Starting phenix.real_space_refine on Sat Jul 4 22:22:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jx8_36692/07_2026/8jx8_36692.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jx8_36692/07_2026/8jx8_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_36692/07_2026/8jx8_36692.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jx8_36692/07_2026/8jx8_36692.map" model { file = "/net/cci-nas-00/data/ceres_data/8jx8_36692/07_2026/8jx8_36692.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jx8_36692/07_2026/8jx8_36692.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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, 70 Ad-hoc single atom residues: {' CA': 5, ' NI': 1} Unusual residues: {'A2G': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain breaks: 6 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, 70 Ad-hoc single atom residues: {' CA': 5, ' NI': 1} Unusual residues: {'A2G': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain breaks: 6 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: 5.77, per 1000 atoms: 0.25 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: 2.29 Conformation dependent library (CDL) restraints added in 1.1 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: 1.51 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: 7.94 Time building geometry restraints manager: 2.91 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 2.920 nonbonded pdb=" OE2 GLU B1923 " pdb="NI NI B4711 " model vdw 2.068 2.920 nonbonded pdb=" NE2 HIS B1963 " pdb="NI NI B4711 " model vdw 2.080 3.000 nonbonded pdb=" NE2 HIS B1921 " pdb="NI NI B4711 " model vdw 2.161 3.000 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 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: 1.230 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: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 26.830 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (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 ARG 0.008 0.000 ARG B2506 TYR 0.016 0.001 TYR A2210 PHE 0.026 0.001 PHE B2706 TRP 0.019 0.002 TRP A1574 HIS 0.004 0.001 HIS B1803 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.21 (24002) covalent geometry : angle 0.72578 / 0.38 (32682) SS BOND : bond 0.00295 / 0.19 ( 49) SS BOND : angle 0.91199 / 0.61 ( 98) hydrogen bonds : bond 0.22985 / 15.44 ( 730) hydrogen bonds : angle 10.20353 / 7.19 ( 1734) Misc. bond : bond 0.01985 / 1.04 ( 2) link_ALPHA1-3 : bond 0.00233 / 0.11 ( 4) link_ALPHA1-3 : angle 0.92105 / 0.59 ( 12) link_ALPHA1-6 : bond 0.00232 / 0.12 ( 4) link_ALPHA1-6 : angle 0.91781 / 0.61 ( 12) link_BETA1-4 : bond 0.00634 / 0.41 ( 24) link_BETA1-4 : angle 1.92419 / 1.25 ( 72) link_NAG-ASN : bond 0.00885 / 0.58 ( 26) link_NAG-ASN : angle 4.70937 / 2.87 ( 78) link_TRANS : bond 0.00166 / 0.08 ( 2) link_TRANS : angle 0.58750 / 0.33 ( 6) *********************** 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 : 1.147 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: 0.1582 time to fit residues: 41.6769 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 : 0.606 ------------------------------------------------------------------------------- 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 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 0.6980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1458 ASN A1632 ASN A1645 HIS A1712 HIS A1755 ASN A1864 ASN A1920 GLN A2322 ASN A2349 GLN A2595 HIS A2660 ASN A2710 ASN A2712 HIS A2715 ASN B1576 HIS B1798 ASN B2097 ASN B2107 ASN B2710 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.117557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.085360 restraints weight = 34439.970| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 1.73 r_work: 0.2880 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.0862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 24113 Z= 0.214 Angle : 0.711 17.943 32960 Z= 0.355 Chirality : 0.052 0.483 3762 Planarity : 0.005 0.043 4189 Dihedral : 10.309 77.965 4468 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 3.80 % Allowed : 12.19 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.15), residues: 2866 helix: -3.36 (0.41), residues: 73 sheet: -0.63 (0.15), residues: 1120 loop : -0.91 (0.15), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1409 TYR 0.021 0.002 TYR A2210 PHE 0.019 0.002 PHE B2065 TRP 0.012 0.002 TRP B1888 HIS 0.005 0.001 HIS B1645 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.21 (24002) covalent geometry : angle 0.66776 / 0.35 (32682) SS BOND : bond 0.00577 / 0.38 ( 49) SS BOND : angle 0.94290 / 0.63 ( 98) hydrogen bonds : bond 0.04533 / 2.98 ( 730) hydrogen bonds : angle 7.38301 / 5.11 ( 1734) Misc. bond : bond 0.00050 / 0.03 ( 2) link_ALPHA1-3 : bond 0.00795 / 0.39 ( 4) link_ALPHA1-3 : angle 1.80796 / 1.01 ( 12) link_ALPHA1-6 : bond 0.00327 / 0.17 ( 4) link_ALPHA1-6 : angle 1.67573 / 1.09 ( 12) link_BETA1-4 : bond 0.00540 / 0.35 ( 24) link_BETA1-4 : angle 2.37347 / 1.52 ( 72) link_NAG-ASN : bond 0.00725 / 0.50 ( 26) link_NAG-ASN : angle 4.38784 / 2.84 ( 78) link_TRANS : bond 0.00124 / 0.07 ( 2) link_TRANS : angle 0.62422 / 0.38 ( 6) *********************** 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 232 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 137 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1363 HIS cc_start: 0.5935 (OUTLIER) cc_final: 0.5343 (t70) REVERT: A 2013 ARG cc_start: 0.7705 (mmt180) cc_final: 0.7421 (mmt180) REVERT: A 2481 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8533 (pt) REVERT: A 2599 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8352 (tp) REVERT: A 2685 TYR cc_start: 0.7377 (OUTLIER) cc_final: 0.6883 (p90) REVERT: B 1387 LYS cc_start: 0.4905 (mmpt) cc_final: 0.4601 (mmtm) REVERT: B 1590 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.7739 (ttm170) REVERT: B 1808 ASP cc_start: 0.8956 (OUTLIER) cc_final: 0.8673 (p0) REVERT: B 2079 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8292 (mm) REVERT: B 2097 ASN cc_start: 0.8852 (OUTLIER) cc_final: 0.8239 (t0) REVERT: B 2127 ARG cc_start: 0.9273 (OUTLIER) cc_final: 0.8889 (ptm160) REVERT: B 2171 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8658 (mp) REVERT: B 2213 LYS cc_start: 0.9160 (OUTLIER) cc_final: 0.8802 (mtmt) REVERT: B 2318 ARG cc_start: 0.9127 (OUTLIER) cc_final: 0.7660 (mmt-90) REVERT: B 2596 SER cc_start: 0.9100 (OUTLIER) cc_final: 0.8761 (t) REVERT: B 2706 PHE cc_start: 0.5175 (t80) cc_final: 0.4819 (t80) outliers start: 95 outliers final: 51 residues processed: 210 average time/residue: 0.1577 time to fit residues: 51.9328 Evaluate side-chains 188 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 124 time to evaluate : 0.865 ------------------------------------------------------------------------------- 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 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 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 2174 VAL 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 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 A residue 2685 TYR Chi-restraints excluded: chain B residue 1421 THR Chi-restraints excluded: chain B residue 1449 VAL Chi-restraints excluded: chain B residue 1469 VAL Chi-restraints excluded: chain B residue 1590 ARG 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 1789 SER Chi-restraints excluded: chain B residue 1808 ASP Chi-restraints excluded: chain B residue 1833 SER Chi-restraints excluded: chain B residue 1955 MET 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 105 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 282 optimal weight: 9.9990 chunk 247 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1780 HIS A1803 HIS A2084 HIS A2715 ASN B2097 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.118869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.085912 restraints weight = 34475.904| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 1.86 r_work: 0.2872 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24113 Z= 0.181 Angle : 0.667 17.640 32960 Z= 0.332 Chirality : 0.051 0.524 3762 Planarity : 0.004 0.042 4189 Dihedral : 9.241 71.798 4446 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 3.72 % Allowed : 12.91 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.15), residues: 2866 helix: -3.34 (0.41), residues: 73 sheet: -0.72 (0.15), residues: 1120 loop : -0.96 (0.15), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B2096 TYR 0.019 0.002 TYR A2210 PHE 0.018 0.002 PHE A1625 TRP 0.012 0.002 TRP A1492 HIS 0.005 0.001 HIS A1803 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 (24002) covalent geometry : angle 0.62736 / 0.32 (32682) SS BOND : bond 0.00326 / 0.20 ( 49) SS BOND : angle 0.98192 / 0.65 ( 98) hydrogen bonds : bond 0.03879 / 2.57 ( 730) hydrogen bonds : angle 6.93345 / 4.81 ( 1734) Misc. bond : bond 0.00033 / 0.02 ( 2) link_ALPHA1-3 : bond 0.01031 / 0.51 ( 4) link_ALPHA1-3 : angle 1.64295 / 0.95 ( 12) link_ALPHA1-6 : bond 0.00475 / 0.24 ( 4) link_ALPHA1-6 : angle 1.67032 / 1.08 ( 12) link_BETA1-4 : bond 0.00435 / 0.28 ( 24) link_BETA1-4 : angle 2.12597 / 1.36 ( 72) link_NAG-ASN : bond 0.00781 / 0.50 ( 26) link_NAG-ASN : angle 4.07440 / 2.64 ( 78) link_TRANS : bond 0.00066 / 0.03 ( 2) link_TRANS : angle 0.59228 / 0.36 ( 6) *********************** 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 225 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 132 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1363 HIS cc_start: 0.5896 (OUTLIER) cc_final: 0.5217 (t70) REVERT: A 1585 MET cc_start: 0.9298 (OUTLIER) cc_final: 0.9069 (mtm) REVERT: A 2127 ARG cc_start: 0.9307 (OUTLIER) cc_final: 0.9029 (ptp-170) REVERT: A 2481 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8520 (pt) REVERT: A 2599 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8357 (tp) REVERT: B 1387 LYS cc_start: 0.4787 (mmpt) cc_final: 0.4537 (mmtm) REVERT: B 1560 LEU cc_start: 0.9222 (pp) cc_final: 0.8941 (pp) REVERT: B 1808 ASP cc_start: 0.9023 (OUTLIER) cc_final: 0.8667 (p0) REVERT: B 2079 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8341 (mm) REVERT: B 2094 GLN cc_start: 0.8639 (tp40) cc_final: 0.8398 (tp40) REVERT: B 2127 ARG cc_start: 0.9276 (OUTLIER) cc_final: 0.8904 (ptm160) REVERT: B 2213 LYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8820 (mtmt) REVERT: B 2242 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.7577 (tpp) REVERT: B 2318 ARG cc_start: 0.9147 (OUTLIER) cc_final: 0.7579 (mmt-90) REVERT: B 2494 MET cc_start: 0.8125 (ptm) cc_final: 0.7862 (ptp) REVERT: B 2596 SER cc_start: 0.9084 (OUTLIER) cc_final: 0.8738 (t) outliers start: 93 outliers final: 59 residues processed: 204 average time/residue: 0.1743 time to fit residues: 55.1980 Evaluate side-chains 195 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 124 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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 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 1585 MET 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 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 2127 ARG 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 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 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 1449 VAL Chi-restraints excluded: chain B residue 1463 VAL Chi-restraints excluded: chain B residue 1466 VAL Chi-restraints excluded: chain B residue 1469 VAL Chi-restraints excluded: chain B residue 1598 ILE 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 1821 LEU Chi-restraints excluded: chain B residue 1955 MET Chi-restraints excluded: chain B residue 1967 LEU Chi-restraints excluded: chain B residue 1987 VAL Chi-restraints excluded: chain B residue 2041 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 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 2557 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 266 optimal weight: 2.9990 chunk 257 optimal weight: 8.9990 chunk 261 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 135 optimal weight: 0.0060 chunk 154 optimal weight: 5.9990 chunk 213 optimal weight: 2.9990 chunk 252 optimal weight: 2.9990 chunk 142 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 overall best weight: 2.