Starting phenix.real_space_refine on Tue Aug 26 15:17:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rqb_19436/08_2025/8rqb_19436.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rqb_19436/08_2025/8rqb_19436.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rqb_19436/08_2025/8rqb_19436.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rqb_19436/08_2025/8rqb_19436.map" model { file = "/net/cci-nas-00/data/ceres_data/8rqb_19436/08_2025/8rqb_19436.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rqb_19436/08_2025/8rqb_19436.cif" } resolution = 1.09 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= 0.037 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 Fe 6 7.16 5 Zn 24 6.06 5 S 216 5.16 5 C 23328 2.51 5 N 6672 2.21 5 O 9750 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39996 Number of models: 1 Model: "" Number of chains: 72 Chain: "A" Number of atoms: 1556 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1275 Chain: "B" Number of atoms: 1556 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1275 Chain: "C" Number of atoms: 1556 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1275 Chain: "D" Number of atoms: 1556 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1275 Chain: "E" Number of atoms: 1556 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1275 Chain: "F" Number of atoms: 1556 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1275 Chain: "G" Number of atoms: 1556 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1275 Chain: "H" Number of atoms: 1556 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1275 Chain: "I" Number of atoms: 1556 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1275 Chain: "J" Number of atoms: 1556 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1275 Chain: "K" Number of atoms: 1556 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1275 Chain: "L" Number of atoms: 1556 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1275 Chain: "M" Number of atoms: 1556 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1275 Chain: "N" Number of atoms: 1556 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1275 Chain: "O" Number of atoms: 1556 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1275 Chain: "P" Number of atoms: 1556 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1275 Chain: "Q" Number of atoms: 1556 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1275 Chain: "R" Number of atoms: 1556 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1275 Chain: "S" Number of atoms: 1556 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1275 Chain: "T" Number of atoms: 1556 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1275 Chain: "U" Number of atoms: 1556 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1275 Chain: "V" Number of atoms: 1556 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1275 Chain: "W" Number of atoms: 1556 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1275 Chain: "X" Number of atoms: 1556 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1275 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 110 Classifications: {'water': 110} Link IDs: {None: 109} Chain: "B" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 109 Classifications: {'water': 109} Link IDs: {None: 108} Chain: "C" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 110 Classifications: {'water': 110} Link IDs: {None: 109} Chain: "D" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 110 Classifications: {'water': 110} Link IDs: {None: 109} Chain: "E" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 109 Classifications: {'water': 109} Link IDs: {None: 108} Chain: "F" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 109 Classifications: {'water': 109} Link IDs: {None: 108} Chain: "G" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 109 Classifications: {'water': 109} Link IDs: {None: 108} Chain: "H" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 110 Classifications: {'water': 110} Link IDs: {None: 109} Chain: "I" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 109 Classifications: {'water': 109} Link IDs: {None: 108} Chain: "J" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 109 Classifications: {'water': 109} Link IDs: {None: 108} Chain: "K" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 109 Classifications: {'water': 109} Link IDs: {None: 108} Chain: "L" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 109 Classifications: {'water': 109} Link IDs: {None: 108} Chain: "M" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 109 Classifications: {'water': 109} Link IDs: {None: 108} Chain: "N" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 109 Classifications: {'water': 109} Link IDs: {None: 108} Chain: "O" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 109 Classifications: {'water': 109} Link IDs: {None: 108} Chain: "P" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 109 Classifications: {'water': 109} Link IDs: {None: 108} Chain: "Q" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 109 Classifications: {'water': 109} Link IDs: {None: 108} Chain: "R" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 109 Classifications: {'water': 109} Link IDs: {None: 108} Chain: "S" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 109 Classifications: {'water': 109} Link IDs: {None: 108} Chain: "T" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 109 Classifications: {'water': 109} Link IDs: {None: 108} Chain: "U" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 110 Classifications: {'water': 110} Link IDs: {None: 109} Chain: "V" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 109 Classifications: {'water': 109} Link IDs: {None: 108} Chain: "W" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 110 Classifications: {'water': 110} Link IDs: {None: 109} Chain: "X" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 109 Classifications: {'water': 109} Link IDs: {None: 108} Residues with excluded nonbonded symmetry interactions: 514 residue: pdb=" N AARG A 22 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 22 " occ=0.50 residue: pdb=" N ATYR A 34 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR A 34 " occ=0.50 residue: pdb=" N ASER A 38 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 38 " occ=0.50 residue: pdb=" N ACYS A 39 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS A 39 " occ=0.50 residue: pdb=" N AARG A 63 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 63 " occ=0.50 residue: pdb=" N AGLU A 64 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU A 64 " occ=0.50 residue: pdb=" N AHIS A 65 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 65 " occ=0.50 residue: pdb=" N AGLU A 94 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU A 94 " occ=0.50 residue: pdb=" N ASER A 109 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 109 " occ=0.50 residue: pdb=" N ASER A 113 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 113 " occ=0.50 residue: pdb=" N APHE A 132 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 132 " occ=0.50 residue: pdb=" N AILE A 133 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE A 133 " occ=0.50 ... (remaining 502 not shown) Time building chain proxies: 12.95, per 1000 atoms: 0.32 Number of scatterers: 39996 At special positions: 0 Unit cell: (131.576, 131.576, 131.576, 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) Zn 24 29.99 Fe 6 26.01 S 216 16.00 O 9750 8.00 N 6672 7.00 C 23328 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.36 Conformation dependent library (CDL) restraints added in 2.8 seconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 202 " pdb="ZN ZN A 202 " - pdb=" ND1AHIS A 65 " pdb=" ZN B 202 " pdb="ZN ZN B 202 " - pdb=" ND1AHIS B 65 " pdb=" ZN C 202 " pdb="ZN ZN C 202 " - pdb=" ND1AHIS C 65 " pdb=" ZN D 201 " pdb="ZN ZN D 201 " - pdb=" ND1AHIS D 65 " pdb=" ZN E 201 " pdb="ZN ZN E 201 " - pdb=" ND1AHIS E 65 " pdb=" ZN F 201 " pdb="ZN ZN F 201 " - pdb=" ND1AHIS F 65 " pdb=" ZN G 201 " pdb="ZN ZN G 201 " - pdb=" ND1AHIS G 65 " pdb=" ZN H 201 " pdb="ZN ZN H 201 " - pdb=" ND1AHIS H 65 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" ND1AHIS I 65 " pdb=" ZN J 201 " pdb="ZN ZN J 201 " - pdb=" ND1AHIS J 65 " pdb=" ZN K 201 " pdb="ZN ZN K 201 " - pdb=" ND1AHIS K 65 " pdb=" ZN L 201 " pdb="ZN ZN L 201 " - pdb=" ND1AHIS L 65 " pdb=" ZN M 201 " pdb="ZN ZN M 201 " - pdb=" ND1AHIS M 65 " pdb=" ZN N 201 " pdb="ZN ZN N 201 " - pdb=" ND1AHIS N 65 " pdb=" ZN O 202 " pdb="ZN ZN O 202 " - pdb=" ND1AHIS O 65 " pdb=" ZN P 201 " pdb="ZN ZN P 201 " - pdb=" ND1AHIS P 65 " pdb=" ZN Q 201 " pdb="ZN ZN Q 201 " - pdb=" ND1AHIS Q 65 " pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" ND1AHIS R 65 " pdb=" ZN S 201 " pdb="ZN ZN S 201 " - pdb=" ND1AHIS S 65 " pdb=" ZN T 201 " pdb="ZN ZN T 201 " - pdb=" ND1AHIS T 65 " pdb=" ZN U 201 " pdb="ZN ZN U 201 " - pdb=" ND1AHIS U 65 " pdb=" ZN V 201 " pdb="ZN ZN V 201 " - pdb=" ND1AHIS V 65 " pdb=" ZN W 201 " pdb="ZN ZN W 201 " - pdb=" ND1AHIS W 65 " pdb=" ZN X 201 " pdb="ZN ZN X 201 " - pdb=" ND1AHIS X 65 " 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8736 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 78.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 13 through 42 Processing helix chain 'A' and resid 48 through 76 Processing helix chain 'A' and resid 95 through 124 Processing helix chain 'A' and resid 126 through 137 Processing helix chain 'A' and resid 137 through 159 Processing helix chain 'A' and resid 164 through 174 removed outlier: 4.331A pdb=" N TYR A 168 " --> pdb=" O GLY A 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 42 Processing helix chain 'B' and resid 48 through 76 Processing helix chain 'B' and resid 95 through 124 Processing helix chain 'B' and resid 126 through 137 Processing helix chain 'B' and resid 137 through 159 Processing helix chain 'B' and resid 164 through 174 removed outlier: 4.331A pdb=" N TYR B 168 " --> pdb=" O GLY B 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 42 Processing helix chain 'C' and resid 48 through 76 Processing helix chain 'C' and resid 95 through 124 Processing helix chain 'C' and resid 126 through 137 Processing helix chain 'C' and resid 137 through 159 Processing helix chain 'C' and resid 164 through 174 removed outlier: 4.331A pdb=" N TYR C 168 " --> pdb=" O GLY C 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 42 Processing helix chain 'D' and resid 48 through 76 Processing helix chain 'D' and resid 95 through 124 Processing helix chain 'D' and resid 126 through 137 Processing helix chain 'D' and resid 137 through 159 Processing helix chain 'D' and resid 164 through 174 removed outlier: 4.331A pdb=" N TYR D 168 " --> pdb=" O GLY D 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 42 Processing helix chain 'E' and resid 48 through 76 Processing helix chain 'E' and resid 95 through 124 Processing helix chain 'E' and resid 126 through 137 Processing helix chain 'E' and resid 137 through 159 Processing helix chain 'E' and resid 164 through 174 removed outlier: 4.331A pdb=" N TYR E 168 " --> pdb=" O GLY E 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 42 Processing helix chain 'F' and resid 48 through 76 Processing helix chain 'F' and resid 95 through 124 Processing helix chain 'F' and resid 126 through 137 Processing helix chain 'F' and resid 137 through 159 Processing helix chain 'F' and resid 164 through 174 removed outlier: 4.331A pdb=" N TYR F 168 " --> pdb=" O GLY F 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 42 Processing helix chain 'G' and resid 48 through 76 Processing helix chain 'G' and resid 95 through 124 Processing helix chain 'G' and resid 126 through 137 Processing helix chain 'G' and resid 137 through 159 Processing helix chain 'G' and resid 164 through 174 removed outlier: 4.332A pdb=" N TYR G 168 " --> pdb=" O GLY G 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 42 Processing helix chain 'H' and resid 48 through 76 Processing helix chain 'H' and resid 95 through 124 Processing helix chain 'H' and resid 126 through 137 Processing helix chain 'H' and resid 137 through 159 Processing helix chain 'H' and resid 164 through 174 removed outlier: 4.332A pdb=" N TYR H 168 " --> pdb=" O GLY H 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 42 Processing helix chain 'I' and resid 48 through 76 Processing helix chain 'I' and resid 95 through 124 Processing helix chain 'I' and resid 126 through 137 Processing helix chain 'I' and resid 137 through 159 Processing helix chain 'I' and resid 164 through 174 removed outlier: 4.330A pdb=" N TYR I 168 " --> pdb=" O GLY I 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 42 Processing helix chain 'J' and resid 48 through 76 Processing helix chain 'J' and resid 95 through 124 Processing helix chain 'J' and resid 126 through 137 Processing helix chain 'J' and resid 137 through 159 Processing helix chain 'J' and resid 164 through 174 removed outlier: 4.332A pdb=" N TYR J 168 " --> pdb=" O GLY J 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 13 through 42 Processing helix chain 'K' and resid 48 through 76 Processing helix chain 'K' and resid 95 through 124 Processing helix chain 'K' and resid 126 through 137 Processing helix chain 'K' and resid 137 through 159 Processing helix chain 'K' and resid 164 through 174 removed outlier: 4.330A pdb=" N TYR K 168 " --> pdb=" O GLY K 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 13 through 42 Processing helix chain 'L' and resid 48 through 76 Processing helix chain 'L' and resid 95 through 124 Processing helix chain 'L' and resid 126 through 137 Processing helix chain 'L' and resid 137 through 159 Processing helix chain 'L' and resid 164 through 174 removed outlier: 4.332A pdb=" N TYR L 168 " --> pdb=" O GLY L 164 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 42 Processing helix chain 'M' and resid 48 through 76 Processing helix chain 'M' and resid 95 through 124 Processing helix chain 'M' and resid 126 through 137 Processing helix chain 'M' and resid 137 through 159 Processing helix chain 'M' and resid 164 through 174 removed outlier: 4.332A pdb=" N TYR M 168 " --> pdb=" O GLY M 164 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 42 Processing helix chain 'N' and resid 48 through 76 Processing helix chain 'N' and resid 95 through 124 Processing helix chain 'N' and resid 126 through 137 Processing helix chain 'N' and resid 137 through 159 Processing helix chain 'N' and resid 164 through 174 removed outlier: 4.332A pdb=" N TYR N 168 " --> pdb=" O GLY N 164 " (cutoff:3.500A) Processing helix chain 'O' and resid 13 through 42 Processing helix chain 'O' and resid 48 through 76 Processing helix chain 'O' and resid 95 through 124 Processing helix chain 'O' and resid 126 through 137 Processing helix chain 'O' and resid 137 through 159 Processing helix chain 'O' and resid 164 through 174 removed outlier: 4.332A pdb=" N TYR O 168 " --> pdb=" O GLY O 164 " (cutoff:3.500A) Processing helix chain 'P' and resid 13 through 42 Processing helix chain 'P' and resid 48 through 76 Processing helix chain 'P' and resid 95 through 124 Processing helix