Starting phenix.real_space_refine on Tue Dec 31 04:09:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8emq_28259/12_2024/8emq_28259.cif Found real_map, /net/cci-nas-00/data/ceres_data/8emq_28259/12_2024/8emq_28259.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8emq_28259/12_2024/8emq_28259.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8emq_28259/12_2024/8emq_28259.map" model { file = "/net/cci-nas-00/data/ceres_data/8emq_28259/12_2024/8emq_28259.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8emq_28259/12_2024/8emq_28259.cif" } resolution = 1.66 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 34800 atoms to isotropic. 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 192 5.16 5 C 21816 2.51 5 N 6072 2.21 5 O 9695 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 168 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 37805 Number of models: 1 Model: "" Number of chains: 72 Chain: "A" Number of atoms: 1450 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: 1392 Chain: "B" Number of atoms: 1450 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: 1392 Chain: "C" Number of atoms: 1450 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: 1392 Chain: "D" Number of atoms: 1450 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: 1392 Chain: "E" Number of atoms: 1450 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: 1392 Chain: "F" Number of atoms: 1450 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: 1392 Chain: "G" Number of atoms: 1450 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: 1392 Chain: "H" Number of atoms: 1450 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: 1392 Chain: "I" Number of atoms: 1450 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: 1392 Chain: "J" Number of atoms: 1450 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: 1392 Chain: "K" Number of atoms: 1450 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: 1392 Chain: "L" Number of atoms: 1450 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: 1392 Chain: "M" Number of atoms: 1450 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: 1392 Chain: "N" Number of atoms: 1450 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: 1392 Chain: "O" Number of atoms: 1450 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: 1392 Chain: "P" Number of atoms: 1450 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: 1392 Chain: "Q" Number of atoms: 1450 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: 1392 Chain: "R" Number of atoms: 1450 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: 1392 Chain: "S" Number of atoms: 1450 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: 1392 Chain: "T" Number of atoms: 1450 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: 1392 Chain: "U" Number of atoms: 1450 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: 1392 Chain: "V" Number of atoms: 1450 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: 1392 Chain: "W" Number of atoms: 1450 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: 1392 Chain: "X" Number of atoms: 1450 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: 1392 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" 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: "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: 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: "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: 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: "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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 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: 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: "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: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "B" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "C" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "D" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "E" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "F" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "G" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "H" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "I" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "J" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "K" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 123 Classifications: {'water': 123} Link IDs: {None: 122} Chain: "L" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "M" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "N" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "O" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "P" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "Q" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "R" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "S" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "T" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "U" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "V" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "W" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "X" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Residues with excluded nonbonded symmetry interactions: 126 residue: pdb=" N AGLU A 94 " occ=0.49 ... (16 atoms not shown) pdb=" OE2BGLU A 94 " occ=0.51 residue: pdb=" N AILE A 133 " occ=0.65 ... (14 atoms not shown) pdb=" CD1BILE A 133 " occ=0.35 residue: pdb=" N AGLU A 140 " occ=0.46 ... (16 atoms not shown) pdb=" OE2BGLU A 140 " occ=0.54 residue: pdb=" N ASER A 144 " occ=0.55 ... (10 atoms not shown) pdb=" OG BSER A 144 " occ=0.45 residue: pdb=" N ALYS A 172 " occ=0.65 ... (16 atoms not shown) pdb=" NZ BLYS A 172 " occ=0.35 residue: pdb=" N AGLU B 94 " occ=0.48 ... (16 atoms not shown) pdb=" OE2BGLU B 94 " occ=0.52 residue: pdb=" N AILE B 133 " occ=0.64 ... (14 atoms not shown) pdb=" CD1BILE B 133 " occ=0.36 residue: pdb=" N AGLU B 140 " occ=0.48 ... (16 atoms not shown) pdb=" OE2BGLU B 140 " occ=0.52 residue: pdb=" N ASER B 144 " occ=0.55 ... (10 atoms not shown) pdb=" OG BSER B 144 " occ=0.45 residue: pdb=" N ALYS B 172 " occ=0.65 ... (16 atoms not shown) pdb=" NZ BLYS B 172 " occ=0.35 residue: pdb=" N AGLU C 94 " occ=0.49 ... (16 atoms not shown) pdb=" OE2BGLU C 94 " occ=0.51 residue: pdb=" N AILE C 133 " occ=0.66 ... (14 atoms not shown) pdb=" CD1BILE C 133 " occ=0.34 ... (remaining 114 not shown) Time building chain proxies: 27.46, per 1000 atoms: 0.73 Number of scatterers: 37805 At special positions: 0 Unit cell: (132.379, 132.379, 132.379, 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 192 16.00 O 9695 8.00 N 6072 7.00 C 21816 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: 7.23 Conformation dependent library (CDL) restraints added in 5.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 201 " pdb="ZN ZN A 201 " - pdb=" ND1 HIS A 65 " pdb=" ZN B 202 " pdb="ZN ZN B 202 " - pdb=" ND1 HIS B 65 " pdb=" ZN C 201 " pdb="ZN ZN C 201 " - pdb=" ND1 HIS C 65 " pdb=" ZN D 201 " pdb="ZN ZN D 201 " - pdb=" ND1 HIS D 65 " pdb=" ZN E 202 " pdb="ZN ZN E 202 " - pdb=" ND1 HIS E 65 " pdb=" ZN F 201 " pdb="ZN ZN F 201 " - pdb=" ND1 HIS F 65 " pdb=" ZN G 201 " pdb="ZN ZN G 201 " - pdb=" ND1 HIS G 65 " pdb=" ZN H 201 " pdb="ZN ZN H 201 " - pdb=" ND1 HIS H 65 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" ND1 HIS I 65 " pdb=" ZN J 202 " pdb="ZN ZN J 202 " - pdb=" ND1 HIS J 65 " pdb=" ZN K 201 " pdb="ZN ZN K 201 " - pdb=" ND1 HIS K 65 " pdb=" ZN L 201 " pdb="ZN ZN L 201 " - pdb=" ND1 HIS L 65 " pdb=" ZN M 201 " pdb="ZN ZN M 201 " - pdb=" ND1 HIS M 65 " pdb=" ZN N 201 " pdb="ZN ZN N 201 " - pdb=" ND1 HIS N 65 " pdb=" ZN O 201 " pdb="ZN ZN O 201 " - pdb=" ND1 HIS O 65 " pdb=" ZN P 201 " pdb="ZN ZN P 201 " - pdb=" ND1 HIS P 65 " pdb=" ZN Q 201 " pdb="ZN ZN Q 201 " - pdb=" ND1 HIS Q 65 " pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" ND1 HIS R 65 " pdb=" ZN S 201 " pdb="ZN ZN S 201 " - pdb=" ND1 HIS S 65 " pdb=" ZN T 201 " pdb="ZN ZN T 201 " - pdb=" ND1 HIS T 65 " pdb=" ZN U 201 " pdb="ZN ZN U 201 " - pdb=" ND1 HIS U 65 " pdb=" ZN V 201 " pdb="ZN ZN V 201 " - pdb=" ND1 HIS V 65 " pdb=" ZN W 201 " pdb="ZN ZN W 201 " - pdb=" ND1 HIS W 65 " pdb=" ZN X 201 " pdb="ZN ZN X 201 " - pdb=" ND1 HIS X 65 " 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8160 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 77.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.99 Creating SS restraints... Processing helix chain 'A' and resid 13 through 41 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: 4.226A pdb=" N TYR A 168 " --> pdb=" O GLY A 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 41 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: 4.226A pdb=" N TYR B 168 " --> pdb=" O GLY B 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 41 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: 4.226A pdb=" N TYR C 168 " --> pdb=" O GLY C 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 41 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: 4.226A pdb=" N TYR D 168 " --> pdb=" O GLY D 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 41 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: 4.226A pdb=" N TYR E 168 " --> pdb=" O GLY E 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 41 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: 4.226A pdb=" N TYR F 168 " --> pdb=" O GLY F 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 41 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: 4.226A pdb=" N TYR G 168 " --> pdb=" O GLY G 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 41 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: 4.226A pdb=" N TYR H 168 " --> pdb=" O GLY H 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 41 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: 4.226A pdb=" N TYR I 168 " --> pdb=" O GLY I 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 41 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: 4.226A pdb=" N TYR J 168 " --> pdb=" O GLY J 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 13 through 41 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: 4.226A pdb=" N TYR K 168 " --> pdb=" O GLY K 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 13 through 41 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: 4.226A pdb=" N TYR L 168 " --> pdb=" O GLY L 164 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 41 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: 4.226A pdb=" N TYR M 168 " --> pdb=" O GLY M 164 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 41 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: 4.226A pdb=" N TYR N 168 " --> pdb=" O GLY N 164 " (cutoff:3.500A) Processing helix chain 'O' and resid 13 through 41 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: 4.226A pdb=" N TYR O 168 " --> pdb=" O GLY O 164 " (cutoff:3.500A) Processing helix chain 'P' and resid 13 through 41 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: 4.226A pdb=" N TYR P 168 " --> pdb=" O GLY P 164 " (cutoff:3.500A) Processing helix chain 'Q' and resid 13 through 41 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: 4.226A pdb=" N TYR Q 168 " --> pdb=" O GLY Q 164 " (cutoff:3.500A) Processing helix chain 'R' and resid 13 through 41 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: 4.226A pdb=" N TYR R 168 " --> pdb=" O GLY R 164 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 41 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: 4.226A pdb=" N TYR S 168 " --> pdb=" O GLY S 164 " (cutoff:3.500A) Processing helix chain 'T' and resid 13 through 41 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: 4.226A pdb=" N TYR T 168 " --> pdb=" O GLY T 164 " (cutoff:3.500A) Processing helix chain 'U' and resid 13 through 41 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: 4.226A pdb=" N TYR U 168 " --> pdb=" O GLY U 164 " (cutoff:3.500A) Processing helix chain 'V' and resid 13 through 41 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: 4.226A pdb=" N TYR V 168 " --> pdb=" O GLY V 164 " (cutoff:3.500A) Processing helix chain 'W' and resid 13 through 41 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: 4.226A pdb=" N TYR W 168 " --> pdb=" O GLY W 164 " (cutoff:3.500A) Processing helix chain 'X' and resid 13 through 41 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: 4.226A pdb=" N TYR X 168 " --> pdb=" O GLY X 164 " (cutoff:3.500A) 2736 hydrogen bonds defined for protein. 8304 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: 9.90 Time building geometry restraints manager: 8.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 8785 1.33 - 1.45: 8782 1.45 - 1.58: 17737 1.58 - 1.71: 0 1.71 - 1.83: 312 Bond restraints: 35616 Sorted by residual: bond pdb=" C ARG J 63 " pdb=" N GLU J 64 " ideal model delta sigma weight residual 1.335 1.225 0.110 1.31e-02 5.83e+03 7.08e+01 bond pdb=" C ARG R 63 " pdb=" N GLU R 64 " ideal model delta sigma weight residual 1.335 1.225 0.110 1.31e-02 5.83e+03 7.08e+01 bond pdb=" C ARG D 63 " pdb=" N GLU D 64 " ideal model delta sigma weight residual 1.335 1.225 0.110 1.31e-02 5.83e+03 7.08e+01 bond pdb=" C ARG I 63 " pdb=" N GLU I 64 " ideal model delta sigma weight residual 1.335 1.225 0.110 1.31e-02 5.83e+03 7.08e+01 bond pdb=" C ARG K 63 " pdb=" N GLU K 64 " ideal model delta sigma weight residual 1.335 1.225 0.110 1.31e-02 5.83e+03 7.08e+01 ... (remaining 35611 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 44425 2.13 - 4.27: 3096 4.27 - 6.40: 408 6.40 - 8.54: 71 8.54 - 10.67: 72 Bond angle restraints: 48072 Sorted by residual: angle pdb=" C BILE D 133 " pdb=" N GLU D 134 " pdb=" CA GLU D 134 " ideal model delta sigma weight residual 120.44 131.08 -10.64 1.30e+00 5.92e-01 6.70e+01 angle pdb=" C BILE S 133 " pdb=" N GLU S 134 " pdb=" CA GLU S 134 " ideal model delta sigma weight residual 120.44 131.08 -10.64 1.30e+00 5.92e-01 6.70e+01 angle pdb=" C BILE K 133 " pdb=" N GLU K 134 " pdb=" CA GLU K 134 " ideal model delta sigma weight residual 120.44 131.08 -10.64 1.30e+00 5.92e-01 6.70e+01 angle pdb=" C BILE L 133 " pdb=" N GLU L 134 " pdb=" CA GLU L 134 " ideal model delta sigma weight residual 120.44 131.08 -10.64 1.30e+00 5.92e-01 6.70e+01 angle pdb=" C BILE H 133 " pdb=" N GLU H 134 " pdb=" CA GLU H 134 " ideal model delta sigma weight residual 120.44 131.08 -10.64 1.30e+00 5.92e-01 6.70e+01 ... (remaining 48067 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.04: 20976 28.04 - 56.08: 648 56.08 - 84.12: 144 84.12 - 112.16: 0 112.16 - 140.20: 24 Dihedral angle restraints: 21792 sinusoidal: 9072 harmonic: 12720 Sorted by residual: dihedral pdb=" CB BGLU H 140 " pdb=" CG BGLU H 140 " pdb=" CD BGLU H 140 " pdb=" OE1BGLU H 140 " ideal model delta sinusoidal sigma weight residual 0.00 140.20 -140.20 1 3.00e+01 1.11e-03 1.89e+01 dihedral pdb=" CB BGLU C 140 " pdb=" CG BGLU C 140 " pdb=" CD BGLU C 140 " pdb=" OE1BGLU C 140 " ideal model delta sinusoidal sigma weight residual 0.00 140.20 -140.20 1 3.00e+01 1.11e-03 1.89e+01 dihedral pdb=" CB BGLU A 140 " pdb=" CG BGLU A 140 " pdb=" CD BGLU A 140 " pdb=" OE1BGLU A 140 " ideal model delta sinusoidal sigma weight residual 0.00 140.20 -140.20 1 3.00e+01 1.11e-03 1.89e+01 ... (remaining 21789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 3336 0.068 - 0.135: 1416 0.135 - 0.202: 144 0.202 - 0.270: 72 0.270 - 0.337: 24 Chirality restraints: 4992 Sorted by residual: chirality pdb=" CB VAL O 8 " pdb=" CA