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A2715 ASN B2084 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.118837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.087765 restraints weight = 34514.715| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.02 r_work: 0.2824 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 24113 Z= 0.287 Angle : 0.736 16.975 32960 Z= 0.368 Chirality : 0.054 0.570 3762 Planarity : 0.005 0.054 4189 Dihedral : 8.972 68.132 4441 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.78 % Favored : 92.18 % Rotamer: Outliers : 4.68 % Allowed : 13.31 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.15), residues: 2866 helix: -3.33 (0.42), residues: 73 sheet: -0.92 (0.15), residues: 1117 loop : -1.11 (0.15), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1413 TYR 0.022 0.002 TYR A2210 PHE 0.027 0.002 PHE B2706 TRP 0.017 0.002 TRP A1492 HIS 0.007 0.001 HIS B1645 Details of bonding type rmsd/Z covalent geometry : bond 0.00690 / 0.29 (24002) covalent geometry : angle 0.70121 / 0.36 (32682) SS BOND : bond 0.00407 / 0.25 ( 49) SS BOND : angle 1.15458 / 0.76 ( 98) hydrogen bonds : bond 0.04028 / 2.65 ( 730) hydrogen bonds : angle 6.90193 / 4.78 ( 1734) Misc. bond : bond 0.00045 / 0.02 ( 2) link_ALPHA1-3 : bond 0.00920 / 0.46 ( 4) link_ALPHA1-3 : angle 1.81104 / 1.01 ( 12) link_ALPHA1-6 : bond 0.00498 / 0.25 ( 4) link_ALPHA1-6 : angle 1.62668 / 1.03 ( 12) link_BETA1-4 : bond 0.00432 / 0.28 ( 24) link_BETA1-4 : angle 2.18794 / 1.38 ( 72) link_NAG-ASN : bond 0.00721 / 0.46 ( 26) link_NAG-ASN : angle 3.95818 / 2.55 ( 78) link_TRANS : bond 0.00143 / 0.08 ( 2) link_TRANS : angle 0.78321 / 0.47 ( 6) *********************** 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 242 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 125 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1363 HIS cc_start: 0.5862 (OUTLIER) cc_final: 0.5467 (t70) REVERT: A 2079 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8388 (mm) REVERT: A 2127 ARG cc_start: 0.9350 (OUTLIER) cc_final: 0.9028 (ptp-170) REVERT: B 1387 LYS cc_start: 0.4838 (mmpt) cc_final: 0.4580 (mmtm) REVERT: B 1808 ASP cc_start: 0.9039 (OUTLIER) cc_final: 0.8641 (p0) REVERT: B 2079 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8257 (mm) REVERT: B 2127 ARG cc_start: 0.9306 (OUTLIER) cc_final: 0.7840 (ptp-170) REVERT: B 2213 LYS cc_start: 0.9242 (OUTLIER) cc_final: 0.8814 (mtmt) REVERT: B 2649 ARG cc_start: 0.7056 (OUTLIER) cc_final: 0.6399 (mtt180) outliers start: 117 outliers final: 90 residues processed: 216 average time/residue: 0.1730 time to fit residues: 58.0166 Evaluate side-chains 214 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 116 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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 1406 VAL 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 1613 ILE Chi-restraints excluded: chain A residue 1616 MET 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 2066 MET 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 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 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 2596 SER 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 1466 VAL Chi-restraints excluded: chain B residue 1469 VAL Chi-restraints excluded: chain B residue 1540 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 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 1833 SER 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 2253 ASP Chi-restraints excluded: chain B residue 2286 VAL Chi-restraints excluded: chain B residue 2315 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 2557 LEU 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 21 optimal weight: 0.6980 chunk 216 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 252 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 chunk 123 optimal weight: 7.9990 chunk 145 optimal weight: 0.4980 chunk 209 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 110 optimal weight: 0.0980 chunk 225 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1665 GLN A1905 ASN A2001 ASN A2710 ASN A2715 ASN B2648 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.119819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.087671 restraints weight = 34107.085| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.76 r_work: 0.2903 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24113 Z= 0.113 Angle : 0.599 16.137 32960 Z= 0.301 Chirality : 0.048 0.535 3762 Planarity : 0.004 0.049 4189 Dihedral : 8.050 62.941 4441 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.60 % Allowed : 14.71 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.16), residues: 2866 helix: -3.26 (0.42), residues: 73 sheet: -0.75 (0.15), residues: 1110 loop : -0.98 (0.16), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1413 TYR 0.018 0.001 TYR A2210 PHE 0.014 0.001 PHE B1786 TRP 0.013 0.001 TRP B1483 HIS 0.003 0.001 HIS A1803 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (24002) covalent geometry : angle 0.56568 / 0.29 (32682) SS BOND : bond 0.00250 / 0.14 ( 49) SS BOND : angle 0.91947 / 0.60 ( 98) hydrogen bonds : bond 