chain 'P' and resid 126 through 137 Processing helix chain 'P' and resid 137 through 159 Processing helix chain 'P' and resid 164 through 174 removed outlier: 4.331A pdb=" N TYR P 168 " --> pdb=" O GLY P 164 " (cutoff:3.500A) Processing helix chain 'Q' and resid 13 through 42 Processing helix chain 'Q' and resid 48 through 76 Processing helix chain 'Q' and resid 95 through 124 Processing helix chain 'Q' and resid 126 through 137 Processing helix chain 'Q' and resid 137 through 159 Processing helix chain 'Q' and resid 164 through 174 removed outlier: 4.331A pdb=" N TYR Q 168 " --> pdb=" O GLY Q 164 " (cutoff:3.500A) Processing helix chain 'R' and resid 13 through 42 Processing helix chain 'R' and resid 48 through 76 Processing helix chain 'R' and resid 95 through 124 Processing helix chain 'R' and resid 126 through 137 Processing helix chain 'R' and resid 137 through 159 Processing helix chain 'R' and resid 164 through 174 removed outlier: 4.331A pdb=" N TYR R 168 " --> pdb=" O GLY R 164 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 42 Processing helix chain 'S' and resid 48 through 76 Processing helix chain 'S' and resid 95 through 124 Processing helix chain 'S' and resid 126 through 137 Processing helix chain 'S' and resid 137 through 159 Processing helix chain 'S' and resid 164 through 174 removed outlier: 4.331A pdb=" N TYR S 168 " --> pdb=" O GLY S 164 " (cutoff:3.500A) Processing helix chain 'T' and resid 13 through 42 Processing helix chain 'T' and resid 48 through 76 Processing helix chain 'T' and resid 95 through 124 Processing helix chain 'T' and resid 126 through 137 Processing helix chain 'T' and resid 137 through 159 Processing helix chain 'T' and resid 164 through 174 removed outlier: 4.331A pdb=" N TYR T 168 " --> pdb=" O GLY T 164 " (cutoff:3.500A) Processing helix chain 'U' and resid 13 through 42 Processing helix chain 'U' and resid 48 through 76 Processing helix chain 'U' and resid 95 through 124 Processing helix chain 'U' and resid 126 through 137 Processing helix chain 'U' and resid 137 through 159 Processing helix chain 'U' and resid 164 through 174 removed outlier: 4.330A pdb=" N TYR U 168 " --> pdb=" O GLY U 164 " (cutoff:3.500A) Processing helix chain 'V' and resid 13 through 42 Processing helix chain 'V' and resid 48 through 76 Processing helix chain 'V' and resid 95 through 124 Processing helix chain 'V' and resid 126 through 137 Processing helix chain 'V' and resid 137 through 159 Processing helix chain 'V' and resid 164 through 174 removed outlier: 4.332A pdb=" N TYR V 168 " --> pdb=" O GLY V 164 " (cutoff:3.500A) Processing helix chain 'W' and resid 13 through 42 Processing helix chain 'W' and resid 48 through 76 Processing helix chain 'W' and resid 95 through 124 Processing helix chain 'W' and resid 126 through 137 Processing helix chain 'W' and resid 137 through 159 Processing helix chain 'W' and resid 164 through 174 removed outlier: 4.331A pdb=" N TYR W 168 " --> pdb=" O GLY W 164 " (cutoff:3.500A) Processing helix chain 'X' and resid 13 through 42 Processing helix chain 'X' and resid 48 through 76 Processing helix chain 'X' and resid 95 through 124 Processing helix chain 'X' and resid 126 through 137 Processing helix chain 'X' and resid 137 through 159 Processing helix chain 'X' and resid 164 through 174 removed outlier: 4.331A pdb=" N TYR X 168 " --> pdb=" O GLY X 164 " (cutoff:3.500A) 3240 hydrogen bonds defined for protein. 9960 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: 7.83 Time building geometry restraints manager: 4.16 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: 11309 1.33 - 1.45: 9426 1.45 - 1.57: 17353 1.57 - 1.69: 0 1.69 - 1.81: 336 Bond restraints: 38424 Sorted by residual: bond pdb=" CA ASER V 38 " pdb=" CB ASER V 38 " ideal model delta sigma weight residual 1.528 1.491 0.038 1.56e-02 4.11e+03 5.81e+00 bond pdb=" CA ASER A 38 " pdb=" CB ASER A 38 " ideal model delta sigma weight residual 1.528 1.491 0.038 1.56e-02 4.11e+03 5.81e+00 bond pdb=" CA ASER T 38 " pdb=" CB ASER T 38 " ideal model delta sigma weight residual 1.528 1.491 0.037 1.56e-02 4.11e+03 5.77e+00 bond pdb=" CA ASER W 38 " pdb=" CB ASER W 38 " ideal model delta sigma weight residual 1.528 1.491 0.037 1.56e-02 4.11e+03 5.77e+00 bond pdb=" CA ASER S 38 " pdb=" CB ASER S 38 " ideal model delta sigma weight residual 1.528 1.491 0.037 1.56e-02 4.11e+03 5.77e+00 ... (remaining 38419 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 43306 1.30 - 2.61: 7443 2.61 - 3.91: 1047 3.91 - 5.21: 242 5.21 - 6.51: 42 Bond angle restraints: 52080 Sorted by residual: angle pdb=" CB GLU X 167 " pdb=" CG GLU X 167 " pdb=" CD GLU X 167 " ideal model delta sigma weight residual 112.60 119.11 -6.51 1.70e+00 3.46e-01 1.47e+01 angle pdb=" CB GLU M 167 " pdb=" CG GLU M 167 " pdb=" CD GLU M 167 " ideal model delta sigma weight residual 112.60 119.11 -6.51 1.70e+00 3.46e-01 1.47e+01 angle pdb=" CB GLU U 167 " pdb=" CG GLU U 167 " pdb=" CD GLU U 167 " ideal model delta sigma weight residual 112.60 119.11 -6.51 1.70e+00 3.46e-01 1.47e+01 angle pdb=" CB GLU R 167 " pdb=" CG GLU R 167 " pdb=" CD GLU R 167 " ideal model delta sigma weight residual 112.60 119.11 -6.51 1.70e+00 3.46e-01 1.47e+01 angle pdb=" CB GLU V 167 " pdb=" CG GLU V 167 " pdb=" CD GLU V 167 " ideal model delta sigma weight residual 112.60 119.10 -6.50 1.70e+00 3.46e-01 1.46e+01 ... (remaining 52075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.14: 21360 15.14 - 30.28: 1680 30.28 - 45.42: 354 45.42 - 60.56: 54 60.56 - 75.70: 72 Dihedral angle restraints: 23520 sinusoidal: 9744 harmonic: 13776 Sorted by residual: dihedral pdb=" CA VAL U 46 " pdb=" C VAL U 46 " pdb=" N ALA U 47 " pdb=" CA ALA U 47 " ideal model delta harmonic sigma weight residual 180.00 161.57 18.43 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA VAL A 46 " pdb=" C VAL A 46 " pdb=" N ALA A 47 " pdb=" CA ALA A 47 " ideal model delta harmonic sigma weight residual 180.00 161.58 18.42 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA VAL I 46 " pdb=" C VAL I 46 " pdb=" N ALA I 47 " pdb=" CA ALA I 47 " ideal model delta harmonic sigma weight residual 180.00 161.59 18.41 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 23517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 3354 0.049 - 0.098: 1340 0.098 - 0.147: 405 0.147 - 0.197: 133 0.197 - 0.246: 48 Chirality restraints: 5280 Sorted by residual: chirality pdb=" CA AGLU V 94 " pdb=" N AGLU V 94 " pdb=" C AGLU V 94 " pdb=" CB AGLU V 94 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA AGLU R 94 " pdb=" N AGLU R 94 " pdb=" C AGLU R 94 " pdb=" CB AGLU R 94 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA AGLU S 94 " pdb=" N AGLU S 94 " pdb=" C AGLU S 94 " pdb=" CB AGLU S 94 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.25 2.00e-01 2.50e+01 1.50e+00 ... (remaining 5277 not shown) Planarity restraints: 7008 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 137 " -0.063 2.00e-02 2.50e+03 3.30e-02 2.17e+01 pdb=" CG TYR D 137 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR D 137 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR D 137 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR D 137 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR D 137 " 0.018 2.00e-02 2.50e+03 pdb=" CZ TYR D 137 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR D 137 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR J 137 " -0.063 2.00e-02 2.50e+03 3.29e-02 2.17e+01 pdb=" CG TYR J 137 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR J 137 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR J 137 