VAL O 8 " pdb=" CG1 VAL O 8 " pdb=" CG2 VAL O 8 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" CB VAL D 8 " pdb=" CA VAL D 8 " pdb=" CG1 VAL D 8 " pdb=" CG2 VAL D 8 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" CB VAL H 8 " pdb=" CA VAL H 8 " pdb=" CG1 VAL H 8 " pdb=" CG2 VAL H 8 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.84e+00 ... (remaining 4989 not shown) Planarity restraints: 6384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 137 " -0.092 2.00e-02 2.50e+03 4.93e-02 4.86e+01 pdb=" CG TYR D 137 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR D 137 " 0.058 2.00e-02 2.50e+03 pdb=" CD2 TYR D 137 " 0.030 2.00e-02 2.50e+03 pdb=" CE1 TYR D 137 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR D 137 " 0.034 2.00e-02 2.50e+03 pdb=" CZ TYR D 137 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR D 137 " -0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR S 137 " -0.092 2.00e-02 2.50e+03 4.93e-02 4.86e+01 pdb=" CG TYR S 137 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR S 137 " 0.058 2.00e-02 2.50e+03 pdb=" CD2 TYR S 137 " 0.030 2.00e-02 2.50e+03 pdb=" CE1 TYR S 137 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR S 137 " 0.034 2.00e-02 2.50e+03 pdb=" CZ TYR S 137 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR S 137 " -0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR O 137 " -0.092 2.00e-02 2.50e+03 4.93e-02 4.86e+01 pdb=" CG TYR O 137 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR O 137 " 0.058 2.00e-02 2.50e+03 pdb=" CD2 TYR O 137 " 0.030 2.00e-02 2.50e+03 pdb=" CE1 TYR O 137 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR O 137 " 0.034 2.00e-02 2.50e+03 pdb=" CZ TYR O 137 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR O 137 " -0.065 2.00e-02 2.50e+03 ... (remaining 6381 not shown) Histogram of nonbonded interaction distances: 0.73 - 1.57: 96 1.57 - 2.40: 324 2.40 - 3.23: 43119 3.23 - 4.07: 122976 4.07 - 4.90: 212416 Warning: very small nonbonded interaction distances. Nonbonded interactions: 378931 Sorted by model distance: nonbonded pdb=" NH2 ARG C 63 " pdb=" NH2 ARG E 63 " model vdw 0.733 3.200 nonbonded pdb=" NH2 ARG G 63 " pdb=" NH2 ARG U 63 " model vdw 0.733 3.200 nonbonded pdb=" NH2 ARG A 63 " pdb=" NH2 ARG K 63 " model vdw 0.733 3.200 nonbonded pdb=" NH2 ARG D 63 " pdb=" NH2 ARG Q 63 " model vdw 0.733 3.200 nonbonded pdb=" NH2 ARG F 63 " pdb=" NH2 ARG N 63 " model vdw 0.733 3.200 ... (remaining 378926 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 93 or resid 95 through 132 or resid 134 through \ 139 or resid 141 through 143 or resid 145 through 171 or resid 173 through 176)) \ selection = (chain 'B' and (resid 5 through 93 or resid 95 through 132 or resid 134 through \ 139 or resid 141 through 143 or resid 145 through 171 or resid 173 through 176)) \ selection = (chain 'C' and (resid 5 through 93 or resid 95 through 132 or resid 134 through \ 139 or resid 141 through 143 or resid 145 through 171 or resid 173 through 176)) \ selection = (chain 'D' and (resid 5 through 93 or resid 95 through 132 or resid 134 through \ 139 or resid 141 through 143 or resid 145 through 171 or resid 173 through 176)) \ selection = (chain 'E' and (resid 5 through 93 or resid 95 through 132 or resid 134 through \ 139 or resid 141 through 143 or resid 145 through 171 or resid 173 through 176)) \ selection = (chain 'F' and (resid 5 through 93 or resid 95 through 132 or resid 134 through \ 139 or resid 141 through 143 or resid 145 through 171 or resid 173 through 176)) \ selection = (chain 'G' and (resid 5 through 93 or resid 95 through 132 or resid 134 through \ 139 or resid 141 through 143 or resid 145 through 171 or resid 173 through 176)) \ selection = (chain 'H' and (resid 5 through 93 or resid 95 through 132 or resid 134 through \ 139 or resid 141 through 143 or resid 145 through 171 or resid 173 through 176)) \ selection = (chain 'I' and (resid 5 through 93 or resid 95 through 132 or resid 134 through \ 139 or resid 141 through 143 or resid 145 through 171 or resid 173 through 176)) \ selection = (chain 'J' and (resid 5 through 93 or resid 95 through 132 or resid 134 through \ 139 or resid 141 through 143 or resid 145 through 171 or resid 173 through 176)) \ selection = (chain 'K' and (resid 5 through 93 or resid 95 through 132 or resid 134 through \ 139 or resid 141 through 143 or resid 145 through 171 or resid 173 through 176)) \ selection = (chain 'L' and (resid 5 through 93 or resid 95 through 132 or resid 134 through \ 139 or resid 141 through 143 or resid 145 through 171 or resid 173 through 176)) \ selection = (chain 'M' and (resid 5 through 93 or resid 95 through 132 or resid 134 through \ 139 or resid 141 through 143 or resid 145 through 171 or resid 173 through 176)) \ selection = (chain 'N' and (resid 5 through 93 or resid 95 through 132 or resid 134 through \ 139 or resid 141 through 143 or resid 145 through 171 or resid 173 through 176)) \ selection = (chain 'O' and (resid 5 through 93 or resid 95 through 132 or resid 134 through \ 139 or resid 141 through 143 or resid 145 through 171 or resid 173 through 176)) \ selection = (chain 'P' and (resid 5 through 93 or resid 95 through 132 or resid 134 through \ 139 or resid 141 through 143 or resid 145 through 171 or resid 173 through 176)) \ selection = (chain 'Q' and (resid 5 through 93 or resid 95 through 132 or resid 134 through \ 139 or resid 141 through 143 or resid 145 through 171 or resid 173 through 176)) \ selection = (chain 'R' and (resid 5 through 93 or resid 95 through 132 or resid 134 through \ 139 or resid 141 through 143 or resid 145 through 171 or resid 173 through 176)) \ selection = (chain 'S' and (resid 5 through 93 or resid 95 through 132 or resid 134 through \ 139 or resid 141 through 143 or resid 145 through 171 or resid 173 through 176)) \ selection = (chain 'T' and (resid 5 through 93 or resid 95 through 132 or resid 134 through \ 139 or resid 141 through 143 or resid 145 through 171 or resid 173 through 176)) \ selection = (chain 'U' and (resid 5 through 93 or resid 95 through 132 or resid 134 through \ 139 or resid 141 through 143 or resid 145 through 171 or resid 173 through 176)) \ selection = (chain 'V' and (resid 5 through 93 or resid 95 through 132 or resid 134 through \ 139 or resid 141 through 143 or resid 145 through 171 or resid 173 through 176)) \ selection = (chain 'W' and (resid 5 through 93 or resid 95 through 132 or resid 134 through \ 139 or resid 141 through 143 or resid 145 through 171 or resid 173 through 176)) \ selection = (chain 'X' and (resid 5 through 93 or resid 95 through 132 or resid 134 through \ 139 or resid 141 through 143 or resid 145 through 171 or resid 173 through 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=0.22 max=1.00 mean=0.97 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: 6.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.330 Construct map_model_manager: 0.030 Extract box with map and model: 1.270 Check model and map are aligned: 0.200 Set scattering table: 0.280 Process input model: 82.770 Find NCS groups from input model: 1.720 Set up NCS constraints: 0.180 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:10.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 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 : 0.011 0.110 35616 Z= 0.705 Angle : 1.312 10.670 48072 Z= 0.887 Chirality : 0.072 0.337 4992 Planarity : 0.009 0.049 6384 Dihedral : 15.252 140.203 13632 Min Nonbonded Distance : 0.733 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 1.91 % Allowed : 3.18 % Favored : 94.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.12), residues: 4440 helix: 1.86 (0.08), residues: 3480 sheet: None (None), residues: 0 loop : 0.72 (0.23), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.009 TRP H 93 HIS 0.013 0.002 HIS L 60 PHE 0.028 0.007 PHE V 51 TYR 0.092 0.013 TYR O 137 ARG 0.015 0.002 ARG T 79 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1008 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 936 time to evaluate : 3.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLN cc_start: 0.7751 (mm-40) cc_final: 0.6946 (mp10) REVERT: A 49 LYS cc_start: 0.8089 (mttm) cc_final: 0.7849 (mtmm) REVERT: A 53 LYS cc_start: 0.8155 (ttpp) cc_final: 0.7755 (ttpp) REVERT: A 68 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.7572 (ttmm) REVERT: A 92 ASP cc_start: 0.7575 (t0) cc_final: 0.7197 (t0) REVERT: A 119 LYS cc_start: 0.7397 (ttmp) cc_final: 0.7143 (ttpt) REVERT: B 14 GLN cc_start: 0.7742 (mm-40) cc_final: 0.6934 (mp10) REVERT: B 49 LYS cc_start: 0.8092 (mttm) cc_final: 0.7852 (mtmm) REVERT: B 53 LYS cc_start: 0.8154 (ttpp) cc_final: 0.7755 (ttpp) REVERT: B 68 LYS cc_start: 0.7808 (OUTLIER) cc_final: 0.7573 (ttmm) REVERT: B 92 ASP cc_start: 0.7577 (t0) cc_final: 0.7199 (t0) REVERT: B 119 LYS cc_start: 0.7400 (ttmp) cc_final: 0.7145 (ttpt) REVERT: C 14 GLN cc_start: 0.7741 (mm-40) cc_final: 0.6935 (mp10) REVERT: C 49 LYS cc_start: 0.8092 (mttm) cc_final: 0.7852 (mtmm) REVERT: C 53 LYS cc_start: 0.8155 (ttpp) cc_final: 0.7754 (ttpp) REVERT: C 68 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7569 (ttmm) REVERT: C 92 ASP cc_start: 0.7585 (t0) cc_final: 0.7211 (t0) REVERT: C 119 LYS cc_start: 0.7396 (ttmp) cc_final: 0.7142 (ttpt) REVERT: D 14 GLN cc_start: 0.7743 (mm-40) cc_final: 0.6937 (mp10) REVERT: D 49 LYS cc_start: 0.8089 (mttm) cc_final: 0.7850 (mtmm) REVERT: D 53 LYS cc_start: 0.8155 (ttpp) cc_final: 0.7755 (ttpp) REVERT: D 68 LYS cc_start: 0.7810 (OUTLIER) cc_final: 0.7576 (ttmm) REVERT: D 92 ASP cc_start: 0.7578 (t0) cc_final: 0.7200 (t0) REVERT: D 119 LYS cc_start: 0.7398 (ttmp) cc_final: 0.7145 (ttpt) REVERT: E 14 GLN cc_start: 0.7743 (mm-40) cc_final: 0.6936 (mp10) REVERT: E 49 LYS cc_start: 0.8093 (mttm) cc_final: 0.7853 (mtmm) REVERT: E 53 LYS cc_start: 0.8157 (ttpp) cc_final: 0.7757 (ttpp) REVERT: E 68 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7571 (ttmm) REVERT: E 92 ASP cc_start: 0.7583 (t0) cc_final: 0.7210 (t0) REVERT: E 119 LYS cc_start: 0.7393 (ttmp) cc_final: 0.7140 (ttpt) REVERT: F 14 GLN cc_start: 0.7762 (mm-40) cc_final: 0.6957 (mp10) REVERT: F 49 LYS cc_start: 0.8089 (mttm) cc_final: 0.7850 (mtmm) REVERT: F 53 LYS cc_start: 0.8154 (ttpp) cc_final: 0.7754 (ttpp) REVERT: F 68 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7572 (ttmm) REVERT: F 92 ASP cc_start: 0.7584 (t0) cc_final: 0.7210 (t0) REVERT: F 119 LYS cc_start: 0.7398 (ttmp) cc_final: 0.7144 (ttpt) REVERT: G 14 GLN cc_start: 0.7744 (mm-40) cc_final: 0.6937 (mp10) REVERT: G 49 LYS cc_start: 0.8090 (mttm) cc_final: 0.7851 (mtmm) REVERT: G 53 LYS cc_start: 0.8153 (ttpp) cc_final: 0.7754 (ttpp) REVERT: G 68 LYS cc_start: 0.7808 (OUTLIER) cc_final: 0.7574 (ttmm) REVERT: G 92 ASP cc_start: 0.7576 (t0) cc_final: 0.7197 (t0) REVERT: G 119 LYS cc_start: 0.7401 (ttmp) cc_final: 0.7147 (ttpt) REVERT: H 14 GLN cc_start: 0.7748 (mm-40) cc_final: 0.6945 (mp10) REVERT: H 49 LYS cc_start: 0.8091 (mttm) cc_final: 0.7853 (mtmm) REVERT: H 53 LYS cc_start: 0.8156 (ttpp) cc_final: 0.7755 (ttpp) REVERT: H 68 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7558 (tttm) REVERT: H 92 ASP cc_start: 0.7584 (t0) cc_final: 0.7208 (t0) REVERT: H 119 LYS cc_start: 0.7394 (ttmp) cc_final: 0.7139 (ttpt) REVERT: I 14 GLN cc_start: 0.7742 (mm-40) cc_final: 0.6936 (mp10) REVERT: I 49 LYS cc_start: 0.8089 (mttm) cc_final: 0.7850 (mtmm) REVERT: I 53 LYS cc_start: 0.8152 (ttpp) cc_final: 0.7752 (ttpp) REVERT: I 68 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7569 (ttmm) REVERT: I 92 ASP cc_start: 0.7581 (t0) cc_final: 0.7205 (t0) REVERT: I 119 LYS cc_start: 0.7400 (ttmp) cc_final: 0.7146 (ttpt) REVERT: J 14 GLN cc_start: 0.7745 (mm-40) cc_final: 0.6937 (mp10) REVERT: J 49 LYS cc_start: 0.8090 (mttm) cc_final: 0.7849 (mtmm) REVERT: J 53 LYS cc_start: 0.8153 (ttpp) cc_final: 0.7753 (ttpp) REVERT: J 68 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.7572 (ttmm) REVERT: J 92 ASP cc_start: 0.7577 (t0) cc_final: 0.7200 (t0) REVERT: J 119 LYS cc_start: 0.7401 (ttmp) cc_final: 0.7146 (ttpt) REVERT: K 14 GLN cc_start: 0.7763 (mm-40) cc_final: 0.6957 (mp10) REVERT: K 49 LYS cc_start: 0.8093 (mttm) cc_final: 0.7852 (mtmm) REVERT: K 53 LYS cc_start: 0.8155 (ttpp) cc_final: 0.7754 (ttpp) REVERT: K 68 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.7565 (ttmm) REVERT: K 92 ASP cc_start: 0.7584 (t0) cc_final: 0.7211 (t0) REVERT: K 119 LYS cc_start: 0.7396 (ttmp) cc_final: 0.7141 (ttpt) REVERT: L 14 GLN cc_start: 0.7764 (mm-40) cc_final: 0.6957 (mp10) REVERT: L 49 LYS cc_start: 0.8091 (mttm) cc_final: 0.7849 (mtmm) REVERT: L 53 LYS cc_start: 0.8155 (ttpp) cc_final: 0.7755 (ttpp) REVERT: L 68 LYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7569 (ttmm) REVERT: L 92 ASP cc_start: 0.7584 (t0) cc_final: 0.7211 (t0) REVERT: L 119 LYS cc_start: 0.7397 (ttmp) cc_final: 0.7143 (ttpt) REVERT: M 14 GLN cc_start: 0.7749 (mm-40) cc_final: 0.6946 (mp10) REVERT: M 49 LYS cc_start: 0.8087 (mttm) cc_final: 0.7850 (mtmm) REVERT: M 53 LYS cc_start: 0.8153 (ttpp) cc_final: 0.7754 (ttpp) REVERT: M 68 LYS cc_start: 0.7809 (OUTLIER) cc_final: 0.7574 (ttmm) REVERT: M 92 ASP cc_start: 0.7574 (t0) cc_final: 0.7196 (t0) REVERT: M 119 LYS cc_start: 0.7398 (ttmp) cc_final: 0.7144 (ttpt) REVERT: N 14 GLN cc_start: 0.7748 (mm-40) cc_final: 0.6944 (mp10) REVERT: N 49 LYS cc_start: 0.8091 (mttm) cc_final: 0.7854 (mtmm) REVERT: N 53 LYS cc_start: 0.8156 (ttpp) cc_final: 0.7756 (ttpp) REVERT: N 68 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7560 (tttm) REVERT: N 92 ASP cc_start: 0.7583 (t0) cc_final: 0.7204 (t0) REVERT: N 119 LYS cc_start: 0.7393 (ttmp) cc_final: 0.7139 (ttpt) REVERT: O 14 GLN cc_start: 0.7744 (mm-40) cc_final: 0.6935 (mp10) REVERT: O 49 LYS cc_start: 0.8093 (mttm) cc_final: 0.7851 (mtmm) REVERT: O 53 LYS cc_start: 0.8155 (ttpp) cc_final: 0.7755 (ttpp) REVERT: O 68 LYS cc_start: 0.7801 (OUTLIER) cc_final: 0.7566 (ttmm) REVERT: O 92 ASP cc_start: 0.7582 (t0) cc_final: 0.7205 (t0) REVERT: O 119 LYS cc_start: 0.7394 (ttmp) cc_final: 0.7139 (ttpt) REVERT: P 14 GLN cc_start: 0.7749 (mm-40) cc_final: 0.6946 (mp10) REVERT: P 49 LYS cc_start: 0.8090 (mttm) cc_final: 0.7852 (mtmm) REVERT: P 53 LYS cc_start: 0.8153 (ttpp) cc_final: 0.7752 (ttpp) REVERT: P 68 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7558 (tttm) REVERT: P 92 ASP cc_start: 0.7583 (t0) cc_final: 0.7206 (t0) REVERT: P 119 LYS cc_start: 0.7396 (ttmp) cc_final: 0.7142 (ttpt) REVERT: Q 14 GLN cc_start: 0.7741 (mm-40) cc_final: 0.6933 (mp10) REVERT: Q 49 LYS cc_start: 0.8097 (mttm) cc_final: 0.7856 (mtmm) REVERT: Q 53 LYS cc_start: 0.8155 (ttpp) cc_final: 0.7756 (ttpp) REVERT: Q 68 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7556 (tttm) REVERT: Q 92 ASP cc_start: 0.7582 (t0) cc_final: 0.7207 (t0) REVERT: Q 119 LYS cc_start: 0.7393 (ttmp) cc_final: 0.7139 (ttpt) REVERT: R 14 GLN cc_start: 0.7745 (mm-40) cc_final: 0.6938 (mp10) REVERT: R 49 LYS cc_start: 0.8090 (mttm) cc_final: 0.7850 (mtmm) REVERT: R 53 LYS cc_start: 0.8154 (ttpp) cc_final: 0.7753 (ttpp) REVERT: R 68 LYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7570 (ttmm) REVERT: R 92 ASP cc_start: 0.7581 (t0) cc_final: 0.7204 (t0) REVERT: R 119 LYS cc_start: 0.7399 (ttmp) cc_final: 0.7145 (ttpt) REVERT: S 14 GLN cc_start: 0.7745 (mm-40) cc_final: 0.6938 (mp10) REVERT: S 49 LYS cc_start: 0.8091 (mttm) cc_final: 0.7851 (mtmm) REVERT: S 53 LYS