0.03092 / 2.06 ( 730) hydrogen bonds : angle 6.51642 / 4.52 ( 1734) Misc. bond : bond 0.00011 / 0.01 ( 2) link_ALPHA1-3 : bond 0.01117 / 0.56 ( 4) link_ALPHA1-3 : angle 1.69325 / 1.00 ( 12) link_ALPHA1-6 : bond 0.00556 / 0.28 ( 4) link_ALPHA1-6 : angle 1.73370 / 1.06 ( 12) link_BETA1-4 : bond 0.00424 / 0.27 ( 24) link_BETA1-4 : angle 1.78294 / 1.13 ( 72) link_NAG-ASN : bond 0.00677 / 0.45 ( 26) link_NAG-ASN : angle 3.53798 / 2.27 ( 78) link_TRANS : bond 0.00034 / 0.02 ( 2) link_TRANS : angle 0.51038 / 0.31 ( 6) *********************** 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 227 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 137 time to evaluate : 0.897 Fit side-chains REVERT: A 1363 HIS cc_start: 0.5989 (OUTLIER) cc_final: 0.5271 (t70) REVERT: A 1585 MET cc_start: 0.9292 (mtm) cc_final: 0.8890 (mtm) REVERT: A 1590 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8196 (ttt90) REVERT: A 1798 ASN cc_start: 0.7464 (t0) cc_final: 0.7211 (t0) REVERT: A 2127 ARG cc_start: 0.9246 (OUTLIER) cc_final: 0.8606 (ptp-170) REVERT: A 2599 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8268 (tp) REVERT: B 1598 ILE cc_start: 0.9160 (OUTLIER) cc_final: 0.8935 (tt) REVERT: B 1808 ASP cc_start: 0.9022 (OUTLIER) cc_final: 0.8652 (p0) REVERT: B 2079 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8108 (mm) REVERT: B 2094 GLN cc_start: 0.8585 (tp40) cc_final: 0.8366 (tp40) REVERT: B 2127 ARG cc_start: 0.9259 (OUTLIER) cc_final: 0.8918 (ptm160) REVERT: B 2213 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8812 (mtmt) REVERT: B 2242 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.7576 (tpp) REVERT: B 2596 SER cc_start: 0.8971 (OUTLIER) cc_final: 0.8680 (t) REVERT: B 2649 ARG cc_start: 0.7196 (OUTLIER) cc_final: 0.6498 (mtt180) REVERT: B 2656 CYS cc_start: 0.5600 (OUTLIER) cc_final: 0.5260 (t) outliers start: 90 outliers final: 55 residues processed: 206 average time/residue: 0.1731 time to fit residues: 55.5068 Evaluate side-chains 193 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 125 time to evaluate : 0.879 ------------------------------------------------------------------------------- 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 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 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 1814 VAL Chi-restraints excluded: chain A residue 1840 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 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 2549 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 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 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 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 2507 VAL Chi-restraints excluded: chain B residue 2530 ASN Chi-restraints excluded: chain B residue 2557 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 2649 ARG Chi-restraints excluded: chain B residue 2656 CYS Chi-restraints excluded: chain B residue 2707 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 102 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 258 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 163 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1905 ASN A2715 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.120535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.088006 restraints weight = 34280.042| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 1.85 r_work: 0.2853 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 24113 Z= 0.194 Angle : 0.655 15.656 32960 Z= 0.326 Chirality : 0.050 0.558 3762 Planarity : 0.004 0.052 4189 Dihedral : 8.041 61.118 4439 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 4.36 % Allowed : 14.35 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.16), residues: 2866 helix: -3.25 (0.43), residues: 73 sheet: -0.89 (0.15), residues: 1132 loop : -0.99 (0.16), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1413 TYR 0.020 0.002 TYR A2210 PHE 0.020 0.002 PHE B2706 TRP 0.014 0.002 TRP A1492 HIS 0.005 0.001 HIS B1645 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.19 (24002) covalent geometry : angle 0.62120 / 0.32 (32682) SS BOND : bond 0.00308 / 0.19 ( 49) SS BOND : angle 0.99252 / 0.65 ( 98) hydrogen bonds : bond 0.03389 / 2.24 ( 730) hydrogen bonds : angle 6.51868 / 4.51 ( 1734) Misc. bond : bond 0.00037 / 0.02 ( 2) link_ALPHA1-3 : bond 0.01086 / 0.54 ( 4) link_ALPHA1-3 : angle 1.87958 / 1.06 ( 12) link_ALPHA1-6 : bond 0.00486 / 0.24 ( 4) link_ALPHA1-6 : angle 1.60665 / 0.98 ( 12) link_BETA1-4 : bond 0.00397 / 0.26 ( 24) link_BETA1-4 : angle 1.88304 / 1.21 ( 72) link_NAG-ASN : bond 0.00680 / 0.43 ( 26) link_NAG-ASN : angle 3.72226 / 2.44 ( 78) link_TRANS : bond 0.00085 / 0.04 ( 2) link_TRANS : angle 0.61250 / 0.37 ( 6) *********************** 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 236 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 127 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1363 HIS cc_start: 0.5734 (OUTLIER) cc_final: 0.5352 (t70) REVERT: A 1450 ASP cc_start: 0.8627 (t0) cc_final: 0.8364 (t70) REVERT: A 1585 MET cc_start: 0.9342 (mtm) cc_final: 0.8982 (mtm) REVERT: A 1849 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8702 (tp) REVERT: A 1955 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.8109 (ppp) REVERT: A 2079 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8379 (mm) REVERT: A 2127 ARG cc_start: 0.9324 (OUTLIER) cc_final: 0.9048 (ptp-170) REVERT: A 2599 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8411 (tp) REVERT: B 1387 LYS cc_start: 0.5630 (mmtm) cc_final: 0.5240 (mmmt) REVERT: B 1808 ASP cc_start: 0.9045 (OUTLIER) cc_final: 0.8637 (p0) REVERT: B 2079 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8163 (mm) REVERT: B 2094 GLN cc_start: 0.8618 (tp40) cc_final: 