi-restraints excluded: chain B residue 1829 LEU Chi-restraints excluded: chain B residue 1911 LEU Chi-restraints excluded: chain B residue 1936 TRP Chi-restraints excluded: chain B residue 2002 VAL Chi-restraints excluded: chain B residue 2013 ARG Chi-restraints excluded: chain B residue 2066 MET Chi-restraints excluded: chain B residue 2081 LEU Chi-restraints excluded: chain B residue 2224 THR Chi-restraints excluded: chain B residue 2258 LEU Chi-restraints excluded: chain B residue 2323 LEU Chi-restraints excluded: chain B residue 2366 THR Chi-restraints excluded: chain B residue 2522 MET Chi-restraints excluded: chain B residue 2533 ILE Chi-restraints excluded: chain B residue 2563 THR Chi-restraints excluded: chain B residue 2592 THR Chi-restraints excluded: chain B residue 2628 VAL Chi-restraints excluded: chain B residue 2677 GLN Chi-restraints excluded: chain B residue 2705 GLN Chi-restraints excluded: chain B residue 2706 PHE Chi-restraints excluded: chain B residue 2736 VAL Chi-restraints excluded: chain B residue 2749 CYS Chi-restraints excluded: chain B residue 2759 TYR Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain G residue 3 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 12 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 259 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 197 optimal weight: 1.9990 chunk 251 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 157 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2032 GLN ** A2441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2530 ASN ** A2665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2107 ASN B2244 HIS B2677 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.124157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.086534 restraints weight = 33586.435| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 1.92 r_work: 0.2825 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 24648 Z= 0.143 Angle : 0.625 16.069 33687 Z= 0.308 Chirality : 0.049 0.384 3825 Planarity : 0.004 0.045 4291 Dihedral : 8.070 65.929 4514 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.79 % Allowed : 13.69 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.15), residues: 2933 helix: -2.54 (0.58), residues: 56 sheet: -0.55 (0.15), residues: 1073 loop : -0.57 (0.15), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B1492 HIS 0.006 0.001 HIS A2665 PHE 0.013 0.001 PHE B2413 TYR 0.027 0.001 TYR A2210 ARG 0.005 0.000 ARG A1702 Details of bonding type rmsd link_TRANS : bond 0.00120 ( 2) link_TRANS : angle 0.50453 ( 6) link_NAG-ASN : bond 0.00680 ( 26) link_NAG-ASN : angle 3.27693 ( 78) link_ALPHA1-6 : bond 0.00568 ( 4) link_ALPHA1-6 : angle 2.08683 ( 12) link_BETA1-4 : bond 0.00554 ( 22) link_BETA1-4 : angle 2.29820 ( 66) link_ALPHA1-3 : bond 0.01078 ( 4) link_ALPHA1-3 : angle 1.47260 ( 12) hydrogen bonds : bond 0.03336 ( 736) hydrogen bonds : angle 6.38282 ( 1719) SS BOND : bond 0.00255 ( 55) SS BOND : angle 1.04125 ( 110) link_BETA1-3 : bond 0.02651 ( 2) link_BETA1-3 : angle 6.58502 ( 6) covalent geometry : bond 0.00334 (24531) covalent geometry : angle 0.58687 (33397) Misc. bond : bond 0.00134 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 175 time to evaluate : 2.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1339 CYS cc_start: 0.5030 (OUTLIER) cc_final: 0.4480 (t) REVERT: A 1444 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.8103 (ttm170) REVERT: A 1539 ILE cc_start: 0.9219 (OUTLIER) cc_final: 0.8881 (tp) REVERT: A 1745 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.7809 (m-30) REVERT: A 1847 GLU cc_start: 0.8790 (pm20) cc_final: 0.8394 (pm20) REVERT: A 2578 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.7387 (ptm-80) REVERT: B 1798 ASN cc_start: 0.8319 (t0) cc_final: 0.7895 (t0) REVERT: B 1808 ASP cc_start: 0.8559 (OUTLIER) cc_final: 0.8137 (m-30) REVERT: B 2013 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7452 (ttp80) REVERT: B 2258 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8640 (pt) REVERT: B 2592 THR cc_start: 0.8678 (OUTLIER) cc_final: 0.8249 (m) REVERT: B 2690 ASN cc_start: 0.7626 (m-40) cc_final: 0.7295 (m110) REVERT: B 2703 GLN cc_start: 0.6654 (mm110) cc_final: 0.6321 (mm-40) REVERT: B 2705 GLN cc_start: 0.6361 (OUTLIER) cc_final: 0.5986 (mt0) REVERT: C 3 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7843 (tt) outliers start: 97 outliers final: 73 residues processed: 246 average time/residue: 0.3910 time to fit residues: 147.5989 Evaluate side-chains 251 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 167 time to evaluate : 2.