Starting phenix.real_space_refine on Fri May 23 07:14:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jx8_36692/05_2025/8jx8_36692.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jx8_36692/05_2025/8jx8_36692.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jx8_36692/05_2025/8jx8_36692.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jx8_36692/05_2025/8jx8_36692.map" model { file = "/net/cci-nas-00/data/ceres_data/8jx8_36692/05_2025/8jx8_36692.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jx8_36692/05_2025/8jx8_36692.cif" } resolution = 3.3 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= 0.006 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 10 9.91 5 Ni 2 6.56 5 S 157 5.16 5 C 14660 2.51 5 N 4018 2.21 5 O 4612 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 23459 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 11221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1436, 11221 Classifications: {'peptide': 1436} Link IDs: {'PTRANS': 73, 'TRANS': 1362} Chain: "B" Number of atoms: 11208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1434, 11208 Classifications: {'peptide': 1434} Link IDs: {'PTRANS': 72, 'TRANS': 1361} 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: "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: "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: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 76 Unusual residues: {' CA': 5, ' NI': 1, 'A2G': 1, 'NAG': 4} Classifications: {'undetermined': 11} Link IDs: {None: 10} 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: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 76 Unusual residues: {' CA': 5, ' NI': 1, 'A2G': 1, 'NAG': 4} Classifications: {'undetermined': 11} Link IDs: {None: 10} 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 22583 SG CYS J 2 59.807 83.330 109.697 1.00 34.72 S ATOM 22473 SG CYS D 2 80.185 87.910 110.601 1.00 29.77 S Time building chain proxies: 14.68, per 1000 atoms: 0.63 Number of scatterers: 23459 At special positions: 0 Unit cell: (142.511, 170.731, 145.333, 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 10 19.99 S 157 16.00 O 4612 8.00 N 4018 7.00 C 14660 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=49, symmetry=0 Simple disulfide: pdb=" SG CYS A1313 " - pdb=" SG CYS A1326 " distance=2.04 Simple disulfide: pdb=" SG CYS A1320 " - pdb=" SG CYS A1339 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A1710 " - pdb=" SG CYS A1726 " distance=2.03 Simple disulfide: pdb=" SG CYS A1728 " - pdb=" SG CYS A1741 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS A2656 " - pdb=" SG CYS A2667 " distance=2.03 Simple disulfide: pdb=" SG CYS A2663 " - pdb=" SG CYS A2676 " distance=2.02 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 B1313 " - pdb=" SG CYS B1326 " distance=2.03 Simple disulfide: pdb=" SG CYS B1320 " - pdb=" SG CYS B1339 " distance=2.04 Simple disulfide: pdb=" SG CYS B1333 " - pdb=" SG CYS B1349 " distance=2.03 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 B1705 " - pdb=" SG CYS B1714 " 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 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 " BETA1-4 " 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 R 1 " - " NAG R 2 " " 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 1 " - " NAG Z 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: 6.70 Conformation dependent library (CDL) restraints added in 3.3 seconds 5732 Ramachandran restraints generated. 2866 Oldfield, 0 Emsley, 2866 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5368 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 76 sheets defined 4.0% alpha, 36.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.67 Creating SS restraints... Processing helix chain 'A' and resid 1328 through 1332 Processing helix chain 'A' and resid 1356 through 1361 Processing helix chain 'A' and resid 1694 through 1698 Processing helix chain 'A' and resid 2021 through 2026 Processing helix chain 'A' and resid 2350 through 2354 Processing helix chain 'A' and resid 2654 through 2663 removed outlier: 3.978A pdb=" N ASP A2657 " --> pdb=" O ASN A2654 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN A2658 " --> pdb=" O PRO A2655 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N PHE A2659 " --> pdb=" O CYS A2656 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASN A2660 " --> pdb=" O ASP A2657 " (cutoff:3.500A) Processing helix chain 'A' and resid 2709 through 2711 No H-bonds generated for 'chain 'A' and resid 2709 through 2711' Processing helix chain 'A' and resid 2733 through 2738 Processing helix chain 'B' and resid 1357 through 1361 Processing helix chain 'B' and resid 1694 through 1698 Processing helix chain 'B' and resid 1703 through 1708 Processing helix chain 'B' and resid 1881 through 1883 No H-bonds generated for 'chain 'B' and resid 1881 through 1883' Processing helix chain 'B' and resid 2016 through 2020 removed outlier: 3.664A pdb=" N SER B2020 " --> pdb=" O ALA B2017 " (cutoff:3.500A) Processing helix chain 'B' and resid 2021 through 2026 Processing helix chain 'B' and resid 2331 through 2335 Processing helix chain 'B' and resid 2349 through 2354 Processing helix chain 'B' and resid 2517 through 2519 No H-bonds generated for 'chain 'B' and resid 2517 through 2519' Processing helix chain 'B' and resid 2657 through 2663 Processing helix chain 'B' and resid 2687 through 2691 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 2729 through 2732 Processing helix chain 'B' and resid 2733 through 2738 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 1365 through 1368 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 1408 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 1458 through 1461 removed outlier: 4.074A pdb=" N GLY A1689 " --> pdb=" O ALA A1442 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1469 through 1475 removed outlier: 4.087A pdb=" N ALA A1471 " --> pdb=" O SER A1484 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER A1484 " --> pdb=" O ALA A1471 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS A1490 " --> pdb=" O ASP A1485 " (cutoff:3.500A) removed outlier: 6.501A 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: 3.909A pdb=" N MET A1514 " --> pdb=" O THR A1527 " (cutoff:3.500A) removed outlier: 6.678A 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: 3.628A pdb=" N GLY A1557 " --> pdb=" O SER A1572 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL A1568 " --> pdb=" O ASP A1561 " (cutoff:3.500A) removed outlier: 6.801A 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: 5.019A pdb=" N GLY A1603 " --> pdb=" O MET A1616 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET A1616 " --> pdb=" O GLY A1603 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE A1623 " --> pdb=" O VAL A1636 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1646 through 1651 removed outlier: 3.879A pdb=" N ALA A1648 " --> pdb=" O THR A1659 " (cutoff:3.500A) removed outlier: 6.801A 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 1775 through 1776 removed outlier: 3.507A pdb=" N ILE A1756 " --> pdb=" O ARG A1753 " (cutoff:3.500A) removed outlier: 4.112A 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: 3.513A pdb=" N GLU A1801 " --> pdb=" O GLU A1797 " (cutoff:3.500A) removed outlier: 6.873A 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: 3.509A pdb=" N SER A1845 " --> pdb=" O THR A1840 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE A1846 " --> pdb=" O LEU A1861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1874 through 1880 removed outlier: 6.474A pdb=" N SER A1889 " --> pdb=" O VAL A1875 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ILE A1877 " --> pdb=" O TYR A1887 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TYR A1887 " --> pdb=" O ILE A1877 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N VAL A1879 " --> pdb=" O LYS A1885 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LYS A1885 " --> pdb=" O VAL A1879 " (cutoff:3.500A) removed outlier: 6.550A 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: 5.211A pdb=" N VAL A1924 " --> pdb=" O ALA A1937 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA A1937 " --> pdb=" O VAL A1924 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE A1944 " --> pdb=" O LEU A1957 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1964 through 1970 removed outlier: 3.838A pdb=" N GLY A1966 " --> pdb=" O SER A1977 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE A1984 " --> pdb=" O LEU A1998 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 2033 through 2036 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 2086 through 2091 removed outlier: 6.866A pdb=" N VAL A2089 " --> pdb=" O GLY A2076 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLY A2076 " --> pdb=" O VAL A2089 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 2098 through 2104 removed outlier: 4.159A pdb=" N HIS A2100 " --> pdb=" O CYS A2113 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY A2124 " --> pdb=" O ASP A2114 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE A2125 " --> pdb=" O VAL A2138 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 2146 through 2153 removed outlier: 6.678A pdb=" N ILE A2148 " --> pdb=" O ALA A2165 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ALA A2165 " --> pdb=" O ILE A2148 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLY A2150 " --> pdb=" O THR A2163 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N THR A2170 " --> pdb=" O LYS A2187 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LYS A2187 " --> pdb=" O THR A2170 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE A2172 " --> pdb=" O LEU A2185 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 2193 through 2199 removed outlier: 3.738A pdb=" N HIS A2195 " --> pdb=" O ALA A2208 " (cutoff:3.500A) removed outlier: 6.819A 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: 4.054A pdb=" N GLY A2239 " --> pdb=" O VAL A2252 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 2281 through 2287 removed outlier: 3.919A pdb=" N GLY A2283 " --> pdb=" O VAL A2294 " (cutoff:3.500A) removed outlier: 6.889A 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 removed outlier: 3.881A pdb=" N PHE A2357 " --> pdb=" O GLY A2370 " (cutoff:3.500A) 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: 3.503A pdb=" N SER A2394 " --> pdb=" O GLY A2640 " (cutoff:3.500A) removed outlier: 4.961A 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: 6.032A pdb=" N ALA A2422 " --> pdb=" O LYS A2439 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LYS A2439 " --> pdb=" O ALA A2422 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ALA A2424 " --> pdb=" O THR A2437 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE A2447 " --> pdb=" O LEU A2462 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 2473 through 2475 removed outlier: 3.693A pdb=" N ARG A2480 " --> pdb=" O ASP A2475 " (cutoff:3.500A) removed outlier: 6.727A 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: 4.101A pdb=" N ALA A2512 " --> pdb=" O THR A2525 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE A2533 " --> pdb=" O ILE A2546 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 2554 through 2559 removed outlier: 3.601A pdb=" N GLY A2556 " --> pdb=" O ALA A2569 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ARG A2578 " --> pdb=" O VAL A2588 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N VAL A2588 " --> pdb=" O ARG A2578 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 2596 through 2602 removed outlier: 4.570A pdb=" N THR A2609 " --> pdb=" O PHE A2597 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LEU A2599 " --> pdb=" O TYR A2607 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N TYR A2607 " --> pdb=" O LEU A2599 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N VAL A2601 " --> pdb=" O TYR A2605 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N TYR A2605 " --> pdb=" O VAL A2601 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 2667 through 2669 Processing sheet with id=AE1, first strand: chain 'A' and resid 2684 through 2687 Processing sheet with id=AE2, first strand: chain 'A' and resid 2705 through 2707 Processing sheet with id=AE3, first strand: chain 'B' and resid 1317 through 1319 Processing sheet with id=AE4, first strand: chain 'B' and resid 1364 through 1368 removed outlier: 3.621A pdb=" N GLN B1364 " --> pdb=" O LEU B1375 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 1380 through 1382 Processing sheet with id=AE6, first strand: chain 'B' and resid 1404 through 1408 Processing sheet with id=AE7, first strand: chain 'B' and resid 1420 through 1422 Processing sheet