0.8385 (tp40) REVERT: B 2127 ARG cc_start: 0.9286 (OUTLIER) cc_final: 0.8908 (ptm160) REVERT: B 2213 LYS cc_start: 0.9223 (OUTLIER) cc_final: 0.8815 (mtmt) REVERT: B 2242 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.7543 (tpp) REVERT: B 2307 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.7611 (mp10) REVERT: B 2649 ARG cc_start: 0.7218 (OUTLIER) cc_final: 0.6514 (mtt180) outliers start: 109 outliers final: 80 residues processed: 213 average time/residue: 0.1683 time to fit residues: 56.2860 Evaluate side-chains 215 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 122 time to evaluate : 0.872 ------------------------------------------------------------------------------- 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 1397 ILE 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 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 1836 ILE 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 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 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 2596 SER 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 1463 VAL Chi-restraints excluded: chain B residue 1469 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 1660 ASP Chi-restraints excluded: chain B residue 1681 MET 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 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 2242 MET Chi-restraints excluded: chain B residue 2253 ASP 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 2557 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 30 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 198 optimal weight: 2.9990 chunk 227 optimal weight: 1.9990 chunk 205 optimal weight: 2.9990 chunk 41 optimal weight: 0.3980 chunk 89 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 201 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1905 ASN A2715 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.121411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.088864 restraints weight = 34154.521| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.85 r_work: 0.2867 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24113 Z= 0.165 Angle : 0.622 15.249 32960 Z= 0.311 Chirality : 0.049 0.550 3762 Planarity : 0.004 0.053 4189 Dihedral : 7.705 59.363 4437 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 4.40 % Allowed : 14.51 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.16), residues: 2866 helix: -3.24 (0.43), residues: 73 sheet: -0.84 (0.15), residues: 1117 loop : -1.00 (0.16), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B2506 TYR 0.020 0.001 TYR A2210 PHE 0.017 0.002 PHE A1625 TRP 0.012 0.002 TRP B1483 HIS 0.004 0.001 HIS B1645 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 (24002) covalent geometry : angle 0.59082 / 0.30 (32682) SS BOND : bond 0.00275 / 0.17 ( 49) SS BOND : angle 0.88073 / 0.58 ( 98) hydrogen bonds : bond 0.03195 / 2.11 ( 730) hydrogen bonds : angle 6.44863 / 4.46 ( 1734) Misc. bond : bond 0.00024 / 0.01 ( 2) link_ALPHA1-3 : bond 0.01019 / 0.51 ( 4) link_ALPHA1-3 : angle 1.77480 / 1.01 ( 12) link_ALPHA1-6 : bond 0.00494 / 0.25 ( 4) link_ALPHA1-6 : angle 1.80732 / 1.08 ( 12) link_BETA1-4 : bond 0.00407 / 0.27 ( 24) link_BETA1-4 : angle 1.76828 / 1.12 ( 72) link_NAG-ASN : bond 0.00653 / 0.42 ( 26) link_NAG-ASN : angle 3.54977 / 2.32 ( 78) link_TRANS : bond 0.00067 / 0.03 ( 2) link_TRANS : angle 0.54999 / 0.33 ( 6) *********************** 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 236 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 126 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1363 HIS cc_start: 0.5743 (OUTLIER) cc_final: 0.5347 (t70) REVERT: A 1450 ASP cc_start: 0.8615 (t0) cc_final: 0.8353 (t70) REVERT: A 1585 MET cc_start: 0.9331 (OUTLIER) cc_final: 0.8937 (mtm) REVERT: A 1590 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.8256 (ttt90) REVERT: A 1849 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8677 (tp) REVERT: A 2079 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8301 (mm) REVERT: A 2127 ARG cc_start: 0.9297 (OUTLIER) cc_final: 0.9027 (ptp-170) REVERT: A 2599 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8342 (tp) REVERT: B 1808 ASP cc_start: 0.9057 (OUTLIER) cc_final: 0.8638 (p0) REVERT: B 2079 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8021 (mm) REVERT: B 2094 GLN cc_start: 0.8602 (tp40) cc_final: 0.8381 (tp40) REVERT: B 2127 ARG cc_start: 0.9293 (OUTLIER) cc_final: 0.8934 (ptm160) REVERT: B 2213 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8786 (mtmt) REVERT: B 2242 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.7520 (tpp) REVERT: B 2307 GLN cc_start: 0.9026 (OUTLIER) cc_final: 0.7627 (mp10) REVERT: B 2596 SER cc_start: 0.9075 (OUTLIER) cc_final: 0.8761 (t) REVERT: B 2649 ARG cc_start: 0.7189 (OUTLIER) cc_final: 0.6475 (mtt180) REVERT: B 2656 CYS cc_start: 0.5504 (OUTLIER) cc_final: 0.5165 (t) REVERT: B 2731 ASP cc_start: 0.6748 (OUTLIER) cc_final: 0.6207 (p0) outliers start: 110 outliers final: 76 residues processed: 214 average time/residue: 0.1692 time to fit residues: 56.5266 Evaluate side-chains 218 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 125 time to evaluate : 0.744 ------------------------------------------------------------------------------- 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 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 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 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 1836 ILE 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 1900 LYS Chi-restraints excluded: chain A residue 1911 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 2127 ARG 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 2515 LEU Chi-restraints excluded: chain A residue 2538 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 2596 SER 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 1469 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 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 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 2557 LEU Chi-restraints excluded: chain B residue 2561 LEU Chi-restraints excluded: chain B residue 2590 VAL Chi-restraints excluded: chain B residue 2591 SER 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 2731 ASP 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 169 optimal weight: 3.9990 chunk 186 optimal weight: 6.9990 chunk 242 optimal weight: 2.9990 chunk 21 optimal weight: 0.0770 chunk 184 optimal weight: 4.9990 chunk 139 optimal weight: 20.0000 chunk 29 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 176 optimal weight: 4.