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR J 137 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR J 137 " 0.018 2.00e-02 2.50e+03 pdb=" CZ TYR J 137 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR J 137 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR U 137 " -0.063 2.00e-02 2.50e+03 3.29e-02 2.17e+01 pdb=" CG TYR U 137 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR U 137 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR U 137 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR U 137 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR U 137 " 0.018 2.00e-02 2.50e+03 pdb=" CZ TYR U 137 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR U 137 " -0.044 2.00e-02 2.50e+03 ... (remaining 7005 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 528 2.59 - 3.17: 39294 3.17 - 3.74: 83252 3.74 - 4.32: 114369 4.32 - 4.90: 178426 Nonbonded interactions: 415869 Sorted by model distance: nonbonded pdb="ZN ZN I 202 " pdb=" O HOH I 325 " model vdw 2.010 2.230 nonbonded pdb="ZN ZN M 201 " pdb=" O HOH M 325 " model vdw 2.010 2.230 nonbonded pdb="ZN ZN N 201 " pdb=" O HOH N 325 " model vdw 2.010 2.230 nonbonded pdb="ZN ZN F 201 " pdb=" O HOH F 325 " model vdw 2.010 2.230 nonbonded pdb="ZN ZN K 201 " pdb=" O HOH K 325 " model vdw 2.010 2.230 ... (remaining 415864 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 21 or resid 23 through 33 or resid 35 through 37 \ or resid 40 through 62 or resid 66 through 93 or resid 95 through 108 or resid \ 110 through 112 or resid 114 through 131 or resid 134 through 138 or resid 140 t \ hrough 143 or resid 145 through 155 or resid 157 through 171 or resid 174 throug \ h 176)) selection = (chain 'B' and (resid 5 through 21 or resid 23 through 33 or resid 35 through 37 \ or resid 40 through 62 or resid 66 through 93 or resid 95 through 108 or resid \ 110 through 112 or resid 114 through 131 or resid 134 through 138 or resid 140 t \ hrough 143 or resid 145 through 155 or resid 157 through 171 or resid 174 throug \ h 176)) selection = (chain 'C' and (resid 5 through 21 or resid 23 through 33 or resid 35 through 37 \ or resid 40 through 62 or resid 66 through 93 or resid 95 through 108 or resid \ 110 through 112 or resid 114 through 131 or resid 134 through 138 or resid 140 t \ hrough 143 or resid 145 through 155 or resid 157 through 171 or resid 174 throug \ h 176)) selection = (chain 'D' and (resid 5 through 21 or resid 23 through 33 or resid 35 through 37 \ or resid 40 through 62 or resid 66 through 93 or resid 95 through 108 or resid \ 110 through 112 or resid 114 through 131 or resid 134 through 138 or resid 140 t \ hrough 143 or resid 145 through 155 or resid 157 through 171 or resid 174 throug \ h 176)) selection = (chain 'E' and (resid 5 through 21 or resid 23 through 33 or resid 35 through 37 \ or resid 40 through 62 or resid 66 through 93 or resid 95 through 108 or resid \ 110 through 112 or resid 114 through 131 or resid 134 through 138 or resid 140 t \ hrough 143 or resid 145 through 155 or resid 157 through 171 or resid 174 throug \ h 176)) selection = (chain 'F' and (resid 5 through 21 or resid 23 through 33 or resid 35 through 37 \ or resid 40 through 62 or resid 66 through 93 or resid 95 through 108 or resid \ 110 through 112 or resid 114 through 131 or resid 134 through 138 or resid 140 t \ hrough 143 or resid 145 through 155 or resid 157 through 171 or resid 174 throug \ h 176)) selection = (chain 'G' and (resid 5 through 21 or resid 23 through 33 or resid 35 through 37 \ or resid 40 through 62 or resid 66 through 93 or resid 95 through 108 or resid \ 110 through 112 or resid 114 through 131 or resid 134 through 138 or resid 140 t \ hrough 143 or resid 145 through 155 or resid 157 through 171 or resid 174 throug \ h 176)) selection = (chain 'H' and (resid 5 through 21 or resid 23 through 33 or resid 35 through 37 \ or resid 40 through 62 or resid 66 through 93 or resid 95 through 108 or resid \ 110 through 112 or resid 114 through 131 or resid 134 through 138 or resid 140 t \ hrough 143 or resid 145 through 155 or resid 157 through 171 or resid 174 throug \ h 176)) selection = (chain 'I' and (resid 5 through 21 or resid 23 through 33 or resid 35 through 37 \ or resid 40 through 62 or resid 66 through 93 or resid 95 through 108 or resid \ 110 through 112 or resid 114 through 131 or resid 134 through 138 or resid 140 t \ hrough 143 or resid 145 through 155 or resid 157 through 171 or resid 174 throug \ h 176)) selection = (chain 'J' and (resid 5 through 21 or resid 23 through 33 or resid 35 through 37 \ or resid 40 through 62 or resid 66 through 93 or resid 95 through 108 or resid \ 110 through 112 or resid 114 through 131 or resid 134 through 138 or resid 140 t \ hrough 143 or resid 145 through 155 or resid 157 through 171 or resid 174 throug \ h 176)) selection = (chain 'K' and (resid 5 through 21 or resid 23 through 33 or resid 35 through 37 \ or resid 40 through 62 or resid 66 through 93 or resid 95 through 108 or resid \ 110 through 112 or resid 114 through 131 or resid 134 through 138 or resid 140 t \ hrough 143 or resid 145 through 155 or resid 157 through 171 or resid 174 throug \ h 176)) selection = (chain 'L' and (resid 5 through 21 or resid 23 through 33 or resid 35 through 37 \ or resid 40 through 62 or resid 66 through 93 or resid 95 through 108 or resid \ 110 through 112 or resid 114 through 131 or resid 134 through 138 or resid 140 t \ hrough 143 or resid 145 through 155 or resid 157 through 171 or resid 174 throug \ h 176)) selection = (chain 'M' and (resid 5 through 21 or resid 23 through 33 or resid 35 through 37 \ or resid 40 through 62 or resid 66 through 93 or resid 95 through 108 or resid \ 110 through 112 or resid 114 through 131 or resid 134 through 138 or resid 140 t \ hrough 143 or resid 145 through 155 or resid 157 through 171 or resid 174 throug \ h 176)) selection = (chain 'N' and (resid 5 through 21 or resid 23 through 33 or resid 35 through 37 \ or resid 40 through 62 or resid 66 through 93 or resid 95 through 108 or resid \ 110 through 112 or resid 114 through 131 or resid 134 through 138 or resid 140 t \ hrough 143 or resid 145 through 155 or resid 157 through 171 or resid 174 throug \ h 176)) selection = (chain 'O' and (resid 5 through 21 or resid 23 through 33 or resid 35 through 37 \ or resid 40 through 62 or resid 66 through 93 or resid 95 through 108 or resid \ 110 through 112 or resid 114 through 131 or resid 134 through 138 or resid 140 t \ hrough 143 or resid 145 through 155 or resid 157 through 171 or resid 174 throug \ h 176)) selection = (chain 'P' and (resid 5 through 21 or resid 23 through 33 or resid 35 through 37 \ or resid 40 through 62 or resid 66 through 93 or resid 95 through 108 or resid \ 110 through 112 or resid 114 through 131 or resid 134 through 138 or resid 140 t \ hrough 143 or resid 145 through 155 or resid 157 through 171 or resid 174 throug \ h 176)) selection = (chain 'Q' and (resid 5 through 21 or resid 23 through 33 or resid 35 through 37 \ or resid 40 through 62 or resid 66 through 93 or resid 95 through 108 or resid \ 110 through 112 or resid 114 through 131 or resid 134 through 138 or resid 140 t \ hrough 143 or resid 145 through 155 or resid 157 through 171 or resid 174 throug \ h 176)) selection = (chain 'R' and (resid 5 through 21 or resid 23 through 33 or resid 35 through 37 \ or resid 40 through 62 or resid 66 through 93 or resid 95 through 108 or resid \ 110 through 112 or resid 114 through 131 or resid 134 through 138 or resid 140 t \ hrough 143 or resid 145 through 155 or resid 157 