with id=AE8, first strand: chain 'B' and resid 1459 through 1461 Processing sheet with id=AE9, first strand: chain 'B' and resid 1469 through 1475 removed outlier: 4.187A pdb=" N ALA B1471 " --> pdb=" O SER B1484 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N THR B1491 " --> pdb=" O VAL B1504 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 1512 through 1518 removed outlier: 3.814A pdb=" N MET B1514 " --> pdb=" O THR B1527 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE B1534 " --> pdb=" O LEU B1547 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 1555 through 1561 removed outlier: 3.516A pdb=" N GLY B1557 " --> pdb=" O SER B1572 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE B1580 " --> pdb=" O ILE B1593 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 1601 through 1607 removed outlier: 4.882A pdb=" N GLY B1603 " --> pdb=" O MET B1616 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET B1616 " --> pdb=" O GLY B1603 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE B1623 " --> pdb=" O VAL B1636 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 1646 through 1652 removed outlier: 4.081A pdb=" N ALA B1648 " --> pdb=" O THR B1659 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE B1655 " --> pdb=" O PHE B1652 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN B1665 " --> pdb=" O ASP B1660 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N GLN B1668 " --> pdb=" O VAL B1679 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N VAL B1679 " --> pdb=" O GLN B1668 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 1713 through 1716 Processing sheet with id=AF6, first strand: chain 'B' and resid 1732 through 1734 Processing sheet with id=AF7, first strand: chain 'B' and resid 1757 through 1761 removed outlier: 3.550A pdb=" N VAL B1752 " --> pdb=" O GLY B2007 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLY B2007 " --> pdb=" O VAL B1752 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B' and resid 1785 through 1787 removed outlier: 3.523A pdb=" N GLU B1801 " --> pdb=" O GLU B1797 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE B1802 " --> pdb=" O PHE B1815 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'B' and resid 1827 through 1830 removed outlier: 6.649A pdb=" N ILE B1846 " --> pdb=" O LEU B1861 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'B' and resid 1874 through 1880 removed outlier: 3.857A pdb=" N GLY B1876 " --> pdb=" O SER B1889 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE B1901 " --> pdb=" O LEU B1914 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'B' and resid 1922 through 1928 removed outlier: 5.329A pdb=" N VAL B1924 " --> pdb=" O ALA B1937 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA B1937 " --> pdb=" O VAL B1924 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE B1944 " --> pdb=" O LEU B1957 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 1964 through 1970 removed outlier: 3.639A pdb=" N GLY B1966 " --> pdb=" O SER B1977 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE B1984 " --> pdb=" O LEU B1998 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'B' and resid 2033 through 2036 Processing sheet with id=AG5, first strand: chain 'B' and resid 2050 through 2052 Processing sheet with id=AG6, first strand: chain 'B' and resid 2074 through 2078 Processing sheet with id=AG7, first strand: chain 'B' and resid 2098 through 2104 removed outlier: 4.275A pdb=" N HIS B2100 " --> pdb=" O CYS B2113 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE B2125 " --> pdb=" O VAL B2138 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'B' and resid 2148 through 2154 removed outlier: 6.089A pdb=" N ILE B2148 " --> pdb=" O ALA B2165 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ALA B2165 " --> pdb=" O ILE B2148 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY B2150 " --> pdb=" O THR B2163 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N THR B2170 " --> pdb=" O LYS B2187 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N LYS B2187 " --> pdb=" O THR B2170 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE B2172 " --> pdb=" O LEU B2185 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'B' and resid 2193 through 2199 removed outlier: 3.784A pdb=" N HIS B2195 " --> pdb=" O ALA B2208 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE B2216 " --> pdb=" O LEU B2229 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'B' and resid 2237 through 2243 removed outlier: 4.307A pdb=" N GLY B2239 " --> pdb=" O VAL B2252 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP B2243 " --> pdb=" O TYR B2248 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TYR B2248 " --> pdb=" O ASP B2243 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ARG B2261 " --> pdb=" O VAL B2271 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N VAL B2271 " --> pdb=" O ARG B2261 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'B' and resid 2281 through 2287 removed outlier: 4.059A pdb=" N GLY B2283 " --> pdb=" O VAL B2294 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS B2300 " --> pdb=" O ASP B2295 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL B2301 " --> pdb=" O ILE B2317 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'B' and resid 2357 through 2359 Processing sheet with id=AH4, first strand: chain 'B' and resid 2375 through 2376 Processing sheet with id=AH5, first strand: chain 'B' and resid 2416 through 2417 removed outlier: 4.033A pdb=" N GLY B2640 " --> pdb=" O SER B2394 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'B' and resid 2421 through 2428 removed outlier: 5.766A pdb=" N ALA B2422 " --> pdb=" O LYS B2439 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LYS B2439 " --> pdb=" O ALA B2422 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA B2424 " --> pdb=" O THR B2437 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N GLY B2445 " --> pdb=" O SER B2464 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N SER B2464 " --> pdb=" O GLY B2445 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE B2447 " --> pdb=" O LEU B2462 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'B' and resid 2469 through 2474 removed outlier: 4.216A pdb=" N GLY B2471 " --> pdb=" O SER B2484 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR B2490 " --> pdb=" O ASP B2485 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE B2491 " --> pdb=" O ILE B2504 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ASN B2500 " --> pdb=" O ALA B2495 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'B' and resid 2510 through 2516 removed outlier: 6.779A pdb=" N TRP B2527 " --> pdb=" O PRO B2510 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ALA B2512 " --> pdb=" O THR B2525 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE B2533 " --> pdb=" O ILE B2546 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'B' and resid 2554 through 2560 removed outlier: 7.056A pdb=" N ILE B2576 " --> pdb=" O VAL B2589 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'B' and resid 2596 through 2602 removed outlier: 3.838A pdb=" N GLY B2598 " --> pdb=" O THR B2609 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS B2615 " --> pdb=" O ASP B2610 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'B' and resid 2666 through 2668 removed outlier: 3.533A pdb=" N ILE B2666 " --> pdb=" O GLN B2677 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'B' and resid 2684 through 2686 Processing sheet with id=AI4, first strand: chain 'B' and resid 2705 through 2708 removed outlier: 6.173A pdb=" N PHE B2706 " --> pdb=" O CYS B2713 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N CYS B2713 " --> pdb=" O PHE B2706 " (cutoff:3.500A) 730 hydrogen bonds defined for protein. 1734 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: 13.58 Time building geometry restraints manager: 7.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7369 1.33 - 1.46: 5966 1.46 - 1.59: 10463 1.59 - 1.71: 1 1.71 - 1.84: 203 Bond restraints: 24002 Sorted by residual: bond pdb=" CB PRO B1398 " pdb=" CG PRO B1398 " ideal model delta sigma weight residual 1.492 1.610 -0.118 5.00e-02 4.00e+02 5.53e+00 bond pdb=" C3 NAG B4704 " pdb=" O3 NAG B4704 " ideal model delta sigma weight residual 1.403 1.446 -0.043 2.00e-02 2.50e+03 4.65e+00 bond pdb=" CA SER A2122 " pdb=" C SER A2122 " ideal model delta sigma weight residual 1.523 1.492 0.030 1.48e-02 4.57e+03 4.24e+00 bond pdb=" C1 NAG B4702 " pdb=" O5 NAG B4702 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.07e+00 bond pdb=" C ASN A1798 " pdb=" N PRO A1799 " ideal model delta sigma weight residual 1.336 1.356 -0.021 1.08e-02 8.57e+03 3.64e+00 ... (remaining 23997 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 31651 1.94 - 3.88: 924 3.88 - 5.82: 92 5.82 - 7.76: 12 7.76 - 9.70: 3 Bond angle restraints: 32682 Sorted by residual: angle pdb=" CA PRO B1398 " pdb=" N PRO B1398 " pdb=" CD PRO B1398 " ideal model delta sigma weight residual 112.00 105.22 6.78 1.40e+00 5.10e-01 2.35e+01 angle pdb=" C LEU A2440 " pdb=" N ASN A2441 " pdb=" CA ASN A2441 " ideal model delta sigma weight residual 121.54 128.22 -6.68 1.91e+00 2.74e-01 1.22e+01 angle pdb=" N VAL A1832 " pdb=" CA VAL A1832 " pdb=" C VAL A1832 " ideal model delta sigma weight residual 112.96 109.66 3.30 1.00e+00 1.00e+00 1.09e+01 angle pdb=" C1 NAG A4701 " pdb=" O5 NAG A4701 " pdb=" C5 NAG A4701 " ideal model delta sigma weight residual 113.21 122.91 -9.70 3.00e+00 1.11e-01 1.05e+01 angle pdb=" C1 NAG B4704 " pdb=" O5 NAG B4704 " pdb=" C5 NAG B4704 " ideal model delta sigma weight residual 113.21 103.72 9.49 3.00e+00 1.11e-01 1.00e+01 ... (remaining 32677 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.39: 13879 21.39 - 42.77: 924 42.77 - 64.16: 156 64.16 - 85.54: 71 85.54 - 106.93: 33 Dihedral angle restraints: 15063 sinusoidal: 6681 harmonic: 8382 Sorted by residual: dihedral pdb=" CB CYS B1401 " pdb=" SG CYS B1401 " pdb=" SG CYS B1414 " pdb=" CB CYS B1414 " ideal model delta sinusoidal sigma weight residual 93.00 -178.81 -88.19 1 1.00e+01 1.00e-02 9.30e+01 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 -179.55 -87.45 1 1.00e+01 1.00e-02 9.17e+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 93.00 178.94 -85.94 1 1.00e+01 1.00e-02 8.92e+01 ... (remaining 15060 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 3613 0.108 - 0.217: 138 0.217 - 0.325: 6 0.325 - 0.433: 3 0.433 - 0.542: 2 Chirality restraints: 3762 Sorted by residual: chirality pdb=" C1 NAG A4704 " pdb=" ND2 ASN A2488 " pdb=" C2 NAG A4704 " pdb=" O5 NAG A4704 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.34e+00 chirality pdb=" C1 NAG V 1 " pdb=" ND2 ASN B1551 " pdb=" C2 NAG V 1 " pdb=" O5 NAG V 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.58e+00 chirality pdb=" C1 NAG A4703 " pdb=" ND2 ASN A2225 " pdb=" C2 NAG A4703 " pdb=" O5 NAG A4703 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.52e+00 ... (remaining 3759 not shown) Planarity restraints: 4217 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A4704 " -0.334 2.00e-02 2.50e+03 2.88e-01 1.04e+03 pdb=" C7 NAG A4704 " 0.079 2.00e-02 2.50e+03 pdb=" C8 NAG A4704 " -0.147 2.00e-02 2.50e+03 pdb=" N2 NAG A4704 " 0.513 2.00e-02 2.50e+03 pdb=" O7 NAG A4704 " -0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B4704 " 0.332 2.00e-02 2.50e+03 2.85e-01 1.02e+03 pdb=" C7 NAG B4704 " -0.074 2.00e-02 2.50e+03 pdb=" C8 NAG B4704 " 0.151 2.00e-02 2.50e+03 pdb=" N2 NAG B4704 " -0.509 2.00e-02 2.50e+03 pdb=" O7 NAG B4704 " 0.100 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " -0.255 2.00e-02 2.50e+03 2.11e-01 5.55e+02 pdb=" C7 NAG F 1 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " -0.179 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " 0.346 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " 0.016 2.00e-02 2.50e+03 ... (remaining 4214 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 209 2.60 - 3.17: 19729 3.17 - 3.75: 34583 3.75 - 4.32: 51251 4.32 - 4.90: 86418 Nonbonded interactions: 192190 Sorted by model distance: nonbonded pdb=" OE2 GLU A1923 " pdb="NI NI A4711 " model vdw 2.024 2.180 nonbonded pdb=" OE2 GLU B1923 " pdb="NI NI B4711 " model vdw 2.068 2.180 nonbonded pdb=" NE2 HIS B1963 " pdb="NI NI B4711 " model vdw 2.080 2.260 nonbonded pdb=" NE2 HIS B1921 " pdb="NI NI B4711 " model vdw 2.161 2.260 nonbonded pdb=" OD2 ASP A1830 " pdb=" OG SER A1833 " model vdw 2.228 3.040 ... (remaining 192185 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 1308 through 2741 or resid 4701 through 4711)) 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.950 Check model and map are aligned: 0.190 Set scattering table: 0.210 Process input model: 61.570 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 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 0.118 24113 Z= 0.213 Angle : 0.766 17.724 32960 Z= 0.388 Chirality : 0.052 0.542 3762 Planarity : 0.012 0.288 4189 Dihedral : 15.648 106.931 9542 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 1.64 % Allowed : 13.67 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.30 (0.15), residues: 2866 helix: -3.53 (0.39), residues: 79 sheet: -0.59 (0.15), residues: 1127 loop : -0.86 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1574 HIS 0.004 0.001 HIS B1803 PHE 0.026 0.001 PHE B2706 TYR 0.016 0.001 TYR A2210 ARG 0.008 0.000 ARG B2506 Details of bonding type rmsd link_TRANS : bond 0.00166 ( 2) link_TRANS : angle 0.58750 ( 6) link_NAG-ASN : bond 0.00885 ( 26) link_NAG-ASN : angle 4.70937 ( 78) link_ALPHA1-6 : bond 0.00232 ( 4) link_ALPHA1-6 : angle 0.91781 ( 12) link_BETA1-4 : bond 0.00634 ( 24) link_BETA1-4 : angle 1.92419 ( 72) link_ALPHA1-3 : bond 0.00233 ( 4) link_ALPHA1-3 : angle 0.92105 ( 12) hydrogen bonds : bond 0.22985 ( 730) hydrogen bonds : angle 10.20353 ( 1734) SS BOND : bond 0.00295 ( 49) SS BOND : angle 0.91199 ( 98) covalent geometry : bond 0.00436 (24002) covalent geometry : angle 0.72578 (32682) Misc. bond : bond 0.01985 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5732 Ramachandran restraints generated. 