cc_start: 0.8153 (ttpp) cc_final: 0.7754 (ttpp) REVERT: S 68 LYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7570 (ttmm) REVERT: S 92 ASP cc_start: 0.7580 (t0) cc_final: 0.7203 (t0) REVERT: S 119 LYS cc_start: 0.7398 (ttmp) cc_final: 0.7145 (ttpt) REVERT: T 14 GLN cc_start: 0.7762 (mm-40) cc_final: 0.6956 (mp10) REVERT: T 49 LYS cc_start: 0.8093 (mttm) cc_final: 0.7853 (mtmm) REVERT: T 53 LYS cc_start: 0.8154 (ttpp) cc_final: 0.7755 (ttpp) REVERT: T 68 LYS cc_start: 0.7802 (OUTLIER) cc_final: 0.7568 (ttmm) REVERT: T 92 ASP cc_start: 0.7583 (t0) cc_final: 0.7209 (t0) REVERT: T 119 LYS cc_start: 0.7395 (ttmp) cc_final: 0.7141 (ttpt) REVERT: U 14 GLN cc_start: 0.7742 (mm-40) cc_final: 0.6935 (mp10) REVERT: U 49 LYS cc_start: 0.8091 (mttm) cc_final: 0.7852 (mtmm) REVERT: U 53 LYS cc_start: 0.8154 (ttpp) cc_final: 0.7753 (ttpp) REVERT: U 68 LYS cc_start: 0.7802 (OUTLIER) cc_final: 0.7568 (ttmm) REVERT: U 92 ASP cc_start: 0.7583 (t0) cc_final: 0.7205 (t0) REVERT: U 119 LYS cc_start: 0.7394 (ttmp) cc_final: 0.7139 (ttpt) REVERT: V 14 GLN cc_start: 0.7750 (mm-40) cc_final: 0.6947 (mp10) REVERT: V 49 LYS cc_start: 0.8091 (mttm) cc_final: 0.7852 (mtmm) REVERT: V 53 LYS cc_start: 0.8155 (ttpp) cc_final: 0.7755 (ttpp) REVERT: V 68 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7559 (tttm) REVERT: V 92 ASP cc_start: 0.7582 (t0) cc_final: 0.7205 (t0) REVERT: V 119 LYS cc_start: 0.7394 (ttmp) cc_final: 0.7140 (ttpt) REVERT: W 14 GLN cc_start: 0.7744 (mm-40) cc_final: 0.6935 (mp10) REVERT: W 49 LYS cc_start: 0.8093 (mttm) cc_final: 0.7853 (mtmm) REVERT: W 53 LYS cc_start: 0.8153 (ttpp) cc_final: 0.7754 (ttpp) REVERT: W 68 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7570 (ttmm) REVERT: W 92 ASP cc_start: 0.7581 (t0) cc_final: 0.7203 (t0) REVERT: W 119 LYS cc_start: 0.7399 (ttmp) cc_final: 0.7144 (ttpt) REVERT: X 14 GLN cc_start: 0.7742 (mm-40) cc_final: 0.6935 (mp10) REVERT: X 49 LYS cc_start: 0.8093 (mttm) cc_final: 0.7853 (mtmm) REVERT: X 53 LYS cc_start: 0.8156 (ttpp) cc_final: 0.7756 (ttpp) REVERT: X 68 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7559 (tttm) REVERT: X 92 ASP cc_start: 0.7583 (t0) cc_final: 0.7210 (t0) REVERT: X 119 LYS cc_start: 0.7392 (ttmp) cc_final: 0.7138 (ttpt) outliers start: 72 outliers final: 24 residues processed: 936 average time/residue: 1.7905 time to fit residues: 1913.2570 Evaluate side-chains 834 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 786 time to evaluate : 3.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 165 MET Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain C residue 68 LYS Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain F residue 165 MET Chi-restraints excluded: chain G residue 68 LYS Chi-restraints excluded: chain G residue 165 MET Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain I residue 68 LYS Chi-restraints excluded: chain I residue 165 MET Chi-restraints excluded: chain J residue 68 LYS Chi-restraints excluded: chain J residue 165 MET Chi-restraints excluded: chain K residue 68 LYS Chi-restraints excluded: chain K residue 165 MET Chi-restraints excluded: chain L residue 68 LYS Chi-restraints excluded: chain L residue 165 MET Chi-restraints excluded: chain M residue 68 LYS Chi-restraints excluded: chain M residue 165 MET Chi-restraints excluded: chain N residue 68 LYS Chi-restraints excluded: chain N residue 165 MET Chi-restraints excluded: chain O residue 68 LYS Chi-restraints excluded: chain O residue 165 MET Chi-restraints excluded: chain P residue 68 LYS Chi-restraints excluded: chain P residue 165 MET Chi-restraints excluded: chain Q residue 68 LYS Chi-restraints excluded: chain Q residue 165 MET Chi-restraints excluded: chain R residue 68 LYS Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain S residue 68 LYS Chi-restraints excluded: chain S residue 165 MET Chi-restraints excluded: chain T residue 68 LYS Chi-restraints excluded: chain T residue 165 MET Chi-restraints excluded: chain U residue 68 LYS Chi-restraints excluded: chain U residue 165 MET Chi-restraints excluded: chain V residue 68 LYS Chi-restraints excluded: chain V residue 165 MET Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain X residue 68 LYS Chi-restraints excluded: chain X residue 165 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 0.6980 chunk 309 optimal weight: 0.7980 chunk 171 optimal weight: 0.9990 chunk 105 optimal weight: 0.6980 chunk 208 optimal weight: 0.9980 chunk 165 optimal weight: 0.8980 chunk 319 optimal weight: 5.9990 chunk 123 optimal weight: 0.9980 chunk 194 optimal weight: 2.9990 chunk 238 optimal weight: 0.5980 chunk 370 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 75 GLN A 83 GLN A 112 GLN B 58 GLN B 75 GLN B 83 GLN B 112 GLN C 58 GLN C 75 GLN C 83 GLN C 112 GLN D 58 GLN D 75 GLN D 83 GLN D 112 GLN E 58 GLN E 75 GLN E 83 GLN E 112 GLN F 58 GLN F 75 GLN F 83 GLN F 112 GLN G 58 GLN G 75 GLN G 83 GLN G 112 GLN H 58 GLN H 75 GLN H 83 GLN H 112 GLN I 58 GLN I 75 GLN I 83 GLN I 112 GLN J 58 GLN J 75 GLN J 83 GLN J 112 GLN K 58 GLN K 75 GLN K 83 GLN K 112 GLN L 58 GLN L 75 GLN L 83 GLN L 112 GLN M 58 GLN M 75 GLN M 83 GLN M 112 GLN N 58 GLN N 75 GLN N 83 GLN N 112 GLN O 58 GLN O 75 GLN O 83 GLN O 112 GLN P 58 GLN P 75 GLN P 83 GLN P 112 GLN Q 58 GLN Q 75 GLN Q 83 GLN Q 112 GLN R 58 GLN R 75 GLN R 83 GLN R 112 GLN S 58 GLN S 75 GLN S 83 GLN S 112 GLN T 58 GLN T 75 GLN T 83 GLN T 112 GLN U 58 GLN U 75 GLN U 83 GLN U 112 GLN V 58 GLN V 75 GLN V 83 GLN V 112 GLN W 58 GLN W 75 GLN W 83 GLN W 112 GLN X 58 GLN X 75 GLN X 83 GLN X 112 GLN Total number of N/Q/H flips: 96 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 35616 Z= 0.159 Angle : 0.575 5.673 48072 Z= 0.317 Chirality : 0.037 0.120 4992 Planarity : 0.003 0.023 6384 Dihedral : 5.505 39.965 4920 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.27 % Allowed : 3.82 % Favored : 94.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.83 (0.12), residues: 4440 helix: 3.68 (0.08), residues: 3528 sheet: None (None), residues: 0 loop : 1.03 (0.24), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP K 93 HIS 0.008 0.001 HIS B 60 PHE 0.015 0.002 PHE J 41 TYR 0.018 0.002 TYR C 32 ARG 0.002 0.000 ARG A 79 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 960 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 912 time to evaluate : 3.177 Fit side-chains REVERT: A 49 LYS cc_start: 0.8075 (mttm) cc_final: 0.7563 (mmpt) REVERT: A 62 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7065 (mm-30) REVERT: A 63 ARG cc_start: 0.7327 (ttp-170) cc_final: 0.7112 (ttt90) REVERT: A 68 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7702 (ttmm) REVERT: A 92 ASP cc_start: 0.7745 (t0) cc_final: 0.7504 (t0) REVERT: A 119 LYS cc_start: 0.7957 (ttmp) cc_final: 0.7637 (tttm) REVERT: B 49 LYS cc_start: 0.8075 (mttm) cc_final: 0.7564 (mmpt) REVERT: B 62 GLU cc_start: 0.7510 (mm-30) cc_final: 0.7120 (mm-30) REVERT: B 63 ARG cc_start: 0.7329 (ttp-170) cc_final: 0.7113 (ttt90) REVERT: B 68 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7711 (ttmm) REVERT: B 92 ASP cc_start: 0.7747 (t0) cc_final: 0.7506 (t0) REVERT: B 119 LYS cc_start: 0.7955 (ttmp) cc_final: 0.7636 (tttm) REVERT: C 49 LYS cc_start: 0.8073 (mttm) cc_final: 0.7562 (mmpt) REVERT: C 62 GLU cc_start: 0.7508 (mm-30) cc_final: 0.7119 (mm-30) REVERT: C 63 ARG cc_start: 0.7330 (ttp-170) cc_final: 0.7108 (ttt90) REVERT: C 68 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7711 (ttmm) REVERT: C 92 ASP cc_start: 0.7745 (t0) cc_final: 0.7505 (t0) REVERT: C 119 LYS cc_start: 0.7953 (ttmp) cc_final: 0.7634 (tttm) REVERT: D 49 LYS cc_start: 0.8076 (mttm) cc_final: 0.7565 (mmpt) REVERT: D 62 GLU cc_start: 0.7510 (mm-30) cc_final: 0.7119 (mm-30) REVERT: D 63 ARG cc_start: 0.7327 (ttp-170) cc_final: 0.7113 (ttt90) REVERT: D 68 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7709 (ttmm) REVERT: D 92 ASP cc_start: 0.7747 (t0) cc_final: 0.7506 (t0) REVERT: D 119 LYS cc_start: 0.7953 (ttmp) cc_final: 0.7634 (tttm) REVERT: E 49 LYS cc_start: 0.8076 (mttm) cc_final: 0.7565 (mmpt) REVERT: E 62 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7120 (mm-30) REVERT: E 63 ARG cc_start: 0.7330 (ttp-170) cc_final: 0.7109 (ttt90) REVERT: E 68 LYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7710 (ttmm) REVERT: E 92 ASP cc_start: 0.7745 (t0) cc_final: 0.7505 (t0) REVERT: E 119 LYS cc_start: 0.7957 (ttmp) cc_final: 0.7638 (tttm) REVERT: F 49 LYS cc_start: 0.8075 (mttm) cc_final: 0.7564 (mmpt) REVERT: F 62 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7119 (mm-30) REVERT: F 63 ARG cc_start: 0.7330 (ttp-170) cc_final: 0.7108 (ttt90) REVERT: F 68 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7710 (ttmm) REVERT: F 92 ASP cc_start: 0.7747 (t0) cc_final: 0.7507 (t0) REVERT: F 119 LYS cc_start: 0.7954 (ttmp) cc_final: 0.7635 (tttm) REVERT: G 49 LYS cc_start: 0.8077 (mttm) cc_final: 0.7566 (mmpt) REVERT: G 62 GLU cc_start: 0.7511 (mm-30) cc_final: 0.7121 (mm-30) REVERT: G 63 ARG cc_start: 0.7328 (ttp-170) cc_final: 0.7113 (ttt90) REVERT: G 68 LYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7710 (ttmm) REVERT: G 92 ASP cc_start: 0.7745 (t0) cc_final: 0.7505 (t0) REVERT: G 119 LYS cc_start: 0.7957 (ttmp) cc_final: 0.7638 (tttm) REVERT: H 49 LYS cc_start: 0.8075 (mttm) cc_final: 0.7563 (mmpt) REVERT: H 62 GLU cc_start: 0.7507 (mm-30) cc_final: 0.7118 (mm-30) REVERT: H 63 ARG cc_start: 0.7325 (ttp-170) cc_final: 0.7108 (ttt90) REVERT: H 68 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7708 (ttmm) REVERT: H 92 ASP cc_start: 0.7745 (t0) cc_final: 0.7505 (t0) REVERT: H 119 LYS cc_start: 0.7954 (ttmp) cc_final: 0.7634 (tttm) REVERT: I 49 LYS cc_start: 0.8073 (mttm) cc_final: 0.7562 (mmpt) REVERT: I 62 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7119 (mm-30) REVERT: I 63 ARG cc_start: 0.7328 (ttp-170) cc_final: 0.7112 (ttt90) REVERT: I 68 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7710 (ttmm) REVERT: I 92 ASP cc_start: 0.7747 (t0) cc_final: 0.7505 (t0) REVERT: I 119 LYS cc_start: 0.7954 (ttmp) cc_final: 0.7634 (tttm) REVERT: J 49 LYS cc_start: 0.8074 (mttm) cc_final: 0.7562 (mmpt) REVERT: J 62 GLU cc_start: 0.7507 (mm-30) cc_final: 0.7117 (mm-30) REVERT: J 63 ARG cc_start: 0.7327 (ttp-170) cc_final: 0.7112 (ttt90) REVERT: J 68 LYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7709 (ttmm) REVERT: J 92 ASP cc_start: 0.7746 (t0) cc_final: 0.7505 (t0) REVERT: J 119 LYS cc_start: 0.7954 (ttmp) cc_final: 0.7634 (tttm) REVERT: K 49 LYS cc_start: 0.8075 (mttm) cc_final: 0.7563 (mmpt) REVERT: K 62 GLU cc_start: 0.7511 (mm-30) cc_final: 0.7121 (mm-30) REVERT: K 63 ARG cc_start: 0.7327 (ttp-170) cc_final: 0.7112 (ttt90) REVERT: K 68 LYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7710 (ttmm) REVERT: K 92 ASP cc_start: 0.7746 (t0) cc_final: 0.7505 (t0) REVERT: K 119 LYS cc_start: 0.7954 (ttmp) cc_final: 0.7634 (tttm) REVERT: L 49 LYS cc_start: 0.8075 (mttm) cc_final: 0.7563 (mmpt) REVERT: L 62 GLU cc_start: 0.7506 (mm-30) cc_final: 0.7117 (mm-30) REVERT: L 63 ARG cc_start: 0.7330 (ttp-170) cc_final: 0.7109 (ttt90) REVERT: L 68 LYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7710 (ttmm) REVERT: L 92 ASP cc_start: 0.7746 (t0) cc_final: 0.7505 (t0) REVERT: L 119 LYS cc_start: 0.7957 (ttmp) cc_final: 0.7637 (tttm) REVERT: M 49 LYS cc_start: 0.8075 (mttm) cc_final: 0.7564 (mmpt) REVERT: M 62 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7119 (mm-30) REVERT: M 63 ARG cc_start: 0.7327 (ttp-170) cc_final: 0.7112 (ttt90) REVERT: M 68 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7710 (ttmm) REVERT: M 92 ASP cc_start: 0.7745 (t0) cc_final: 0.7505 (t0) REVERT: M 119 LYS cc_start: 0.7954 (ttmp) cc_final: 0.7635 (tttm) REVERT: N 49 LYS cc_start: 0.8077 (mttm) cc_final: 0.7567 (mmpt) REVERT: N 62 GLU cc_start: 0.7511 (mm-30) cc_final: 0.7121 (mm-30) REVERT: N 63 ARG cc_start: 0.7326 (ttp-170) cc_final: 0.7109 (ttt90) REVERT: N 68 LYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7709 (ttmm) REVERT: N 92 ASP cc_start: 0.7743 (t0) cc_final: 0.7504 (t0) REVERT: N 119 LYS cc_start: 0.7957 (ttmp) cc_final: 0.7638 (tttm) REVERT: O 49 LYS cc_start: 0.8076 (mttm) cc_final: 0.7564 (mmpt) REVERT: O 62 GLU cc_start: 0.7510 (mm-30) cc_final: 0.7120 (mm-30) REVERT: O 63 ARG cc_start: 0.7326 (ttp-170) cc_final: 0.7109 (ttt90) REVERT: O 68 LYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7709 (ttmm) REVERT: O 92 ASP cc_start: 0.7745 (t0) cc_final: 0.7505 (t0) REVERT: O 119 LYS cc_start: 0.7957 (ttmp) cc_final: 0.7637 (tttm) REVERT: P 49 LYS cc_start: 0.8073 (mttm) cc_final: 0.7562 (mmpt) REVERT: P 62 GLU cc_start: 0.7510 (mm-30) cc_final: 0.7120 (mm-30) REVERT: P 63 ARG cc_start: 0.7326 (ttp-170) cc_final: 0.7109 (ttt90) REVERT: P 68 LYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7710 (ttmm) REVERT: P 92 ASP cc_start: 0.7744 (t0) cc_final: 0.7504 (t0) REVERT: P 119 LYS cc_start: 0.7954 (ttmp) cc_final: 0.7635 (tttm) REVERT: Q 49 LYS cc_start: 0.8075 (mttm) cc_final: 0.7564 (mmpt) REVERT: Q 62 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7119 (mm-30) REVERT: Q 63 ARG cc_start: 0.7327 (ttp-170) cc_final: 0.7109 (ttt90) REVERT: Q 68 LYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7709 (ttmm) REVERT: Q 92 ASP cc_start: 0.7745 (t0) cc_final: 0.7506 (t0) REVERT: Q 119 LYS cc_start: 0.7956 (ttmp) cc_final: 0.7637 (tttm) REVERT: R 49 LYS cc_start: 0.8076 (mttm) cc_final: 0.7565 (mmpt) REVERT: R 62 GLU cc_start: 0.7510 (mm-30) cc_final: 0.7120 (mm-30) REVERT: R 63 ARG cc_start: 0.7327 (ttp-170) cc_final: 0.7112 (ttt90) REVERT: R 68 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7708 (ttmm) REVERT: R 92 ASP cc_start: 0.7745 (t0) cc_final: 0.7505 (t0) REVERT: R 119 LYS cc_start: 0.7954 (ttmp) cc_final: 0.7635 (tttm) REVERT: S 49 LYS cc_start: 0.8076 (mttm) cc_final: 0.7565 (mmpt) REVERT: S 62 GLU cc_start: 0.7510 (mm-30) cc_final: 0.7120 (mm-30) REVERT: S 63 ARG cc_start: 0.7328 (ttp-170) cc_final: 0.7113 (ttt90) REVERT: S 68 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7709 (ttmm) REVERT: S 92 ASP cc_start: 0.7746 (t0) cc_final: 0.7506 (t0) REVERT: S 119 LYS cc_start: 0.7958 (ttmp) cc_final: 0.7638 (tttm) REVERT: T 49 LYS cc_start: 0.8077 (mttm) cc_final: 0.7566 (mmpt) REVERT: T 62 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7124 (mm-30) REVERT: T 63 ARG cc_start: 0.7327 (ttp-170) cc_final: 0.7112 (ttt90) REVERT: T 68 LYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7711 (ttmm) REVERT: T 92 ASP cc_start: 0.7744 (t0) cc_final: 0.7504 (t0) REVERT: T 119 LYS cc_start: 0.7957 (ttmp) cc_final: 0.7638 (tttm) REVERT: U 49 LYS cc_start: 0.8075 (mttm) cc_final: 0.7565 (mmpt) REVERT: U 62 GLU cc_start: 0.7510 (mm-30) cc_final: 0.7121 (mm-30) REVERT: U 63 ARG cc_start: 0.7325 (ttp-170) cc_final: 0.7109 (ttt90) REVERT: U 68 LYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7709 (ttmm) REVERT: U 92 ASP cc_start: 0.7746 (t0) cc_final: 0.7506 (t0) REVERT: U 119 LYS cc_start: 0.7955 (ttmp) cc_final: 0.7635 (tttm) REVERT: V 49 LYS cc_start: 0.8076 (mttm) cc_final: 0.7565 (mmpt) REVERT: V 62 GLU cc_start: 0.7511 (mm-30) cc_final: 0.7121 (mm-30) REVERT: V 63 ARG cc_start: 0.7325 (ttp-170) cc_final: 0.7109 (ttt90) REVERT: V 68 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7708 (ttmm) REVERT: V 92 ASP cc_start: 0.7744 (t0) cc_final: 0.7504 (t0) REVERT: V 119 LYS cc_start: 0.7958 (ttmp) cc_final: 0.7638 (tttm) REVERT: W 49 LYS cc_start: 0.8075 (mttm) cc_final: 0.7564 (mmpt) REVERT: W 62 GLU cc_start: 0.7510 (mm-30) cc_final: 0.7120 (mm-30) REVERT: W 63 ARG cc_start: 0.7328 (ttp-170) cc_final: 0.7113 (ttt90) REVERT: W 68 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7711 (ttmm) REVERT: W 92 ASP cc_start: 0.7746 (t0) cc_final: 0.7506 (t0) REVERT: W 119 LYS cc_start: 0.7956 (ttmp) cc_final: 0.7637 (tttm) REVERT: X 49 LYS cc_start: 0.8076 (mttm) cc_final: 0.7565 (mmpt) REVERT: X 62 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7119 (mm-30) REVERT: X 63 ARG cc_start: 0.7325 (ttp-170) cc_final: 0.7110 (ttt90) REVERT: X 68 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7708 (ttmm) REVERT: X 92 ASP cc_start: 0.7745 (t0) cc_final: 0.7505 (t0) REVERT: X 119 LYS cc_start: 0.7954 (ttmp) cc_final: 0.7634 (tttm) outliers start: 48 outliers final: 0 residues processed: 912 average time/residue: 1.8340 time to fit residues: 1904.3932 Evaluate side-chains 912 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 888 time to evaluate : 3.