through 171 or resid 174 throug \ h 176)) selection = (chain 'S' and (resid 5 through 21 or resid 23 through 33 or resid 35 through 37 \ or resid 40 through 62 or resid 66 through 93 or resid 95 through 108 or resid \ 110 through 112 or resid 114 through 131 or resid 134 through 138 or resid 140 t \ hrough 143 or resid 145 through 155 or resid 157 through 171 or resid 174 throug \ h 176)) selection = (chain 'T' and (resid 5 through 21 or resid 23 through 33 or resid 35 through 37 \ or resid 40 through 62 or resid 66 through 93 or resid 95 through 108 or resid \ 110 through 112 or resid 114 through 131 or resid 134 through 138 or resid 140 t \ hrough 143 or resid 145 through 155 or resid 157 through 171 or resid 174 throug \ h 176)) selection = (chain 'U' and (resid 5 through 21 or resid 23 through 33 or resid 35 through 37 \ or resid 40 through 62 or resid 66 through 93 or resid 95 through 108 or resid \ 110 through 112 or resid 114 through 131 or resid 134 through 138 or resid 140 t \ hrough 143 or resid 145 through 155 or resid 157 through 171 or resid 174 throug \ h 176)) selection = (chain 'V' and (resid 5 through 21 or resid 23 through 33 or resid 35 through 37 \ or resid 40 through 62 or resid 66 through 93 or resid 95 through 108 or resid \ 110 through 112 or resid 114 through 131 or resid 134 through 138 or resid 140 t \ hrough 143 or resid 145 through 155 or resid 157 through 171 or resid 174 throug \ h 176)) selection = (chain 'W' and (resid 5 through 21 or resid 23 through 33 or resid 35 through 37 \ or resid 40 through 62 or resid 66 through 93 or resid 95 through 108 or resid \ 110 through 112 or resid 114 through 131 or resid 134 through 138 or resid 140 t \ hrough 143 or resid 145 through 155 or resid 157 through 171 or resid 174 throug \ h 176)) selection = (chain 'X' and (resid 5 through 21 or resid 23 through 33 or resid 35 through 37 \ or resid 40 through 62 or resid 66 through 93 or resid 95 through 108 or resid \ 110 through 112 or resid 114 through 131 or resid 134 through 138 or resid 140 t \ hrough 143 or resid 145 through 155 or resid 157 through 171 or resid 174 throug \ h 176)) } 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=0.25 max=1.00 mean=0.91 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: 7.750 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: 0.030 Extract box with map and model: 2.410 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 46.420 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.110 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:6.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 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 : 0.007 0.043 38448 Z= 0.480 Angle : 1.041 6.514 52080 Z= 0.690 Chirality : 0.062 0.246 5280 Planarity : 0.008 0.049 7008 Dihedral : 12.157 75.701 14784 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.18 % Allowed : 1.78 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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 aren not related in a simple way. whole: 3.51 (0.11), residues: 5064 helix: 2.80 (0.07), residues: 4104 sheet: None (None), residues: 0 loop : 0.13 (0.22), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG A 79 TYR 0.063 0.010 TYR D 137 PHE 0.032 0.009 PHE I 41 TRP 0.025 0.009 TRP P 93 HIS 0.017 0.004 HIS F 60 Details of bonding type rmsd covalent geometry : bond 0.00706 (38424) covalent geometry : angle 1.04095 (52080) hydrogen bonds : bond 0.12353 ( 3240) hydrogen bonds : angle 4.73383 ( 9960) metal coordination : bond 0.01451 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 874 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 826 time to evaluate : 1.403 Fit side-chains REVERT: C 157 LYS cc_start: 0.6745 (mttt) cc_final: 0.6508 (mtpt) REVERT: D 90 ARG cc_start: 0.5944 (mtt-85) cc_final: 0.5659 (mtt90) REVERT: F 157 LYS cc_start: 0.6744 (mttt) cc_final: 0.6514 (mtpt) REVERT: G 157 LYS cc_start: 0.6803 (mttt) cc_final: 0.6580 (mtpt) REVERT: H 157 LYS cc_start: 0.6774 (mttt) cc_final: 0.6552 (mtpt) REVERT: I 157 LYS cc_start: 0.6805 (mttt) cc_final: 0.6589 (mtpt) REVERT: K 157 LYS cc_start: 0.6803 (mttt) cc_final: 0.6569 (mtpt) REVERT: M 157 LYS cc_start: 0.6763 (mttt) cc_final: 0.6516 (mtpt) REVERT: P 157 LYS cc_start: 0.6782 (mttt) cc_final: 0.6552 (mtpt) REVERT: R 157 LYS cc_start: 0.6795 (mttt) cc_final: 0.6571 (mtpt) REVERT: U 157 LYS cc_start: 0.6736 (mttt) cc_final: 0.6500 (mtpt) REVERT: W 157 LYS cc_start: 0.6816 (mttt) cc_final: 0.6593 (mtpt) outliers start: 48 outliers final: 0 residues processed: 826 average time/residue: 0.9200 time to fit residues: 883.9272 Evaluate side-chains 782 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 782 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 30.0000 chunk 388 optimal weight: 50.0000 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 20.0000 chunk 401 optimal weight: 30.0000 chunk 155 optimal weight: 50.0000 chunk 244 optimal weight: 7.9990 overall best weight: 9.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 125 ASN ** A 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN C 112 GLN ** C 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 GLN ** D 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 GLN ** G 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** J 75 GLN ** J 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** K 75 GLN ** K 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** L 125 ASN ** L 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** M 75 GLN M 112 GLN ** M 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** N 125 ASN ** N 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** P 75 GLN ** P 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Q 75 GLN ** Q 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** R 75 GLN ** R 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** T 75 GLN ** T 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** U 112 GLN ** U 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** V 125 ASN ** V 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.155631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.122643 restraints weight = 130960.192| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 0.75 r_work: 0.3140 rms_B_bonded: 0.90 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 1.25 restraints_weight: 0.2500 r_work: 0.2919 rms_B_bonded: 2.45 restraints_weight: 0.1250 r_work: 0.2885 rms_B_bonded: 4.70 restraints_weight: 0.0625 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2836 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2836 r_free = 0.2836 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2835 r_free = 0.2835 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2835 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 38448 Z= 0.298 Angle : 0.881 7.926 52080 Z= 0.489 Chirality : 0.045 0.175 5280 Planarity : 0.007 0.052 7008 Dihedral : 4.596 18.853 5304 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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 aren not related in a simple way. whole: 4.05 (0.11), residues: 5064 helix: 3.16 (0.07), residues: 4104 sheet: None (None), residues: 0 loop : 0.42 (0.23), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.002 ARG N 79 TYR 0.037 0.005 TYR Q 137 PHE 0.042 0.006 PHE P 41 TRP 0.023 0.005 TRP M 93 HIS 0.013 0.004 HIS I 60 Details of bonding type rmsd covalent geometry : bond 0.00618 (38424) covalent geometry : angle 0.88138 (52080) hydrogen bonds : bond 0.07898 ( 3240) hydrogen bonds : angle 4.31784 ( 9960) metal coordination : bond 0.00994 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 710 time to evaluate : 1.432 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 710 average time/residue: 0.9133 time to fit residues: 754.6912 Evaluate side-chains 710 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 710 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 136 optimal weight: 50.0000 chunk 219 optimal weight: 7.9990 chunk 375 optimal weight: 30.0000 chunk 31 optimal weight: 20.0000 chunk 44 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 349 optimal weight: 50.0000 chunk 46 optimal weight: 9.9990 chunk 145 optimal weight: 0.9980 chunk 329 optimal weight: 10.0000 overall best weight: 4.