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1339 CYS Chi-restraints excluded: chain A residue 1343 THR Chi-restraints excluded: chain A residue 1356 HIS Chi-restraints excluded: chain A residue 1444 ARG Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain A residue 1450 ASP Chi-restraints excluded: chain A residue 1466 VAL Chi-restraints excluded: chain A residue 1469 VAL Chi-restraints excluded: chain A residue 1539 ILE Chi-restraints excluded: chain A residue 1569 MET Chi-restraints excluded: chain A residue 1585 MET Chi-restraints excluded: chain A residue 1594 VAL Chi-restraints excluded: chain A residue 1598 ILE Chi-restraints excluded: chain A residue 1636 VAL Chi-restraints excluded: chain A residue 1656 VAL Chi-restraints excluded: chain A residue 1667 MET Chi-restraints excluded: chain A residue 1728 CYS Chi-restraints excluded: chain A residue 1745 ASP Chi-restraints excluded: chain A residue 1752 VAL Chi-restraints excluded: chain A residue 1814 VAL Chi-restraints excluded: chain A residue 1886 LEU Chi-restraints excluded: chain A residue 1897 VAL Chi-restraints excluded: chain A residue 1925 VAL Chi-restraints excluded: chain A residue 1926 THR Chi-restraints excluded: chain A residue 1969 VAL Chi-restraints excluded: chain A residue 1985 GLU Chi-restraints excluded: chain A residue 2002 VAL Chi-restraints excluded: chain A residue 2037 VAL Chi-restraints excluded: chain A residue 2070 MET Chi-restraints excluded: chain A residue 2088 MET Chi-restraints excluded: chain A residue 2170 THR Chi-restraints excluded: chain A residue 2174 VAL Chi-restraints excluded: chain A residue 2230 VAL Chi-restraints excluded: chain A residue 2285 THR Chi-restraints excluded: chain A residue 2361 LEU Chi-restraints excluded: chain A residue 2394 SER Chi-restraints excluded: chain A residue 2472 ILE Chi-restraints excluded: chain A residue 2497 ASP Chi-restraints excluded: chain A residue 2507 VAL Chi-restraints excluded: chain A residue 2578 ARG Chi-restraints excluded: chain A residue 2601 VAL Chi-restraints excluded: chain A residue 2636 THR Chi-restraints excluded: chain A residue 2649 ARG Chi-restraints excluded: chain A residue 2741 THR Chi-restraints excluded: chain A residue 2773 GLU Chi-restraints excluded: chain B residue 1397 ILE Chi-restraints excluded: chain B residue 1445 ASP Chi-restraints excluded: chain B residue 1449 VAL Chi-restraints excluded: chain B residue 1463 VAL Chi-restraints excluded: chain B residue 1469 VAL Chi-restraints excluded: chain B residue 1504 VAL Chi-restraints excluded: chain B residue 1517 VAL Chi-restraints excluded: chain B residue 1589 MET Chi-restraints excluded: chain B residue 1636 VAL Chi-restraints excluded: chain B residue 1650 THR Chi-restraints excluded: chain B residue 1666 VAL Chi-restraints excluded: chain B residue 1667 MET Chi-restraints excluded: chain B residue 1726 CYS Chi-restraints excluded: chain B residue 1728 CYS Chi-restraints excluded: chain B residue 1752 VAL Chi-restraints excluded: chain B residue 1789 SER Chi-restraints excluded: chain B residue 1808 ASP Chi-restraints excluded: chain B residue 1829 LEU Chi-restraints excluded: chain B residue 1911 LEU Chi-restraints excluded: chain B residue 1936 TRP Chi-restraints excluded: chain B residue 1967 LEU Chi-restraints excluded: chain B residue 2002 VAL Chi-restraints excluded: chain B residue 2013 ARG Chi-restraints excluded: chain B residue 2081 LEU Chi-restraints excluded: chain B residue 2258 LEU Chi-restraints excluded: chain B residue 2323 LEU Chi-restraints excluded: chain B residue 2366 THR Chi-restraints excluded: chain B residue 2522 MET Chi-restraints excluded: chain B residue 2533 ILE Chi-restraints excluded: chain B residue 2563 THR Chi-restraints excluded: chain B residue 2592 THR Chi-restraints excluded: chain B residue 2677 GLN Chi-restraints excluded: chain B residue 2705 GLN Chi-restraints excluded: chain B residue 2706 PHE Chi-restraints excluded: chain B residue 2736 VAL Chi-restraints excluded: chain B residue 2749 CYS Chi-restraints excluded: chain B residue 2759 TYR Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain G residue 3 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 59 optimal weight: 0.4980 chunk 218 optimal weight: 0.5980 chunk 104 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 265 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 161 optimal weight: 8.9990 chunk 202 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2530 ASN ** A2665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2244 HIS B2677 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.123407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.086900 restraints weight = 33880.224| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.10 r_work: 0.2801 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 24648 Z= 0.181 Angle : 0.647 15.568 33687 Z= 0.319 Chirality : 0.050 0.385 3825 Planarity : 0.004 0.042 4291 Dihedral : 8.015 62.873 4512 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.91 % Allowed : 13.85 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.15), residues: 2933 helix: -2.50 (0.58), residues: 56 sheet: -0.63 (0.15), residues: 1087 loop : -0.61 (0.15), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B1492 HIS 0.006 0.001 HIS A2665 PHE 0.017 0.001 PHE B2413 TYR 0.029 0.002 TYR A2210 ARG 