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain C residue 68 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain G residue 68 LYS Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain I residue 68 LYS Chi-restraints excluded: chain J residue 68 LYS Chi-restraints excluded: chain K residue 68 LYS Chi-restraints excluded: chain L residue 68 LYS Chi-restraints excluded: chain M residue 68 LYS Chi-restraints excluded: chain N residue 68 LYS Chi-restraints excluded: chain O residue 68 LYS Chi-restraints excluded: chain P residue 68 LYS Chi-restraints excluded: chain Q residue 68 LYS Chi-restraints excluded: chain R residue 68 LYS Chi-restraints excluded: chain S residue 68 LYS Chi-restraints excluded: chain T residue 68 LYS Chi-restraints excluded: chain U residue 68 LYS Chi-restraints excluded: chain V residue 68 LYS Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain X residue 68 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 7.9990 chunk 114 optimal weight: 10.0000 chunk 308 optimal weight: 5.9990 chunk 252 optimal weight: 0.9990 chunk 102 optimal weight: 10.0000 chunk 371 optimal weight: 5.9990 chunk 400 optimal weight: 2.9990 chunk 330 optimal weight: 0.9990 chunk 368 optimal weight: 10.0000 chunk 126 optimal weight: 5.9990 chunk 297 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 60 HIS A 75 GLN A 112 GLN B 14 GLN B 60 HIS B 75 GLN B 112 GLN C 14 GLN C 60 HIS C 75 GLN C 112 GLN D 14 GLN D 60 HIS D 75 GLN D 112 GLN E 14 GLN E 60 HIS E 75 GLN E 112 GLN F 14 GLN F 60 HIS F 75 GLN F 112 GLN G 14 GLN G 60 HIS G 75 GLN G 112 GLN H 14 GLN H 60 HIS H 75 GLN H 112 GLN I 14 GLN I 60 HIS I 75 GLN I 112 GLN J 14 GLN J 60 HIS J 75 GLN J 112 GLN K 14 GLN K 60 HIS K 75 GLN K 112 GLN L 14 GLN L 60 HIS L 75 GLN L 112 GLN M 14 GLN M 60 HIS M 75 GLN M 112 GLN N 14 GLN N 60 HIS N 75 GLN N 112 GLN O 14 GLN O 60 HIS O 75 GLN O 112 GLN P 14 GLN P 60 HIS P 75 GLN P 112 GLN Q 14 GLN Q 60 HIS Q 75 GLN Q 112 GLN R 14 GLN R 60 HIS R 75 GLN R 112 GLN S 14 GLN S 60 HIS S 75 GLN S 112 GLN T 14 GLN T 60 HIS T 75 GLN T 112 GLN U 14 GLN U 60 HIS U 75 GLN U 112 GLN V 14 GLN V 60 HIS V 75 GLN V 112 GLN W 14 GLN W 60 HIS W 75 GLN W 112 GLN X 14 GLN X 60 HIS X 75 GLN X 112 GLN Total number of N/Q/H flips: 96 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 35616 Z= 0.267 Angle : 0.700 5.663 48072 Z= 0.382 Chirality : 0.040 0.132 4992 Planarity : 0.004 0.022 6384 Dihedral : 4.564 16.817 4848 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.27 % Allowed : 6.37 % Favored : 92.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.00 (0.12), residues: 4440 helix: 3.82 (0.08), residues: 3528 sheet: None (None), residues: 0 loop : 0.99 (0.25), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.004 TRP K 93 HIS 0.003 0.001 HIS B 151 PHE 0.023 0.003 PHE O 41 TYR 0.021 0.003 TYR C 32 ARG 0.005 0.001 ARG C 79 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 840 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 792 time to evaluate : 3.185 Fit side-chains REVERT: A 49 LYS cc_start: 0.8150 (mttm) cc_final: 0.7940 (mtpm) REVERT: A 62 GLU cc_start: 0.7397 (mm-30) cc_final: 0.7086 (mm-30) REVERT: A 68 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7714 (tttm) REVERT: A 92 ASP cc_start: 0.7902 (t0) cc_final: 0.7655 (t0) REVERT: A 119 LYS cc_start: 0.7940 (ttmp) cc_final: 0.7616 (tttm) REVERT: B 49 LYS cc_start: 0.8156 (mttm) cc_final: 0.7946 (mtpm) REVERT: B 62 GLU cc_start: 0.7402 (mm-30) cc_final: 0.7094 (mm-30) REVERT: B 68 LYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7716 (tttm) REVERT: B 92 ASP cc_start: 0.7904 (t0) cc_final: 0.7656 (t0) REVERT: B 119 LYS cc_start: 0.7942 (ttmp) cc_final: 0.7618 (tttm) REVERT: C 49 LYS cc_start: 0.8142 (mttm) cc_final: 0.7931 (mtpm) REVERT: C 62 GLU cc_start: 0.7401 (mm-30) cc_final: 0.7093 (mm-30) REVERT: C 68 LYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7715 (tttm) REVERT: C 92 ASP cc_start: 0.7904 (t0) cc_final: 0.7658 (t0) REVERT: C 119 LYS cc_start: 0.7939 (ttmp) cc_final: 0.7615 (tttm) REVERT: D 49 LYS cc_start: 0.8153 (mttm) cc_final: 0.7943 (mtpm) REVERT: D 62 GLU cc_start: 0.7402 (mm-30) cc_final: 0.7093 (mm-30) REVERT: D 68 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7714 (tttm) REVERT: D 92 ASP cc_start: 0.7906 (t0) cc_final: 0.7659 (t0) REVERT: D 119 LYS cc_start: 0.7941 (ttmp) cc_final: 0.7616 (tttm) REVERT: E 49 LYS cc_start: 0.8140 (mttm) cc_final: 0.7929 (mtpm) REVERT: E 62 GLU cc_start: 0.7402 (mm-30) cc_final: 0.7094 (mm-30) REVERT: E 68 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7714 (tttm) REVERT: E 92 ASP cc_start: 0.7902 (t0) cc_final: 0.7655 (t0) REVERT: E 119 LYS cc_start: 0.7942 (ttmp) cc_final: 0.7619 (tttm) REVERT: F 49 LYS cc_start: 0.8142 (mttm) cc_final: 0.7931 (mtpm) REVERT: F 62 GLU cc_start: 0.7402 (mm-30) cc_final: 0.7094 (mm-30) REVERT: F 68 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7715 (tttm) REVERT: F 92 ASP cc_start: 0.7904 (t0) cc_final: 0.7658 (t0) REVERT: F 119 LYS cc_start: 0.7940 (ttmp) cc_final: 0.7616 (tttm) REVERT: G 49 LYS cc_start: 0.8153 (mttm) cc_final: 0.7943 (mtpm) REVERT: G 62 GLU cc_start: 0.7399 (mm-30) cc_final: 0.7091 (mm-30) REVERT: G 68 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7714 (tttm) REVERT: G 92 ASP cc_start: 0.7904 (t0) cc_final: 0.7656 (t0) REVERT: G 119 LYS cc_start: 0.7942 (ttmp) cc_final: 0.7617 (tttm) REVERT: H 49 LYS cc_start: 0.8152 (mttm) cc_final: 0.7942 (mtpm) REVERT: H 62 GLU cc_start: 0.7401 (mm-30) cc_final: 0.7092 (mm-30) REVERT: H 68 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7714 (tttm) REVERT: H 92 ASP cc_start: 0.7905 (t0) cc_final: 0.7658 (t0) REVERT: H 119 LYS cc_start: 0.7940 (ttmp) cc_final: 0.7614 (tttm) REVERT: I 49 LYS cc_start: 0.8140 (mttm) cc_final: 0.7929 (mtpm) REVERT: I 62 GLU cc_start: 0.7401 (mm-30) cc_final: 0.7092 (mm-30) REVERT: I 68 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7715 (tttm) REVERT: I 92 ASP cc_start: 0.7906 (t0) cc_final: 0.7659 (t0) REVERT: I 119 LYS cc_start: 0.7940 (ttmp) cc_final: 0.7615 (tttm) REVERT: J 49 LYS cc_start: 0.8150 (mttm) cc_final: 0.7939 (mtpm) REVERT: J 62 GLU cc_start: 0.7399 (mm-30) cc_final: 0.7090 (mm-30) REVERT: J 68 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7715 (tttm) REVERT: J 92 ASP cc_start: 0.7906 (t0) cc_final: 0.7658 (t0) REVERT: J 119 LYS cc_start: 0.7940 (ttmp) cc_final: 0.7614 (tttm) REVERT: K 49 LYS cc_start: 0.8138 (mttm) cc_final: 0.7927 (mtpm) REVERT: K 62 GLU cc_start: 0.7400 (mm-30) cc_final: 0.7091 (mm-30) REVERT: K 68 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7715 (tttm) REVERT: K 92 ASP cc_start: 0.7904 (t0) cc_final: 0.7657 (t0) REVERT: K 119 LYS cc_start: 0.7938 (ttmp) cc_final: 0.7614 (tttm) REVERT: L 49 LYS cc_start: 0.8140 (mttm) cc_final: 0.7930 (mtpm) REVERT: L 62 GLU cc_start: 0.7401 (mm-30) cc_final: 0.7093 (mm-30) REVERT: L 68 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7713 (tttm) REVERT: L 92 ASP cc_start: 0.7904 (t0) cc_final: 0.7657 (t0) REVERT: L 119 LYS cc_start: 0.7941 (ttmp) cc_final: 0.7616 (tttm) REVERT: M 49 LYS cc_start: 0.8152 (mttm) cc_final: 0.7942 (mtpm) REVERT: M 62 GLU cc_start: 0.7403 (mm-30) cc_final: 0.7094 (mm-30) REVERT: M 68 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7715 (tttm) REVERT: M 92 ASP cc_start: 0.7904 (t0) cc_final: 0.7658 (t0) REVERT: M 119 LYS cc_start: 0.7939 (ttmp) cc_final: 0.7616 (tttm) REVERT: N 49 LYS cc_start: 0.8153 (mttm) cc_final: 0.7943 (mtpm) REVERT: N 62 GLU cc_start: 0.7401 (mm-30) cc_final: 0.7092 (mm-30) REVERT: N 68 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7714 (tttm) REVERT: N 92 ASP cc_start: 0.7903 (t0) cc_final: 0.7656 (t0) REVERT: N 119 LYS cc_start: 0.7942 (ttmp) cc_final: 0.7617 (tttm) REVERT: O 49 LYS cc_start: 0.8138 (mttm) cc_final: 0.7928 (mtpm) REVERT: O 62 GLU cc_start: 0.7401 (mm-30) cc_final: 0.7093 (mm-30) REVERT: O 68 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7713 (tttm) REVERT: O 92 ASP cc_start: 0.7903 (t0) cc_final: 0.7656 (t0) REVERT: O 119 LYS cc_start: 0.7940 (ttmp) cc_final: 0.7616 (tttm) REVERT: P 49 LYS cc_start: 0.8152 (mttm) cc_final: 0.7941 (mtpm) REVERT: P 62 GLU cc_start: 0.7401 (mm-30) cc_final: 0.7092 (mm-30) REVERT: P 68 LYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7715 (tttm) REVERT: P 92 ASP cc_start: 0.7904 (t0) cc_final: 0.7657 (t0) REVERT: P 119 LYS cc_start: 0.7939 (ttmp) cc_final: 0.7615 (tttm) REVERT: Q 49 LYS cc_start: 0.8141 (mttm) cc_final: 0.7931 (mtpm) REVERT: Q 62 GLU cc_start: 0.7402 (mm-30) cc_final: 0.7094 (mm-30) REVERT: Q 68 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7714 (tttm) REVERT: Q 92 ASP cc_start: 0.7904 (t0) cc_final: 0.7656 (t0) REVERT: Q 119 LYS cc_start: 0.7943 (ttmp) cc_final: 0.7618 (tttm) REVERT: R 49 LYS cc_start: 0.8150 (mttm) cc_final: 0.7939 (mtpm) REVERT: R 62 GLU cc_start: 0.7402 (mm-30) cc_final: 0.7093 (mm-30) REVERT: R 68 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7714 (tttm) REVERT: R 92 ASP cc_start: 0.7905 (t0) cc_final: 0.7657 (t0) REVERT: R 119 LYS cc_start: 0.7941 (ttmp) cc_final: 0.7616 (tttm) REVERT: S 49 LYS cc_start: 0.8139 (mttm) cc_final: 0.7928 (mtpm) REVERT: S 62 GLU cc_start: 0.7401 (mm-30) cc_final: 0.7093 (mm-30) REVERT: S 68 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7714 (tttm) REVERT: S 92 ASP cc_start: 0.7902 (t0) cc_final: 0.7656 (t0) REVERT: S 119 LYS cc_start: 0.7943 (ttmp) cc_final: 0.7618 (tttm) REVERT: T 49 LYS cc_start: 0.8142 (mttm) cc_final: 0.7931 (mtpm) REVERT: T 62 GLU cc_start: 0.7400 (mm-30) cc_final: 0.7092 (mm-30) REVERT: T 68 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7714 (tttm) REVERT: T 92 ASP cc_start: 0.7902 (t0) cc_final: 0.7655 (t0) REVERT: T 119 LYS cc_start: 0.7941 (ttmp) cc_final: 0.7617 (tttm) REVERT: U 49 LYS cc_start: 0.8140 (mttm) cc_final: 0.7929 (mtpm) REVERT: U 62 GLU cc_start: 0.7402 (mm-30) cc_final: 0.7093 (mm-30) REVERT: U 68 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7715 (tttm) REVERT: U 92 ASP cc_start: 0.7905 (t0) cc_final: 0.7659 (t0) REVERT: U 119 LYS cc_start: 0.7940 (ttmp) cc_final: 0.7615 (tttm) REVERT: V 49 LYS cc_start: 0.8150 (mttm) cc_final: 0.7940 (mtpm) REVERT: V 62 GLU cc_start: 0.7402 (mm-30) cc_final: 0.7094 (mm-30) REVERT: V 68 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7714 (tttm) REVERT: V 92 ASP cc_start: 0.7903 (t0) cc_final: 0.7656 (t0) REVERT: V 119 LYS cc_start: 0.7942 (ttmp) cc_final: 0.7618 (tttm) REVERT: W 49 LYS cc_start: 0.8153 (mttm) cc_final: 0.7943 (mtpm) REVERT: W 62 GLU cc_start: 0.7402 (mm-30) cc_final: 0.7094 (mm-30) REVERT: W 68 LYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7716 (tttm) REVERT: W 92 ASP cc_start: 0.7903 (t0) cc_final: 0.7654 (t0) REVERT: W 119 LYS cc_start: 0.7943 (ttmp) cc_final: 0.7618 (tttm) REVERT: X 49 LYS cc_start: 0.8137 (mttm) cc_final: 0.7927 (mtpm) REVERT: X 62 GLU cc_start: 0.7403 (mm-30) cc_final: 0.7094 (mm-30) REVERT: X 68 LYS cc_start: 0.7920 (OUTLIER) cc_final: 0.7713 (tttm) REVERT: X 92 ASP cc_start: 0.7906 (t0) cc_final: 0.7659 (t0) REVERT: X 119 LYS cc_start: 0.7941 (ttmp) cc_final: 0.7616 (tttm) outliers start: 48 outliers final: 0 residues processed: 816 average time/residue: 1.7761 time to fit residues: 1657.8986 Evaluate side-chains 816 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 792 time to evaluate : 3.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain C residue 68 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain G residue 68 LYS Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain I residue 68 LYS Chi-restraints excluded: chain J residue 68 LYS Chi-restraints excluded: chain K residue 68 LYS Chi-restraints excluded: chain L residue 68 LYS Chi-restraints excluded: chain M residue 68 LYS Chi-restraints excluded: chain N residue 68 LYS Chi-restraints excluded: chain O residue 68 LYS Chi-restraints excluded: chain P residue 68 LYS Chi-restraints excluded: chain Q residue 68 LYS Chi-restraints excluded: chain R residue 68 LYS Chi-restraints excluded: chain S residue 68 LYS Chi-restraints excluded: chain T residue 68 LYS Chi-restraints excluded: chain U residue 68 LYS Chi-restraints excluded: chain V residue 68 LYS Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain X residue 68 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 5.9990 chunk 279 optimal weight: 0.9980 chunk 192 optimal weight: 10.0000 chunk 41 optimal weight: 0.9980 chunk 177 optimal weight: 0.9990 chunk 249 optimal weight: 3.9990 chunk 372 optimal weight: 0.2980 chunk 394 optimal weight: 0.5980 chunk 194 optimal weight: 0.7980 chunk 353 optimal weight: 1.9990 chunk 106 optimal weight: 9.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 60 HIS B 14 GLN B 60 HIS C 14 GLN C 60 HIS D 14 GLN D 60 HIS E 14 GLN E 60 HIS F 14 GLN F 60 HIS G 14 GLN G 60 HIS H 14 GLN H 60 HIS I 14 GLN I 60 HIS J 14 GLN J 60 HIS K 14 GLN K 60 HIS L 14 GLN L 60 HIS M 14 GLN M 60 HIS N 14 GLN N 60 HIS O 14 GLN O 60 HIS P 14 GLN P 60 HIS Q 14 GLN Q 60 HIS R 14 GLN R 60 HIS S 14 GLN S 60 HIS T 14 GLN T 60 HIS U 14 GLN U 60 HIS V 14 GLN V 60 HIS W 14 GLN W 60 HIS X 14 GLN X 60 HIS Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 35616 Z= 0.150 Angle : 0.544 4.909 48072 Z= 0.296 Chirality : 0.037 0.126 4992 Planarity : 0.004 0.048 6384 Dihedral : 4.567 18.875 4848 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.91 % Allowed : 5.73 % Favored : 92.