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.156046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.123792 restraints weight = 139769.406| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 0.77 r_work: 0.3158 rms_B_bonded: 0.91 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 1.34 restraints_weight: 0.2500 r_work: 0.2945 rms_B_bonded: 2.42 restraints_weight: 0.1250 r_work: 0.2910 rms_B_bonded: 4.71 restraints_weight: 0.0625 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2861 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2861 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 38448 Z= 0.209 Angle : 0.725 7.321 52080 Z= 0.403 Chirality : 0.040 0.136 5280 Planarity : 0.005 0.040 7008 Dihedral : 4.556 18.056 5304 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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 aren not related in a simple way. whole: 4.43 (0.11), residues: 5064 helix: 3.44 (0.07), residues: 4104 sheet: None (None), residues: 0 loop : 0.45 (0.22), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 79 TYR 0.027 0.003 TYR V 137 PHE 0.033 0.004 PHE A 41 TRP 0.019 0.004 TRP A 93 HIS 0.010 0.003 HIS J 60 Details of bonding type rmsd covalent geometry : bond 0.00400 (38424) covalent geometry : angle 0.72479 (52080) hydrogen bonds : bond 0.06981 ( 3240) hydrogen bonds : angle 4.13001 ( 9960) metal coordination : bond 0.00316 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 739 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 739 time to evaluate : 1.695 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 739 average time/residue: 1.0561 time to fit residues: 910.2004 Evaluate side-chains 665 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 665 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 315 optimal weight: 0.9980 chunk 309 optimal weight: 20.0000 chunk 358 optimal weight: 30.0000 chunk 30 optimal weight: 5.9990 chunk 319 optimal weight: 5.9990 chunk 326 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 32 optimal weight: 0.1980 chunk 237 optimal weight: 6.9990 chunk 308 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.159228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.127110 restraints weight = 141223.345| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 0.78 r_work: 0.3204 rms_B_bonded: 0.92 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 1.35 restraints_weight: 0.2500 r_work: 0.3000 rms_B_bonded: 2.38 restraints_weight: 0.1250 r_work: 0.2964 rms_B_bonded: 4.22 restraints_weight: 0.0625 r_work: 0.2964 rms_B_bonded: 4.22 restraints_weight: 0.0312 r_work: 0.2964 rms_B_bonded: 4.22 restraints_weight: 0.0156 r_work: 0.2964 rms_B_bonded: 4.22 restraints_weight: 0.0078 r_work: 0.2964 rms_B_bonded: 4.22 restraints_weight: 0.0039 r_work: 0.2964 rms_B_bonded: 4.22 restraints_weight: 0.0020 r_work: 0.2964 rms_B_bonded: 4.22 restraints_weight: 0.0010 r_work: 0.2964 rms_B_bonded: 4.22 restraints_weight: 0.0005 r_work: 0.2964 rms_B_bonded: 4.22 restraints_weight: 0.0002 r_work: 0.2964 rms_B_bonded: 4.22 restraints_weight: 0.0001 r_work: 0.2964 rms_B_bonded: 4.22 restraints_weight: 0.0001 r_work: 0.2964 rms_B_bonded: 4.22 restraints_weight: 0.0000 r_work: 0.2964 rms_B_bonded: 4.22 restraints_weight: 0.0000 r_work: 0.2964 rms_B_bonded: 4.22 restraints_weight: 0.0000 r_work: 0.2964 rms_B_bonded: 4.22 restraints_weight: 0.0000 r_work: 0.2964 rms_B_bonded: 4.22 restraints_weight: 0.0000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2921 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2921 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 38448 Z= 0.159 Angle : 0.611 6.126 52080 Z= 0.339 Chirality : 0.037 0.116 5280 Planarity : 0.004 0.024 7008 Dihedral : 4.483 18.746 5304 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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 aren not related in a simple way. whole: 4.94 (0.11), residues: 5064 helix: 3.81 (0.07), residues: 4104 sheet: None (None), residues: 0 loop : 0.52 (0.23), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 79 TYR 0.021 0.002 TYR R 137 PHE 0.026 0.003 PHE A 41 TRP 0.016 0.003 TRP I 93 HIS 0.013 0.002 HIS V 60 Details of bonding type rmsd covalent geometry : bond 0.00283 (38424) covalent geometry : angle 0.61128 (52080) hydrogen bonds : bond 0.05950 ( 3240) hydrogen bonds : angle 3.91612 ( 9960) metal coordination : bond 0.00037 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 725 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 725 time to evaluate : 1.574 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 725 average time/residue: 0.9758 time to fit residues: 831.2121 Evaluate side-chains 656 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 656 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 280 optimal weight: 2.9990 chunk 1 optimal weight: 30.0000 chunk 395 optimal weight: 5.9990 chunk 134 optimal weight: 0.9980 chunk 112 optimal weight: 30.0000 chunk 389 optimal weight: 0.1980 chunk 39 optimal weight: 20.0000 chunk 211 optimal weight: 3.9990 chunk 380 optimal weight: 20.0000 chunk 384 optimal weight: 50.0000 chunk 84 optimal weight: 6.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.157407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.124997 restraints weight = 141367.349| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 0.86 r_work: 0.3179 rms_B_bonded: 0.91 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 1.34 restraints_weight: 0.2500 r_work: 0.2973 rms_B_bonded: 2.34 restraints_weight: 0.1250 r_work: 0.2934 rms_B_bonded: 4.54 restraints_weight: 0.0625 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2892 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2892 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 38448 Z= 0.181 Angle : 0.660 6.617 52080 Z= 0.367 Chirality : 0.038 0.122 5280 Planarity : 0.004 0.026 7008 Dihedral : 4.509 18.540 5304 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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 aren not related in a simple way. whole: 4.78 (0.11), residues: 5064 helix: 3.70 (0.07), residues: 4104 sheet: None (None), residues: 0 loop : 0.48 (0.23), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG J 79 TYR 0.023 0.003 TYR M 137 PHE 0.029 0.004 PHE E 41 TRP 0.017 0.004 TRP I 93 HIS 0.005 0.001 HIS V 128 Details of bonding type rmsd covalent geometry : bond 0.00334 (38424) covalent geometry : angle 0.66043 (52080) hydrogen bonds : bond 0.06442 ( 3240) hydrogen bonds : angle 4.00265 ( 9960) metal coordination : bond 0.00146 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 682 time to evaluate : 1.621 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 682 average time/residue: 0.9038 time to fit residues: 725.1295 Evaluate side-chains 672 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 672 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 21 optimal weight: 6.9990 chunk 5 optimal