0.007 0.000 ARG A1413 Details of bonding type rmsd link_TRANS : bond 0.00168 ( 2) link_TRANS : angle 0.53187 ( 6) link_NAG-ASN : bond 0.00647 ( 26) link_NAG-ASN : angle 3.27537 ( 78) link_ALPHA1-6 : bond 0.00544 ( 4) link_ALPHA1-6 : angle 2.10495 ( 12) link_BETA1-4 : bond 0.00554 ( 22) link_BETA1-4 : angle 2.29734 ( 66) link_ALPHA1-3 : bond 0.01066 ( 4) link_ALPHA1-3 : angle 1.48218 ( 12) hydrogen bonds : bond 0.03502 ( 736) hydrogen bonds : angle 6.39984 ( 1719) SS BOND : bond 0.00275 ( 55) SS BOND : angle 1.12986 ( 110) link_BETA1-3 : bond 0.02646 ( 2) link_BETA1-3 : angle 6.66392 ( 6) covalent geometry : bond 0.00430 (24531) covalent geometry : angle 0.61032 (33397) Misc. bond : bond 0.00134 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 171 time to evaluate : 2.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1339 CYS cc_start: 0.4948 (OUTLIER) cc_final: 0.4277 (t) REVERT: A 1413 ARG cc_start: 0.7769 (mtm110) cc_final: 0.7184 (mtm-85) REVERT: A 1444 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.8143 (ttm170) REVERT: A 1539 ILE cc_start: 0.9215 (OUTLIER) cc_final: 0.8884 (tp) REVERT: A 1745 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.7819 (m-30) REVERT: A 1847 GLU cc_start: 0.8773 (pm20) cc_final: 0.8406 (pm20) REVERT: A 2578 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.7432 (ptm-80) REVERT: B 1798 ASN cc_start: 0.8308 (t0) cc_final: 0.7890 (t0) REVERT: B 1808 ASP cc_start: 0.8605 (OUTLIER) cc_final: 0.8179 (m-30) REVERT: B 2013 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7500 (ttp80) REVERT: B 2258 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8636 (pt) REVERT: B 2592 THR cc_start: 0.8768 (OUTLIER) cc_final: 0.8340 (m) REVERT: B 2649 ARG cc_start: 0.6940 (ttp-110) cc_final: 0.6571 (ttp-110) REVERT: B 2690 ASN cc_start: 0.7632 (m-40) cc_final: 0.7294 (m110) REVERT: B 2703 GLN cc_start: 0.6690 (mm110) cc_final: 0.6363 (mm-40) REVERT: B 2705 GLN cc_start: 0.6394 (OUTLIER) cc_final: 0.6031 (mt0) REVERT: C 3 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.7932 (tt) outliers start: 100 outliers final: 79 residues processed: 245 average time/residue: 0.3994 time to fit residues: 150.4769 Evaluate side-chains 258 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 168 time to evaluate : 2.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1339 CYS Chi-restraints excluded: chain A residue 1343 THR Chi-restraints excluded: chain A residue 1356 HIS Chi-restraints excluded: chain A residue 1444 ARG Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain A residue 1450 ASP Chi-restraints excluded: chain A residue 1466 VAL Chi-restraints excluded: chain A residue 1469 VAL Chi-restraints excluded: chain A residue 1539 ILE Chi-restraints excluded: chain A residue 1569 MET Chi-restraints excluded: chain A residue 1585 MET Chi-restraints excluded: chain A residue 1594 VAL Chi-restraints excluded: chain A residue 1598 ILE Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 1636 VAL Chi-restraints excluded: chain A residue 1650 THR Chi-restraints excluded: chain A residue 1656 VAL Chi-restraints excluded: chain A residue 1667 MET Chi-restraints excluded: chain A residue 1728 CYS Chi-restraints excluded: chain A residue 1745 ASP Chi-restraints excluded: chain A residue 1752 VAL Chi-restraints excluded: chain A residue 1814 VAL Chi-restraints excluded: chain A residue 1886 LEU Chi-restraints excluded: chain A residue 1897 VAL Chi-restraints excluded: chain A residue 1925 VAL Chi-restraints excluded: chain A residue 1926 THR Chi-restraints excluded: chain A residue 1969 VAL Chi-restraints excluded: chain A residue 1985 GLU Chi-restraints excluded: chain A residue 2002 VAL Chi-restraints excluded: chain A residue 2037 VAL Chi-restraints excluded: chain A residue 2070 MET Chi-restraints excluded: chain A residue 2088 MET Chi-restraints excluded: chain A residue 2170 THR Chi-restraints excluded: chain A residue 2174 VAL Chi-restraints excluded: chain A residue 2230 VAL Chi-restraints excluded: chain A residue 2285 THR Chi-restraints excluded: chain A residue 2361 LEU Chi-restraints excluded: chain A residue 2394 SER Chi-restraints excluded: chain A residue 2472 ILE Chi-restraints excluded: chain A residue 2497 ASP Chi-restraints excluded: chain A residue 2507 VAL Chi-restraints excluded: chain A residue 2578 ARG Chi-restraints excluded: chain A residue 2601 VAL Chi-restraints excluded: chain A residue 2636 THR Chi-restraints excluded: chain A residue 2649 ARG Chi-restraints excluded: chain A residue 2657 ASP Chi-restraints excluded: chain A residue 2741 THR Chi-restraints excluded: chain A residue 2773 GLU Chi-restraints excluded: chain B residue 1397 ILE Chi-restraints excluded: chain B residue 1409 ARG Chi-restraints excluded: chain B residue 1445 ASP Chi-restraints excluded: chain B residue 1449 VAL Chi-restraints excluded: chain B residue 1463 VAL Chi-restraints excluded: chain B residue 1469 VAL Chi-restraints excluded: chain B residue 