2866 Oldfield, 0 Emsley, 2866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5732 Ramachandran restraints generated. 2866 Oldfield, 0 Emsley, 2866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 135 time to evaluate : 2.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2013 ARG cc_start: 0.7464 (mmt180) cc_final: 0.7055 (mmt180) REVERT: B 1387 LYS cc_start: 0.4810 (mmpt) cc_final: 0.4346 (mmtm) outliers start: 41 outliers final: 40 residues processed: 170 average time/residue: 0.3681 time to fit residues: 97.8004 Evaluate side-chains 163 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 123 time to evaluate : 2.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1401 CYS Chi-restraints excluded: chain A residue 1455 HIS Chi-restraints excluded: chain A residue 1477 VAL Chi-restraints excluded: chain A residue 1517 VAL Chi-restraints excluded: chain A residue 1569 MET Chi-restraints excluded: chain A residue 1650 THR Chi-restraints excluded: chain A residue 1684 VAL Chi-restraints excluded: chain A residue 1726 CYS Chi-restraints excluded: chain A residue 1737 ASP Chi-restraints excluded: chain A residue 1789 SER Chi-restraints excluded: chain A residue 1900 LYS Chi-restraints excluded: chain A residue 1910 SER Chi-restraints excluded: chain A residue 1919 LEU Chi-restraints excluded: chain A residue 2062 TYR Chi-restraints excluded: chain A residue 2174 VAL Chi-restraints excluded: chain A residue 2299 LYS Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2507 VAL Chi-restraints excluded: chain A residue 2514 VAL Chi-restraints excluded: chain A residue 2515 LEU Chi-restraints excluded: chain A residue 2588 VAL Chi-restraints excluded: chain A residue 2590 VAL Chi-restraints excluded: chain A residue 2596 SER Chi-restraints excluded: chain B residue 1449 VAL Chi-restraints excluded: chain B residue 1463 VAL Chi-restraints excluded: chain B residue 1466 VAL Chi-restraints excluded: chain B residue 1598 ILE Chi-restraints excluded: chain B residue 1660 ASP Chi-restraints excluded: chain B residue 1987 VAL Chi-restraints excluded: chain B residue 2070 MET Chi-restraints excluded: chain B residue 2098 VAL Chi-restraints excluded: chain B residue 2221 LEU Chi-restraints excluded: chain B residue 2286 VAL Chi-restraints excluded: chain B residue 2507 VAL Chi-restraints excluded: chain B residue 2590 VAL Chi-restraints excluded: chain B residue 2599 LEU Chi-restraints excluded: chain B residue 2656 CYS Chi-restraints excluded: chain B residue 2707 THR Chi-restraints excluded: chain B residue 2736 VAL Chi-restraints excluded: chain G residue 3 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 241 optimal weight: 1.9990 chunk 216 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 chunk 224 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 136 optimal weight: 8.9990 chunk 166 optimal weight: 1.9990 chunk 259 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1458 ASN A1645 HIS A1712 HIS A1755 ASN A1780 HIS A1803 HIS A1864 ASN A1920 GLN A2084 HIS A2322 ASN A2349 GLN A2595 HIS A2660 ASN A2710 ASN A2712 HIS A2715 ASN B1576 HIS B1798 ASN B2084 HIS B2097 ASN B2107 ASN B2710 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.120348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.088444 restraints weight = 34139.194| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.72 r_work: 0.2872 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.0889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 24113 Z= 0.239 Angle : 0.729 18.729 32960 Z= 0.364 Chirality : 0.052 0.454 3762 Planarity : 0.005 0.043 4189 Dihedral : 10.342 77.715 4468 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 3.92 % Allowed : 12.47 % Favored : 83.61 % 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: -1.40 (0.15), residues: 2866 helix: -3.35 (0.41), residues: 73 sheet: -0.68 (0.15), residues: 1114 loop : -0.93 (0.15), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1492 HIS 0.007 0.001 HIS B1645 PHE 0.021 0.002 PHE B2065 TYR 0.021 0.002 TYR A2210 ARG 0.005 0.001 ARG B2182 Details of bonding type rmsd link_TRANS : bond 0.00140 ( 2) link_TRANS : angle 0.65654 ( 6) link_NAG-ASN : bond 0.00710 ( 26) link_NAG-ASN : angle 4.38256 ( 78) link_ALPHA1-6 : bond 0.00340 ( 4) link_ALPHA1-6 : angle 1.63183 ( 12) link_BETA1-4 : bond 0.00516 ( 24) link_BETA1-4 : angle 2.37269 ( 72) link_ALPHA1-3 : bond 0.00818 ( 4) link_ALPHA1-3 : angle 1.77674 ( 12) hydrogen bonds : bond 0.04622 ( 730) hydrogen bonds : angle 7.38390 ( 1734) SS BOND : bond 0.00345 ( 49) SS BOND : angle 0.96657 ( 98) covalent geometry : bond 0.00571 (24002) covalent geometry : angle 0.68720 (32682) Misc. bond : bond 0.00065 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5732 Ramachandran restraints generated. 2866 Oldfield, 0 Emsley, 2866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5732 Ramachandran restraints generated. 2866 Oldfield, 0 Emsley, 2866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 135 time to evaluate : 2.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1363 HIS cc_start: 0.5885 (OUTLIER) cc_final: 0.5294 (t70) REVERT: A 1408 MET cc_start: 0.7223 (OUTLIER) cc_final: 0.6914 (mtm) REVERT: A 1409 ARG cc_start: 0.7887 (mtp85) cc_final: 0.7514 (mmm-85) REVERT: A 2127 ARG cc_start: 0.9312 (OUTLIER) cc_final: 0.9081 (ptp-170) REVERT: A 2481 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8570 (pt) REVERT: A 2599 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8370 (tp) REVERT: B 1387 LYS cc_start: 0.5010 (mmpt) cc_final: 0.4760 (mmtm) REVERT: B 1808 ASP cc_start: 0.8975 (OUTLIER) cc_final: 0.8683 (p0) REVERT: B 2079 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8326 (mm) REVERT: B 2097 ASN cc_start: 0.8858 (OUTLIER) cc_final: 0.8244 (t0) REVERT: B 2127 ARG cc_start: 0.9279 (OUTLIER) cc_final: 0.7825 (ptp-170) REVERT: B 2171 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8677 (mp) REVERT: B 2213 LYS cc_start: 0.9183 (OUTLIER) cc_final: 0.8818 (mtmt) REVERT: B 2318 ARG cc_start: 0.9133 (OUTLIER) cc_final: 0.8340 (mmt-90) outliers start: 98 outliers final: 54 residues processed: 210 average time/residue: 0.3658 time to fit residues: 118.8396 Evaluate side-chains 190 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 124 time to evaluate : 2.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1363 HIS Chi-restraints excluded: chain A residue 1365 CYS Chi-restraints excluded: chain A residue 1401 CYS Chi-restraints excluded: chain A residue 1408 MET Chi-restraints excluded: chain A residue 1455 HIS Chi-restraints excluded: chain A residue 1477 VAL Chi-restraints excluded: chain A residue 1517 VAL Chi-restraints excluded: chain A residue 1539 ILE Chi-restraints excluded: chain A residue 1569 MET Chi-restraints excluded: chain A residue 1598 ILE Chi-restraints excluded: chain A residue 1650 THR Chi-restraints excluded: chain A residue 1651 LEU Chi-restraints excluded: chain A residue 1684 VAL Chi-restraints excluded: chain A residue 1737 ASP Chi-restraints excluded: chain A residue 1739 VAL Chi-restraints excluded: chain A residue 1779 GLN Chi-restraints excluded: chain A residue 1900 LYS Chi-restraints excluded: chain A residue 1911 LEU Chi-restraints excluded: chain A residue 1919 LEU Chi-restraints excluded: chain A residue 1974 LEU Chi-restraints excluded: chain A residue 2070 MET Chi-restraints excluded: chain A residue 2088 MET Chi-restraints excluded: chain A residue 2127 ARG 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 2452 LEU Chi-restraints excluded: chain A residue 2481 ILE Chi-restraints excluded: chain A residue 2499 SER Chi-restraints excluded: chain A residue 2507 VAL Chi-restraints excluded: chain A residue 2515 LEU Chi-restraints excluded: chain A residue 2547 VAL Chi-restraints excluded: chain A residue 2580 THR Chi-restraints excluded: chain A residue 2588 VAL Chi-restraints excluded: chain A residue 2590 VAL Chi-restraints excluded: chain A residue 2596 SER Chi-restraints excluded: chain A residue 2599 LEU Chi-restraints excluded: chain B residue 1421 THR Chi-restraints excluded: chain B residue 1449 VAL Chi-restraints excluded: chain B residue 1466 VAL Chi-restraints excluded: chain B residue 1469 VAL Chi-restraints excluded: chain B residue 1651 LEU Chi-restraints excluded: chain B residue 1660 ASP Chi-restraints excluded: chain B residue 1681 MET Chi-restraints excluded: chain B residue 1808 ASP Chi-restraints excluded: chain B residue 1833 SER Chi-restraints excluded: chain B residue 1967 LEU Chi-restraints excluded: chain B residue 1987 VAL Chi-restraints excluded: chain B residue 2070 MET Chi-restraints excluded: chain B residue 2079 LEU Chi-restraints excluded: chain B residue 2097 ASN Chi-restraints excluded: chain B residue 2098 VAL Chi-restraints excluded: chain B residue 2127 ARG Chi-restraints excluded: chain B residue 2171 LEU Chi-restraints excluded: chain B residue 2213 LYS Chi-restraints excluded: chain B residue 2221 LEU Chi-restraints excluded: chain B residue 2286 VAL Chi-restraints excluded: chain B residue 2318 ARG Chi-restraints excluded: chain B residue 2507 VAL Chi-restraints excluded: chain B residue 2530 ASN Chi-restraints excluded: chain B residue 2561 LEU Chi-restraints excluded: chain B residue 2590 VAL Chi-restraints excluded: chain B residue 2596 SER Chi-restraints excluded: chain B residue 2599 LEU Chi-restraints excluded: chain B residue 2656 CYS Chi-restraints excluded: chain B residue 2707 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 50 optimal weight: 0.1980 chunk 283 optimal weight: 20.0000 chunk 280 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 222 optimal weight: 3.9990 chunk 64 optimal weight: 0.0980 chunk 32 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 246 optimal weight: 4.9990 chunk 179 optimal weight: 3.9990 chunk 81 optimal weight: 0.0970 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1665 GLN A2715 ASN B2097 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.121079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.088405 restraints weight = 34026.256| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 1.84 r_work: 0.2918 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24113 Z= 0.109 Angle : 0.614 17.484 32960 Z= 0.305 Chirality : 0.049 0.511 3762 Planarity : 0.004 0.046 4189 Dihedral : 8.904 70.323 4451 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.20 % Allowed : 13.19 % Favored : 83.61 % 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: -1.30 (0.15), residues: 2866 helix: -3.30 (0.41), residues: 73 sheet: -0.60 (0.15), residues: 1092 loop : -0.89 (0.15), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B1483 HIS 0.003 0.001 HIS A2665 PHE 0.023 0.001 PHE B2706 TYR 0.018 0.001 TYR A2210 ARG 0.003 0.000 ARG B1590 Details of bonding type rmsd link_TRANS : bond 0.00039 ( 2) link_TRANS : angle 0.47705 ( 6) link_NAG-ASN : bond 0.00779 ( 26) link_NAG-ASN : angle 3.94431 ( 78) link_ALPHA1-6 : bond 0.00487 ( 4) link_ALPHA1-6 : angle 1.74649 ( 12) link_BETA1-4 : bond 0.00448 ( 24) link_BETA1-4 : angle 1.99234 ( 72) link_ALPHA1-3 : bond 0.01092 ( 4) link_ALPHA1-3 : angle 1.56946 ( 12) hydrogen bonds : bond 0.03474 ( 730) hydrogen bonds : angle 6.80470 ( 1734) SS BOND : bond 0.00268 ( 49) SS BOND : angle 0.85057 ( 98) covalent geometry : bond 0.00239 (24002) covalent geometry : angle 0.57485 (32682) Misc. bond : bond 0.00013 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5732 Ramachandran restraints generated. 