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.42 (0.13), residues: 4440 helix: 4.13 (0.08), residues: 3528 sheet: None (None), residues: 0 loop : 1.12 (0.25), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP E 93 HIS 0.002 0.001 HIS R 128 PHE 0.015 0.002 PHE C 41 TYR 0.015 0.002 TYR R 137 ARG 0.002 0.000 ARG D 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 864 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 792 time to evaluate : 3.162 Fit side-chains REVERT: A 49 LYS cc_start: 0.8093 (mttm) cc_final: 0.7878 (mtpm) REVERT: A 62 GLU cc_start: 0.7467 (mm-30) cc_final: 0.7146 (mm-30) REVERT: A 68 LYS cc_start: 0.7942 (OUTLIER) cc_final: 0.7738 (tttm) REVERT: A 92 ASP cc_start: 0.7735 (t0) cc_final: 0.7517 (t0) REVERT: A 162 GLU cc_start: 0.6588 (mp0) cc_final: 0.6308 (mm-30) REVERT: B 49 LYS cc_start: 0.8095 (mttm) cc_final: 0.7879 (mtpm) REVERT: B 62 GLU cc_start: 0.7470 (mm-30) cc_final: 0.7160 (mm-30) REVERT: B 68 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7739 (tttm) REVERT: B 92 ASP cc_start: 0.7735 (t0) cc_final: 0.7517 (t0) REVERT: B 162 GLU cc_start: 0.6588 (mp0) cc_final: 0.6308 (mm-30) REVERT: C 49 LYS cc_start: 0.8093 (mttm) cc_final: 0.7877 (mtpm) REVERT: C 62 GLU cc_start: 0.7472 (mm-30) cc_final: 0.7161 (mm-30) REVERT: C 68 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7739 (tttm) REVERT: C 92 ASP cc_start: 0.7736 (t0) cc_final: 0.7518 (t0) REVERT: C 162 GLU cc_start: 0.6587 (mp0) cc_final: 0.6308 (mm-30) REVERT: D 49 LYS cc_start: 0.8094 (mttm) cc_final: 0.7879 (mtpm) REVERT: D 62 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7158 (mm-30) REVERT: D 68 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7738 (tttm) REVERT: D 92 ASP cc_start: 0.7736 (t0) cc_final: 0.7518 (t0) REVERT: D 162 GLU cc_start: 0.6588 (mp0) cc_final: 0.6307 (mm-30) REVERT: E 49 LYS cc_start: 0.8095 (mttm) cc_final: 0.7880 (mtpm) REVERT: E 62 GLU cc_start: 0.7470 (mm-30) cc_final: 0.7161 (mm-30) REVERT: E 68 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7737 (tttm) REVERT: E 92 ASP cc_start: 0.7735 (t0) cc_final: 0.7518 (t0) REVERT: E 162 GLU cc_start: 0.6590 (mp0) cc_final: 0.6309 (mm-30) REVERT: F 49 LYS cc_start: 0.8094 (mttm) cc_final: 0.7878 (mtpm) REVERT: F 62 GLU cc_start: 0.7477 (mm-30) cc_final: 0.7166 (mm-30) REVERT: F 68 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7736 (tttm) REVERT: F 92 ASP cc_start: 0.7734 (t0) cc_final: 0.7516 (t0) REVERT: F 162 GLU cc_start: 0.6587 (mp0) cc_final: 0.6308 (mm-30) REVERT: G 49 LYS cc_start: 0.8096 (mttm) cc_final: 0.7880 (mtpm) REVERT: G 62 GLU cc_start: 0.7480 (mm-30) cc_final: 0.7170 (mm-30) REVERT: G 68 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7736 (tttm) REVERT: G 92 ASP cc_start: 0.7735 (t0) cc_final: 0.7516 (t0) REVERT: G 162 GLU cc_start: 0.6588 (mp0) cc_final: 0.6309 (mm-30) REVERT: H 49 LYS cc_start: 0.8092 (mttm) cc_final: 0.7877 (mtpm) REVERT: H 62 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7166 (mm-30) REVERT: H 68 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7737 (tttm) REVERT: H 92 ASP cc_start: 0.7735 (t0) cc_final: 0.7517 (t0) REVERT: H 162 GLU cc_start: 0.6588 (mp0) cc_final: 0.6308 (mm-30) REVERT: I 49 LYS cc_start: 0.8087 (mttm) cc_final: 0.7870 (mtpm) REVERT: I 62 GLU cc_start: 0.7480 (mm-30) cc_final: 0.7169 (mm-30) REVERT: I 68 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7735 (tttm) REVERT: I 92 ASP cc_start: 0.7736 (t0) cc_final: 0.7518 (t0) REVERT: I 162 GLU cc_start: 0.6587 (mp0) cc_final: 0.6308 (mm-30) REVERT: J 49 LYS cc_start: 0.8093 (mttm) cc_final: 0.7877 (mtpm) REVERT: J 62 GLU cc_start: 0.7477 (mm-30) cc_final: 0.7167 (mm-30) REVERT: J 68 LYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7735 (tttm) REVERT: J 92 ASP cc_start: 0.7737 (t0) cc_final: 0.7518 (t0) REVERT: J 162 GLU cc_start: 0.6589 (mp0) cc_final: 0.6308 (mm-30) REVERT: K 49 LYS cc_start: 0.8086 (mttm) cc_final: 0.7870 (mtpm) REVERT: K 62 GLU cc_start: 0.7481 (mm-30) cc_final: 0.7170 (mm-30) REVERT: K 68 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7737 (tttm) REVERT: K 92 ASP cc_start: 0.7736 (t0) cc_final: 0.7517 (t0) REVERT: K 162 GLU cc_start: 0.6588 (mp0) cc_final: 0.6308 (mm-30) REVERT: L 49 LYS cc_start: 0.8093 (mttm) cc_final: 0.7878 (mtpm) REVERT: L 62 GLU cc_start: 0.7478 (mm-30) cc_final: 0.7168 (mm-30) REVERT: L 68 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7736 (tttm) REVERT: L 92 ASP cc_start: 0.7736 (t0) cc_final: 0.7517 (t0) REVERT: L 162 GLU cc_start: 0.6589 (mp0) cc_final: 0.6308 (mm-30) REVERT: M 49 LYS cc_start: 0.8095 (mttm) cc_final: 0.7879 (mtpm) REVERT: M 62 GLU cc_start: 0.7468 (mm-30) cc_final: 0.7158 (mm-30) REVERT: M 68 LYS cc_start: 0.7942 (OUTLIER) cc_final: 0.7738 (tttm) REVERT: M 92 ASP cc_start: 0.7734 (t0) cc_final: 0.7516 (t0) REVERT: M 162 GLU cc_start: 0.6587 (mp0) cc_final: 0.6308 (mm-30) REVERT: N 49 LYS cc_start: 0.8096 (mttm) cc_final: 0.7880 (mtpm) REVERT: N 62 GLU cc_start: 0.7475 (mm-30) cc_final: 0.7166 (mm-30) REVERT: N 68 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7737 (tttm) REVERT: N 92 ASP cc_start: 0.7734 (t0) cc_final: 0.7516 (t0) REVERT: N 162 GLU cc_start: 0.6587 (mp0) cc_final: 0.6309 (mm-30) REVERT: O 49 LYS cc_start: 0.8086 (mttm) cc_final: 0.7870 (mtpm) REVERT: O 62 GLU cc_start: 0.7473 (mm-30) cc_final: 0.7164 (mm-30) REVERT: O 68 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7736 (tttm) REVERT: O 92 ASP cc_start: 0.7735 (t0) cc_final: 0.7516 (t0) REVERT: O 162 GLU cc_start: 0.6588 (mp0) cc_final: 0.6308 (mm-30) REVERT: P 49 LYS cc_start: 0.8093 (mttm) cc_final: 0.7877 (mtpm) REVERT: P 62 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7166 (mm-30) REVERT: P 68 LYS cc_start: 0.7942 (OUTLIER) cc_final: 0.7737 (tttm) REVERT: P 92 ASP cc_start: 0.7735 (t0) cc_final: 0.7518 (t0) REVERT: P 162 GLU cc_start: 0.6587 (mp0) cc_final: 0.6308 (mm-30) REVERT: Q 49 LYS cc_start: 0.8087 (mttm) cc_final: 0.7871 (mtpm) REVERT: Q 62 GLU cc_start: 0.7474 (mm-30) cc_final: 0.7165 (mm-30) REVERT: Q 68 LYS cc_start: 0.7942 (OUTLIER) cc_final: 0.7737 (tttm) REVERT: Q 92 ASP cc_start: 0.7735 (t0) cc_final: 0.7517 (t0) REVERT: Q 162 GLU cc_start: 0.6588 (mp0) cc_final: 0.6309 (mm-30) REVERT: R 49 LYS cc_start: 0.8094 (mttm) cc_final: 0.7878 (mtpm) REVERT: R 62 GLU cc_start: 0.7484 (mm-30) cc_final: 0.7174 (mm-30) REVERT: R 68 LYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7735 (tttm) REVERT: R 92 ASP cc_start: 0.7736 (t0) cc_final: 0.7518 (t0) REVERT: R 162 GLU cc_start: 0.6588 (mp0) cc_final: 0.6307 (mm-30) REVERT: S 49 LYS cc_start: 0.8088 (mttm) cc_final: 0.7872 (mtpm) REVERT: S 62 GLU cc_start: 0.7482 (mm-30) cc_final: 0.7172 (mm-30) REVERT: S 68 LYS cc_start: 0.7937 (OUTLIER) cc_final: 0.7734 (tttm) REVERT: S 92 ASP cc_start: 0.7735 (t0) cc_final: 0.7517 (t0) REVERT: S 162 GLU cc_start: 0.6590 (mp0) cc_final: 0.6309 (mm-30) REVERT: T 49 LYS cc_start: 0.8089 (mttm) cc_final: 0.7873 (mtpm) REVERT: T 62 GLU cc_start: 0.7477 (mm-30) cc_final: 0.7167 (mm-30) REVERT: T 68 LYS cc_start: 0.7942 (OUTLIER) cc_final: 0.7738 (tttm) REVERT: T 92 ASP cc_start: 0.7734 (t0) cc_final: 0.7515 (t0) REVERT: T 162 GLU cc_start: 0.6588 (mp0) cc_final: 0.6309 (mm-30) REVERT: U 49 LYS cc_start: 0.8088 (mttm) cc_final: 0.7871 (mtpm) REVERT: U 62 GLU cc_start: 0.7474 (mm-30) cc_final: 0.7164 (mm-30) REVERT: U 68 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7737 (tttm) REVERT: U 92 ASP cc_start: 0.7734 (t0) cc_final: 0.7516 (t0) REVERT: U 162 GLU cc_start: 0.6587 (mp0) cc_final: 0.6308 (mm-30) REVERT: V 49 LYS cc_start: 0.8095 (mttm) cc_final: 0.7880 (mtpm) REVERT: V 62 GLU cc_start: 0.7475 (mm-30) cc_final: 0.7166 (mm-30) REVERT: V 68 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7736 (tttm) REVERT: V 92 ASP cc_start: 0.7735 (t0) cc_final: 0.7517 (t0) REVERT: V 162 GLU cc_start: 0.6589 (mp0) cc_final: 0.6309 (mm-30) REVERT: W 49 LYS cc_start: 0.8094 (mttm) cc_final: 0.7879 (mtpm) REVERT: W 62 GLU cc_start: 0.7481 (mm-30) cc_final: 0.7171 (mm-30) REVERT: W 68 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7736 (tttm) REVERT: W 92 ASP cc_start: 0.7735 (t0) cc_final: 0.7517 (t0) REVERT: W 162 GLU cc_start: 0.6588 (mp0) cc_final: 0.6309 (mm-30) REVERT: X 49 LYS cc_start: 0.8087 (mttm) cc_final: 0.7870 (mtpm) REVERT: X 62 GLU cc_start: 0.7475 (mm-30) cc_final: 0.7165 (mm-30) REVERT: X 68 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7736 (tttm) REVERT: X 92 ASP cc_start: 0.7735 (t0) cc_final: 0.7518 (t0) REVERT: X 162 GLU cc_start: 0.6588 (mp0) cc_final: 0.6308 (mm-30) outliers start: 72 outliers final: 0 residues processed: 816 average time/residue: 1.7914 time to fit residues: 1673.5331 Evaluate side-chains 816 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 792 time to evaluate : 3.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain C residue 68 LYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain F residue 68 LYS Chi-restraints excluded: chain G residue 68 LYS Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain I residue 68 LYS Chi-restraints excluded: chain J residue 68 LYS Chi-restraints excluded: chain K residue 68 LYS Chi-restraints excluded: chain L residue 68 LYS Chi-restraints excluded: chain M residue 68 LYS Chi-restraints excluded: chain N residue 68 LYS Chi-restraints excluded: chain O residue 68 LYS Chi-restraints excluded: chain P residue 68 LYS Chi-restraints excluded: chain Q residue 68 LYS Chi-restraints excluded: chain R residue 68 LYS Chi-restraints excluded: chain S residue 68 LYS Chi-restraints excluded: chain T residue 68 LYS Chi-restraints excluded: chain U residue 68 LYS Chi-restraints excluded: chain V residue 68 LYS Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain X residue 68 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 3.9990 chunk 223 optimal weight: 6.9990 chunk 5 optimal weight: 0.5980 chunk 293 optimal weight: 8.9990 chunk 162 optimal weight: 1.9990 chunk 336 optimal weight: 2.9990 chunk 272 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 201 optimal weight: 20.0000 chunk 353 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 112 GLN B 14 GLN B 112 GLN C 14 GLN C 112 GLN D 14 GLN D 112 GLN E 14 GLN E 112 GLN F 14 GLN F 112 GLN G 14 GLN G 112 GLN H 14 GLN H 112 GLN I 14 GLN I 112 GLN J 14 GLN J 112 GLN K 14 GLN K 112 GLN L 14 GLN L 112 GLN M 14 GLN M 112 GLN N 14 GLN N 112 GLN O 14 GLN O 112 GLN P 14 GLN P 112 GLN Q 14 GLN Q 112 GLN R 14 GLN R 112 GLN S 14 GLN S 112 GLN T 14 GLN T 112 GLN U 14 GLN U 112 GLN V 14 GLN V 112 GLN W 14 GLN W 112 GLN X 14 GLN X 112 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 35616 Z= 0.200 Angle : 0.614 5.383 48072 Z= 0.334 Chirality : 0.038 0.127 4992 Planarity : 0.005 0.047 6384 Dihedral : 4.571 18.306 4848 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.27 % Allowed : 7.01 % Favored : 91.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.31 (0.13), residues: 4440 helix: 4.04 (0.08), residues: 3528 sheet: None (None), residues: 0 loop : 1.12 (0.25), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP E 93 HIS 0.003 0.001 HIS K 60 PHE 0.020 0.002 PHE F 41 TYR 0.016 0.002 TYR R 137 ARG 0.003 0.001 ARG S 79 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 840 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 792 time to evaluate : 3.285 Fit side-chains REVERT: A 49 LYS cc_start: 0.8132 (mttm) cc_final: 0.7921 (mtpm) REVERT: A 62 GLU cc_start: 0.7441 (mm-30) cc_final: 0.7137 (mm-30) REVERT: A 92 ASP cc_start: 0.7834 (t0) cc_final: 0.7586 (t0) REVERT: A 162 GLU cc_start: 0.6596 (mp0) cc_final: 0.6333 (mm-30) REVERT: B 49 LYS cc_start: 0.8142 (mttm) cc_final: 0.7928 (mtpm) REVERT: B 62 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7144 (mm-30) REVERT: B 92 ASP cc_start: 0.7834 (t0) cc_final: 0.7586 (t0) REVERT: B 162 GLU cc_start: 0.6596 (mp0) cc_final: 0.6334 (mm-30) REVERT: C 49 LYS cc_start: 0.8141 (mttm) cc_final: 0.7927 (mtpm) REVERT: C 62 GLU cc_start: 0.7446 (mm-30) cc_final: 0.7145 (mm-30) REVERT: C 92 ASP cc_start: 0.7835 (t0) cc_final: 0.7587 (t0) REVERT: C 162 GLU cc_start: 0.6596 (mp0) cc_final: 0.6333 (mm-30) REVERT: D 49 LYS cc_start: 0.8140 (mttm) cc_final: 0.7926 (mtpm) REVERT: D 62 GLU cc_start: 0.7443 (mm-30) cc_final: 0.7141 (mm-30) REVERT: D 92 ASP cc_start: 0.7835 (t0) cc_final: 0.7586 (t0) REVERT: D 162 GLU cc_start: 0.6594 (mp0) cc_final: 0.6332 (mm-30) REVERT: E 49 LYS cc_start: 0.8140 (mttm) cc_final: 0.7927 (mtpm) REVERT: E 62 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7144 (mm-30) REVERT: E 92 ASP cc_start: 0.7835 (t0) cc_final: 0.7587 (t0) REVERT: E 162 GLU cc_start: 0.6594 (mp0) cc_final: 0.6332 (mm-30) REVERT: F 49 LYS cc_start: 0.8141 (mttm) cc_final: 0.7926 (mtpm) REVERT: F 62 GLU cc_start: 0.7448 (mm-30) cc_final: 0.7147 (mm-30) REVERT: F 92 ASP cc_start: 0.7835 (t0) cc_final: 0.7587 (t0) REVERT: F 162 GLU cc_start: 0.6594 (mp0) cc_final: 0.6332 (mm-30) REVERT: G 49 LYS cc_start: 0.8133 (mttm) cc_final: 0.7922 (mtpm) REVERT: G 62 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7143 (mm-30) REVERT: G 68 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7711 (tttm) REVERT: G 92 ASP cc_start: 0.7834 (t0) cc_final: 0.7586 (t0) REVERT: G 162 GLU cc_start: 0.6596 (mp0) cc_final: 0.6334 (mm-30) REVERT: H 49 LYS cc_start: 0.8141 (mttm) cc_final: 0.7927 (mtpm) REVERT: H 62 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7143 (mm-30) REVERT: H 68 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7710 (tttm) REVERT: H 92 ASP cc_start: 0.7835 (t0) cc_final: 0.7587 (t0) REVERT: H 162 GLU cc_start: 0.6595 (mp0) cc_final: 0.6333 (mm-30) REVERT: I 49 LYS cc_start: 0.8134 (mttm) cc_final: 0.7918 (mtpm) REVERT: I 62 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7145 (mm-30) REVERT: I 68 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7711 (tttm) REVERT: I 92 ASP cc_start: 0.7835 (t0) cc_final: 0.7587 (t0) REVERT: I 162 GLU cc_start: 0.6595 (mp0) cc_final: 0.6333 (mm-30) REVERT: J 49 LYS cc_start: 0.8132 (mttm) cc_final: 0.7921 (mtpm) REVERT: J 62 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7142 (mm-30) REVERT: J 68 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7710 (tttm) REVERT: J 92 ASP cc_start: 0.7836 (t0) cc_final: 0.7587 (t0) REVERT: J 162 GLU cc_start: 0.6595 (mp0) cc_final: 0.6333 (mm-30) REVERT: K 49 LYS cc_start: 0.8133 (mttm) cc_final: 0.7918 (mtpm) REVERT: K 62 GLU cc_start: 0.7442 (mm-30) cc_final: 0.7141 (mm-30) REVERT: K 92 ASP cc_start: 0.7835 (t0) cc_final: 0.7587 (t0) REVERT: K 162 GLU cc_start: 0.6595 (mp0) cc_final: 0.6333 (mm-30) REVERT: L 49 LYS cc_start: 0.8141 (mttm) cc_final: 0.7927 (mtpm) REVERT: L 62 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7144 (mm-30) REVERT: L 92 ASP cc_start: 0.7835 (t0) cc_final: 0.7586 (t0) REVERT: L 162 GLU cc_start: 0.6596 (mp0) cc_final: 0.6333 (mm-30) REVERT: M 49 LYS cc_start: 0.8133 (mttm) cc_final: 0.7921 (mtpm) REVERT: M 62 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7144 (mm-30) REVERT: M 92 ASP cc_start: 0.7835 (t0) cc_final: 0.7586 (t0) REVERT: M 162 GLU cc_start: 0.6594 (mp0) cc_final: 0.6332 (mm-30) REVERT: N 49 LYS cc_start: 0.8133 (mttm) cc_final: 0.7922 (mtpm) REVERT: N 62 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7142 (mm-30) REVERT: N 68 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7711 (tttm) REVERT: N 92 ASP cc_start: 0.7834 (t0) cc_final: 0.7586 (t0) REVERT: N 162 GLU cc_start: 0.6595 (mp0) cc_final: 0.6334 (mm-30) REVERT: O 49 LYS cc_start: 0.8134 (mttm) cc_final: 0.7919 (mtpm) REVERT: O 62 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7143 (mm-30) REVERT: O 68 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7710 (tttm) REVERT: O 92 ASP cc_start: 0.7834 (t0) cc_final: 0.7586 (t0) REVERT: O 162 GLU cc_start: 0.6596 (mp0) cc_final: 0.6333 (mm-30) REVERT: P 49 LYS cc_start: 0.8133 (mttm) cc_final: 0.7921 (mtpm) REVERT: P 62 GLU cc_start: 0.7446 (mm-30) cc_final: 0.7144 (mm-30) REVERT: P 68 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7711 (tttm) REVERT: P 92 ASP cc_start: 0.7835 (t0) cc_final: 0.7586 (t0) REVERT: P 162 GLU cc_start: 0.6595 (mp0) cc_final: 0.6333 (mm-30) REVERT: Q 49 LYS cc_start: 0.8135 (mttm) cc_final: 0.7920 (mtpm) REVERT: Q 62 GLU cc_start: 0.7446 (mm-30) cc_final: 0.7145 (mm-30) REVERT: Q 68 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7710 (tttm) REVERT: Q 92 ASP cc_start: 0.7834 (t0) cc_final: 0.7586 (t0) REVERT: Q 162 GLU