1504 VAL Chi-restraints excluded: chain B residue 1517 VAL Chi-restraints excluded: chain B residue 1589 MET Chi-restraints excluded: chain B residue 1636 VAL Chi-restraints excluded: chain B residue 1650 THR Chi-restraints excluded: chain B residue 1666 VAL Chi-restraints excluded: chain B residue 1667 MET Chi-restraints excluded: chain B residue 1726 CYS Chi-restraints excluded: chain B residue 1728 CYS Chi-restraints excluded: chain B residue 1789 SER Chi-restraints excluded: chain B residue 1808 ASP Chi-restraints excluded: chain B residue 1829 LEU Chi-restraints excluded: chain B residue 1911 LEU Chi-restraints excluded: chain B residue 1926 THR Chi-restraints excluded: chain B residue 1936 TRP Chi-restraints excluded: chain B residue 1967 LEU Chi-restraints excluded: chain B residue 2002 VAL Chi-restraints excluded: chain B residue 2013 ARG Chi-restraints excluded: chain B residue 2081 LEU Chi-restraints excluded: chain B residue 2224 THR Chi-restraints excluded: chain B residue 2258 LEU Chi-restraints excluded: chain B residue 2323 LEU Chi-restraints excluded: chain B residue 2366 THR Chi-restraints excluded: chain B residue 2522 MET Chi-restraints excluded: chain B residue 2533 ILE Chi-restraints excluded: chain B residue 2563 THR Chi-restraints excluded: chain B residue 2592 THR Chi-restraints excluded: chain B residue 2628 VAL Chi-restraints excluded: chain B residue 2677 GLN Chi-restraints excluded: chain B residue 2705 GLN Chi-restraints excluded: chain B residue 2706 PHE Chi-restraints excluded: chain B residue 2736 VAL Chi-restraints excluded: chain B residue 2749 CYS Chi-restraints excluded: chain B residue 2759 TYR Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain G residue 3 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 110 optimal weight: 2.9990 chunk 197 optimal weight: 0.7980 chunk 139 optimal weight: 0.6980 chunk 196 optimal weight: 0.9980 chunk 243 optimal weight: 1.9990 chunk 244 optimal weight: 0.9980 chunk 285 optimal weight: 9.9990 chunk 99 optimal weight: 0.6980 chunk 153 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2530 ASN ** A2665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2244 HIS B2677 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.124251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.088242 restraints weight = 33657.667| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.23 r_work: 0.2808 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 24648 Z= 0.136 Angle : 0.624 15.389 33687 Z= 0.308 Chirality : 0.049 0.389 3825 Planarity : 0.004 0.041 4291 Dihedral : 7.844 60.810 4512 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.64 % Allowed : 14.40 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.15), residues: 2933 helix: -2.44 (0.59), residues: 56 sheet: -0.57 (0.15), residues: 1061 loop : -0.57 (0.15), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B2684 HIS 0.006 0.001 HIS A2665 PHE 0.013 0.001 PHE B2413 TYR 0.027 0.001 TYR A2210 ARG 0.007 0.000 ARG A1702 Details of bonding type rmsd link_TRANS : bond 0.00108 ( 2) link_TRANS : angle 0.51328 ( 6) link_NAG-ASN : bond 0.00641 ( 26) link_NAG-ASN : angle 3.24551 ( 78) link_ALPHA1-6 : bond 0.00574 ( 4) link_ALPHA1-6 : angle 2.09564 ( 12) link_BETA1-4 : bond 0.00554 ( 22) link_BETA1-4 : angle 2.22311 ( 66) link_ALPHA1-3 : bond 0.01054 ( 4) link_ALPHA1-3 : angle 1.49648 ( 12) hydrogen bonds : bond 0.03266 ( 736) hydrogen bonds : angle 6.33781 ( 1719) SS BOND : bond 0.00235 ( 55) SS BOND : angle 0.97731 ( 110) link_BETA1-3 : bond 0.02621 ( 2) link_BETA1-3 : angle 6.46780 ( 6) covalent geometry : bond 0.00314 (24531) covalent geometry : angle 0.58806 (33397) Misc. bond : bond 0.00120 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 174 time to evaluate : 2.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1339 CYS cc_start: 0.4941 (OUTLIER) cc_final: 0.4272 (t) REVERT: A 1413 ARG cc_start: 0.7792 (mtm110) cc_final: 0.7175 (mtm-85) REVERT: A 1444 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8129 (ttm170) REVERT: A 1539 ILE cc_start: 0.9200 (OUTLIER) cc_final: 0.8855 (tp) REVERT: A 1745 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7834 (m-30) REVERT: A 1847 GLU cc_start: 0.8765 (pm20) cc_final: 0.8432 (pm20) REVERT: A 2578 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7431 (ptm-80) REVERT: B 1798 ASN cc_start: 0.8286 (t0) cc_final: 0.7867 (t0) REVERT: B 1808 ASP cc_start: 0.8612 (OUTLIER) cc_final: 0.8176 (m-30) REVERT: B 2258 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8665 (pt) REVERT: B 2592 THR cc_start: 0.8750 (OUTLIER) cc_final: 0.8307 (m) REVERT: B 2690 ASN cc_start: 0.7580 (m-40) cc_final: 0.7250 (m110) REVERT: B 2703 GLN cc_start: 0.6648 (mm110) cc_final: 0.6317 (mm-40) REVERT: B 2705 GLN cc_start: 0.6380 (OUTLIER) cc_final: 0.5972 (mt0) REVERT: C 3 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7881 (tt) outliers start: 93 outliers final: 76 residues processed: 243 average time/residue: 0.4013 time to fit residues: 148.7296 Evaluate side-chains 255 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 169 time to evaluate : 2.