weight: 20.0000 chunk 212 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 312 optimal weight: 8.9990 chunk 120 optimal weight: 50.0000 chunk 0 optimal weight: 60.0000 chunk 367 optimal weight: 30.0000 chunk 337 optimal weight: 50.0000 chunk 107 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.155231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.123138 restraints weight = 137869.041| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 0.77 r_work: 0.3148 rms_B_bonded: 0.91 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 1.26 restraints_weight: 0.2500 r_work: 0.2937 rms_B_bonded: 2.32 restraints_weight: 0.1250 r_work: 0.2901 rms_B_bonded: 4.59 restraints_weight: 0.0625 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2852 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2852 r_free = 0.2852 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2852 r_free = 0.2852 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2852 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 38448 Z= 0.242 Angle : 0.779 7.549 52080 Z= 0.432 Chirality : 0.042 0.167 5280 Planarity : 0.006 0.031 7008 Dihedral : 4.558 18.300 5304 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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 aren not related in a simple way. whole: 4.44 (0.11), residues: 5064 helix: 3.45 (0.07), residues: 4104 sheet: None (None), residues: 0 loop : 0.45 (0.22), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG U 79 TYR 0.029 0.004 TYR M 137 PHE 0.036 0.005 PHE V 41 TRP 0.019 0.004 TRP S 93 HIS 0.007 0.003 HIS Q 57 Details of bonding type rmsd covalent geometry : bond 0.00484 (38424) covalent geometry : angle 0.77909 (52080) hydrogen bonds : bond 0.07352 ( 3240) hydrogen bonds : angle 4.18525 ( 9960) metal coordination : bond 0.00533 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 675 time to evaluate : 0.949 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 675 average time/residue: 0.6289 time to fit residues: 498.1563 Evaluate side-chains 670 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 670 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 145 optimal weight: 5.9990 chunk 217 optimal weight: 3.9990 chunk 310 optimal weight: 4.9990 chunk 163 optimal weight: 30.0000 chunk 263 optimal weight: 7.9990 chunk 134 optimal weight: 4.9990 chunk 252 optimal weight: 20.0000 chunk 390 optimal weight: 6.9990 chunk 142 optimal weight: 10.0000 chunk 288 optimal weight: 6.9990 chunk 342 optimal weight: 40.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.155559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.123384 restraints weight = 140723.110| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 0.77 r_work: 0.3152 rms_B_bonded: 0.91 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 1.33 restraints_weight: 0.2500 r_work: 0.2944 rms_B_bonded: 2.32 restraints_weight: 0.1250 r_work: 0.2909 rms_B_bonded: 4.04 restraints_weight: 0.0625 r_work: 0.2909 rms_B_bonded: 4.04 restraints_weight: 0.0312 r_work: 0.2909 rms_B_bonded: 4.04 restraints_weight: 0.0156 r_work: 0.2909 rms_B_bonded: 4.04 restraints_weight: 0.0078 r_work: 0.2909 rms_B_bonded: 4.04 restraints_weight: 0.0039 r_work: 0.2909 rms_B_bonded: 4.04 restraints_weight: 0.0020 r_work: 0.2909 rms_B_bonded: 4.04 restraints_weight: 0.0010 r_work: 0.2909 rms_B_bonded: 4.04 restraints_weight: 0.0005 r_work: 0.2909 rms_B_bonded: 4.04 restraints_weight: 0.0002 r_work: 0.2909 rms_B_bonded: 4.04 restraints_weight: 0.0001 r_work: 0.2909 rms_B_bonded: 4.04 restraints_weight: 0.0001 r_work: 0.2909 rms_B_bonded: 4.04 restraints_weight: 0.0000 r_work: 0.2909 rms_B_bonded: 4.04 restraints_weight: 0.0000 r_work: 0.2909 rms_B_bonded: 4.04 restraints_weight: 0.0000 r_work: 0.2909 rms_B_bonded: 4.04 restraints_weight: 0.0000 r_work: 0.2909 rms_B_bonded: 4.04 restraints_weight: 0.0000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2866 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2866 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 38448 Z= 0.229 Angle : 0.755 7.429 52080 Z= 0.419 Chirality : 0.041 0.157 5280 Planarity : 0.005 0.034 7008 Dihedral : 4.557 18.293 5304 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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 aren not related in a simple way. whole: 4.39 (0.11), residues: 5064 helix: 3.41 (0.07), residues: 4104 sheet: None (None), residues: 0 loop : 0.46 (0.22), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 79 TYR 0.028 0.003 TYR R 137 PHE 0.034 0.005 PHE N 41 TRP 0.019 0.004 TRP S 93 HIS 0.008 0.002 HIS I 57 Details of bonding type rmsd covalent geometry : bond 0.00451 (38424) covalent geometry : angle 0.75483 (52080) hydrogen bonds : bond 0.07220 ( 3240) hydrogen bonds : angle 4.16956 ( 9960) metal coordination : bond 0.00422 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 640 time to evaluate : 0.926 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 640 average time/residue: 0.5766 time to fit residues: 434.8981 Evaluate side-chains 640 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 640 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 172 optimal weight: 20.0000 chunk 269 optimal weight: 40.0000 chunk 185 optimal weight: 6.9990 chunk 308 optimal weight: 50.0000 chunk 387 optimal weight: 8.9990 chunk 73 optimal weight: 30.0000 chunk 110 optimal weight: 3.9990 chunk 156 optimal weight: 0.7980 chunk 288 optimal weight: 6.9990 chunk 365 optimal weight: 2.9990 chunk 398 optimal weight: 4.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.156352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.124202 restraints weight = 138732.097| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 0.77 r_work: 0.3164 rms_B_bonded: 0.91 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 1.31 restraints_weight: 0.2500 r_work: 0.2945 rms_B_bonded: 2.52 restraints_weight: 0.1250 r_work: 0.2917 rms_B_bonded: 4.95 restraints_weight: 0.0625 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2874 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2874 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 38448 Z= 0.203 Angle : 0.709 7.078 52080 Z= 0.394 Chirality : 0.039 0.137 5280 Planarity : 0.005 0.032 7008 Dihedral : 4.540 17.883 5304 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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 aren not related in a simple way. whole: 4.52 (0.11), residues: 5064 helix: 3.50 (0.07), residues: 4104 sheet: None (None), residues: 0 loop : 0.49 (0.23), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG U 79 TYR 0.025 0.003 TYR V 137 PHE 0.032 0.004 PHE I 41 TRP 0.018 0.004 TRP B 93 HIS 0.007 0.002 HIS W 57 Details of bonding type rmsd covalent geometry : bond 0.00390 (38424) covalent geometry : angle 0.70924 (52080) hydrogen bonds : bond 0.06830 ( 3240) hydrogen bonds : angle 4.09334 ( 9960) metal coordination : bond 0.00284 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 640 time to evaluate : 0.853 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 640 average time/residue: 0.5502 time to fit residues: 415.0383 Evaluate side-chains 640 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 640 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 106 optimal weight: 6.9990 chunk 182 optimal weight: 9.9990 chunk 73 optimal weight: 30.0000 chunk 71 optimal weight: 0.6980 chunk 232 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 155 optimal weight: 0.9990 chunk 345 optimal weight: 30.0000 chunk 15 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.159500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.127368 