cc_start: 0.6596 (mp0) cc_final: 0.6334 (mm-30) REVERT: R 49 LYS cc_start: 0.8131 (mttm) cc_final: 0.7920 (mtpm) REVERT: R 62 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7143 (mm-30) REVERT: R 68 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7709 (tttm) REVERT: R 92 ASP cc_start: 0.7834 (t0) cc_final: 0.7586 (t0) REVERT: R 162 GLU cc_start: 0.6594 (mp0) cc_final: 0.6332 (mm-30) REVERT: S 49 LYS cc_start: 0.8134 (mttm) cc_final: 0.7919 (mtpm) REVERT: S 62 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7143 (mm-30) REVERT: S 68 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7711 (tttm) REVERT: S 92 ASP cc_start: 0.7835 (t0) cc_final: 0.7586 (t0) REVERT: S 162 GLU cc_start: 0.6594 (mp0) cc_final: 0.6332 (mm-30) REVERT: T 49 LYS cc_start: 0.8135 (mttm) cc_final: 0.7919 (mtpm) REVERT: T 62 GLU cc_start: 0.7446 (mm-30) cc_final: 0.7144 (mm-30) REVERT: T 92 ASP cc_start: 0.7834 (t0) cc_final: 0.7586 (t0) REVERT: T 162 GLU cc_start: 0.6596 (mp0) cc_final: 0.6334 (mm-30) REVERT: U 49 LYS cc_start: 0.8134 (mttm) cc_final: 0.7918 (mtpm) REVERT: U 62 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7142 (mm-30) REVERT: U 68 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7710 (tttm) REVERT: U 92 ASP cc_start: 0.7835 (t0) cc_final: 0.7586 (t0) REVERT: U 162 GLU cc_start: 0.6594 (mp0) cc_final: 0.6332 (mm-30) REVERT: V 49 LYS cc_start: 0.8132 (mttm) cc_final: 0.7921 (mtpm) REVERT: V 62 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7142 (mm-30) REVERT: V 68 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7710 (tttm) REVERT: V 92 ASP cc_start: 0.7835 (t0) cc_final: 0.7586 (t0) REVERT: V 162 GLU cc_start: 0.6594 (mp0) cc_final: 0.6332 (mm-30) REVERT: W 49 LYS cc_start: 0.8134 (mttm) cc_final: 0.7922 (mtpm) REVERT: W 62 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7146 (mm-30) REVERT: W 68 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7711 (tttm) REVERT: W 92 ASP cc_start: 0.7834 (t0) cc_final: 0.7586 (t0) REVERT: W 162 GLU cc_start: 0.6596 (mp0) cc_final: 0.6334 (mm-30) REVERT: X 49 LYS cc_start: 0.8132 (mttm) cc_final: 0.7917 (mtpm) REVERT: X 62 GLU cc_start: 0.7443 (mm-30) cc_final: 0.7141 (mm-30) REVERT: X 68 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7709 (tttm) REVERT: X 92 ASP cc_start: 0.7835 (t0) cc_final: 0.7586 (t0) REVERT: X 162 GLU cc_start: 0.6594 (mp0) cc_final: 0.6332 (mm-30) outliers start: 48 outliers final: 0 residues processed: 816 average time/residue: 1.7755 time to fit residues: 1657.1810 Evaluate side-chains 796 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 782 time to evaluate : 3.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 68 LYS Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain I residue 68 LYS Chi-restraints excluded: chain J residue 68 LYS Chi-restraints excluded: chain N residue 68 LYS Chi-restraints excluded: chain O residue 68 LYS Chi-restraints excluded: chain P residue 68 LYS Chi-restraints excluded: chain Q residue 68 LYS Chi-restraints excluded: chain R residue 68 LYS Chi-restraints excluded: chain S residue 68 LYS Chi-restraints excluded: chain U residue 68 LYS Chi-restraints excluded: chain V residue 68 LYS Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain X residue 68 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 10.0000 chunk 355 optimal weight: 0.4980 chunk 77 optimal weight: 6.9990 chunk 231 optimal weight: 0.9990 chunk 97 optimal weight: 10.0000 chunk 394 optimal weight: 0.5980 chunk 327 optimal weight: 0.9990 chunk 182 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 207 optimal weight: 8.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 60 HIS A 112 GLN B 14 GLN B 60 HIS B 112 GLN C 14 GLN C 60 HIS C 112 GLN D 14 GLN D 60 HIS D 112 GLN E 14 GLN E 60 HIS E 112 GLN F 14 GLN F 60 HIS F 112 GLN G 14 GLN G 60 HIS G 112 GLN H 14 GLN H 60 HIS H 112 GLN I 14 GLN I 60 HIS I 112 GLN J 14 GLN J 60 HIS J 112 GLN K 14 GLN K 60 HIS K 112 GLN L 14 GLN L 60 HIS L 112 GLN M 14 GLN M 60 HIS M 112 GLN N 14 GLN N 60 HIS N 112 GLN O 14 GLN O 60 HIS O 112 GLN P 14 GLN P 60 HIS P 112 GLN Q 14 GLN Q 60 HIS Q 112 GLN R 14 GLN R 60 HIS R 112 GLN S 14 GLN S 60 HIS S 112 GLN T 14 GLN T 60 HIS T 112 GLN U 14 GLN U 60 HIS U 112 GLN V 14 GLN V 60 HIS V 112 GLN W 14 GLN W 60 HIS W 112 GLN X 14 GLN X 60 HIS X 112 GLN Total number of N/Q/H flips: 72 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 35616 Z= 0.182 Angle : 0.589 5.175 48072 Z= 0.321 Chirality : 0.038 0.126 4992 Planarity : 0.004 0.043 6384 Dihedral : 4.434 19.600 4808 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.01 % Allowed : 7.27 % Favored : 91.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.37 (0.13), residues: 4440 helix: 4.09 (0.08), residues: 3528 sheet: None (None), residues: 0 loop : 1.12 (0.25), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP W 93 HIS 0.003 0.001 HIS T 128 PHE 0.019 0.002 PHE H 41 TYR 0.016 0.002 TYR R 137 ARG 0.002 0.001 ARG B 79 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 820 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 782 time to evaluate : 3.237 Fit side-chains REVERT: A 49 LYS cc_start: 0.8116 (mttm) cc_final: 0.7903 (mtpm) REVERT: A 62 GLU cc_start: 0.7443 (mm-30) cc_final: 0.7149 (mm-30) REVERT: A 92 ASP cc_start: 0.7820 (t0) cc_final: 0.7575 (t0) REVERT: A 162 GLU cc_start: 0.6569 (mp0) cc_final: 0.6302 (mm-30) REVERT: B 49 LYS cc_start: 0.8116 (mttm) cc_final: 0.7903 (mtpm) REVERT: B 62 GLU cc_start: 0.7457 (mm-30) cc_final: 0.7166 (mm-30) REVERT: B 92 ASP cc_start: 0.7820 (t0) cc_final: 0.7575 (t0) REVERT: B 162 GLU cc_start: 0.6569 (mp0) cc_final: 0.6303 (mm-30) REVERT: C 49 LYS cc_start: 0.8115 (mttm) cc_final: 0.7902 (mtpm) REVERT: C 62 GLU cc_start: 0.7450 (mm-30) cc_final: 0.7158 (mm-30) REVERT: C 92 ASP cc_start: 0.7821 (t0) cc_final: 0.7576 (t0) REVERT: C 162 GLU cc_start: 0.6569 (mp0) cc_final: 0.6304 (mm-30) REVERT: D 49 LYS cc_start: 0.8115 (mttm) cc_final: 0.7902 (mtpm) REVERT: D 62 GLU cc_start: 0.7456 (mm-30) cc_final: 0.7164 (mm-30) REVERT: D 92 ASP cc_start: 0.7819 (t0) cc_final: 0.7575 (t0) REVERT: D 162 GLU cc_start: 0.6569 (mp0) cc_final: 0.6303 (mm-30) REVERT: E 49 LYS cc_start: 0.8116 (mttm) cc_final: 0.7903 (mtpm) REVERT: E 62 GLU cc_start: 0.7450 (mm-30) cc_final: 0.7157 (mm-30) REVERT: E 92 ASP cc_start: 0.7820 (t0) cc_final: 0.7575 (t0) REVERT: E 162 GLU cc_start: 0.6569 (mp0) cc_final: 0.6303 (mm-30) REVERT: F 49 LYS cc_start: 0.8116 (mttm) cc_final: 0.7902 (mtpm) REVERT: F 62 GLU cc_start: 0.7451 (mm-30) cc_final: 0.7158 (mm-30) REVERT: F 92 ASP cc_start: 0.7820 (t0) cc_final: 0.7575 (t0) REVERT: F 162 GLU cc_start: 0.6567 (mp0) cc_final: 0.6302 (mm-30) REVERT: G 49 LYS cc_start: 0.8116 (mttm) cc_final: 0.7903 (mtpm) REVERT: G 62 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7157 (mm-30) REVERT: G 68 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7692 (tttm) REVERT: G 92 ASP cc_start: 0.7819 (t0) cc_final: 0.7574 (t0) REVERT: G 162 GLU cc_start: 0.6568 (mp0) cc_final: 0.6303 (mm-30) REVERT: H 49 LYS cc_start: 0.8115 (mttm) cc_final: 0.7902 (mtpm) REVERT: H 62 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7157 (mm-30) REVERT: H 68 LYS cc_start: 0.7897 (OUTLIER) cc_final: 0.7690 (tttm) REVERT: H 92 ASP cc_start: 0.7821 (t0) cc_final: 0.7575 (t0) REVERT: H 162 GLU cc_start: 0.6569 (mp0) cc_final: 0.6303 (mm-30) REVERT: I 49 LYS cc_start: 0.8124 (mttm) cc_final: 0.7908 (mtpm) REVERT: I 62 GLU cc_start: 0.7450 (mm-30) cc_final: 0.7157 (mm-30) REVERT: I 68 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7691 (tttm) REVERT: I 92 ASP cc_start: 0.7821 (t0) cc_final: 0.7576 (t0) REVERT: I 162 GLU cc_start: 0.6569 (mp0) cc_final: 0.6304 (mm-30) REVERT: J 49 LYS cc_start: 0.8114 (mttm) cc_final: 0.7902 (mtpm) REVERT: J 62 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7157 (mm-30) REVERT: J 68 LYS cc_start: 0.7897 (OUTLIER) cc_final: 0.7690 (tttm) REVERT: J 92 ASP cc_start: 0.7820 (t0) cc_final: 0.7575 (t0) REVERT: J 162 GLU cc_start: 0.6569 (mp0) cc_final: 0.6303 (mm-30) REVERT: K 49 LYS cc_start: 0.8125 (mttm) cc_final: 0.7909 (mtpm) REVERT: K 62 GLU cc_start: 0.7448 (mm-30) cc_final: 0.7156 (mm-30) REVERT: K 92 ASP cc_start: 0.7820 (t0) cc_final: 0.7575 (t0) REVERT: K 162 GLU cc_start: 0.6569 (mp0) cc_final: 0.6303 (mm-30) REVERT: L 49 LYS cc_start: 0.8116 (mttm) cc_final: 0.7903 (mtpm) REVERT: L 62 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7157 (mm-30) REVERT: L 92 ASP cc_start: 0.7820 (t0) cc_final: 0.7576 (t0) REVERT: L 162 GLU cc_start: 0.6569 (mp0) cc_final: 0.6302 (mm-30) REVERT: M 49 LYS cc_start: 0.8116 (mttm) cc_final: 0.7902 (mtpm) REVERT: M 62 GLU cc_start: 0.7452 (mm-30) cc_final: 0.7160 (mm-30) REVERT: M 92 ASP cc_start: 0.7820 (t0) cc_final: 0.7575 (t0) REVERT: M 162 GLU cc_start: 0.6567 (mp0) cc_final: 0.6302 (mm-30) REVERT: N 49 LYS cc_start: 0.8116 (mttm) cc_final: 0.7903 (mtpm) REVERT: N 62 GLU cc_start: 0.7450 (mm-30) cc_final: 0.7157 (mm-30) REVERT: N 68 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7691 (tttm) REVERT: N 92 ASP cc_start: 0.7819 (t0) cc_final: 0.7574 (t0) REVERT: N 162 GLU cc_start: 0.6568 (mp0) cc_final: 0.6303 (mm-30) REVERT: O 49 LYS cc_start: 0.8126 (mttm) cc_final: 0.7910 (mtpm) REVERT: O 62 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7158 (mm-30) REVERT: O 68 LYS cc_start: 0.7897 (OUTLIER) cc_final: 0.7690 (tttm) REVERT: O 92 ASP cc_start: 0.7820 (t0) cc_final: 0.7576 (t0) REVERT: O 162 GLU cc_start: 0.6569 (mp0) cc_final: 0.6302 (mm-30) REVERT: P 49 LYS cc_start: 0.8115 (mttm) cc_final: 0.7901 (mtpm) REVERT: P 62 GLU cc_start: 0.7450 (mm-30) cc_final: 0.7158 (mm-30) REVERT: P 68 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7691 (tttm) REVERT: P 92 ASP cc_start: 0.7821 (t0) cc_final: 0.7576 (t0) REVERT: P 162 GLU cc_start: 0.6569 (mp0) cc_final: 0.6304 (mm-30) REVERT: Q 49 LYS cc_start: 0.8126 (mttm) cc_final: 0.7910 (mtpm) REVERT: Q 62 GLU cc_start: 0.7450 (mm-30) cc_final: 0.7158 (mm-30) REVERT: Q 68 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7691 (tttm) REVERT: Q 92 ASP cc_start: 0.7820 (t0) cc_final: 0.7575 (t0) REVERT: Q 162 GLU cc_start: 0.6568 (mp0) cc_final: 0.6303 (mm-30) REVERT: R 49 LYS cc_start: 0.8115 (mttm) cc_final: 0.7902 (mtpm) REVERT: R 62 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7157 (mm-30) REVERT: R 68 LYS cc_start: 0.7897 (OUTLIER) cc_final: 0.7690 (tttm) REVERT: R 92 ASP cc_start: 0.7819 (t0) cc_final: 0.7575 (t0) REVERT: R 162 GLU cc_start: 0.6569 (mp0) cc_final: 0.6303 (mm-30) REVERT: S 49 LYS cc_start: 0.8125 (mttm) cc_final: 0.7909 (mtpm) REVERT: S 62 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7156 (mm-30) REVERT: S 68 LYS cc_start: 0.7897 (OUTLIER) cc_final: 0.7690 (tttm) REVERT: S 92 ASP cc_start: 0.7820 (t0) cc_final: 0.7575 (t0) REVERT: S 162 GLU cc_start: 0.6569 (mp0) cc_final: 0.6302 (mm-30) REVERT: T 49 LYS cc_start: 0.8126 (mttm) cc_final: 0.7910 (mtpm) REVERT: T 62 GLU cc_start: 0.7448 (mm-30) cc_final: 0.7156 (mm-30) REVERT: T 92 ASP cc_start: 0.7818 (t0) cc_final: 0.7574 (t0) REVERT: T 162 GLU cc_start: 0.6568 (mp0) cc_final: 0.6303 (mm-30) REVERT: U 49 LYS cc_start: 0.8126 (mttm) cc_final: 0.7909 (mtpm) REVERT: U 62 GLU cc_start: 0.7451 (mm-30) cc_final: 0.7158 (mm-30) REVERT: U 68 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7690 (tttm) REVERT: U 92 ASP cc_start: 0.7820 (t0) cc_final: 0.7576 (t0) REVERT: U 162 GLU cc_start: 0.6567 (mp0) cc_final: 0.6302 (mm-30) REVERT: V 49 LYS cc_start: 0.8115 (mttm) cc_final: 0.7902 (mtpm) REVERT: V 62 GLU cc_start: 0.7448 (mm-30) cc_final: 0.7155 (mm-30) REVERT: V 68 LYS cc_start: 0.7897 (OUTLIER) cc_final: 0.7690 (tttm) REVERT: V 92 ASP cc_start: 0.7820 (t0) cc_final: 0.7575 (t0) REVERT: V 162 GLU cc_start: 0.6569 (mp0) cc_final: 0.6303 (mm-30) REVERT: W 49 LYS cc_start: 0.8116 (mttm) cc_final: 0.7903 (mtpm) REVERT: W 62 GLU cc_start: 0.7450 (mm-30) cc_final: 0.7158 (mm-30) REVERT: W 68 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7692 (tttm) REVERT: W 92 ASP cc_start: 0.7820 (t0) cc_final: 0.7576 (t0) REVERT: W 162 GLU cc_start: 0.6569 (mp0) cc_final: 0.6303 (mm-30) REVERT: X 49 LYS cc_start: 0.8125 (mttm) cc_final: 0.7909 (mtpm) REVERT: X 62 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7153 (mm-30) REVERT: X 68 LYS cc_start: 0.7897 (OUTLIER) cc_final: 0.7689 (tttm) REVERT: X 92 ASP cc_start: 0.7819 (t0) cc_final: 0.7574 (t0) REVERT: X 162 GLU cc_start: 0.6569 (mp0) cc_final: 0.6303 (mm-30) outliers start: 38 outliers final: 0 residues processed: 806 average time/residue: 1.7480 time to fit residues: 1613.8443 Evaluate side-chains 796 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 782 time to evaluate : 3.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 68 LYS Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain I residue 68 LYS Chi-restraints excluded: chain J residue 68 LYS Chi-restraints excluded: chain N residue 68 LYS Chi-restraints excluded: chain O residue 68 LYS Chi-restraints excluded: chain P residue 68 LYS Chi-restraints excluded: chain Q residue 68 LYS Chi-restraints excluded: chain R residue 68 LYS Chi-restraints excluded: chain S residue 68 LYS Chi-restraints excluded: chain U residue 68 LYS Chi-restraints excluded: chain V residue 68 LYS Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain X residue 68 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 224 optimal weight: 0.7980 chunk 288 optimal weight: 3.9990 chunk 223 optimal weight: 4.9990 chunk 332 optimal weight: 1.9990 chunk 220 optimal weight: 2.9990 chunk 393 optimal weight: 7.9990 chunk 246 optimal weight: 2.9990 chunk 239 optimal weight: 7.9990 chunk 181 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 112 GLN B 14 GLN B 112 GLN C 14 GLN C 112 GLN D 14 GLN D 112 GLN E 14 GLN E 112 GLN F 14 GLN F 112 GLN G 14 GLN G 112 GLN H 14 GLN H 112 GLN I 14 GLN I 112 GLN J 14 GLN J 112 GLN K 14 GLN K 112 GLN L 14 GLN L 112 GLN M 14 GLN M 112 GLN N 14 GLN N 112 GLN O 14 GLN O 112 GLN P 14 GLN P 112 GLN Q 14 GLN Q 112 GLN R 14 GLN R 112 GLN S 14 GLN S 112 GLN T 14 GLN T 112 GLN U 14 GLN U 112 GLN V 14 GLN V 112 GLN W 14 GLN W 112 GLN X 14 GLN X 112 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 35616 Z= 0.203 Angle : 0.615 5.400 48072 Z= 0.336 Chirality : 0.038 0.129 4992 Planarity : 0.005 0.049 6384 Dihedral : 4.451 20.215 4808 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.01 % Allowed : 7.27 % Favored : 91.