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1339 CYS Chi-restraints excluded: chain A residue 1343 THR Chi-restraints excluded: chain A residue 1356 HIS Chi-restraints excluded: chain A residue 1444 ARG Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain A residue 1450 ASP Chi-restraints excluded: chain A residue 1466 VAL Chi-restraints excluded: chain A residue 1469 VAL Chi-restraints excluded: chain A residue 1539 ILE Chi-restraints excluded: chain A residue 1569 MET Chi-restraints excluded: chain A residue 1585 MET Chi-restraints excluded: chain A residue 1594 VAL Chi-restraints excluded: chain A residue 1598 ILE Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 1636 VAL Chi-restraints excluded: chain A residue 1650 THR Chi-restraints excluded: chain A residue 1656 VAL Chi-restraints excluded: chain A residue 1667 MET Chi-restraints excluded: chain A residue 1728 CYS Chi-restraints excluded: chain A residue 1745 ASP Chi-restraints excluded: chain A residue 1814 VAL Chi-restraints excluded: chain A residue 1829 LEU Chi-restraints excluded: chain A residue 1886 LEU Chi-restraints excluded: chain A residue 1897 VAL Chi-restraints excluded: chain A residue 1926 THR Chi-restraints excluded: chain A residue 1969 VAL Chi-restraints excluded: chain A residue 1985 GLU Chi-restraints excluded: chain A residue 2002 VAL Chi-restraints excluded: chain A residue 2037 VAL Chi-restraints excluded: chain A residue 2070 MET Chi-restraints excluded: chain A residue 2088 MET Chi-restraints excluded: chain A residue 2170 THR Chi-restraints excluded: chain A residue 2174 VAL Chi-restraints excluded: chain A residue 2230 VAL Chi-restraints excluded: chain A residue 2285 THR Chi-restraints excluded: chain A residue 2361 LEU Chi-restraints excluded: chain A residue 2394 SER Chi-restraints excluded: chain A residue 2472 ILE Chi-restraints excluded: chain A residue 2497 ASP Chi-restraints excluded: chain A residue 2507 VAL Chi-restraints excluded: chain A residue 2578 ARG Chi-restraints excluded: chain A residue 2601 VAL Chi-restraints excluded: chain A residue 2636 THR Chi-restraints excluded: chain A residue 2649 ARG Chi-restraints excluded: chain A residue 2741 THR Chi-restraints excluded: chain A residue 2773 GLU Chi-restraints excluded: chain B residue 1397 ILE Chi-restraints excluded: chain B residue 1409 ARG Chi-restraints excluded: chain B residue 1445 ASP Chi-restraints excluded: chain B residue 1449 VAL Chi-restraints excluded: chain B residue 1463 VAL Chi-restraints excluded: chain B residue 1469 VAL Chi-restraints excluded: chain B residue 1504 VAL Chi-restraints excluded: chain B residue 1517 VAL Chi-restraints excluded: chain B residue 1589 MET Chi-restraints excluded: chain B residue 1636 VAL Chi-restraints excluded: chain B residue 1650 THR Chi-restraints excluded: chain B residue 1666 VAL Chi-restraints excluded: chain B residue 1667 MET Chi-restraints excluded: chain B residue 1726 CYS Chi-restraints excluded: chain B residue 1728 CYS Chi-restraints excluded: chain B residue 1752 VAL Chi-restraints excluded: chain B residue 1789 SER Chi-restraints excluded: chain B residue 1808 ASP Chi-restraints excluded: chain B residue 1829 LEU Chi-restraints excluded: chain B residue 1911 LEU Chi-restraints excluded: chain B residue 1926 THR Chi-restraints excluded: chain B residue 1936 TRP Chi-restraints excluded: chain B residue 1967 LEU Chi-restraints excluded: chain B residue 2002 VAL Chi-restraints excluded: chain B residue 2081 LEU Chi-restraints excluded: chain B residue 2258 LEU Chi-restraints excluded: chain B residue 2323 LEU Chi-restraints excluded: chain B residue 2366 THR Chi-restraints excluded: chain B residue 2522 MET Chi-restraints excluded: chain B residue 2533 ILE Chi-restraints excluded: chain B residue 2563 THR Chi-restraints excluded: chain B residue 2592 THR Chi-restraints excluded: chain B residue 2628 VAL Chi-restraints excluded: chain B residue 2705 GLN Chi-restraints excluded: chain B residue 2706 PHE Chi-restraints excluded: chain B residue 2736 VAL Chi-restraints excluded: chain B residue 2749 CYS Chi-restraints excluded: chain B residue 2759 TYR Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain G residue 3 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 30 optimal weight: 2.9990 chunk 213 optimal weight: 0.8980 chunk 240 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 79 optimal weight: 4.9990 chunk 132 optimal weight: 0.7980 chunk 254 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 50 optimal weight: 0.0040 chunk 188 optimal weight: 0.0770 overall best weight: 0.4950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2530 ASN ** A2665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.125782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.088356 restraints weight = 