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A2715 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.116941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.084531 restraints weight = 34305.556| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 1.76 r_work: 0.2848 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 24113 Z= 0.245 Angle : 0.683 14.990 32960 Z= 0.341 Chirality : 0.052 0.573 3762 Planarity : 0.005 0.055 4189 Dihedral : 7.902 59.370 4435 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 4.84 % Allowed : 14.31 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.15), residues: 2866 helix: -3.22 (0.44), residues: 73 sheet: -0.98 (0.15), residues: 1123 loop : -1.06 (0.15), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B2506 TYR 0.021 0.002 TYR A2210 PHE 0.024 0.002 PHE A1625 TRP 0.014 0.002 TRP A1492 HIS 0.005 0.001 HIS B1645 Details of bonding type rmsd/Z covalent geometry : bond 0.00591 / 0.24 (24002) covalent geometry : angle 0.65239 / 0.33 (32682) SS BOND : bond 0.00400 / 0.26 ( 49) SS BOND : angle 1.18483 / 0.76 ( 98) hydrogen bonds : bond 0.03522 / 2.31 ( 730) hydrogen bonds : angle 6.54859 / 4.54 ( 1734) Misc. bond : bond 0.00039 / 0.02 ( 2) link_ALPHA1-3 : bond 0.00946 / 0.47 ( 4) link_ALPHA1-3 : angle 1.84059 / 1.02 ( 12) link_ALPHA1-6 : bond 0.00487 / 0.24 ( 4) link_ALPHA1-6 : angle 1.77667 / 1.05 ( 12) link_BETA1-4 : bond 0.00418 / 0.28 ( 24) link_BETA1-4 : angle 1.88519 / 1.19 ( 72) link_NAG-ASN : bond 0.00666 / 0.42 ( 26) link_NAG-ASN : angle 3.60081 / 2.34 ( 78) link_TRANS : bond 0.00135 / 0.07 ( 2) link_TRANS : angle 0.66593 / 0.40 ( 6) *********************** 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 241 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 120 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1363 HIS cc_start: 0.5711 (OUTLIER) cc_final: 0.5318 (t70) REVERT: A 1450 ASP cc_start: 0.8612 (t0) cc_final: 0.8412 (t70) REVERT: A 1585 MET cc_start: 0.9322 (mtm) cc_final: 0.8961 (mtm) REVERT: A 1590 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.8355 (ttt90) REVERT: A 1849 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8702 (tp) REVERT: A 1955 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.8088 (ppp) REVERT: A 2079 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8383 (mm) REVERT: A 2127 ARG cc_start: 0.9295 (OUTLIER) cc_final: 0.9006 (ptp-170) REVERT: A 2453 TYR cc_start: 0.7472 (OUTLIER) cc_final: 0.7095 (t80) REVERT: A 2599 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8417 (tp) REVERT: B 1387 LYS cc_start: 0.5547 (mmtm) cc_final: 0.5124 (mmtm) REVERT: B 1560 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8911 (pp) REVERT: B 1808 ASP cc_start: 0.9040 (OUTLIER) cc_final: 0.8632 (p0) REVERT: B 2079 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8126 (mm) REVERT: B 2094 GLN cc_start: 0.8603 (tp40) cc_final: 0.8375 (tp40) REVERT: B 2127 ARG cc_start: 0.9292 (OUTLIER) cc_final: 0.7832 (ptp-170) REVERT: B 2213 LYS cc_start: 0.9234 (OUTLIER) cc_final: 0.8836 (mtmt) REVERT: B 2307 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.7627 (mp10) REVERT: B 2318 ARG cc_start: 0.9179 (OUTLIER) cc_final: 0.6733 (mtt-85) REVERT: B 2649 ARG cc_start: 0.7179 (OUTLIER) cc_final: 0.6456 (mtt180) REVERT: B 2731 ASP cc_start: 0.6759 (OUTLIER) cc_final: 0.6176 (p0) outliers start: 121 outliers final: 91 residues processed: 217 average time/residue: 0.1754 time to fit residues: 59.3405 Evaluate side-chains 226 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 118 time to evaluate : 0.875 ------------------------------------------------------------------------------- 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 1408 MET Chi-restraints excluded: chain A residue 1453 THR 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 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 1836 ILE 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 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 2285 THR 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 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 2596 SER 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 1463 VAL Chi-restraints excluded: chain B residue 1466 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 1681 MET Chi-restraints excluded: chain B residue 1714 CYS Chi-restraints excluded: chain B residue 1784 VAL 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 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 2286 VAL Chi-restraints excluded: chain B residue 2307 GLN Chi-restraints excluded: chain B residue 2318 ARG 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 2557 LEU Chi-restraints excluded: chain B residue 2561 LEU Chi-restraints excluded: chain B residue 2590 VAL Chi-restraints excluded: chain B residue 2591 SER 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 2628 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 2731 ASP 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 