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.28 (0.13), residues: 4440 helix: 4.02 (0.08), residues: 3528 sheet: None (None), residues: 0 loop : 1.13 (0.25), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP E 93 HIS 0.003 0.001 HIS V 128 PHE 0.021 0.002 PHE B 41 TYR 0.016 0.002 TYR S 137 ARG 0.003 0.001 ARG J 79 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 820 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 782 time to evaluate : 3.211 Fit side-chains REVERT: A 49 LYS cc_start: 0.8126 (mttm) cc_final: 0.7912 (mtpm) REVERT: A 62 GLU cc_start: 0.7430 (mm-30) cc_final: 0.7133 (mm-30) REVERT: A 92 ASP cc_start: 0.7841 (t0) cc_final: 0.7586 (t0) REVERT: A 162 GLU cc_start: 0.6572 (mp0) cc_final: 0.6306 (mm-30) REVERT: B 49 LYS cc_start: 0.8128 (mttm) cc_final: 0.7915 (mtpm) REVERT: B 62 GLU cc_start: 0.7439 (mm-30) cc_final: 0.7144 (mm-30) REVERT: B 92 ASP cc_start: 0.7842 (t0) cc_final: 0.7587 (t0) REVERT: B 162 GLU cc_start: 0.6572 (mp0) cc_final: 0.6307 (mm-30) REVERT: C 49 LYS cc_start: 0.8127 (mttm) cc_final: 0.7914 (mtpm) REVERT: C 62 GLU cc_start: 0.7438 (mm-30) cc_final: 0.7142 (mm-30) REVERT: C 92 ASP cc_start: 0.7843 (t0) cc_final: 0.7588 (t0) REVERT: C 162 GLU cc_start: 0.6572 (mp0) cc_final: 0.6308 (mm-30) REVERT: D 49 LYS cc_start: 0.8126 (mttm) cc_final: 0.7911 (mtpm) REVERT: D 62 GLU cc_start: 0.7438 (mm-30) cc_final: 0.7142 (mm-30) REVERT: D 92 ASP cc_start: 0.7842 (t0) cc_final: 0.7587 (t0) REVERT: D 162 GLU cc_start: 0.6570 (mp0) cc_final: 0.6306 (mm-30) REVERT: E 49 LYS cc_start: 0.8127 (mttm) cc_final: 0.7912 (mtpm) REVERT: E 62 GLU cc_start: 0.7436 (mm-30) cc_final: 0.7141 (mm-30) REVERT: E 92 ASP cc_start: 0.7842 (t0) cc_final: 0.7587 (t0) REVERT: E 162 GLU cc_start: 0.6571 (mp0) cc_final: 0.6306 (mm-30) REVERT: F 49 LYS cc_start: 0.8128 (mttm) cc_final: 0.7914 (mtpm) REVERT: F 62 GLU cc_start: 0.7439 (mm-30) cc_final: 0.7143 (mm-30) REVERT: F 92 ASP cc_start: 0.7843 (t0) cc_final: 0.7588 (t0) REVERT: F 162 GLU cc_start: 0.6571 (mp0) cc_final: 0.6307 (mm-30) REVERT: G 49 LYS cc_start: 0.8128 (mttm) cc_final: 0.7914 (mtpm) REVERT: G 62 GLU cc_start: 0.7437 (mm-30) cc_final: 0.7141 (mm-30) REVERT: G 68 LYS cc_start: 0.7905 (OUTLIER) cc_final: 0.7698 (tttm) REVERT: G 92 ASP cc_start: 0.7841 (t0) cc_final: 0.7587 (t0) REVERT: G 162 GLU cc_start: 0.6571 (mp0) cc_final: 0.6307 (mm-30) REVERT: H 49 LYS cc_start: 0.8126 (mttm) cc_final: 0.7913 (mtpm) REVERT: H 62 GLU cc_start: 0.7437 (mm-30) cc_final: 0.7141 (mm-30) REVERT: H 68 LYS cc_start: 0.7905 (OUTLIER) cc_final: 0.7698 (tttm) REVERT: H 92 ASP cc_start: 0.7843 (t0) cc_final: 0.7588 (t0) REVERT: H 162 GLU cc_start: 0.6571 (mp0) cc_final: 0.6306 (mm-30) REVERT: I 49 LYS cc_start: 0.8119 (mttm) cc_final: 0.7905 (mtpm) REVERT: I 62 GLU cc_start: 0.7439 (mm-30) cc_final: 0.7143 (mm-30) REVERT: I 68 LYS cc_start: 0.7905 (OUTLIER) cc_final: 0.7697 (tttm) REVERT: I 92 ASP cc_start: 0.7842 (t0) cc_final: 0.7587 (t0) REVERT: I 162 GLU cc_start: 0.6572 (mp0) cc_final: 0.6308 (mm-30) REVERT: J 49 LYS cc_start: 0.8126 (mttm) cc_final: 0.7913 (mtpm) REVERT: J 62 GLU cc_start: 0.7437 (mm-30) cc_final: 0.7141 (mm-30) REVERT: J 68 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7698 (tttm) REVERT: J 92 ASP cc_start: 0.7843 (t0) cc_final: 0.7587 (t0) REVERT: J 162 GLU cc_start: 0.6571 (mp0) cc_final: 0.6306 (mm-30) REVERT: K 49 LYS cc_start: 0.8119 (mttm) cc_final: 0.7905 (mtpm) REVERT: K 62 GLU cc_start: 0.7436 (mm-30) cc_final: 0.7140 (mm-30) REVERT: K 92 ASP cc_start: 0.7843 (t0) cc_final: 0.7588 (t0) REVERT: K 162 GLU cc_start: 0.6571 (mp0) cc_final: 0.6306 (mm-30) REVERT: L 49 LYS cc_start: 0.8126 (mttm) cc_final: 0.7912 (mtpm) REVERT: L 62 GLU cc_start: 0.7436 (mm-30) cc_final: 0.7140 (mm-30) REVERT: L 92 ASP cc_start: 0.7842 (t0) cc_final: 0.7586 (t0) REVERT: L 162 GLU cc_start: 0.6572 (mp0) cc_final: 0.6306 (mm-30) REVERT: M 49 LYS cc_start: 0.8128 (mttm) cc_final: 0.7914 (mtpm) REVERT: M 62 GLU cc_start: 0.7438 (mm-30) cc_final: 0.7142 (mm-30) REVERT: M 92 ASP cc_start: 0.7843 (t0) cc_final: 0.7588 (t0) REVERT: M 162 GLU cc_start: 0.6571 (mp0) cc_final: 0.6307 (mm-30) REVERT: N 49 LYS cc_start: 0.8128 (mttm) cc_final: 0.7914 (mtpm) REVERT: N 62 GLU cc_start: 0.7437 (mm-30) cc_final: 0.7141 (mm-30) REVERT: N 68 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7698 (tttm) REVERT: N 92 ASP cc_start: 0.7842 (t0) cc_final: 0.7587 (t0) REVERT: N 162 GLU cc_start: 0.6571 (mp0) cc_final: 0.6307 (mm-30) REVERT: O 49 LYS cc_start: 0.8119 (mttm) cc_final: 0.7905 (mtpm) REVERT: O 62 GLU cc_start: 0.7437 (mm-30) cc_final: 0.7142 (mm-30) REVERT: O 68 LYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7696 (tttm) REVERT: O 92 ASP cc_start: 0.7841 (t0) cc_final: 0.7586 (t0) REVERT: O 162 GLU cc_start: 0.6572 (mp0) cc_final: 0.6307 (mm-30) REVERT: P 49 LYS cc_start: 0.8126 (mttm) cc_final: 0.7913 (mtpm) REVERT: P 62 GLU cc_start: 0.7439 (mm-30) cc_final: 0.7143 (mm-30) REVERT: P 68 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7696 (tttm) REVERT: P 92 ASP cc_start: 0.7843 (t0) cc_final: 0.7588 (t0) REVERT: P 162 GLU cc_start: 0.6572 (mp0) cc_final: 0.6308 (mm-30) REVERT: Q 49 LYS cc_start: 0.8122 (mttm) cc_final: 0.7908 (mtpm) REVERT: Q 62 GLU cc_start: 0.7439 (mm-30) cc_final: 0.7144 (mm-30) REVERT: Q 68 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7697 (tttm) REVERT: Q 92 ASP cc_start: 0.7842 (t0) cc_final: 0.7587 (t0) REVERT: Q 162 GLU cc_start: 0.6572 (mp0) cc_final: 0.6307 (mm-30) REVERT: R 49 LYS cc_start: 0.8125 (mttm) cc_final: 0.7911 (mtpm) REVERT: R 62 GLU cc_start: 0.7439 (mm-30) cc_final: 0.7142 (mm-30) REVERT: R 68 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7696 (tttm) REVERT: R 92 ASP cc_start: 0.7842 (t0) cc_final: 0.7587 (t0) REVERT: R 162 GLU cc_start: 0.6570 (mp0) cc_final: 0.6307 (mm-30) REVERT: S 49 LYS cc_start: 0.8120 (mttm) cc_final: 0.7906 (mtpm) REVERT: S 62 GLU cc_start: 0.7439 (mm-30) cc_final: 0.7144 (mm-30) REVERT: S 68 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7696 (tttm) REVERT: S 92 ASP cc_start: 0.7842 (t0) cc_final: 0.7587 (t0) REVERT: S 162 GLU cc_start: 0.6571 (mp0) cc_final: 0.6306 (mm-30) REVERT: T 49 LYS cc_start: 0.8121 (mttm) cc_final: 0.7907 (mtpm) REVERT: T 62 GLU cc_start: 0.7437 (mm-30) cc_final: 0.7141 (mm-30) REVERT: T 92 ASP cc_start: 0.7841 (t0) cc_final: 0.7586 (t0) REVERT: T 162 GLU cc_start: 0.6571 (mp0) cc_final: 0.6307 (mm-30) REVERT: U 49 LYS cc_start: 0.8120 (mttm) cc_final: 0.7905 (mtpm) REVERT: U 62 GLU cc_start: 0.7439 (mm-30) cc_final: 0.7144 (mm-30) REVERT: U 68 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7695 (tttm) REVERT: U 92 ASP cc_start: 0.7843 (t0) cc_final: 0.7588 (t0) REVERT: U 162 GLU cc_start: 0.6571 (mp0) cc_final: 0.6307 (mm-30) REVERT: V 49 LYS cc_start: 0.8126 (mttm) cc_final: 0.7912 (mtpm) REVERT: V 62 GLU cc_start: 0.7438 (mm-30) cc_final: 0.7143 (mm-30) REVERT: V 68 LYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7696 (tttm) REVERT: V 92 ASP cc_start: 0.7842 (t0) cc_final: 0.7587 (t0) REVERT: V 162 GLU cc_start: 0.6571 (mp0) cc_final: 0.6306 (mm-30) REVERT: W 49 LYS cc_start: 0.8128 (mttm) cc_final: 0.7915 (mtpm) REVERT: W 62 GLU cc_start: 0.7439 (mm-30) cc_final: 0.7144 (mm-30) REVERT: W 68 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7698 (tttm) REVERT: W 92 ASP cc_start: 0.7842 (t0) cc_final: 0.7587 (t0) REVERT: W 162 GLU cc_start: 0.6572 (mp0) cc_final: 0.6307 (mm-30) REVERT: X 49 LYS cc_start: 0.8119 (mttm) cc_final: 0.7904 (mtpm) REVERT: X 62 GLU cc_start: 0.7439 (mm-30) cc_final: 0.7143 (mm-30) REVERT: X 68 LYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7694 (tttm) REVERT: X 92 ASP cc_start: 0.7843 (t0) cc_final: 0.7588 (t0) REVERT: X 162 GLU cc_start: 0.6570 (mp0) cc_final: 0.6307 (mm-30) outliers start: 38 outliers final: 0 residues processed: 806 average time/residue: 1.7820 time to fit residues: 1643.5587 Evaluate side-chains 796 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 782 time to evaluate : 3.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 68 LYS Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain I residue 68 LYS Chi-restraints excluded: chain J residue 68 LYS Chi-restraints excluded: chain N residue 68 LYS Chi-restraints excluded: chain O residue 68 LYS Chi-restraints excluded: chain P residue 68 LYS Chi-restraints excluded: chain Q residue 68 LYS Chi-restraints excluded: chain R residue 68 LYS Chi-restraints excluded: chain S residue 68 LYS Chi-restraints excluded: chain U residue 68 LYS Chi-restraints excluded: chain V residue 68 LYS Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain X residue 68 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 5.9990 chunk 157 optimal weight: 7.9990 chunk 234 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 250 optimal weight: 1.9990 chunk 267 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 309 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 112 GLN B 14 GLN B 112 GLN C 14 GLN C 112 GLN D 14 GLN D 112 GLN E 14 GLN E 112 GLN F 14 GLN F 112 GLN G 14 GLN G 112 GLN H 14 GLN H 112 GLN I 14 GLN I 112 GLN J 14 GLN J 112 GLN K 14 GLN K 112 GLN L 14 GLN L 112 GLN M 14 GLN M 112 GLN N 14 GLN N 112 GLN O 14 GLN O 112 GLN P 14 GLN P 112 GLN Q 14 GLN Q 112 GLN R 14 GLN R 112 GLN S 14 GLN S 112 GLN T 14 GLN T 112 GLN U 14 GLN U 112 GLN V 14 GLN V 112 GLN W 14 GLN W 112 GLN X 14 GLN X 112 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 35616 Z= 0.316 Angle : 0.741 5.699 48072 Z= 0.406 Chirality : 0.042 0.137 4992 Planarity : 0.006 0.063 6384 Dihedral : 4.452 20.391 4808 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.01 % Allowed : 7.27 % Favored : 91.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.94 (0.12), residues: 4440 helix: 3.78 (0.08), residues: 3528 sheet: None (None), residues: 0 loop : 0.96 (0.24), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.004 TRP B 93 HIS 0.003 0.001 HIS L 57 PHE 0.027 0.003 PHE K 41 TYR 0.019 0.004 TYR C 137 ARG 0.006 0.001 ARG C 79 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 798 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 760 time to evaluate : 3.187 Fit side-chains REVERT: A 49 LYS cc_start: 0.8144 (mttm) cc_final: 0.7927 (mtpm) REVERT: A 92 ASP cc_start: 0.7884 (t0) cc_final: 0.7639 (t0) REVERT: A 162 GLU cc_start: 0.6604 (mp0) cc_final: 0.6348 (mm-30) REVERT: B 49 LYS cc_start: 0.8146 (mttm) cc_final: 0.7929 (mtpm) REVERT: B 92 ASP cc_start: 0.7883 (t0) cc_final: 0.7637 (t0) REVERT: B 162 GLU cc_start: 0.6604 (mp0) cc_final: 0.6348 (mm-30) REVERT: C 49 LYS cc_start: 0.8144 (mttm) cc_final: 0.7928 (mtpm) REVERT: C 92 ASP cc_start: 0.7884 (t0) cc_final: 0.7641 (t0) REVERT: C 162 GLU cc_start: 0.6604 (mp0) cc_final: 0.6348 (mm-30) REVERT: D 49 LYS cc_start: 0.8144 (mttm) cc_final: 0.7926 (mtpm) REVERT: D 92 ASP cc_start: 0.7884 (t0) cc_final: 0.7641 (t0) REVERT: D 162 GLU cc_start: 0.6600 (mp0) cc_final: 0.6344 (mm-30) REVERT: E 49 LYS cc_start: 0.8144 (mttm) cc_final: 0.7926 (mtpm) REVERT: E 92 ASP cc_start: 0.7883 (t0) cc_final: 0.7638 (t0) REVERT: E 162 GLU cc_start: 0.6603 (mp0) cc_final: 0.6347 (mm-30) REVERT: F 49 LYS cc_start: 0.8144 (mttm) cc_final: 0.7927 (mtpm) REVERT: F 92 ASP cc_start: 0.7884 (t0) cc_final: 0.7640 (t0) REVERT: F 162 GLU cc_start: 0.6603 (mp0) cc_final: 0.6347 (mm-30) REVERT: G 49 LYS cc_start: 0.8147 (mttm) cc_final: 0.7930 (mtpm) REVERT: G 68 LYS cc_start: 0.7889 (OUTLIER) cc_final: 0.7670 (tttm) REVERT: G 92 ASP cc_start: 0.7883 (t0) cc_final: 0.7638 (t0) REVERT: G 162 GLU cc_start: 0.6604 (mp0) cc_final: 0.6348 (mm-30) REVERT: H 49 LYS cc_start: 0.8143 (mttm) cc_final: 0.7926 (mtpm) REVERT: H 68 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7668 (tttm) REVERT: H 92 ASP cc_start: 0.7885 (t0) cc_final: 0.7641 (t0) REVERT: H 162 GLU cc_start: 0.6606 (mp0) cc_final: 0.6348 (mm-30) REVERT: I 49 LYS cc_start: 0.8142 (mttm) cc_final: 0.7932 (mtpm) REVERT: I 68 LYS cc_start: 0.7889 (OUTLIER) cc_final: 0.7669 (tttm) REVERT: I 92 ASP cc_start: 0.7884 (t0) cc_final: 0.7641 (t0) REVERT: I 162 GLU cc_start: 0.6604 (mp0) cc_final: 0.6348 (mm-30) REVERT: J 49 LYS cc_start: 0.8143 (mttm) cc_final: 0.7926 (mtpm) REVERT: J 68 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7667 (tttm) REVERT: J 92 ASP cc_start: 0.7885 (t0) cc_final: 0.7641 (t0) REVERT: J 162 GLU cc_start: 0.6606 (mp0) cc_final: 0.6348 (mm-30) REVERT: K 49 LYS cc_start: 0.8142 (mttm) cc_final: 0.7931 (mtpm) REVERT: K 92 ASP cc_start: 0.7885 (t0) cc_final: 0.7641 (t0) REVERT: K 162 GLU cc_start: 0.6606 (mp0) cc_final: 0.6348 (mm-30) REVERT: L 49 LYS cc_start: 0.8144 (mttm) cc_final: 0.7927 (mtpm) REVERT: L 92 ASP cc_start: 0.7896 (t0) cc_final: 0.7651 (t0) REVERT: L 162 GLU cc_start: 0.6602 (mp0) cc_final: 0.6345 (mm-30) REVERT: M 49 LYS cc_start: 0.8144 (mttm) cc_final: 0.7927 (mtpm) REVERT: M 92 ASP cc_start: 0.7884 (t0) cc_final: 0.7640 (t0) REVERT: M 162 GLU cc_start: 0.6603 (mp0) cc_final: 0.6348 (mm-30) REVERT: N 49 LYS cc_start: 0.8147 (mttm) cc_final: 0.7930 (mtpm) REVERT: N 68 LYS cc_start: 0.7889 (OUTLIER) cc_final: 0.7669 (tttm) REVERT: N 92 ASP cc_start: 0.7883 (t0) cc_final: 0.7639 (t0) REVERT: N 162 GLU cc_start: 0.6601 (mp0) cc_final: 0.6346 (mm-30) REVERT: O 49 LYS cc_start: 0.8141 (mttm) cc_final: 0.7932 (mtpm) REVERT: O 68 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7669 (tttm) REVERT: O 92 ASP cc_start: 0.7884 (t0) cc_final: 0.7632 (t0) REVERT: O 162 GLU cc_start: 0.6602 (mp0) cc_final: 0.6345 (mm-30) REVERT: P 49 LYS cc_start: 0.8144 (mttm) cc_final: 0.7928 (mtpm) REVERT: P 68 LYS cc_start: 0.7889 (OUTLIER) cc_final: 0.7669 (tttm) REVERT: P 92 ASP cc_start: 0.7884 (t0) cc_final: 0.7641 (t0) REVERT: P 162 GLU cc_start: 0.6604 (mp0) cc_final: 0.6348 (mm-30) REVERT: Q 49 LYS cc_start: 0.8144 (mttm) cc_final: 0.7934 (mtpm) REVERT: Q 68 LYS cc_start: 0.7889 (OUTLIER) cc_final: 0.7670 (tttm) REVERT: Q 92 ASP cc_start: 0.7883 (t0) cc_final: 0.7638 (t0) REVERT: Q 162 GLU cc_start: 0.6601 (mp0) cc_final: 0.6345 (mm-30) REVERT: R 49 LYS cc_start: 0.8144 (mttm) cc_final: 0.7926 (mtpm) REVERT: R 68 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7667 (tttm) REVERT: R 92 ASP cc_start: 0.7885 (t0) cc_final: 0.7641 (t0) REVERT: R 162 GLU cc_start: 0.6603 (mp0) cc_final: 0.6347 (mm-30) REVERT: S 49 LYS cc_start: 0.8142 (mttm) cc_final: 0.7932 (mtpm) REVERT: S 68 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7656 (ttmm) REVERT: S 92 ASP cc_start: 0.7883 (t0) cc_final: 0.7639 (t0) REVERT: S 162 GLU cc_start: 0.6600 (mp0) cc_final: 0.6344 (mm-30) REVERT: T 49 LYS cc_start: 0.8144 (mttm) cc_final: 0.7935 (mtpm) REVERT: T 92 ASP cc_start: 0.7884 (t0) cc_final: 0.7631 (t0) REVERT: T 162 GLU cc_start: 0.6604 (mp0) cc_final: 0.6348 (mm-30) REVERT: U 49 LYS cc_start: 0.8142 (mttm) cc_final: 0.7932 (mtpm) REVERT: U 68 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7656 (ttmm) REVERT: U 92 ASP cc_start: 0.7884 (t0) cc_final: 0.7640 (t0) REVERT: U 162 GLU cc_start: 0.6603 (mp0) cc_final: 0.6347 (mm-30) REVERT: V 49 LYS cc_start: 0.8144 (mttm) cc_final: 0.7926 (mtpm) REVERT: V 68 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7668 (tttm) REVERT: V 92 ASP cc_start: 0.7883 (t0) cc_final: 0.7639 (t0) REVERT: V 162 GLU cc_start: 0.6603 (mp0) cc_final: 0.6347 (mm-30) REVERT: W 49 LYS cc_start: 0.8145 (mttm) cc_final: 0.7929 (mtpm) REVERT: W 68 LYS cc_start: 0.7889 (OUTLIER) cc_final: 0.7657 (ttmm) REVERT: W 92 ASP cc_start: 0.7883 (t0) cc_final: 0.7637 (t0) REVERT: W 162 GLU cc_start: 0.6601 (mp0) cc_final: 0.6346 (mm-30) REVERT: X 49 LYS cc_start: 0.8141 (mttm) cc_final: 0.7931 (mtpm) REVERT: X 68 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7668 (tttm) REVERT: X 92 ASP cc_start: 0.7885 (t0) cc_final: 0.7641 (t0) REVERT: X 162 GLU cc_start: 0.6600 (mp0) cc_final: 0.6344 (mm-30) outliers start: 38 outliers final: 0 residues processed: 784 average time/residue: 1.7546 time to fit residues: 1574.7914 Evaluate side-chains 750 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 736 time to evaluate : 4.