33669.034| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 1.92 r_work: 0.2801 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 24648 Z= 0.108 Angle : 0.598 15.114 33687 Z= 0.294 Chirality : 0.048 0.395 3825 Planarity : 0.003 0.039 4291 Dihedral : 7.436 59.836 4512 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.09 % Allowed : 15.10 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.16), residues: 2933 helix: -2.67 (0.51), residues: 68 sheet: -0.50 (0.15), residues: 1070 loop : -0.52 (0.15), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B2684 HIS 0.006 0.001 HIS A2665 PHE 0.011 0.001 PHE B2413 TYR 0.024 0.001 TYR A2210 ARG 0.007 0.000 ARG A1702 Details of bonding type rmsd link_TRANS : bond 0.00075 ( 2) link_TRANS : angle 0.46605 ( 6) link_NAG-ASN : bond 0.00643 ( 26) link_NAG-ASN : angle 3.19424 ( 78) link_ALPHA1-6 : bond 0.00629 ( 4) link_ALPHA1-6 : angle 2.02014 ( 12) link_BETA1-4 : bond 0.00580 ( 22) link_BETA1-4 : angle 2.12712 ( 66) link_ALPHA1-3 : bond 0.01083 ( 4) link_ALPHA1-3 : angle 1.49832 ( 12) hydrogen bonds : bond 0.03002 ( 736) hydrogen bonds : angle 6.19477 ( 1719) SS BOND : bond 0.00198 ( 55) SS BOND : angle 0.81802 ( 110) link_BETA1-3 : bond 0.02478 ( 2) link_BETA1-3 : angle 6.04221 ( 6) covalent geometry : bond 0.00242 (24531) covalent geometry : angle 0.56286 (33397) Misc. bond : bond 0.00104 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 190 time to evaluate : 2.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1339 CYS cc_start: 0.5001 (OUTLIER) cc_final: 0.4407 (t) REVERT: A 1413 ARG cc_start: 0.7788 (mtm110) cc_final: 0.7195 (mtm-85) REVERT: A 1444 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.8084 (ttm170) REVERT: A 1847 GLU cc_start: 0.8778 (pm20) cc_final: 0.8306 (pm20) REVERT: A 2426 ASP cc_start: 0.8098 (t0) cc_final: 0.7690 (t0) REVERT: B 1798 ASN cc_start: 0.8211 (t0) cc_final: 0.7802 (t0) REVERT: B 1954 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.7595 (ttm-80) REVERT: B 2258 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8737 (pt) REVERT: B 2592 THR cc_start: 0.8631 (OUTLIER) cc_final: 0.8216 (m) REVERT: B 2690 ASN cc_start: 0.7469 (m-40) cc_final: 0.7154 (m110) REVERT: C 3 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7859 (tt) outliers start: 79 outliers final: 65 residues processed: 248 average time/residue: 0.4094 time to fit residues: 153.2418 Evaluate side-chains 251 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 180 time to evaluate : 2.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1339 CYS Chi-restraints excluded: chain A residue 1343 THR Chi-restraints excluded: chain A residue 1356 HIS Chi-restraints excluded: chain A residue 1444 ARG Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain A residue 1450 ASP Chi-restraints excluded: chain A residue 1466 VAL Chi-restraints excluded: chain A residue 1539 ILE Chi-restraints excluded: chain A residue 1569 MET Chi-restraints excluded: chain A residue 1585 MET Chi-restraints excluded: chain A residue 1594 VAL Chi-restraints excluded: chain A residue 1598 ILE Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 1636 VAL Chi-restraints excluded: chain A residue 1656 VAL Chi-restraints excluded: chain A residue 1667 MET Chi-restraints excluded: chain A residue 1728 CYS Chi-restraints excluded: chain A residue 1752 VAL Chi-restraints excluded: chain A residue 1829 LEU Chi-restraints excluded: chain A residue 1886 LEU Chi-restraints excluded: chain A residue 1897 VAL Chi-restraints excluded: chain A residue 1969 VAL Chi-restraints excluded: chain A residue 1985 GLU Chi-restraints excluded: chain A residue 2002 VAL Chi-restraints excluded: chain A residue 2037 VAL Chi-restraints excluded: chain A residue 2070 MET Chi-restraints excluded: chain A residue 2088 MET Chi-restraints excluded: chain A residue 2174 VAL Chi-restraints excluded: chain A residue 2230 VAL Chi-restraints excluded: chain A residue 2361 LEU Chi-restraints excluded: chain A residue 2394 SER Chi-restraints excluded: chain A residue 2497 ASP Chi-restraints excluded: chain A residue 2507 VAL Chi-restraints excluded: chain A residue 2601 VAL Chi-restraints excluded: chain A residue 2636 THR Chi-restraints excluded: chain A residue 2649 ARG Chi-restraints excluded: chain A residue 2741 THR Chi-restraints excluded: chain A residue 2773 GLU Chi-restraints excluded: chain B residue 1397 ILE Chi-restraints excluded: chain B residue 1445 ASP Chi-restraints excluded: chain B residue 1449 VAL Chi-restraints excluded: chain B residue 1463 VAL Chi-restraints excluded: chain B residue 1504 VAL Chi-restraints excluded: chain B residue 1517 VAL Chi-restraints excluded: chain B residue 1636 VAL Chi-restraints excluded: chain B residue 1650 THR Chi-restraints excluded: chain B residue 1666 VAL Chi-restraints excluded: chain B residue 1667 MET Chi-restraints excluded: chain B residue 1726 CYS Chi-restraints excluded: chain B residue 1728 CYS Chi-restraints excluded: chain B residue 1752 VAL Chi-restraints