101 optimal weight: 0.9980 chunk 185 optimal weight: 0.9990 chunk 255 optimal weight: 0.9980 chunk 151 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 149 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A2026 ASN A2715 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.121585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.089200 restraints weight = 34249.138| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 1.82 r_work: 0.2870 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24113 Z= 0.143 Angle : 0.621 19.447 32960 Z= 0.309 Chirality : 0.048 0.382 3762 Planarity : 0.004 0.053 4189 Dihedral : 7.536 58.435 4435 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 4.40 % Allowed : 14.75 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.16), residues: 2866 helix: -3.22 (0.44), residues: 73 sheet: -0.87 (0.15), residues: 1113 loop : -0.98 (0.16), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B2506 TYR 0.019 0.001 TYR A2210 PHE 0.015 0.001 PHE B1625 TRP 0.014 0.001 TRP B1483 HIS 0.004 0.001 HIS B1645 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (24002) covalent geometry : angle 0.58397 / 0.30 (32682) SS BOND : bond 0.00271 / 0.17 ( 49) SS BOND : angle 0.98755 / 0.63 ( 98) hydrogen bonds : bond 0.03092 / 2.05 ( 730) hydrogen bonds : angle 6.40844 / 4.44 ( 1734) Misc. bond : bond 0.00018 / 0.01 ( 2) link_ALPHA1-3 : bond 0.00998 / 0.50 ( 4) link_ALPHA1-3 : angle 1.69822 / 0.99 ( 12) link_ALPHA1-6 : bond 0.00497 / 0.25 ( 4) link_ALPHA1-6 : angle 1.76232 / 1.06 ( 12) link_BETA1-4 : bond 0.00410 / 0.27 ( 24) link_BETA1-4 : angle 1.71252 / 1.08 ( 72) link_NAG-ASN : bond 0.00857 / 0.63 ( 26) link_NAG-ASN : angle 3.87969 / 2.43 ( 78) link_TRANS : bond 0.00060 / 0.03 ( 2) link_TRANS : angle 0.48961 / 0.30 ( 6) *********************** 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 230 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 120 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1363 HIS cc_start: 0.5684 (OUTLIER) cc_final: 0.5301 (t70) REVERT: A 1450 ASP cc_start: 0.8595 (t0) cc_final: 0.8341 (t70) REVERT: A 1585 MET cc_start: 0.9322 (OUTLIER) cc_final: 0.8921 (mtm) REVERT: A 1590 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.8318 (ttt90) REVERT: A 1849 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8660 (tp) REVERT: A 2079 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8287 (mm) REVERT: A 2127 ARG cc_start: 0.9289 (OUTLIER) cc_final: 0.9026 (ptp-170) REVERT: A 2599 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8326 (tp) REVERT: B 1387 LYS cc_start: 0.5451 (mmtm) cc_final: 0.5080 (mmmt) REVERT: B 1560 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8952 (pp) REVERT: B 1598 ILE cc_start: 0.9222 (OUTLIER) cc_final: 0.8979 (tt) REVERT: B 1808 ASP cc_start: 0.9064 (OUTLIER) cc_final: 0.8636 (p0) REVERT: B 2079 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.7995 (mm) REVERT: B 2094 GLN cc_start: 0.8599 (tp40) cc_final: 0.8379 (tp40) REVERT: B 2127 ARG cc_start: 0.9286 (OUTLIER) cc_final: 0.8928 (ptm160) REVERT: B 2213 LYS cc_start: 0.9184 (OUTLIER) cc_final: 0.8828 (mtmt) REVERT: B 2242 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.7548 (tpp) REVERT: B 2307 GLN cc_start: 0.9024 (OUTLIER) cc_final: 0.7625 (mp10) REVERT: B 2596 SER cc_start: 0.9054 (OUTLIER) cc_final: 0.8747 (t) REVERT: B 2649 ARG cc_start: 0.7179 (OUTLIER) cc_final: 0.6458 (mtt180) REVERT: B 2656 CYS cc_start: 0.5299 (OUTLIER) cc_final: 0.5052 (t) outliers start: 110 outliers final: 84 residues processed: 207 average time/residue: 0.1811 time to fit residues: 58.3896 Evaluate side-chains 220 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 118 time to evaluate : 0.856 ------------------------------------------------------------------------------- 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 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 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 1836 ILE 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 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 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 2596 SER 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 1463 VAL Chi-restraints excluded: chain B residue 1466 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 1681 MET 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 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 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 2557 LEU Chi-restraints excluded: chain B residue 2561 LEU Chi-restraints excluded: chain B residue 2590 VAL Chi-restraints excluded: chain B residue 2591 SER 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 2628 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 227 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 208 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 191 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A2715 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.121769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.089203 restraints weight = 34181.360| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 1.85 r_work: 0.2875 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.1789 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= 0.144 Angle : 0.613 18.107 32960 Z= 0.306 Chirality : 0.048 0.381 3762 Planarity : 0.004 0.052 4189 Dihedral : 7.352 58.664 4435 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 4.28 % Allowed : 14.91 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.16), residues: 2866 helix: -3.21 (0.44), residues: 73 sheet: -0.84 (0.15), residues: 1107 loop : -0.94 (0.16), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B2506 TYR 0.019 0.001 TYR A2210 PHE 0.025 0.002 PHE B2706 TRP 0.013 0.001 TRP B1483 HIS 0.004 0.001 