restraints weight = 138556.244| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 0.78 r_work: 0.3208 rms_B_bonded: 0.92 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 1.35 restraints_weight: 0.2500 r_work: 0.3001 rms_B_bonded: 2.39 restraints_weight: 0.1250 r_work: 0.2967 rms_B_bonded: 4.66 restraints_weight: 0.0625 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2924 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2924 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 38448 Z= 0.160 Angle : 0.611 6.086 52080 Z= 0.339 Chirality : 0.037 0.114 5280 Planarity : 0.004 0.024 7008 Dihedral : 4.489 18.817 5304 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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 aren not related in a simple way. whole: 4.96 (0.11), residues: 5064 helix: 3.82 (0.07), residues: 4104 sheet: None (None), residues: 0 loop : 0.56 (0.23), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG O 79 TYR 0.020 0.002 TYR I 137 PHE 0.025 0.003 PHE V 41 TRP 0.017 0.003 TRP A 93 HIS 0.004 0.001 HIS W 57 Details of bonding type rmsd covalent geometry : bond 0.00288 (38424) covalent geometry : angle 0.61088 (52080) hydrogen bonds : bond 0.05902 ( 3240) hydrogen bonds : angle 3.88158 ( 9960) metal coordination : bond 0.00011 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 680 time to evaluate : 0.833 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 680 average time/residue: 0.5181 time to fit residues: 417.9130 Evaluate side-chains 652 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 652 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 278 optimal weight: 20.0000 chunk 78 optimal weight: 30.0000 chunk 280 optimal weight: 0.8980 chunk 140 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 124 optimal weight: 30.0000 chunk 347 optimal weight: 6.9990 chunk 56 optimal weight: 40.0000 chunk 245 optimal weight: 1.9990 chunk 295 optimal weight: 20.0000 chunk 47 optimal weight: 10.0000 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.156964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.124505 restraints weight = 140616.811| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 0.86 r_work: 0.3171 rms_B_bonded: 0.92 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 1.33 restraints_weight: 0.2500 r_work: 0.2965 rms_B_bonded: 2.38 restraints_weight: 0.1250 r_work: 0.2932 rms_B_bonded: 4.28 restraints_weight: 0.0625 r_work: 0.2932 rms_B_bonded: 4.28 restraints_weight: 0.0312 r_work: 0.2932 rms_B_bonded: 4.28 restraints_weight: 0.0156 r_work: 0.2932 rms_B_bonded: 4.28 restraints_weight: 0.0078 r_work: 0.2932 rms_B_bonded: 4.28 restraints_weight: 0.0039 r_work: 0.2932 rms_B_bonded: 4.28 restraints_weight: 0.0020 r_work: 0.2932 rms_B_bonded: 4.28 restraints_weight: 0.0010 r_work: 0.2932 rms_B_bonded: 4.28 restraints_weight: 0.0005 r_work: 0.2932 rms_B_bonded: 4.28 restraints_weight: 0.0002 r_work: 0.2932 rms_B_bonded: 4.28 restraints_weight: 0.0001 r_work: 0.2932 rms_B_bonded: 4.28 restraints_weight: 0.0001 r_work: 0.2932 rms_B_bonded: 4.28 restraints_weight: 0.0000 r_work: 0.2932 rms_B_bonded: 4.28 restraints_weight: 0.0000 r_work: 0.2932 rms_B_bonded: 4.28 restraints_weight: 0.0000 r_work: 0.2932 rms_B_bonded: 4.28 restraints_weight: 0.0000 r_work: 0.2932 rms_B_bonded: 4.28 restraints_weight: 0.0000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2889 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2889 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 38448 Z= 0.195 Angle : 0.689 6.793 52080 Z= 0.383 Chirality : 0.039 0.130 5280 Planarity : 0.005 0.027 7008 Dihedral : 4.533 18.027 5304 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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 aren not related in a simple way. whole: 4.68 (0.11), residues: 5064 helix: 3.62 (0.07), residues: 4104 sheet: None (None), residues: 0 loop : 0.49 (0.23), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG U 79 TYR 0.023 0.003 TYR K 137 PHE 0.031 0.004 PHE S 41 TRP 0.018 0.004 TRP W 93 HIS 0.005 0.002 HIS I 128 Details of bonding type rmsd covalent geometry : bond 0.00372 (38424) covalent geometry : angle 0.68869 (52080) hydrogen bonds : bond 0.06658 ( 3240) hydrogen bonds : angle 4.03219 ( 9960) metal coordination : bond 0.00200 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 645 time to evaluate : 0.818 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 645 average time/residue: 0.5472 time to fit residues: 415.0893 Evaluate side-chains 645 residues out of total 3240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 645 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 156 optimal weight: 0.6980 chunk 88 optimal weight: 0.8980 chunk 254 optimal weight: 20.0000 chunk 162 optimal weight: 4.9990 chunk 365 optimal weight: 0.0020 chunk 374 optimal weight: 1.9990 chunk 58 optimal weight: 20.0000 chunk 62 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 320 optimal weight: 40.0000 chunk 154 optimal weight: 40.0000 overall best weight: 1.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 173 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 173 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.159578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.127420 restraints weight = 141932.363| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 0.79 r_work: 0.3209 rms_B_bonded: 0.92 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 1.36 restraints_weight: 0.2500 r_work: 0.3001 rms_B_bonded: 2.47 restraints_weight: 0.1250 r_work: 0.2976 rms_B_bonded: 3.70 restraints_weight: 0.0625 r_work: 0.2976 rms_B_bonded: 3.70 restraints_weight: 0.0312 r_work: 0.2976 rms_B_bonded: 3.70 restraints_weight: 0.0156 r_work: 0.2976 rms_B_bonded: 3.70 restraints_weight: 0.0078 r_work: 0.2976 rms_B_bonded: 3.70 restraints_weight: 0.0039 r_work: 0.2976 rms_B_bonded: 3.70 restraints_weight: 0.0020 r_work: 0.2976 rms_B_bonded: 3.70 restraints_weight: 0.0010 r_work: 0.2976 rms_B_bonded: 3.70 restraints_weight: 0.0005 r_work: 0.2976 rms_B_bonded: 3.70 restraints_weight: 0.0002 r_work: 0.2976 rms_B_bonded: 3.70 restraints_weight: 0.0001 r_work: 0.2976 rms_B_bonded: 3.70 restraints_weight: 0.0001 r_work: 0.2976 rms_B_bonded: 3.70 restraints_weight: 0.0000 r_work: 0.2976 rms_B_bonded: 3.70 restraints_weight: 0.0000 r_work: 0.2976 rms_B_bonded: 3.70 restraints_weight: 0.0000 r_work: 0.2976 rms_B_bonded: 3.70 restraints_weight: 0.0000 r_work: 0.2976 rms_B_bonded: 3.70 restraints_weight: 0.0000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2933 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2932 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 38448 Z= 0.161 Angle : 0.612 6.065 52080 Z= 0.341 Chirality : 0.037 0.114 5280 Planarity : 0.004 0.024 7008 Dihedral : 4.476 18.687 5304 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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 aren not related in a simple way. whole: 4.98 (0.11), residues: 5064 helix: 3.83 (0.07), residues: 4104 sheet: None (None), residues: 0 loop : 0.57 (0.23), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 79 TYR 0.020 0.002 TYR L 137 PHE 0.025 0.003 PHE I 41 TRP 0.017 0.003 TRP I 93 HIS 0.004 0.001 HIS L 57 Details of bonding type rmsd covalent geometry : bond 0.00294 (38424) covalent geometry : angle 0.61195 (52080) hydrogen bonds : bond 0.05922 ( 3240) hydrogen bonds : angle 3.86974 ( 9960) metal coordination : bond 0.00051 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 78384.62 seconds wall clock time: 1317 minutes 26.07 seconds (79046.07 seconds total)