2866 Oldfield, 0 Emsley, 2866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5732 Ramachandran restraints generated. 2866 Oldfield, 0 Emsley, 2866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 144 time to evaluate : 2.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1363 HIS cc_start: 0.5837 (OUTLIER) cc_final: 0.5134 (t70) REVERT: A 1408 MET cc_start: 0.7187 (OUTLIER) cc_final: 0.6982 (mtm) REVERT: A 1409 ARG cc_start: 0.7887 (mtp85) cc_final: 0.7589 (mmm-85) REVERT: A 1585 MET cc_start: 0.9326 (OUTLIER) cc_final: 0.8946 (mtm) REVERT: A 2176 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.8180 (mtp180) REVERT: A 2481 ILE cc_start: 0.8788 (OUTLIER) cc_final: 0.8450 (pt) REVERT: A 2599 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8217 (tp) REVERT: B 1387 LYS cc_start: 0.4881 (mmpt) cc_final: 0.4638 (mmtm) REVERT: B 1560 LEU cc_start: 0.9173 (pp) cc_final: 0.8933 (pp) REVERT: B 1808 ASP cc_start: 0.8992 (OUTLIER) cc_final: 0.8668 (p0) REVERT: B 2079 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8252 (mm) REVERT: B 2094 GLN cc_start: 0.8646 (tp40) cc_final: 0.8395 (tp40) REVERT: B 2127 ARG cc_start: 0.9245 (OUTLIER) cc_final: 0.8902 (ptm160) REVERT: B 2171 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8589 (mp) REVERT: B 2213 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8800 (mtmt) REVERT: B 2242 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.7672 (tpp) REVERT: B 2596 SER cc_start: 0.8961 (OUTLIER) cc_final: 0.8650 (t) outliers start: 80 outliers final: 42 residues processed: 202 average time/residue: 0.3837 time to fit residues: 121.0727 Evaluate side-chains 183 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 128 time to evaluate : 2.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1363 HIS Chi-restraints excluded: chain A residue 1365 CYS Chi-restraints excluded: chain A residue 1388 THR Chi-restraints excluded: chain A residue 1401 CYS Chi-restraints excluded: chain A residue 1408 MET Chi-restraints excluded: chain A residue 1477 VAL Chi-restraints excluded: chain A residue 1517 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 1650 THR Chi-restraints excluded: chain A residue 1684 VAL Chi-restraints excluded: chain A residue 1779 GLN Chi-restraints excluded: chain A residue 1840 THR Chi-restraints excluded: chain A residue 1893 THR Chi-restraints excluded: chain A residue 1900 LYS Chi-restraints excluded: chain A residue 1911 LEU Chi-restraints excluded: chain A residue 1919 LEU Chi-restraints excluded: chain A residue 1974 LEU 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 2176 ARG Chi-restraints excluded: chain A residue 2230 VAL Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2481 ILE Chi-restraints excluded: chain A residue 2499 SER Chi-restraints excluded: chain A residue 2507 VAL Chi-restraints excluded: chain A residue 2514 VAL Chi-restraints excluded: chain A residue 2515 LEU Chi-restraints excluded: chain A residue 2547 VAL Chi-restraints excluded: chain A residue 2588 VAL Chi-restraints excluded: chain A residue 2590 VAL Chi-restraints excluded: chain A residue 2599 LEU Chi-restraints excluded: chain B residue 1449 VAL Chi-restraints excluded: chain B residue 1463 VAL Chi-restraints excluded: chain B residue 1598 ILE Chi-restraints excluded: chain B residue 1660 ASP Chi-restraints excluded: chain B residue 1808 ASP Chi-restraints excluded: chain B residue 1821 LEU Chi-restraints excluded: chain B residue 1955 MET Chi-restraints excluded: chain B residue 1987 VAL Chi-restraints excluded: chain B residue 2079 LEU Chi-restraints excluded: chain B residue 2098 VAL Chi-restraints excluded: chain B residue 2127 ARG Chi-restraints excluded: chain B residue 2171 LEU Chi-restraints excluded: chain B residue 2213 LYS Chi-restraints excluded: chain B residue 2242 MET Chi-restraints excluded: chain B residue 2507 VAL Chi-restraints excluded: chain B residue 2530 ASN Chi-restraints excluded: chain B residue 2590 VAL Chi-restraints excluded: chain B residue 2596 SER Chi-restraints excluded: chain B residue 2599 LEU Chi-restraints excluded: chain B residue 2656 CYS Chi-restraints excluded: chain B residue 2736 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 55 optimal weight: 4.9990 chunk 246 optimal weight: 0.0070 chunk 128 optimal weight: 4.9990 chunk 166 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 260 optimal weight: 7.9990 chunk 195 optimal weight: 2.9990 chunk 265 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 254 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 overall best weight: 2.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2715 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.118884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.087103 restraints weight = 34416.699| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.69 r_work: 0.2843 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 24113 Z= 0.287 Angle : 0.736 16.885 32960 Z= 0.367 Chirality : 0.054 0.568 3762 Planarity : 0.005 0.060 4189 Dihedral : 8.844 67.810 4438 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.75 % Favored : 92.22 % Rotamer: Outliers : 4.40 % Allowed : 13.19 % Favored : 82.41 % 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: -1.60 (0.15), residues: 2866 helix: -3.34 (0.42), residues: 73 sheet: -0.88 (0.15), residues: 1123 loop : -1.04 (0.15), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1492 HIS 0.007 0.001 HIS B1645 PHE 0.026 0.002 PHE A1625 TYR 0.023 0.002 TYR A2210 ARG 0.006 0.001 ARG A1413 Details of bonding type rmsd link_TRANS : bond 0.00146 ( 2) link_TRANS : angle 0.72123 ( 6) link_NAG-ASN : bond 0.00727 ( 26) link_NAG-ASN : angle 3.93851 ( 78) link_ALPHA1-6 : bond 0.00488 ( 4) link_ALPHA1-6 : angle 1.60918 ( 12) link_BETA1-4 : bond 0.00393 ( 24) link_BETA1-4 : angle 2.17838 ( 72) link_ALPHA1-3 : bond 0.00943 ( 4) link_ALPHA1-3 : angle 1.81545 ( 12) hydrogen bonds : bond 0.04038 ( 730) hydrogen bonds : angle 6.85671 ( 1734) SS BOND : bond 0.00408 ( 49) SS BOND : angle 1.21687 ( 98) covalent geometry : bond 0.00693 (24002) covalent geometry : angle 0.70118 (32682) Misc. bond : bond 0.00046 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5732 Ramachandran restraints generated. 2866 Oldfield, 0 Emsley, 2866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5732 Ramachandran restraints generated. 2866 Oldfield, 0 Emsley, 2866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 121 time to evaluate : 2.724 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1363 HIS cc_start: 0.5871 (OUTLIER) cc_final: 0.5493 (t70) REVERT: A 2127 ARG cc_start: 0.9335 (OUTLIER) cc_final: 0.9066 (ptp-170) REVERT: B 1387 LYS cc_start: 0.4769 (mmpt) cc_final: 0.4524 (mmtm) REVERT: B 1808 ASP cc_start: 0.9007 (OUTLIER) cc_final: 0.8593 (p0) REVERT: B 2079 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8141 (mm) REVERT: B 2127 ARG cc_start: 0.9285 (OUTLIER) cc_final: 0.7814 (ptp-170) REVERT: B 2171 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8753 (mp) REVERT: B 2213 LYS cc_start: 0.9225 (OUTLIER) cc_final: 0.8790 (mtmt) REVERT: B 2242 MET cc_start: 0.8561 (OUTLIER) cc_final: 0.7514 (tpp) REVERT: B 2318 ARG cc_start: 0.9157 (OUTLIER) cc_final: 0.6721 (mtt-85) REVERT: B 2649 ARG cc_start: 0.7182 (OUTLIER) cc_final: 0.6482 (mtt180) outliers start: 110 outliers final: 83 residues processed: 208 average time/residue: 0.3762 time to fit residues: 121.4278 Evaluate side-chains 209 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 116 time to evaluate : 2.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1363 HIS Chi-restraints excluded: chain A residue 1365 CYS Chi-restraints excluded: chain A residue 1366 MET Chi-restraints excluded: chain A residue 1388 THR Chi-restraints excluded: chain A residue 1401 CYS Chi-restraints excluded: chain A residue 1455 HIS Chi-restraints excluded: chain A residue 1477 VAL Chi-restraints excluded: chain A residue 1517 VAL Chi-restraints excluded: chain A residue 1539 ILE Chi-restraints excluded: chain A residue 1569 MET Chi-restraints excluded: chain A residue 1598 ILE Chi-restraints excluded: chain A residue 1650 THR Chi-restraints excluded: chain A residue 1651 LEU Chi-restraints excluded: chain A residue 1684 VAL Chi-restraints excluded: chain A residue 1737 ASP Chi-restraints excluded: chain A residue 1739 VAL Chi-restraints excluded: chain A residue 1779 GLN Chi-restraints excluded: chain A residue 1814 VAL Chi-restraints excluded: chain A residue 1840 THR Chi-restraints excluded: chain A residue 1851 LEU Chi-restraints excluded: chain A residue 1893 THR Chi-restraints excluded: chain A residue 1900 LYS Chi-restraints excluded: chain A residue 1911 LEU Chi-restraints excluded: chain A residue 1919 LEU Chi-restraints excluded: chain A residue 1974 LEU Chi-restraints excluded: chain A residue 2062 TYR Chi-restraints excluded: chain A residue 2070 MET Chi-restraints excluded: chain A residue 2088 MET Chi-restraints excluded: chain A residue 2127 ARG Chi-restraints excluded: chain A residue 2174 VAL Chi-restraints excluded: chain A residue 2230 VAL Chi-restraints excluded: chain A residue 2249 ILE Chi-restraints excluded: chain A residue 2285 THR Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2499 SER Chi-restraints excluded: chain A residue 2507 VAL Chi-restraints excluded: chain A residue 2514 VAL Chi-restraints excluded: chain A residue 2515 LEU Chi-restraints excluded: chain A residue 2547 VAL Chi-restraints excluded: chain A residue 2549 THR Chi-restraints excluded: chain A residue 2561 LEU Chi-restraints excluded: chain A residue 2580 THR Chi-restraints excluded: chain A residue 2588 VAL Chi-restraints excluded: chain A residue 2590 VAL Chi-restraints excluded: chain A residue 2599 LEU Chi-restraints excluded: chain B residue 1378 LEU Chi-restraints excluded: chain B residue 1421 THR 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 1540 ASP Chi-restraints excluded: chain B residue 1589 MET Chi-restraints excluded: chain B residue 1598 ILE Chi-restraints excluded: chain B residue 1610 ASN Chi-restraints excluded: chain B residue 1651 LEU Chi-restraints excluded: chain B residue 1660 ASP Chi-restraints excluded: chain B residue 1681 MET Chi-restraints excluded: chain B residue 1714 CYS Chi-restraints excluded: chain B residue 1789 SER Chi-restraints excluded: chain B residue 1808 ASP Chi-restraints excluded: chain B residue 1813 THR Chi-restraints excluded: chain B residue 1821 LEU Chi-restraints excluded: chain B residue 1847 GLU Chi-restraints excluded: chain B residue 1897 VAL Chi-restraints excluded: chain B residue 1955 MET Chi-restraints excluded: chain B residue 1967 LEU Chi-restraints excluded: chain B residue 1974 LEU Chi-restraints excluded: chain B residue 1987 VAL Chi-restraints excluded: chain B residue 2041 MET Chi-restraints excluded: chain B residue 2070 MET Chi-restraints excluded: chain B residue 2079 LEU Chi-restraints excluded: chain B residue 2098 VAL Chi-restraints excluded: chain B residue 2119 VAL Chi-restraints excluded: chain B residue 2127 ARG Chi-restraints excluded: chain B residue 2171 LEU Chi-restraints excluded: chain B residue 2213 LYS Chi-restraints excluded: chain B residue 2221 LEU Chi-restraints excluded: chain B residue 2242 MET Chi-restraints excluded: chain B residue 2253 ASP Chi-restraints excluded: chain B residue 2286 VAL Chi-restraints excluded: chain B residue 2318 ARG Chi-restraints excluded: chain B residue 2327 VAL Chi-restraints excluded: chain B residue 2464 SER Chi-restraints excluded: chain B residue 2507 VAL Chi-restraints excluded: chain B residue 2530 ASN Chi-restraints excluded: chain B residue 2561 LEU Chi-restraints excluded: chain B residue 2590 VAL Chi-restraints excluded: chain B residue 2596 SER Chi-restraints excluded: chain B residue 2599 LEU Chi-restraints excluded: chain B residue 2601 VAL Chi-restraints excluded: chain B residue 2649 ARG Chi-restraints excluded: chain B residue 2656 CYS Chi-restraints excluded: chain B residue 2736 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 176 optimal weight: 2.9990 chunk 188 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 199 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 268 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 249 optimal weight: 2.9990 chunk 42 optimal weight: 0.4980 chunk 106 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1457 HIS A2715 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.120969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.089030 restraints weight = 34288.018| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.74 r_work: 0.2885 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24113 Z= 0.172 Angle : 0.636 16.259 32960 Z= 0.319 Chirality : 0.050 0.553 3762 Planarity : 0.004 0.051 4189 Dihedral : 8.285 63.949 4438 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 3.52 % Allowed : 14.67 % 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: -1.59 (0.15), residues: 2866 helix: -3.28 (0.43), residues: 73 sheet: -0.90 (0.15), residues: 1121 loop : -1.00 (0.15), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1492 HIS 0.004 0.001 HIS B1645 PHE 0.017 0.002 PHE A1625 TYR 0.019 0.002 TYR A2210 ARG 0.005 0.000 ARG B2506 Details of bonding type rmsd link_TRANS : bond 0.00063 ( 2) link_TRANS : angle 0.62051 ( 6) link_NAG-ASN : bond 0.00680 ( 26) link_NAG-ASN : angle 3.66145 ( 78) link_ALPHA1-6 : bond 0.00508 ( 4) link_ALPHA1-6 : angle 1.65441 ( 12) link_BETA1-4 : bond 0.00414 ( 24) link_BETA1-4 : angle 1.88901 ( 72) link_ALPHA1-3 : bond 0.01072 ( 4) link_ALPHA1-3 : angle 1.73016 ( 12) hydrogen bonds : bond 0.03396 ( 730) hydrogen bonds : angle 6.62390 ( 1734) SS BOND : bond 0.00289 ( 49) SS BOND : angle 0.97820 ( 98) covalent geometry : bond 0.00409 (24002) covalent geometry : angle 0.60299 (32682) Misc. bond : bond 0.00024 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5732 Ramachandran restraints generated. 