HIS B1645 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 (24002) covalent geometry : angle 0.57754 / 0.30 (32682) SS BOND : bond 0.00270 / 0.17 ( 49) SS BOND : angle 0.96311 / 0.62 ( 98) hydrogen bonds : bond 0.03062 / 2.02 ( 730) hydrogen bonds : angle 6.31215 / 4.36 ( 1734) Misc. bond : bond 0.00018 / 0.01 ( 2) link_ALPHA1-3 : bond 0.01010 / 0.50 ( 4) link_ALPHA1-3 : angle 1.71390 / 1.00 ( 12) link_ALPHA1-6 : bond 0.00495 / 0.25 ( 4) link_ALPHA1-6 : angle 1.71578 / 1.04 ( 12) link_BETA1-4 : bond 0.00395 / 0.26 ( 24) link_BETA1-4 : angle 1.68843 / 1.07 ( 72) link_NAG-ASN : bond 0.00824 / 0.60 ( 26) link_NAG-ASN : angle 3.80473 / 2.40 ( 78) link_TRANS : bond 0.00064 / 0.03 ( 2) link_TRANS : angle 0.48178 / 0.29 ( 6) ********************** 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 230 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 123 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1363 HIS cc_start: 0.5716 (OUTLIER) cc_final: 0.5269 (t70) REVERT: A 1450 ASP cc_start: 0.8616 (t0) cc_final: 0.8415 (t70) REVERT: A 1585 MET cc_start: 0.9326 (OUTLIER) cc_final: 0.8893 (mtm) REVERT: A 1590 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8290 (ttt90) REVERT: A 1849 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8647 (tp) REVERT: A 1906 MET cc_start: 0.8928 (mtp) cc_final: 0.8349 (ttm) REVERT: A 2079 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8267 (mm) REVERT: A 2127 ARG cc_start: 0.9289 (OUTLIER) cc_final: 0.9039 (ptp-170) REVERT: A 2599 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8332 (tp) REVERT: B 1387 LYS cc_start: 0.5535 (mmtm) cc_final: 0.5158 (mmmt) REVERT: B 1408 MET cc_start: 0.7868 (mtm) cc_final: 0.7594 (mtm) REVERT: B 1560 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8961 (pp) REVERT: B 1598 ILE cc_start: 0.9220 (OUTLIER) cc_final: 0.8997 (tt) REVERT: B 1808 ASP cc_start: 0.9066 (OUTLIER) cc_final: 0.8637 (p0) REVERT: B 2079 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.7937 (mm) REVERT: B 2094 GLN cc_start: 0.8594 (tp40) cc_final: 0.8387 (tp40) REVERT: B 2127 ARG cc_start: 0.9272 (OUTLIER) cc_final: 0.8900 (ptm160) REVERT: B 2213 LYS cc_start: 0.9170 (OUTLIER) cc_final: 0.8812 (mtmt) REVERT: B 2242 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.7519 (tpp) REVERT: B 2307 GLN cc_start: 0.9027 (OUTLIER) cc_final: 0.7627 (mp10) REVERT: B 2426 ASP cc_start: 0.8497 (t0) cc_final: 0.8220 (t0) REVERT: B 2596 SER cc_start: 0.9057 (OUTLIER) cc_final: 0.8755 (t) REVERT: B 2649 ARG cc_start: 0.7169 (OUTLIER) cc_final: 0.6452 (mtt180) REVERT: B 2656 CYS cc_start: 0.5220 (OUTLIER) cc_final: 0.4986 (t) REVERT: B 2731 ASP cc_start: 0.6698 (OUTLIER) cc_final: 0.6167 (p0) outliers start: 107 outliers final: 84 residues processed: 207 average time/residue: 0.1642 time to fit residues: 52.7495 Evaluate side-chains 223 residues out of total 2502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 120 time to evaluate : 0.700 ------------------------------------------------------------------------------- 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 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 1836 ILE 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 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 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 2596 SER 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 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 1681 MET 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 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 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 2557 LEU Chi-restraints excluded: chain B residue 2561 LEU Chi-restraints excluded: chain B residue 2590 VAL Chi-restraints excluded: chain B residue 2591 SER 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 2628 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 2731 ASP 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 83 optimal weight: 2.9990 chunk 127 optimal weight: 9.9990 chunk 125 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 266 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A2715 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.120531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.087860 restraints weight = 34164.347| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 1.84 r_work: 0.2847 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 24113 Z= 0.199 Angle : 0.650 18.043 32960 Z= 0.324 Chirality : 0.050 0.377 3762 Planarity : 0.004 0.054 4189 Dihedral : 7.541 58.983 4435 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 4.32 % Allowed : 14.83 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.16), residues: 2866 helix: -3.23 (0.44), residues: 73 sheet: -0.96 (0.15), residues: 1117 loop : -1.01 (0.16), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B2506 TYR 0.021 0.002 TYR A2210 PHE 0.020 0.002 PHE A1625 TRP 0.012 0.002 TRP A1492 HIS 0.004 0.001 HIS B1645 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.20 (24002) covalent geometry : angle 0.61518 / 0.32 (32682) SS BOND : bond 0.00316 / 0.19 ( 49) SS BOND : angle 1.03310 / 0.67 ( 98) hydrogen bonds : bond 0.03298 / 2.17 ( 730) hydrogen bonds : angle 6.40992 / 4.43 ( 1734) Misc. bond : bond 0.00028 / 0.01 ( 2) link_ALPHA1-3 : bond 0.00947 / 0.47 ( 4) link_ALPHA1-3 : angle 1.76182 / 1.00 ( 12) link_ALPHA1-6 : bond 0.00477 / 0.24 ( 4) link_ALPHA1-6 : angle 1.69888 / 1.02 ( 12) link_BETA1-4 : bond 0.00401 / 0.27 ( 24) link_BETA1-4 : angle 1.76820 / 1.12 ( 72) link_NAG-ASN : bond 0.00770 / 0.54 ( 26) link_NAG-ASN : angle 3.84238 / 2.43 ( 78) link_TRANS : bond 0.00102 / 0.05 ( 2) link_TRANS : angle 0.58362 / 0.35 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5546.16 seconds wall clock time: 95 minutes 49.25 seconds (5749.25 seconds total)