excluded: chain B residue 1808 ASP Chi-restraints excluded: chain B residue 1829 LEU Chi-restraints excluded: chain B residue 1926 THR Chi-restraints excluded: chain B residue 1936 TRP Chi-restraints excluded: chain B residue 1954 ARG Chi-restraints excluded: chain B residue 2002 VAL Chi-restraints excluded: chain B residue 2081 LEU Chi-restraints excluded: chain B residue 2258 LEU Chi-restraints excluded: chain B residue 2323 LEU Chi-restraints excluded: chain B residue 2366 THR Chi-restraints excluded: chain B residue 2425 LEU Chi-restraints excluded: chain B residue 2522 MET Chi-restraints excluded: chain B residue 2533 ILE Chi-restraints excluded: chain B residue 2563 THR Chi-restraints excluded: chain B residue 2592 THR Chi-restraints excluded: chain B residue 2678 CYS Chi-restraints excluded: chain B residue 2749 CYS Chi-restraints excluded: chain B residue 2759 TYR Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain G residue 3 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 156 optimal weight: 0.9980 chunk 102 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 241 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 275 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 168 optimal weight: 3.9990 chunk 195 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2530 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.124785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.087741 restraints weight = 33822.619| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 2.11 r_work: 0.2823 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 24648 Z= 0.140 Angle : 0.619 14.712 33687 Z= 0.305 Chirality : 0.049 0.396 3825 Planarity : 0.004 0.039 4291 Dihedral : 7.458 59.786 4512 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.21 % Allowed : 15.06 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.15), residues: 2933 helix: -2.65 (0.52), residues: 68 sheet: -0.53 (0.15), residues: 1071 loop : -0.57 (0.15), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP B2684 HIS 0.003 0.001 HIS A1505 PHE 0.017 0.001 PHE B1400 TYR 0.025 0.001 TYR A2210 ARG 0.009 0.000 ARG A1702 Details of bonding type rmsd link_TRANS : bond 0.00123 ( 2) link_TRANS : angle 0.49639 ( 6) link_NAG-ASN : bond 0.00609 ( 26) link_NAG-ASN : angle 3.31738 ( 78) link_ALPHA1-6 : bond 0.00587 ( 4) link_ALPHA1-6 : angle 2.02707 ( 12) link_BETA1-4 : bond 0.00563 ( 22) link_BETA1-4 : angle 2.12060 ( 66) link_ALPHA1-3 : bond 0.01013 ( 4) link_ALPHA1-3 : angle 1.54224 ( 12) hydrogen bonds : bond 0.03173 ( 736) hydrogen bonds : angle 6.19381 ( 1719) SS BOND : bond 0.00227 ( 55) SS BOND : angle 0.88930 ( 110) link_BETA1-3 : bond 0.02516 ( 2) link_BETA1-3 : angle 6.19136 ( 6) covalent geometry : bond 0.00324 (24531) covalent geometry : angle 0.58298 (33397) Misc. bond : bond 0.00098 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5866 Ramachandran restraints generated. 2933 Oldfield, 0 Emsley, 2933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 178 time to evaluate : 3.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1339 CYS cc_start: 0.5008 (OUTLIER) cc_final: 0.4407 (t) REVERT: A 1413 ARG cc_start: 0.7917 (mtm110) cc_final: 0.7250 (mtm-85) REVERT: A 1444 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8096 (ttm170) REVERT: A 1847 GLU cc_start: 0.8795 (pm20) cc_final: 0.8437 (pm20) REVERT: A 2426 ASP cc_start: 0.8172 (t0) cc_final: 0.7749 (t0) REVERT: B 1798 ASN cc_start: 0.8265 (t0) cc_final: 0.7856 (t0) REVERT: B 1954 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.7564 (ttm-80) REVERT: B 2258 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8661 (pt) REVERT: B 2561 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8442 (mp) REVERT: B 2592 THR cc_start: 0.8717 (OUTLIER) cc_final: 0.8247 (m) REVERT: B 2649 ARG cc_start: 0.6829 (ttp-110) cc_final: 0.6460 (ttp-110) REVERT: B 2684 TRP cc_start: 0.6780 (m-90) cc_final: 0.6254 (m-90) REVERT: B 2690 ASN cc_start: 0.7509 (m-40) cc_final: 0.7186 (m110) REVERT: C 3 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7849 (tt) outliers start: 82 outliers final: 70 residues processed: 240 average time/residue: 0.4075 time to fit residues: 149.5700 Evaluate side-chains 253 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 176 time to evaluate : 2.