2866 Oldfield, 0 Emsley, 2866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5732 Ramachandran restraints generated. 2866 Oldfield, 0 Emsley, 2866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 126 time to evaluate : 2.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1363 HIS cc_start: 0.5795 (OUTLIER) cc_final: 0.5379 (t70) REVERT: A 1585 MET cc_start: 0.9295 (mtm) cc_final: 0.8962 (mtm) REVERT: A 2079 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8319 (mm) REVERT: B 1808 ASP cc_start: 0.9004 (OUTLIER) cc_final: 0.8628 (p0) REVERT: B 2079 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8256 (mm) REVERT: B 2094 GLN cc_start: 0.8585 (tp40) cc_final: 0.8354 (tp40) REVERT: B 2127 ARG cc_start: 0.9266 (OUTLIER) cc_final: 0.8892 (ptm160) REVERT: B 2171 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8722 (mp) REVERT: B 2213 LYS cc_start: 0.9202 (OUTLIER) cc_final: 0.8787 (mtmt) REVERT: B 2242 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.7504 (tpp) REVERT: B 2596 SER cc_start: 0.9077 (OUTLIER) cc_final: 0.8752 (t) outliers start: 88 outliers final: 65 residues processed: 197 average time/residue: 0.3510 time to fit residues: 109.4436 Evaluate side-chains 195 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 121 time to evaluate : 2.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1363 HIS Chi-restraints excluded: chain A residue 1365 CYS Chi-restraints excluded: chain A residue 1388 THR Chi-restraints excluded: chain A residue 1401 CYS Chi-restraints excluded: chain A residue 1477 VAL Chi-restraints excluded: chain A residue 1517 VAL Chi-restraints excluded: chain A residue 1539 ILE Chi-restraints excluded: chain A residue 1569 MET Chi-restraints excluded: chain A residue 1598 ILE Chi-restraints excluded: chain A residue 1650 THR Chi-restraints excluded: chain A residue 1651 LEU Chi-restraints excluded: chain A residue 1684 VAL Chi-restraints excluded: chain A residue 1779 GLN Chi-restraints excluded: chain A residue 1814 VAL Chi-restraints excluded: chain A residue 1840 THR Chi-restraints excluded: chain A residue 1893 THR Chi-restraints excluded: chain A residue 1900 LYS Chi-restraints excluded: chain A residue 1911 LEU Chi-restraints excluded: chain A residue 1919 LEU Chi-restraints excluded: chain A residue 1974 LEU Chi-restraints excluded: chain A residue 2062 TYR Chi-restraints excluded: chain A residue 2070 MET Chi-restraints excluded: chain A residue 2079 LEU 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 2452 LEU Chi-restraints excluded: chain A residue 2499 SER Chi-restraints excluded: chain A residue 2507 VAL Chi-restraints excluded: chain A residue 2514 VAL Chi-restraints excluded: chain A residue 2515 LEU Chi-restraints excluded: chain A residue 2547 VAL Chi-restraints excluded: chain A residue 2549 THR Chi-restraints excluded: chain A residue 2561 LEU Chi-restraints excluded: chain A residue 2580 THR Chi-restraints excluded: chain A residue 2588 VAL Chi-restraints excluded: chain A residue 2590 VAL Chi-restraints excluded: chain A residue 2599 LEU Chi-restraints excluded: chain B residue 1378 LEU Chi-restraints excluded: chain B residue 1449 VAL Chi-restraints excluded: chain B residue 1463 VAL Chi-restraints excluded: chain B residue 1540 ASP Chi-restraints excluded: chain B residue 1566 ASP Chi-restraints excluded: chain B residue 1589 MET Chi-restraints excluded: chain B residue 1598 ILE Chi-restraints excluded: chain B residue 1610 ASN Chi-restraints excluded: chain B residue 1660 ASP Chi-restraints excluded: chain B residue 1709 SER Chi-restraints excluded: chain B residue 1714 CYS Chi-restraints excluded: chain B residue 1808 ASP Chi-restraints excluded: chain B residue 1813 THR Chi-restraints excluded: chain B residue 1821 LEU Chi-restraints excluded: chain B residue 1847 GLU Chi-restraints excluded: chain B residue 1955 MET Chi-restraints excluded: chain B residue 1974 LEU Chi-restraints excluded: chain B residue 1987 VAL Chi-restraints excluded: chain B residue 2041 MET Chi-restraints excluded: chain B residue 2070 MET Chi-restraints excluded: chain B residue 2079 LEU Chi-restraints excluded: chain B residue 2098 VAL Chi-restraints excluded: chain B residue 2127 ARG Chi-restraints excluded: chain B residue 2171 LEU Chi-restraints excluded: chain B residue 2213 LYS Chi-restraints excluded: chain B residue 2221 LEU Chi-restraints excluded: chain B residue 2242 MET Chi-restraints excluded: chain B residue 2464 SER Chi-restraints excluded: chain B residue 2507 VAL Chi-restraints excluded: chain B residue 2530 ASN Chi-restraints excluded: chain B residue 2561 LEU Chi-restraints excluded: chain B residue 2590 VAL Chi-restraints excluded: chain B residue 2596 SER Chi-restraints excluded: chain B residue 2599 LEU Chi-restraints excluded: chain B residue 2656 CYS Chi-restraints excluded: chain B residue 2736 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 262 optimal weight: 9.9990 chunk 237 optimal weight: 2.9990 chunk 164 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 188 optimal weight: 0.8980 chunk 184 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 209 optimal weight: 2.9990 chunk 277 optimal weight: 5.9990 chunk 203 optimal weight: 0.5980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1905 ASN A2710 ASN A2715 ASN B2648 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.121572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.089754 restraints weight = 33985.079| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 1.72 r_work: 0.2896 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24113 Z= 0.145 Angle : 0.617 15.675 32960 Z= 0.307 Chirality : 0.049 0.548 3762 Planarity : 0.004 0.051 4189 Dihedral : 7.957 61.224 4438 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 4.12 % Allowed : 14.47 % Favored : 81.41 % 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: -1.53 (0.16), residues: 2866 helix: -3.27 (0.43), residues: 73 sheet: -0.86 (0.15), residues: 1119 loop : -0.96 (0.16), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B1483 HIS 0.003 0.001 HIS A1505 PHE 0.021 0.001 PHE B2706 TYR 0.020 0.001 TYR A2210 ARG 0.009 0.000 ARG A1413 Details of bonding type rmsd link_TRANS : bond 0.00051 ( 2) link_TRANS : angle 0.53330 ( 6) link_NAG-ASN : bond 0.00658 ( 26) link_NAG-ASN : angle 3.67925 ( 78) link_ALPHA1-6 : bond 0.00508 ( 4) link_ALPHA1-6 : angle 1.65939 ( 12) link_BETA1-4 : bond 0.00410 ( 24) link_BETA1-4 : angle 1.79085 ( 72) link_ALPHA1-3 : bond 0.01085 ( 4) link_ALPHA1-3 : angle 1.77244 ( 12) hydrogen bonds : bond 0.03172 ( 730) hydrogen bonds : angle 6.47423 ( 1734) SS BOND : bond 0.00262 ( 49) SS BOND : angle 0.85273 ( 98) covalent geometry : bond 0.00338 (24002) covalent geometry : angle 0.58356 (32682) Misc. bond : bond 0.00019 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5732 Ramachandran restraints generated. 2866 Oldfield, 0 Emsley, 2866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5732 Ramachandran restraints generated. 2866 Oldfield, 0 Emsley, 2866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 128 time to evaluate : 2.489 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1363 HIS cc_start: 0.5755 (OUTLIER) cc_final: 0.5393 (t70) REVERT: A 1585 MET cc_start: 0.9302 (OUTLIER) cc_final: 0.8910 (mtm) REVERT: A 1590 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8267 (ttt90) REVERT: A 1849 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8623 (tp) REVERT: A 1955 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.8059 (ppp) REVERT: A 2079 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8337 (mm) REVERT: A 2127 ARG cc_start: 0.9269 (OUTLIER) cc_final: 0.8673 (ptp-170) REVERT: A 2599 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8302 (tp) REVERT: B 1808 ASP cc_start: 0.9010 (OUTLIER) cc_final: 0.8626 (p0) REVERT: B 2079 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8113 (mm) REVERT: B 2094 GLN cc_start: 0.8561 (tp40) cc_final: 0.8334 (tp40) REVERT: B 2127 ARG cc_start: 0.9280 (OUTLIER) cc_final: 0.8920 (ptm160) REVERT: B 2213 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8795 (mtmt) REVERT: B 2242 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.7507 (tpp) REVERT: B 2435 PHE cc_start: 0.9199 (m-80) cc_final: 0.8948 (m-80) REVERT: B 2494 MET cc_start: 0.7950 (ptm) cc_final: 0.7425 (ptp) REVERT: B 2596 SER cc_start: 0.9069 (OUTLIER) cc_final: 0.8754 (t) REVERT: B 2649 ARG cc_start: 0.7194 (OUTLIER) cc_final: 0.6494 (mtt180) outliers start: 103 outliers final: 71 residues processed: 207 average time/residue: 0.3566 time to fit residues: 116.1339 Evaluate side-chains 207 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 121 time to evaluate : 2.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1363 HIS Chi-restraints excluded: chain A residue 1365 CYS Chi-restraints excluded: chain A residue 1366 MET Chi-restraints excluded: chain A residue 1388 THR Chi-restraints excluded: chain A residue 1401 CYS Chi-restraints excluded: chain A residue 1455 HIS Chi-restraints excluded: chain A residue 1477 VAL Chi-restraints excluded: chain A residue 1517 VAL Chi-restraints excluded: chain A residue 1539 ILE Chi-restraints excluded: chain A residue 1564 MET Chi-restraints excluded: chain A residue 1569 MET Chi-restraints excluded: chain A residue 1585 MET Chi-restraints excluded: chain A residue 1590 ARG Chi-restraints excluded: chain A residue 1650 THR Chi-restraints excluded: chain A residue 1651 LEU Chi-restraints excluded: chain A residue 1684 VAL Chi-restraints excluded: chain A residue 1737 ASP Chi-restraints excluded: chain A residue 1779 GLN Chi-restraints excluded: chain A residue 1814 VAL Chi-restraints excluded: chain A residue 1840 THR Chi-restraints excluded: chain A residue 1849 LEU Chi-restraints excluded: chain A residue 1851 LEU Chi-restraints excluded: chain A residue 1893 THR Chi-restraints excluded: chain A residue 1900 LYS Chi-restraints excluded: chain A residue 1911 LEU Chi-restraints excluded: chain A residue 1955 MET Chi-restraints excluded: chain A residue 1974 LEU Chi-restraints excluded: chain A residue 2062 TYR Chi-restraints excluded: chain A residue 2070 MET Chi-restraints excluded: chain A residue 2079 LEU Chi-restraints excluded: chain A residue 2088 MET Chi-restraints excluded: chain A residue 2127 ARG Chi-restraints excluded: chain A residue 2174 VAL Chi-restraints excluded: chain A residue 2230 VAL Chi-restraints excluded: chain A residue 2315 VAL Chi-restraints excluded: chain A residue 2348 LEU Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2499 SER Chi-restraints excluded: chain A residue 2507 VAL Chi-restraints excluded: chain A residue 2515 LEU Chi-restraints excluded: chain A residue 2547 VAL Chi-restraints excluded: chain A residue 2561 LEU Chi-restraints excluded: chain A residue 2580 THR Chi-restraints excluded: chain A residue 2588 VAL Chi-restraints excluded: chain A residue 2590 VAL Chi-restraints excluded: chain A residue 2599 LEU Chi-restraints excluded: chain B residue 1378 LEU Chi-restraints excluded: chain B residue 1421 THR Chi-restraints excluded: chain B residue 1449 VAL Chi-restraints excluded: chain B residue 1463 VAL Chi-restraints excluded: chain B residue 1540 ASP Chi-restraints excluded: chain B residue 1566 ASP Chi-restraints excluded: chain B residue 1598 ILE Chi-restraints excluded: chain B residue 1610 