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1339 CYS Chi-restraints excluded: chain A residue 1343 THR Chi-restraints excluded: chain A residue 1356 HIS Chi-restraints excluded: chain A residue 1444 ARG Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain A residue 1450 ASP Chi-restraints excluded: chain A residue 1466 VAL Chi-restraints excluded: chain A residue 1469 VAL Chi-restraints excluded: chain A residue 1539 ILE Chi-restraints excluded: chain A residue 1569 MET Chi-restraints excluded: chain A residue 1585 MET Chi-restraints excluded: chain A residue 1594 VAL Chi-restraints excluded: chain A residue 1598 ILE Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 1636 VAL Chi-restraints excluded: chain A residue 1656 VAL Chi-restraints excluded: chain A residue 1667 MET Chi-restraints excluded: chain A residue 1728 CYS Chi-restraints excluded: chain A residue 1752 VAL Chi-restraints excluded: chain A residue 1814 VAL Chi-restraints excluded: chain A residue 1829 LEU Chi-restraints excluded: chain A residue 1886 LEU Chi-restraints excluded: chain A residue 1897 VAL Chi-restraints excluded: chain A residue 1926 THR Chi-restraints excluded: chain A residue 1969 VAL Chi-restraints excluded: chain A residue 1985 GLU Chi-restraints excluded: chain A residue 2002 VAL Chi-restraints excluded: chain A residue 2037 VAL Chi-restraints excluded: chain A residue 2070 MET Chi-restraints excluded: chain A residue 2088 MET Chi-restraints excluded: chain A residue 2174 VAL Chi-restraints excluded: chain A residue 2230 VAL Chi-restraints excluded: chain A residue 2361 LEU Chi-restraints excluded: chain A residue 2394 SER Chi-restraints excluded: chain A residue 2497 ASP Chi-restraints excluded: chain A residue 2507 VAL Chi-restraints excluded: chain A residue 2601 VAL Chi-restraints excluded: chain A residue 2636 THR Chi-restraints excluded: chain A residue 2649 ARG Chi-restraints excluded: chain A residue 2741 THR Chi-restraints excluded: chain A residue 2773 GLU Chi-restraints excluded: chain B residue 1397 ILE Chi-restraints excluded: chain B residue 1445 ASP Chi-restraints excluded: chain B residue 1449 VAL Chi-restraints excluded: chain B residue 1463 VAL Chi-restraints excluded: chain B residue 1504 VAL Chi-restraints excluded: chain B residue 1517 VAL Chi-restraints excluded: chain B residue 1636 VAL Chi-restraints excluded: chain B residue 1650 THR Chi-restraints excluded: chain B residue 1666 VAL Chi-restraints excluded: chain B residue 1667 MET Chi-restraints excluded: chain B residue 1726 CYS Chi-restraints excluded: chain B residue 1728 CYS Chi-restraints excluded: chain B residue 1752 VAL Chi-restraints excluded: chain B residue 1808 ASP Chi-restraints excluded: chain B residue 1829 LEU Chi-restraints excluded: chain B residue 1911 LEU Chi-restraints excluded: chain B residue 1926 THR Chi-restraints excluded: chain B residue 1936 TRP Chi-restraints excluded: chain B residue 1954 ARG Chi-restraints excluded: chain B residue 1967 LEU Chi-restraints excluded: chain B residue 2002 VAL Chi-restraints excluded: chain B residue 2081 LEU Chi-restraints excluded: chain B residue 2258 LEU Chi-restraints excluded: chain B residue 2323 LEU Chi-restraints excluded: chain B residue 2366 THR Chi-restraints excluded: chain B residue 2522 MET Chi-restraints excluded: chain B residue 2533 ILE Chi-restraints excluded: chain B residue 2561 LEU Chi-restraints excluded: chain B residue 2563 THR Chi-restraints excluded: chain B residue 2592 THR Chi-restraints excluded: chain B residue 2628 VAL Chi-restraints excluded: chain B residue 2678 CYS Chi-restraints excluded: chain B residue 2749 CYS Chi-restraints excluded: chain B residue 2759 TYR Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain G residue 3 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 117 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 287 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 144 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2530 ASN A2758 HIS B2244 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.124055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.087797 restraints weight = 33433.161| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 2.29 r_work: 0.2804 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 24648 Z= 0.161 Angle : 0.631 14.327 33687 Z= 0.311 Chirality : 0.049 0.394 3825 Planarity : 0.004 0.040 4291 Dihedral : 7.511 59.557 4512 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.29 % Allowed : 15.10 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.16), residues: 2933 helix: -2.54 (0.57), residues: 62 sheet: -0.58 (0.15), residues: 1077 loop : -0.57 (0.15), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B2684 HIS 0.003 0.001 HIS A1576 PHE 0.014 0.001 PHE B2413 TYR 0.028 0.001 TYR A2210 ARG 0.008 0.000 ARG A1702 Details of bonding type rmsd link_TRANS : bond 0.00144 ( 2) link_TRANS : angle 0.54930 ( 6) link_NAG-ASN : bond 0.00630 ( 26) link_NAG-ASN : angle 3.37745 ( 78) link_ALPHA1-6 : bond 0.00600 ( 4) link_ALPHA1-6 : angle 2.00540 ( 12) link_BETA1-4 : bond 0.00549 ( 22) link_BETA1-4 : angle 2.12468 ( 66) link_ALPHA1-3 : bond 0.01022 ( 4) link_ALPHA1-3 : angle 1.50916 ( 12) hydrogen bonds : bond 0.03289 ( 736) hydrogen bonds : angle 6.22814 ( 1719) SS BOND : bond 0.00244 ( 55) SS BOND : angle 0.91103 ( 110) link_BETA1-3 : bond 0.02528 ( 2) link_BETA1-3 : angle 6.31553 ( 6) covalent geometry : bond 0.00379 (24531) covalent geometry : angle 0.59474 (33397) Misc. bond : bond 0.00102 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12599.34 seconds wall clock time: 218 minutes 22.23 seconds (13102.23 seconds total)