ASN Chi-restraints excluded: chain B residue 1651 LEU Chi-restraints excluded: chain B residue 1660 ASP Chi-restraints excluded: chain B residue 1714 CYS Chi-restraints excluded: chain B residue 1808 ASP Chi-restraints excluded: chain B residue 1813 THR Chi-restraints excluded: chain B residue 1821 LEU Chi-restraints excluded: chain B residue 1847 GLU Chi-restraints excluded: chain B residue 1955 MET Chi-restraints excluded: chain B residue 1967 LEU Chi-restraints excluded: chain B residue 1974 LEU Chi-restraints excluded: chain B residue 1987 VAL Chi-restraints excluded: chain B residue 2041 MET Chi-restraints excluded: chain B residue 2070 MET Chi-restraints excluded: chain B residue 2079 LEU Chi-restraints excluded: chain B residue 2098 VAL Chi-restraints excluded: chain B residue 2127 ARG Chi-restraints excluded: chain B residue 2213 LYS Chi-restraints excluded: chain B residue 2221 LEU Chi-restraints excluded: chain B residue 2242 MET Chi-restraints excluded: chain B residue 2253 ASP Chi-restraints excluded: chain B residue 2315 VAL Chi-restraints excluded: chain B residue 2327 VAL Chi-restraints excluded: chain B residue 2507 VAL Chi-restraints excluded: chain B residue 2530 ASN Chi-restraints excluded: chain B residue 2561 LEU Chi-restraints excluded: chain B residue 2590 VAL Chi-restraints excluded: chain B residue 2596 SER Chi-restraints excluded: chain B residue 2599 LEU Chi-restraints excluded: chain B residue 2601 VAL Chi-restraints excluded: chain B residue 2649 ARG Chi-restraints excluded: chain B residue 2656 CYS Chi-restraints excluded: chain B residue 2736 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 155 optimal weight: 1.9990 chunk 259 optimal weight: 0.7980 chunk 147 optimal weight: 10.0000 chunk 278 optimal weight: 5.9990 chunk 231 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 160 optimal weight: 4.9990 chunk 53 optimal weight: 0.0970 chunk 99 optimal weight: 1.9990 chunk 179 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2715 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.120718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.088770 restraints weight = 34240.942| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 1.73 r_work: 0.2881 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 24113 Z= 0.199 Angle : 0.647 15.229 32960 Z= 0.323 Chirality : 0.050 0.560 3762 Planarity : 0.004 0.054 4189 Dihedral : 7.809 59.870 4436 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 4.60 % Allowed : 14.27 % Favored : 81.14 % 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: -1.61 (0.15), residues: 2866 helix: -3.26 (0.43), residues: 73 sheet: -0.96 (0.15), residues: 1132 loop : -0.98 (0.16), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1492 HIS 0.004 0.001 HIS B1645 PHE 0.020 0.002 PHE A1625 TYR 0.020 0.002 TYR A2210 ARG 0.011 0.000 ARG A1413 Details of bonding type rmsd link_TRANS : bond 0.00096 ( 2) link_TRANS : angle 0.61578 ( 6) link_NAG-ASN : bond 0.00655 ( 26) link_NAG-ASN : angle 3.59883 ( 78) link_ALPHA1-6 : bond 0.00480 ( 4) link_ALPHA1-6 : angle 1.80254 ( 12) link_BETA1-4 : bond 0.00411 ( 24) link_BETA1-4 : angle 1.83461 ( 72) link_ALPHA1-3 : bond 0.01030 ( 4) link_ALPHA1-3 : angle 1.83211 ( 12) hydrogen bonds : bond 0.03367 ( 730) hydrogen bonds : angle 6.51503 ( 1734) SS BOND : bond 0.00303 ( 49) SS BOND : angle 0.89144 ( 98) covalent geometry : bond 0.00477 (24002) covalent geometry : angle 0.61571 (32682) Misc. bond : bond 0.00027 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5732 Ramachandran restraints generated. 2866 Oldfield, 0 Emsley, 2866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5732 Ramachandran restraints generated. 2866 Oldfield, 0 Emsley, 2866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 127 time to evaluate : 2.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1363 HIS cc_start: 0.5722 (OUTLIER) cc_final: 0.5336 (t70) REVERT: A 1585 MET cc_start: 0.9310 (OUTLIER) cc_final: 0.8940 (mtm) REVERT: A 1590 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.8242 (ttt90) REVERT: A 1849 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8681 (tp) REVERT: A 1955 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.8106 (ptp) REVERT: A 2079 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8370 (mm) REVERT: A 2127 ARG cc_start: 0.9310 (OUTLIER) cc_final: 0.9063 (ptp-170) REVERT: A 2599 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8349 (tp) REVERT: B 1387 LYS cc_start: 0.5300 (mmtm) cc_final: 0.4875 (mmtm) REVERT: B 1560 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8951 (pp) REVERT: B 1808 ASP cc_start: 0.9013 (OUTLIER) cc_final: 0.8614 (p0) REVERT: B 2079 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8102 (mm) REVERT: B 2094 GLN cc_start: 0.8576 (tp40) cc_final: 0.8345 (tp40) REVERT: B 2127 ARG cc_start: 0.9278 (OUTLIER) cc_final: 0.8901 (ptm160) REVERT: B 2213 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8790 (mtmt) REVERT: B 2242 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.7429 (tpp) REVERT: B 2307 GLN cc_start: 0.9021 (OUTLIER) cc_final: 0.7622 (mp10) REVERT: B 2649 ARG cc_start: 0.7176 (OUTLIER) cc_final: 0.6469 (mtt180) outliers start: 115 outliers final: 84 residues processed: 218 average time/residue: 0.3596 time to fit residues: 123.5657 Evaluate side-chains 224 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 124 time to evaluate : 2.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1363 HIS Chi-restraints excluded: chain A residue 1365 CYS Chi-restraints excluded: chain A residue 1366 MET Chi-restraints excluded: chain A residue 1388 THR Chi-restraints excluded: chain A residue 1401 CYS Chi-restraints excluded: chain A residue 1455 HIS Chi-restraints excluded: chain A residue 1477 VAL Chi-restraints excluded: chain A residue 1517 VAL Chi-restraints excluded: chain A residue 1539 ILE Chi-restraints excluded: chain A residue 1564 MET Chi-restraints excluded: chain A residue 1569 MET Chi-restraints excluded: chain A residue 1585 MET Chi-restraints excluded: chain A residue 1590 ARG Chi-restraints excluded: chain A residue 1598 ILE Chi-restraints excluded: chain A residue 1650 THR Chi-restraints excluded: chain A residue 1651 LEU Chi-restraints excluded: chain A residue 1684 VAL Chi-restraints excluded: chain A residue 1737 ASP Chi-restraints excluded: chain A residue 1779 GLN Chi-restraints excluded: chain A residue 1814 VAL Chi-restraints excluded: chain A residue 1840 THR Chi-restraints excluded: chain A residue 1849 LEU Chi-restraints excluded: chain A residue 1851 LEU Chi-restraints excluded: chain A residue 1893 THR Chi-restraints excluded: chain A residue 1900 LYS Chi-restraints excluded: chain A residue 1911 LEU Chi-restraints excluded: chain A residue 1919 LEU Chi-restraints excluded: chain A residue 1955 MET Chi-restraints excluded: chain A residue 1974 LEU Chi-restraints excluded: chain A residue 2062 TYR Chi-restraints excluded: chain A residue 2070 MET Chi-restraints excluded: chain A residue 2079 LEU Chi-restraints excluded: chain A residue 2088 MET Chi-restraints excluded: chain A residue 2127 ARG Chi-restraints excluded: chain A residue 2153 LEU Chi-restraints excluded: chain A residue 2174 VAL Chi-restraints excluded: chain A residue 2225 ASN Chi-restraints excluded: chain A residue 2230 VAL Chi-restraints excluded: chain A residue 2315 VAL Chi-restraints excluded: chain A residue 2348 LEU Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2499 SER Chi-restraints excluded: chain A residue 2507 VAL Chi-restraints excluded: chain A residue 2514 VAL Chi-restraints excluded: chain A residue 2515 LEU Chi-restraints excluded: chain A residue 2547 VAL Chi-restraints excluded: chain A residue 2561 LEU Chi-restraints excluded: chain A residue 2580 THR Chi-restraints excluded: chain A residue 2588 VAL Chi-restraints excluded: chain A residue 2590 VAL Chi-restraints excluded: chain A residue 2599 LEU Chi-restraints excluded: chain A residue 2739 PHE Chi-restraints excluded: chain B residue 1378 LEU Chi-restraints excluded: chain B residue 1421 THR Chi-restraints excluded: chain B residue 1449 VAL Chi-restraints excluded: chain B residue 1450 ASP Chi-restraints excluded: chain B residue 1463 VAL Chi-restraints excluded: chain B residue 1469 VAL Chi-restraints excluded: chain B residue 1540 ASP Chi-restraints excluded: chain B residue 1560 LEU Chi-restraints excluded: chain B residue 1566 ASP Chi-restraints excluded: chain B residue 1598 ILE Chi-restraints excluded: chain B residue 1610 ASN Chi-restraints excluded: chain B residue 1651 LEU Chi-restraints excluded: chain B residue 1660 ASP Chi-restraints excluded: chain B residue 1714 CYS Chi-restraints excluded: chain B residue 1808 ASP Chi-restraints excluded: chain B residue 1813 THR Chi-restraints excluded: chain B residue 1821 LEU Chi-restraints excluded: chain B residue 1847 GLU Chi-restraints excluded: chain B residue 1897 VAL Chi-restraints excluded: chain B residue 1955 MET Chi-restraints excluded: chain B residue 1967 LEU Chi-restraints excluded: chain B residue 1974 LEU Chi-restraints excluded: chain B residue 1987 VAL Chi-restraints excluded: chain B residue 2041 MET Chi-restraints excluded: chain B residue 2070 MET Chi-restraints excluded: chain B residue 2079 LEU Chi-restraints excluded: chain B residue 2098 VAL Chi-restraints excluded: chain B residue 2127 ARG Chi-restraints excluded: chain B residue 2171 LEU Chi-restraints excluded: chain B residue 2213 LYS Chi-restraints excluded: chain B residue 2221 LEU Chi-restraints excluded: chain B residue 2242 MET Chi-restraints excluded: chain B residue 2253 ASP Chi-restraints excluded: chain B residue 2286 VAL Chi-restraints excluded: chain B residue 2307 GLN Chi-restraints excluded: chain B residue 2315 VAL Chi-restraints excluded: chain B residue 2327 VAL Chi-restraints excluded: chain B residue 2464 SER Chi-restraints excluded: chain B residue 2507 VAL Chi-restraints excluded: chain B residue 2530 ASN Chi-restraints excluded: chain B residue 2561 LEU Chi-restraints excluded: chain B residue 2590 VAL Chi-restraints excluded: chain B residue 2596 SER Chi-restraints excluded: chain B residue 2599 LEU Chi-restraints excluded: chain B residue 2601 VAL Chi-restraints excluded: chain B residue 2649 ARG Chi-restraints excluded: chain B residue 2656 CYS Chi-restraints excluded: chain B residue 2736 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 108 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 187 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 174 optimal weight: 0.7980 chunk 224 optimal weight: 1.9990 chunk 213 optimal weight: 2.9990 chunk 246 optimal weight: 0.9980 chunk 88 optimal weight: 0.3980 chunk 194 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2212 GLN A2715 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.122501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.090790 restraints weight = 34047.052| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.72 r_work: 0.2912 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24113 Z= 0.125 Angle : 0.598 14.939 32960 Z= 0.299 Chirality : 0.048 0.536 3762 Planarity : 0.004 0.052 4189 Dihedral : 7.445 58.259 4436 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 3.92 % Allowed : 15.03 % Favored : 81.06 % 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: -1.47 (0.16), residues: 2866 helix: -3.24 (0.43), residues: 73 sheet: -0.81 (0.15), residues: 1116 loop : -0.92 (0.16), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B1483 HIS 0.003 0.001 HIS B1645 PHE 0.022 0.001 PHE B2706 TYR 0.019 0.001 TYR A2210 ARG 0.008 0.000 ARG B2506 Details of bonding type rmsd link_TRANS : bond 0.00049 ( 2) link_TRANS : angle 0.45400 ( 6) link_NAG-ASN : bond 0.00636 ( 26) link_NAG-ASN : angle 3.44277 ( 78) link_ALPHA1-6 : bond 0.00542 ( 4) link_ALPHA1-6 : angle 1.78272 ( 12) link_BETA1-4 : bond 0.00420 ( 24) link_BETA1-4 : angle 1.67247 ( 72) link_ALPHA1-3 : bond 0.01044 ( 4) link_ALPHA1-3 : angle 1.71003 ( 12) hydrogen bonds : bond 0.02979 ( 730) hydrogen bonds : angle 6.36106 ( 1734) SS BOND : bond 0.00263 ( 49) SS BOND : angle 1.03316 ( 98) covalent geometry : bond 0.00290 (24002) covalent geometry : angle 0.56589 (32682) Misc. bond : bond 0.00013 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5732 Ramachandran restraints generated. 2866 Oldfield, 0 Emsley, 2866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5732 Ramachandran restraints generated. 2866 Oldfield, 0 Emsley, 2866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 131 time to evaluate : 2.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1363 HIS cc_start: 0.5734 (OUTLIER) cc_final: 0.5344 (t70) REVERT: A 1585 MET cc_start: 0.9293 (OUTLIER) cc_final: 0.8886 (mtm) REVERT: A 1590 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.8213 (ttt90) REVERT: A 1955 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.8079 (ppp) REVERT: A 2079 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8251 (mm) REVERT: A 2127 ARG cc_start: 0.9245 (OUTLIER) cc_final: 0.8629 (ptp-170) REVERT: A 2212 GLN cc_start: 0.9101 (OUTLIER) cc_final: 0.8887 (mm-40) REVERT: A 2453 TYR cc_start: 0.7344 (OUTLIER) cc_final: 0.7036 (t80) REVERT: A 2599 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8265 (tp) REVERT: B 1560 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8943 (pp) REVERT: B 1808 ASP cc_start: 0.9019 (OUTLIER) cc_final: 0.8614 (p0) REVERT: B 2079 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8039 (mm) REVERT: B 2094 GLN cc_start: 0.8554 (tp40) cc_final: 0.8336 (tp40) REVERT: B 2127 ARG cc_start: 0.9274 (OUTLIER) cc_final: 0.8920 (ptm160) REVERT: B 2213 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8759 (mtmt) REVERT: B 2242 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.7488 (tpp) REVERT: B 2307 GLN cc_start: 0.9024 (OUTLIER) cc_final: 0.7623 (mp10) REVERT: B 2435 PHE cc_start: 0.9189 (m-80) cc_final: 0.8917 (m-80) REVERT: B 2596 SER cc_start: 0.9039 (OUTLIER) cc_final: 0.8744 (t) REVERT: B 2649 ARG cc_start: 0.7144 (OUTLIER) cc_final: 0.6445 (mtt180) REVERT: B 2656 CYS cc_start: 0.5295 (OUTLIER) cc_final: 0.5053 (t) outliers start: 98 outliers final: 69 residues processed: 208 average time/residue: 0.3782 time to fit residues: 121.6415 Evaluate side-chains 213 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 125 time to evaluate : 2.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1363 HIS Chi-restraints excluded: chain A residue 1365 CYS Chi-restraints excluded: chain A residue 1388 THR Chi-restraints excluded: chain A residue 1401 CYS Chi-restraints excluded: chain A residue 1455 HIS Chi-restraints excluded: chain A residue 1477 VAL Chi-restraints excluded: chain A residue 1517 VAL Chi-restraints excluded: chain A residue 1539 ILE Chi-restraints excluded: chain A residue 1564 MET Chi-restraints excluded: chain A residue 1569 MET Chi-restraints excluded: chain A residue 1585 MET Chi-restraints excluded: chain A residue 1590 ARG Chi-restraints excluded: chain A residue 1650 THR Chi-restraints excluded: chain A residue 1651 LEU Chi-restraints excluded: chain A residue 1684 VAL Chi-restraints excluded: chain A residue 1726 CYS Chi-restraints excluded: chain A residue 1737 ASP Chi-restraints excluded: chain A residue 1779 GLN Chi-restraints excluded: chain A residue 1814 VAL Chi-restraints excluded: chain A residue 1840 THR Chi-restraints excluded: chain A residue 1893 THR Chi-restraints excluded: chain A residue 1900 LYS Chi-restraints excluded: chain A residue 1911 LEU Chi-restraints excluded: chain A residue 1919 LEU Chi-restraints excluded: chain A residue 1955 MET Chi-restraints excluded: chain A residue 1974 LEU Chi-restraints excluded: chain A residue 2062 TYR Chi-restraints excluded: chain A residue 2070 MET Chi-restraints excluded: chain A residue 2079 LEU Chi-restraints excluded: chain A residue 2088 MET Chi-restraints excluded: chain A residue 2127 ARG Chi-restraints excluded: chain A residue 2153 LEU Chi-restraints excluded: chain A residue 2174 VAL Chi-restraints excluded: chain A residue 2212 GLN Chi-restraints excluded: chain A residue 2225 ASN Chi-restraints excluded: chain A residue 2230 VAL Chi-restraints excluded: chain A residue 2249 ILE Chi-restraints excluded: chain A residue 2348 LEU Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2453 TYR Chi-restraints excluded: chain A residue 2499 SER Chi-restraints excluded: chain A residue 2507 VAL Chi-restraints excluded: chain A residue 2514 VAL Chi-restraints excluded: chain A residue 2515 LEU Chi-restraints excluded: chain A residue 2547 VAL Chi-restraints excluded: chain A residue 2561 LEU Chi-restraints excluded: chain A residue 2580 THR Chi-restraints excluded: chain A residue 2588 VAL Chi-restraints excluded: chain A residue 2590 VAL Chi-restraints excluded: chain A residue 2599 LEU Chi-restraints excluded: chain B residue 1378 LEU Chi-restraints excluded: chain B residue 1421 THR Chi-restraints excluded: chain B residue 1463 VAL Chi-restraints excluded: chain B residue 1540 ASP Chi-restraints excluded: chain B residue 1560 LEU Chi-restraints excluded: chain B residue 1566 ASP Chi-restraints excluded: chain B residue 1598 ILE Chi-restraints excluded: chain B residue 1610 ASN Chi-restraints excluded: chain B residue 1660 ASP Chi-restraints excluded: chain B residue 1714 CYS Chi-restraints excluded: chain B residue 1808 ASP Chi-restraints excluded: chain B residue 1821 LEU Chi-restraints excluded: chain B residue 1897 VAL Chi-restraints excluded: chain B residue 1955 MET Chi-restraints excluded: chain B residue 1974 LEU Chi-restraints excluded: chain B residue 1987 VAL Chi-restraints excluded: chain B residue 2041 MET Chi-restraints excluded: chain B residue 2070 MET Chi-restraints excluded: chain B residue 2079 LEU Chi-restraints excluded: chain B residue 2098 VAL Chi-restraints excluded: chain B residue 2127 ARG Chi-restraints excluded: chain B residue 2171 LEU Chi-restraints excluded: chain B residue 2213 LYS Chi-restraints excluded: chain B residue 2221 LEU Chi-restraints excluded: chain B residue 2242 MET Chi-restraints excluded: chain B residue 2286 VAL Chi-restraints excluded: chain B residue 2307 GLN Chi-restraints excluded: chain B residue 2327 VAL Chi-restraints excluded: chain B residue 2507 VAL Chi-restraints excluded: chain B residue 2530 ASN Chi-restraints excluded: chain B residue 2561 LEU Chi-restraints excluded: chain B residue 2590 VAL Chi-restraints excluded: chain B residue 2596 SER Chi-restraints excluded: chain B residue 2599 LEU Chi-restraints excluded: chain B residue 2601 VAL Chi-restraints excluded: chain B residue 2649 ARG Chi-restraints excluded: chain B residue 2656 CYS Chi-restraints excluded: chain B residue 2736 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 228 optimal weight: 1.9990 chunk 172 optimal weight: 0.6980 chunk 216 optimal weight: 0.4980 chunk 188 optimal weight: 3.9990 chunk 167 optimal weight: 0.0980 chunk 82 optimal weight: 3.9990 chunk 276 optimal weight: 7.9990 chunk 142 optimal weight: 8.9990 chunk 112 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 265 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2492 ASN A2715 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.121939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.090116 restraints weight = 34108.165| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 1.74 r_work: 0.2901 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24113 Z= 0.151 Angle : 0.623 18.521 32960 Z= 0.309 Chirality : 0.048 0.382 3762 Planarity : 0.004 0.052 4189 Dihedral : 7.400 58.526 4435 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 4.24 % Allowed : 14.87 % Favored : 80.90 % 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: -1.47 (0.16), residues: 2866 helix: -3.24 (0.44), residues: 73 sheet: -0.82 (0.15), residues: 1122 loop : -0.92 (0.16), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B1483 HIS 0.003 0.001 HIS B1645 PHE 0.016 0.001 PHE A1625 TYR 0.028 0.001 TYR A2181 ARG 0.008 0.000 ARG B1702 Details of bonding type rmsd link_TRANS : bond 0.00066 ( 2) link_TRANS : angle 0.50973 ( 6) link_NAG-ASN : bond 0.00878 ( 26) link_NAG-ASN : angle 3.96109 ( 78) link_ALPHA1-6 : bond 0.00513 ( 4) link_ALPHA1-6 : angle 1.72905 ( 12) link_BETA1-4 : bond 0.00407 ( 24) link_BETA1-4 : angle 1.70227 ( 72) link_ALPHA1-3 : bond 0.01029 ( 4) link_ALPHA1-3 : angle 1.75488 ( 12) hydrogen bonds : bond 0.03086 ( 730) hydrogen bonds : angle 6.33679 ( 1734) SS BOND : bond 0.00267 ( 49) SS BOND : angle 1.00561 ( 98) covalent geometry : bond 0.00356 (24002) covalent geometry : angle 0.58497 (32682) Misc. bond : bond 0.00019 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5732 Ramachandran restraints generated. 2866 Oldfield, 0 Emsley, 2866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5732 Ramachandran restraints generated. 2866 Oldfield, 0 Emsley, 2866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 126 time to evaluate : 2.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1363 HIS cc_start: 0.5737 (OUTLIER) cc_final: 0.5351 (t70) REVERT: A 1585 MET cc_start: 0.9293 (OUTLIER) cc_final: 0.8885 (mtm) REVERT: A 1590 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.8242 (ttt90) REVERT: A 1849 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8658 (tp) REVERT: A 1955 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.8055 (ppp) REVERT: A 2079 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8247 (mm) REVERT: A 2127 ARG cc_start: 0.9259 (OUTLIER) cc_final: 0.8709 (ptp-170) REVERT: A 2453 TYR cc_start: 0.7362 (OUTLIER) cc_final: 0.7032 (t80) REVERT: A 2599 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8279 (tp) REVERT: B 1387 LYS cc_start: 0.5769 (OUTLIER) cc_final: 0.5029 (mmtt) REVERT: B 1560 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8951 (pp) REVERT: B 1808 ASP cc_start: 0.9022 (OUTLIER) cc_final: 0.8614 (p0) REVERT: B 2079 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.7952 (mm) REVERT: B 2094 GLN cc_start: 0.8565 (tp40) cc_final: 0.8346 (tp40) REVERT: B 2127 ARG cc_start: 0.9264 (OUTLIER) cc_final: 0.8894 (ptm160) REVERT: B 2213 LYS cc_start: 0.9143 (OUTLIER) cc_final: 0.8783 (mtmt) REVERT: B 2242 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.7502 (tpp) REVERT: B 2307 GLN cc_start: 0.9024 (OUTLIER) cc_final: 0.7624 (mp10) REVERT: B 2596 SER cc_start: 0.9066 (OUTLIER) cc_final: 0.8765 (t) REVERT: B 2649 ARG cc_start: 0.7126 (OUTLIER) cc_final: 0.6415 (mtt180) REVERT: B 2656 CYS cc_start: 0.5296 (OUTLIER) cc_final: 0.5052 (t) outliers start: 106 outliers final: 76 residues processed: 210 average time/residue: 0.3804 time to fit residues: 124.3823 Evaluate side-chains 219 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 123 time to evaluate : 3.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1363 HIS Chi-restraints excluded: chain A residue 1365 CYS Chi-restraints excluded: chain A residue 1388 THR Chi-restraints excluded: chain A residue 1401 CYS Chi-restraints excluded: chain A residue 1455 HIS Chi-restraints excluded: chain A residue 1477 VAL Chi-restraints excluded: chain A residue 1515 ILE Chi-restraints excluded: chain A residue 1517 VAL Chi-restraints excluded: chain A residue 1539 ILE Chi-restraints excluded: chain A residue 1564 MET Chi-restraints excluded: chain A residue 1569 MET Chi-restraints excluded: chain A residue 1585 MET Chi-restraints excluded: chain A residue 1590 ARG Chi-restraints excluded: chain A residue 1650 THR Chi-restraints excluded: chain A residue 1651 LEU Chi-restraints excluded: chain A residue 1684 VAL Chi-restraints excluded: chain A residue 1726 CYS Chi-restraints excluded: chain A residue 1737 ASP Chi-restraints excluded: chain A residue 1779 GLN Chi-restraints excluded: chain A residue 1814 VAL Chi-restraints excluded: chain A residue 1840 THR Chi-restraints excluded: chain A residue 1849 LEU Chi-restraints excluded: chain A residue 1893 THR Chi-restraints excluded: chain A residue 1900 LYS Chi-restraints excluded: chain A residue 1911 LEU Chi-restraints excluded: chain A residue 1919 LEU Chi-restraints excluded: chain A residue 1955 MET Chi-restraints excluded: chain A residue 1974 LEU Chi-restraints excluded: chain A residue 2062 TYR Chi-restraints excluded: chain A residue 2070 MET Chi-restraints excluded: chain A residue 2079 LEU Chi-restraints excluded: chain A residue 2088 MET Chi-restraints excluded: chain A residue 2127 ARG Chi-restraints excluded: chain A residue 2153 LEU Chi-restraints excluded: chain A residue 2174 VAL Chi-restraints excluded: chain A residue 2225 ASN Chi-restraints excluded: chain A residue 2230 VAL Chi-restraints excluded: chain A residue 2249 ILE Chi-restraints excluded: chain A residue 2348 LEU Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2453 TYR Chi-restraints excluded: chain A residue 2499 SER Chi-restraints excluded: chain A residue 2507 VAL Chi-restraints excluded: chain A residue 2514 VAL Chi-restraints excluded: chain A residue 2515 LEU Chi-restraints excluded: chain A residue 2547 VAL Chi-restraints excluded: chain A residue 2561 LEU Chi-restraints excluded: chain A residue 2580 THR Chi-restraints excluded: chain A residue 2588 VAL Chi-restraints excluded: chain A residue 2590 VAL Chi-restraints excluded: chain A residue 2599 LEU Chi-restraints excluded: chain B residue 1378 LEU Chi-restraints excluded: chain B residue 1387 LYS Chi-restraints excluded: chain B residue 1421 THR Chi-restraints excluded: chain B residue 1463 VAL Chi-restraints excluded: chain B residue 1540 ASP Chi-restraints excluded: chain B residue 1560 LEU Chi-restraints excluded: chain B residue 1566 ASP Chi-restraints excluded: chain B residue 1598 ILE Chi-restraints excluded: chain B residue 1610 ASN Chi-restraints excluded: chain B residue 1651 LEU Chi-restraints excluded: chain B residue 1660 ASP Chi-restraints excluded: chain B residue 1714 CYS Chi-restraints excluded: chain B residue 1808 ASP Chi-restraints excluded: chain B residue 1813 THR Chi-restraints excluded: chain B residue 1821 LEU Chi-restraints excluded: chain B residue 1871 VAL Chi-restraints excluded: chain B residue 1897 VAL Chi-restraints excluded: chain B residue 1955 MET Chi-restraints excluded: chain B residue 1974 LEU Chi-restraints excluded: chain B residue 1987 VAL Chi-restraints excluded: chain B residue 2041 MET Chi-restraints excluded: chain B residue 2070 MET Chi-restraints excluded: chain B residue 2079 LEU Chi-restraints excluded: chain B residue 2098 VAL Chi-restraints excluded: chain B residue 2127 ARG Chi-restraints excluded: chain B residue 2171 LEU Chi-restraints excluded: chain B residue 2213 LYS Chi-restraints excluded: chain B residue 2221 LEU Chi-restraints excluded: chain B residue 2242 MET Chi-restraints excluded: chain B residue 2253 ASP Chi-restraints excluded: chain B residue 2286 VAL Chi-restraints excluded: chain B residue 2307 GLN Chi-restraints excluded: chain B residue 2315 VAL Chi-restraints excluded: chain B residue 2327 VAL Chi-restraints excluded: chain B residue 2507 VAL Chi-restraints excluded: chain B residue 2530 ASN Chi-restraints excluded: chain B residue 2561 LEU Chi-restraints excluded: chain B residue 2590 VAL Chi-restraints excluded: chain B residue 2596 SER Chi-restraints excluded: chain B residue 2599 LEU Chi-restraints excluded: chain B residue 2601 VAL Chi-restraints excluded: chain B residue 2649 ARG Chi-restraints excluded: chain B residue 2656 CYS Chi-restraints excluded: chain B residue 2707 THR Chi-restraints excluded: chain B residue 2736 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 246 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 195 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 255 optimal weight: 0.9980 chunk 234 optimal weight: 0.9980 chunk 275 optimal weight: 0.5980 chunk 192 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2212 GLN A2715 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.119783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.086918 restraints weight = 34294.867| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 1.87 r_work: 0.2887 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24113 Z= 0.135 Angle : 0.604 18.362 32960 Z= 0.300 Chirality : 0.048 0.377 3762 Planarity : 0.004 0.052 4189 Dihedral : 7.222 58.394 4435 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 3.88 % Allowed : 15.27 % Favored : 80.86 % 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: -1.44 (0.16), residues: 2866 helix: -3.25 (0.43), residues: 73 sheet: -0.82 (0.15), residues: 1117 loop : -0.88 (0.16), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B1483 HIS 0.003 0.001 HIS A1505 PHE 0.023 0.001 PHE B2706 TYR 0.016 0.001 TYR A2210 ARG 0.012 0.000 ARG A1413 Details of bonding type rmsd link_TRANS : bond 0.00055 ( 2) link_TRANS : angle 0.44841 ( 6) link_NAG-ASN : bond 0.00811 ( 26) link_NAG-ASN : angle 3.78568 ( 78) link_ALPHA1-6 : bond 0.00523 ( 4) link_ALPHA1-6 : angle 1.72534 ( 12) link_BETA1-4 : bond 0.00394 ( 24) link_BETA1-4 : angle 1.64252 ( 72) link_ALPHA1-3 : bond 0.01006 ( 4) link_ALPHA1-3 : angle 1.69668 ( 12) hydrogen bonds : bond 0.02977 ( 730) hydrogen bonds : angle 6.26870 ( 1734) SS BOND : bond 0.00252 ( 49) SS BOND : angle 0.92659 ( 98) covalent geometry : bond 0.00316 (24002) covalent geometry : angle 0.56807 (32682) Misc. bond : bond 0.00016 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5732 Ramachandran restraints generated. 2866 Oldfield, 0 Emsley, 2866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5732 Ramachandran restraints generated. 2866 Oldfield, 0 Emsley, 2866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 124 time to evaluate : 2.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1363 HIS cc_start: 0.5693 (OUTLIER) cc_final: 0.5305 (t70) REVERT: A 1585 MET cc_start: 0.9323 (OUTLIER) cc_final: 0.8912 (mtm) REVERT: A 1590 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.8263 (ttt90) REVERT: A 1849 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8639 (tp) REVERT: A 1906 MET cc_start: 0.9005 (mtp) cc_final: 0.8537 (ttm) REVERT: A 1955 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.8184 (ppp) REVERT: A 2079 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8232 (mm) REVERT: A 2127 ARG cc_start: 0.9249 (OUTLIER) cc_final: 0.8653 (ptp-170) REVERT: A 2212 GLN cc_start: 0.9123 (OUTLIER) cc_final: 0.8828 (mm-40) REVERT: A 2453 TYR cc_start: 0.7432 (OUTLIER) cc_final: 0.7052 (t80) REVERT: A 2599 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8315 (tp) REVERT: B 1560 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8931 (pp) REVERT: B 1808 ASP cc_start: 0.9053 (OUTLIER) cc_final: 0.8636 (p0) REVERT: B 2079 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7880 (mm) REVERT: B 2094 GLN cc_start: 0.8645 (tp40) cc_final: 0.8427 (tp40) REVERT: B 2127 ARG cc_start: 0.9269 (OUTLIER) cc_final: 0.8899 (ptm160) REVERT: B 2213 LYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8793 (mtmt) REVERT: B 2242 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.7529 (tpp) REVERT: B 2307 GLN cc_start: 0.9039 (OUTLIER) cc_final: 0.7635 (mp10) REVERT: B 2596 SER cc_start: 0.9052 (OUTLIER) cc_final: 0.8760 (t) REVERT: B 2649 ARG cc_start: 0.7122 (OUTLIER) cc_final: 0.6415 (mtt180) REVERT: B 2656 CYS cc_start: 0.5322 (OUTLIER) cc_final: 0.5117 (t) outliers start: 97 outliers final: 72 residues processed: 199 average time/residue: 0.4034 time to fit residues: 124.3750 Evaluate side-chains 215 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 123 time to evaluate : 2.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1363 HIS Chi-restraints excluded: chain A residue 1365 CYS Chi-restraints excluded: chain A residue 1366 MET Chi-restraints excluded: chain A residue 1388 THR Chi-restraints excluded: chain A residue 1401 CYS Chi-restraints excluded: chain A residue 1455 HIS Chi-restraints excluded: chain A residue 1477 VAL Chi-restraints excluded: chain A residue 1517 VAL Chi-restraints excluded: chain A residue 1539 ILE Chi-restraints excluded: chain A residue 1564 MET Chi-restraints excluded: chain A residue 1569 MET Chi-restraints excluded: chain A residue 1585 MET Chi-restraints excluded: chain A residue 1590 ARG Chi-restraints excluded: chain A residue 1684 VAL Chi-restraints excluded: chain A residue 1726 CYS Chi-restraints excluded: chain A residue 1737 ASP Chi-restraints excluded: chain A residue 1779 GLN Chi-restraints excluded: chain A residue 1814 VAL Chi-restraints excluded: chain A residue 1840 THR Chi-restraints excluded: chain A residue 1849 LEU Chi-restraints excluded: chain A residue 1893 THR Chi-restraints excluded: chain A residue 1900 LYS Chi-restraints excluded: chain A residue 1911 LEU Chi-restraints excluded: chain A residue 1919 LEU Chi-restraints excluded: chain A residue 1955 MET Chi-restraints excluded: chain A residue 1974 LEU Chi-restraints excluded: chain A residue 2062 TYR Chi-restraints excluded: chain A residue 2070 MET Chi-restraints excluded: chain A residue 2079 LEU Chi-restraints excluded: chain A residue 2088 MET Chi-restraints excluded: chain A residue 2127 ARG Chi-restraints excluded: chain A residue 2153 LEU Chi-restraints excluded: chain A residue 2174 VAL Chi-restraints excluded: chain A residue 2212 GLN Chi-restraints excluded: chain A residue 2225 ASN Chi-restraints excluded: chain A residue 2230 VAL Chi-restraints excluded: chain A residue 2249 ILE Chi-restraints excluded: chain A residue 2348 LEU Chi-restraints excluded: chain A residue 2452 LEU Chi-restraints excluded: chain A residue 2453 TYR Chi-restraints excluded: chain A residue 2499 SER Chi-restraints excluded: chain A residue 2507 VAL Chi-restraints excluded: chain A residue 2514 VAL Chi-restraints excluded: chain A residue 2515 LEU Chi-restraints excluded: chain A residue 2547 VAL Chi-restraints excluded: chain A residue 2561 LEU Chi-restraints excluded: chain A residue 2580 THR Chi-restraints excluded: chain A residue 2588 VAL Chi-restraints excluded: chain A residue 2590 VAL Chi-restraints excluded: chain A residue 2599 LEU Chi-restraints excluded: chain B residue 1378 LEU Chi-restraints excluded: chain B residue 1387 LYS Chi-restraints excluded: chain B residue 1421 THR Chi-restraints excluded: chain B residue 1463 VAL Chi-restraints excluded: chain B residue 1540 ASP Chi-restraints excluded: chain B residue 1560 LEU Chi-restraints excluded: chain B residue 1566 ASP Chi-restraints excluded: chain B residue 1598 ILE Chi-restraints excluded: chain B residue 1610 ASN Chi-restraints excluded: chain B residue 1660 ASP Chi-restraints excluded: chain B residue 1714 CYS Chi-restraints excluded: chain B residue 1808 ASP Chi-restraints excluded: chain B residue 1813 THR Chi-restraints excluded: chain B residue 1821 LEU Chi-restraints excluded: chain B residue 1871 VAL Chi-restraints excluded: chain B residue 1897 VAL Chi-restraints excluded: chain B residue 1955 MET Chi-restraints excluded: chain B residue 1974 LEU Chi-restraints excluded: chain B residue 1987 VAL Chi-restraints excluded: chain B residue 2041 MET Chi-restraints excluded: chain B residue 2070 MET Chi-restraints excluded: chain B residue 2079 LEU Chi-restraints excluded: chain B residue 2098 VAL Chi-restraints excluded: chain B residue 2127 ARG Chi-restraints excluded: chain B residue 2171 LEU Chi-restraints excluded: chain B residue 2213 LYS Chi-restraints excluded: chain B residue 2221 LEU Chi-restraints excluded: chain B residue 2242 MET Chi-restraints excluded: chain B residue 2286 VAL Chi-restraints excluded: chain B residue 2307 GLN Chi-restraints excluded: chain B residue 2315 VAL Chi-restraints excluded: chain B residue 2327 VAL Chi-restraints excluded: chain B residue 2507 VAL Chi-restraints excluded: chain B residue 2530 ASN Chi-restraints excluded: chain B residue 2561 LEU Chi-restraints excluded: chain B residue 2590 VAL Chi-restraints excluded: chain B residue 2596 SER Chi-restraints excluded: chain B residue 2599 LEU Chi-restraints excluded: chain B residue 2601 VAL Chi-restraints excluded: chain B residue 2649 ARG Chi-restraints excluded: chain B residue 2656 CYS Chi-restraints excluded: chain B residue 2736 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 67 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 223 optimal weight: 1.9990 chunk 250 optimal weight: 7.9990 chunk 139 optimal weight: 8.9990 chunk 193 optimal weight: 3.9990 chunk 114 optimal weight: 7.9990 chunk 144 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2715 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.119443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.086705 restraints weight = 34200.799| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 1.85 r_work: 0.2886 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.202 24113 Z= 0.234 Angle : 0.750 59.197 32960 Z= 0.404 Chirality : 0.052 0.858 3762 Planarity : 0.004 0.050 4189 Dihedral : 7.217 58.409 4434 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 4.04 % Allowed : 15.15 % Favored : 80.82 % Cbeta Deviations : 0.04 % 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: -1.45 (0.16), residues: 2866 helix: -3.26 (0.43), residues: 73 sheet: -0.82 (0.15), residues: 1117 loop : -0.89 (0.16), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B1483 HIS 0.003 0.001 HIS B2403 PHE 0.016 0.002 PHE A1625 TYR 0.029 0.002 TYR A2181 ARG 0.007 0.000 ARG B2506 Details of bonding type rmsd link_TRANS : bond 0.00094 ( 2) link_TRANS : angle 0.50087 ( 6) link_NAG-ASN : bond 0.00790 ( 26) link_NAG-ASN : angle 3.77860 ( 78) link_ALPHA1-6 : bond 0.00599 ( 4) link_ALPHA1-6 : angle 1.75690 ( 12) link_BETA1-4 : bond 0.00391 ( 24) link_BETA1-4 : angle 1.64990 ( 72) link_ALPHA1-3 : bond 0.01005 ( 4) link_ALPHA1-3 : angle 1.67494 ( 12) hydrogen bonds : bond 0.03048 ( 730) hydrogen bonds : angle 6.26555 ( 1734) SS BOND : bond 0.00321 ( 49) SS BOND : angle 0.91254 ( 98) covalent geometry : bond 0.00507 (24002) covalent geometry : angle 0.72262 (32682) Misc. bond : bond 0.00032 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12082.51 seconds wall clock time: 209 minutes 41.84 seconds (12581.84 seconds total)