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 68 LYS Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain I residue 68 LYS Chi-restraints excluded: chain J residue 68 LYS Chi-restraints excluded: chain N residue 68 LYS Chi-restraints excluded: chain O residue 68 LYS Chi-restraints excluded: chain P residue 68 LYS Chi-restraints excluded: chain Q residue 68 LYS Chi-restraints excluded: chain R residue 68 LYS Chi-restraints excluded: chain S residue 68 LYS Chi-restraints excluded: chain U residue 68 LYS Chi-restraints excluded: chain V residue 68 LYS Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain X residue 68 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 0.7980 chunk 376 optimal weight: 5.9990 chunk 343 optimal weight: 0.6980 chunk 366 optimal weight: 5.9990 chunk 220 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 287 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 chunk 331 optimal weight: 0.6980 chunk 346 optimal weight: 0.7980 chunk 365 optimal weight: 8.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 60 HIS B 14 GLN B 60 HIS C 14 GLN C 60 HIS D 14 GLN D 60 HIS E 14 GLN E 60 HIS F 14 GLN F 60 HIS G 14 GLN G 60 HIS H 14 GLN H 60 HIS I 14 GLN I 60 HIS J 14 GLN J 60 HIS K 14 GLN K 60 HIS L 14 GLN L 60 HIS M 14 GLN M 60 HIS N 14 GLN N 60 HIS O 14 GLN O 60 HIS P 14 GLN P 60 HIS Q 14 GLN Q 60 HIS R 14 GLN R 60 HIS S 14 GLN S 60 HIS T 14 GLN T 60 HIS U 14 GLN U 60 HIS V 14 GLN V 60 HIS W 14 GLN W 60 HIS X 14 GLN X 60 HIS Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 35616 Z= 0.153 Angle : 0.547 4.914 48072 Z= 0.298 Chirality : 0.037 0.129 4992 Planarity : 0.004 0.037 6384 Dihedral : 4.443 22.108 4808 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.36 (0.13), residues: 4440 helix: 4.07 (0.08), residues: 3552 sheet: None (None), residues: 0 loop : 1.04 (0.26), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP B 93 HIS 0.003 0.001 HIS T 128 PHE 0.016 0.002 PHE I 41 TYR 0.014 0.002 TYR Q 137 ARG 0.002 0.000 ARG X 22 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 782 time to evaluate : 3.298 Fit side-chains REVERT: A 49 LYS cc_start: 0.8078 (mttm) cc_final: 0.7867 (mtpm) REVERT: A 62 GLU cc_start: 0.7467 (mm-30) cc_final: 0.7184 (mm-30) REVERT: A 92 ASP cc_start: 0.7696 (t0) cc_final: 0.7473 (t0) REVERT: A 162 GLU cc_start: 0.6603 (mp0) cc_final: 0.6326 (mm-30) REVERT: B 49 LYS cc_start: 0.8078 (mttm) cc_final: 0.7868 (mtpm) REVERT: B 62 GLU cc_start: 0.7473 (mm-30) cc_final: 0.7161 (mm-30) REVERT: B 92 ASP cc_start: 0.7697 (t0) cc_final: 0.7474 (t0) REVERT: B 162 GLU cc_start: 0.6601 (mp0) cc_final: 0.6327 (mm-30) REVERT: C 49 LYS cc_start: 0.8078 (mttm) cc_final: 0.7867 (mtpm) REVERT: C 62 GLU cc_start: 0.7477 (mm-30) cc_final: 0.7167 (mm-30) REVERT: C 92 ASP cc_start: 0.7696 (t0) cc_final: 0.7473 (t0) REVERT: C 162 GLU cc_start: 0.6602 (mp0) cc_final: 0.6327 (mm-30) REVERT: D 49 LYS cc_start: 0.8079 (mttm) cc_final: 0.7867 (mtpm) REVERT: D 62 GLU cc_start: 0.7470 (mm-30) cc_final: 0.7158 (mm-30) REVERT: D 92 ASP cc_start: 0.7696 (t0) cc_final: 0.7473 (t0) REVERT: D 162 GLU cc_start: 0.6602 (mp0) cc_final: 0.6326 (mm-30) REVERT: E 49 LYS cc_start: 0.8079 (mttm) cc_final: 0.7868 (mtpm) REVERT: E 62 GLU cc_start: 0.7470 (mm-30) cc_final: 0.7159 (mm-30) REVERT: E 92 ASP cc_start: 0.7696 (t0) cc_final: 0.7474 (t0) REVERT: E 162 GLU cc_start: 0.6604 (mp0) cc_final: 0.6328 (mm-30) REVERT: F 49 LYS cc_start: 0.8078 (mttm) cc_final: 0.7868 (mtpm) REVERT: F 62 GLU cc_start: 0.7474 (mm-30) cc_final: 0.7162 (mm-30) REVERT: F 92 ASP cc_start: 0.7694 (t0) cc_final: 0.7473 (t0) REVERT: F 162 GLU cc_start: 0.6600 (mp0) cc_final: 0.6326 (mm-30) REVERT: G 49 LYS cc_start: 0.8079 (mttm) cc_final: 0.7869 (mtpm) REVERT: G 62 GLU cc_start: 0.7475 (mm-30) cc_final: 0.7163 (mm-30) REVERT: G 68 LYS cc_start: 0.7904 (ttmp) cc_final: 0.7637 (ttmm) REVERT: G 92 ASP cc_start: 0.7694 (t0) cc_final: 0.7472 (t0) REVERT: G 162 GLU cc_start: 0.6602 (mp0) cc_final: 0.6327 (mm-30) REVERT: H 49 LYS cc_start: 0.8076 (mttm) cc_final: 0.7865 (mtpm) REVERT: H 62 GLU cc_start: 0.7472 (mm-30) cc_final: 0.7161 (mm-30) REVERT: H 68 LYS cc_start: 0.7904 (ttmp) cc_final: 0.7638 (ttmm) REVERT: H 92 ASP cc_start: 0.7696 (t0) cc_final: 0.7473 (t0) REVERT: H 162 GLU cc_start: 0.6602 (mp0) cc_final: 0.6326 (mm-30) REVERT: I 49 LYS cc_start: 0.8081 (mttm) cc_final: 0.7867 (mtpm) REVERT: I 62 GLU cc_start: 0.7475 (mm-30) cc_final: 0.7163 (mm-30) REVERT: I 68 LYS cc_start: 0.7904 (ttmp) cc_final: 0.7637 (ttmm) REVERT: I 92 ASP cc_start: 0.7696 (t0) cc_final: 0.7473 (t0) REVERT: I 162 GLU cc_start: 0.6601 (mp0) cc_final: 0.6327 (mm-30) REVERT: J 49 LYS cc_start: 0.8076 (mttm) cc_final: 0.7865 (mtpm) REVERT: J 62 GLU cc_start: 0.7477 (mm-30) cc_final: 0.7166 (mm-30) REVERT: J 68 LYS cc_start: 0.7904 (ttmp) cc_final: 0.7638 (ttmm) REVERT: J 92 ASP cc_start: 0.7697 (t0) cc_final: 0.7474 (t0) REVERT: J 162 GLU cc_start: 0.6602 (mp0) cc_final: 0.6326 (mm-30) REVERT: K 49 LYS cc_start: 0.8082 (mttm) cc_final: 0.7867 (mtpm) REVERT: K 62 GLU cc_start: 0.7475 (mm-30) cc_final: 0.7164 (mm-30) REVERT: K 92 ASP cc_start: 0.7696 (t0) cc_final: 0.7474 (t0) REVERT: K 162 GLU cc_start: 0.6602 (mp0) cc_final: 0.6326 (mm-30) REVERT: L 49 LYS cc_start: 0.8077 (mttm) cc_final: 0.7867 (mtpm) REVERT: L 62 GLU cc_start: 0.7475 (mm-30) cc_final: 0.7163 (mm-30) REVERT: L 92 ASP cc_start: 0.7696 (t0) cc_final: 0.7473 (t0) REVERT: L 162 GLU cc_start: 0.6603 (mp0) cc_final: 0.6326 (mm-30) REVERT: M 49 LYS cc_start: 0.8079 (mttm) cc_final: 0.7868 (mtpm) REVERT: M 62 GLU cc_start: 0.7473 (mm-30) cc_final: 0.7162 (mm-30) REVERT: M 92 ASP cc_start: 0.7695 (t0) cc_final: 0.7473 (t0) REVERT: M 162 GLU cc_start: 0.6600 (mp0) cc_final: 0.6326 (mm-30) REVERT: N 49 LYS cc_start: 0.8079 (mttm) cc_final: 0.7869 (mtpm) REVERT: N 62 GLU cc_start: 0.7474 (mm-30) cc_final: 0.7162 (mm-30) REVERT: N 68 LYS cc_start: 0.7904 (ttmp) cc_final: 0.7637 (ttmm) REVERT: N 92 ASP cc_start: 0.7694 (t0) cc_final: 0.7472 (t0) REVERT: N 162 GLU cc_start: 0.6602 (mp0) cc_final: 0.6327 (mm-30) REVERT: O 49 LYS cc_start: 0.8083 (mttm) cc_final: 0.7869 (mtpm) REVERT: O 62 GLU cc_start: 0.7474 (mm-30) cc_final: 0.7162 (mm-30) REVERT: O 68 LYS cc_start: 0.7904 (ttmp) cc_final: 0.7638 (ttmm) REVERT: O 92 ASP cc_start: 0.7696 (t0) cc_final: 0.7473 (t0) REVERT: O 162 GLU cc_start: 0.6603 (mp0) cc_final: 0.6326 (mm-30) REVERT: P 49 LYS cc_start: 0.8076 (mttm) cc_final: 0.7866 (mtpm) REVERT: P 62 GLU cc_start: 0.7474 (mm-30) cc_final: 0.7162 (mm-30) REVERT: P 68 LYS cc_start: 0.7905 (ttmp) cc_final: 0.7637 (ttmm) REVERT: P 92 ASP cc_start: 0.7696 (t0) cc_final: 0.7473 (t0) REVERT: P 162 GLU cc_start: 0.6601 (mp0) cc_final: 0.6327 (mm-30) REVERT: Q 49 LYS cc_start: 0.8083 (mttm) cc_final: 0.7869 (mtpm) REVERT: Q 62 GLU cc_start: 0.7472 (mm-30) cc_final: 0.7160 (mm-30) REVERT: Q 68 LYS cc_start: 0.7905 (ttmp) cc_final: 0.7637 (ttmm) REVERT: Q 92 ASP cc_start: 0.7697 (t0) cc_final: 0.7474 (t0) REVERT: Q 162 GLU cc_start: 0.6601 (mp0) cc_final: 0.6327 (mm-30) REVERT: R 49 LYS cc_start: 0.8077 (mttm) cc_final: 0.7866 (mtpm) REVERT: R 62 GLU cc_start: 0.7473 (mm-30) cc_final: 0.7162 (mm-30) REVERT: R 68 LYS cc_start: 0.7902 (ttmp) cc_final: 0.7637 (ttmm) REVERT: R 92 ASP cc_start: 0.7696 (t0) cc_final: 0.7474 (t0) REVERT: R 162 GLU cc_start: 0.6602 (mp0) cc_final: 0.6326 (mm-30) REVERT: S 49 LYS cc_start: 0.8085 (mttm) cc_final: 0.7870 (mtpm) REVERT: S 62 GLU cc_start: 0.7474 (mm-30) cc_final: 0.7163 (mm-30) REVERT: S 68 LYS cc_start: 0.7902 (ttmp) cc_final: 0.7637 (ttmm) REVERT: S 92 ASP cc_start: 0.7696 (t0) cc_final: 0.7474 (t0) REVERT: S 162 GLU cc_start: 0.6604 (mp0) cc_final: 0.6328 (mm-30) REVERT: T 49 LYS cc_start: 0.8085 (mttm) cc_final: 0.7871 (mtpm) REVERT: T 62 GLU cc_start: 0.7473 (mm-30) cc_final: 0.7161 (mm-30) REVERT: T 92 ASP cc_start: 0.7694 (t0) cc_final: 0.7473 (t0) REVERT: T 162 GLU cc_start: 0.6602 (mp0) cc_final: 0.6327 (mm-30) REVERT: U 49 LYS cc_start: 0.8083 (mttm) cc_final: 0.7869 (mtpm) REVERT: U 62 GLU cc_start: 0.7475 (mm-30) cc_final: 0.7162 (mm-30) REVERT: U 68 LYS cc_start: 0.7903 (ttmp) cc_final: 0.7636 (ttmm) REVERT: U 92 ASP cc_start: 0.7695 (t0) cc_final: 0.7473 (t0) REVERT: U 162 GLU cc_start: 0.6600 (mp0) cc_final: 0.6326 (mm-30) REVERT: V 49 LYS cc_start: 0.8078 (mttm) cc_final: 0.7867 (mtpm) REVERT: V 62 GLU cc_start: 0.7473 (mm-30) cc_final: 0.7161 (mm-30) REVERT: V 68 LYS cc_start: 0.7903 (ttmp) cc_final: 0.7638 (ttmm) REVERT: V 92 ASP cc_start: 0.7696 (t0) cc_final: 0.7474 (t0) REVERT: V 162 GLU cc_start: 0.6604 (mp0) cc_final: 0.6328 (mm-30) REVERT: W 49 LYS cc_start: 0.8077 (mttm) cc_final: 0.7867 (mtpm) REVERT: W 62 GLU cc_start: 0.7473 (mm-30) cc_final: 0.7161 (mm-30) REVERT: W 68 LYS cc_start: 0.7905 (ttmp) cc_final: 0.7637 (ttmm) REVERT: W 92 ASP cc_start: 0.7697 (t0) cc_final: 0.7474 (t0) REVERT: W 162 GLU cc_start: 0.6601 (mp0) cc_final: 0.6327 (mm-30) REVERT: X 49 LYS cc_start: 0.8082 (mttm) cc_final: 0.7867 (mtpm) REVERT: X 62 GLU cc_start: 0.7473 (mm-30) cc_final: 0.7162 (mm-30) REVERT: X 68 LYS cc_start: 0.7902 (ttmp) cc_final: 0.7637 (ttmm) REVERT: X 92 ASP cc_start: 0.7696 (t0) cc_final: 0.7474 (t0) REVERT: X 162 GLU cc_start: 0.6602 (mp0) cc_final: 0.6326 (mm-30) outliers start: 0 outliers final: 0 residues processed: 782 average time/residue: 1.8054 time to fit residues: 1610.1533 Evaluate side-chains 782 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 782 time to evaluate : 3.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 5.9990 chunk 387 optimal weight: 2.9990 chunk 236 optimal weight: 3.9990 chunk 183 optimal weight: 0.7980 chunk 269 optimal weight: 5.9990 chunk 406 optimal weight: 0.8980 chunk 374 optimal weight: 0.0870 chunk 323 optimal weight: 0.0370 chunk 33 optimal weight: 3.9990 chunk 250 optimal weight: 1.9990 chunk 198 optimal weight: 3.9990 overall best weight: 0.7638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 35616 Z= 0.155 Angle : 0.551 5.015 48072 Z= 0.299 Chirality : 0.037 0.130 4992 Planarity : 0.004 0.037 6384 Dihedral : 4.217 18.921 4752 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.50 (0.13), residues: 4440 helix: 4.20 (0.08), residues: 3528 sheet: None (None), residues: 0 loop : 1.05 (0.25), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP W 93 HIS 0.003 0.001 HIS D 128 PHE 0.017 0.002 PHE R 41 TYR 0.015 0.002 TYR Q 137 ARG 0.002 0.000 ARG E 22 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 782 time to evaluate : 3.256 Fit side-chains REVERT: A 49 LYS cc_start: 0.8090 (mttm) cc_final: 0.7876 (mtpm) REVERT: A 62 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7193 (mm-30) REVERT: A 92 ASP cc_start: 0.7706 (t0) cc_final: 0.7487 (t0) REVERT: A 162 GLU cc_start: 0.6599 (mp0) cc_final: 0.6327 (mm-30) REVERT: B 49 LYS cc_start: 0.8092 (mttm) cc_final: 0.7877 (mtpm) REVERT: B 62 GLU cc_start: 0.7485 (mm-30) cc_final: 0.7203 (mm-30) REVERT: B 92 ASP cc_start: 0.7717 (t0) cc_final: 0.7498 (t0) REVERT: B 162 GLU cc_start: 0.6598 (mp0) cc_final: 0.6326 (mm-30) REVERT: C 49 LYS cc_start: 0.8091 (mttm) cc_final: 0.7876 (mtpm) REVERT: C 62 GLU cc_start: 0.7482 (mm-30) cc_final: 0.7200 (mm-30) REVERT: C 92 ASP cc_start: 0.7716 (t0) cc_final: 0.7496 (t0) REVERT: C 162 GLU cc_start: 0.6597 (mp0) cc_final: 0.6327 (mm-30) REVERT: D 49 LYS cc_start: 0.8091 (mttm) cc_final: 0.7875 (mtpm) REVERT: D 62 GLU cc_start: 0.7482 (mm-30) cc_final: 0.7200 (mm-30) REVERT: D 92 ASP cc_start: 0.7717 (t0) cc_final: 0.7497 (t0) REVERT: D 162 GLU cc_start: 0.6598 (mp0) cc_final: 0.6326 (mm-30) REVERT: E 49 LYS cc_start: 0.8091 (mttm) cc_final: 0.7876 (mtpm) REVERT: E 62 GLU cc_start: 0.7483 (mm-30) cc_final: 0.7201 (mm-30) REVERT: E 92 ASP cc_start: 0.7717 (t0) cc_final: 0.7497 (t0) REVERT: E 162 GLU cc_start: 0.6599 (mp0) cc_final: 0.6328 (mm-30) REVERT: F 49 LYS cc_start: 0.8092 (mttm) cc_final: 0.7877 (mtpm) REVERT: F 62 GLU cc_start: 0.7488 (mm-30) cc_final: 0.7206 (mm-30) REVERT: F 92 ASP cc_start: 0.7716 (t0) cc_final: 0.7496 (t0) REVERT: F 162 GLU cc_start: 0.6597 (mp0) cc_final: 0.6326 (mm-30) REVERT: G 49 LYS cc_start: 0.8092 (mttm) cc_final: 0.7878 (mtpm) REVERT: G 62 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7209 (mm-30) REVERT: G 68 LYS cc_start: 0.7915 (ttmp) cc_final: 0.7650 (ttmm) REVERT: G 92 ASP cc_start: 0.7716 (t0) cc_final: 0.7496 (t0) REVERT: G 162 GLU cc_start: 0.6598 (mp0) cc_final: 0.6327 (mm-30) REVERT: H 49 LYS cc_start: 0.8091 (mttm) cc_final: 0.7875 (mtpm) REVERT: H 62 GLU cc_start: 0.7490 (mm-30) cc_final: 0.7208 (mm-30) REVERT: H 68 LYS cc_start: 0.7914 (ttmp) cc_final: 0.7650 (ttmm) REVERT: H 92 ASP cc_start: 0.7706 (t0) cc_final: 0.7486 (t0) REVERT: H 162 GLU cc_start: 0.6598 (mp0) cc_final: 0.6327 (mm-30) REVERT: I 49 LYS cc_start: 0.8092 (mttm) cc_final: 0.7878 (mtpm) REVERT: I 62 GLU cc_start: 0.7492 (mm-30) cc_final: 0.7210 (mm-30) REVERT: I 68 LYS cc_start: 0.7915 (ttmp) cc_final: 0.7649 (ttmm) REVERT: I 92 ASP cc_start: 0.7716 (t0) cc_final: 0.7497 (t0) REVERT: I 162 GLU cc_start: 0.6597 (mp0) cc_final: 0.6327 (mm-30) REVERT: J 49 LYS cc_start: 0.8090 (mttm) cc_final: 0.7875 (mtpm) REVERT: J 62 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7209 (mm-30) REVERT: J 68 LYS cc_start: 0.7915 (ttmp) cc_final: 0.7650 (ttmm) REVERT: J 92 ASP cc_start: 0.7717 (t0) cc_final: 0.7496 (t0) REVERT: J 162 GLU cc_start: 0.6598 (mp0) cc_final: 0.6327 (mm-30) REVERT: K 49 LYS cc_start: 0.8092 (mttm) cc_final: 0.7878 (mtpm) REVERT: K 62 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7210 (mm-30) REVERT: K 92 ASP cc_start: 0.7706 (t0) cc_final: 0.7486 (t0) REVERT: K 162 GLU cc_start: 0.6598 (mp0) cc_final: 0.6327 (mm-30) REVERT: L 49 LYS cc_start: 0.8091 (mttm) cc_final: 0.7876 (mtpm) REVERT: L 62 GLU cc_start: 0.7488 (mm-30) cc_final: 0.7206 (mm-30) REVERT: L 92 ASP cc_start: 0.7717 (t0) cc_final: 0.7498 (t0) REVERT: L 162 GLU cc_start: 0.6599 (mp0) cc_final: 0.6327 (mm-30) REVERT: M 49 LYS cc_start: 0.8092 (mttm) cc_final: 0.7877 (mtpm) REVERT: M 62 GLU cc_start: 0.7482 (mm-30) cc_final: 0.7200 (mm-30) REVERT: M 92 ASP cc_start: 0.7705 (t0) cc_final: 0.7486 (t0) REVERT: M 162 GLU cc_start: 0.6598 (mp0) cc_final: 0.6326 (mm-30) REVERT: N 49 LYS cc_start: 0.8092 (mttm) cc_final: 0.7878 (mtpm) REVERT: N 62 GLU cc_start: 0.7490 (mm-30) cc_final: 0.7208 (mm-30) REVERT: N 68 LYS cc_start: 0.7915 (ttmp) cc_final: 0.7649 (ttmm) REVERT: N 92 ASP cc_start: 0.7704 (t0) cc_final: 0.7485 (t0) REVERT: N 162 GLU cc_start: 0.6598 (mp0) cc_final: 0.6327 (mm-30) REVERT: O 49 LYS cc_start: 0.8093 (mttm) cc_final: 0.7879 (mtpm) REVERT: O 62 GLU cc_start: 0.7489 (mm-30) cc_final: 0.7206 (mm-30) REVERT: O 68 LYS cc_start: 0.7914 (ttmp) cc_final: 0.7650 (ttmm) REVERT: O 92 ASP cc_start: 0.7705 (t0) cc_final: 0.7486 (t0) REVERT: O 162 GLU cc_start: 0.6599 (mp0) cc_final: 0.6327 (mm-30) REVERT: P 49 LYS cc_start: 0.8090 (mttm) cc_final: 0.7876 (mtpm) REVERT: P 62 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7208 (mm-30) REVERT: P 68 LYS cc_start: 0.7916 (ttmp) cc_final: 0.7649 (ttmm) REVERT: P 92 ASP cc_start: 0.7705 (t0) cc_final: 0.7486 (t0) REVERT: P 162 GLU cc_start: 0.6597 (mp0) cc_final: 0.6327 (mm-30) REVERT: Q 49 LYS cc_start: 0.8094 (mttm) cc_final: 0.7880 (mtpm) REVERT: Q 62 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7209 (mm-30) REVERT: Q 68 LYS cc_start: 0.7916 (ttmp) cc_final: 0.7650 (ttmm) REVERT: Q 92 ASP cc_start: 0.7706 (t0) cc_final: 0.7487 (t0) REVERT: Q 162 GLU cc_start: 0.6598 (mp0) cc_final: 0.6326 (mm-30) REVERT: R 49 LYS cc_start: 0.8091 (mttm) cc_final: 0.7875 (mtpm) REVERT: R 62 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7212 (mm-30) REVERT: R 68 LYS cc_start: 0.7912 (ttmp) cc_final: 0.7648 (ttmm) REVERT: R 92 ASP cc_start: 0.7718 (t0) cc_final: 0.7497 (t0) REVERT: R 162 GLU cc_start: 0.6598 (mp0) cc_final: 0.6326 (mm-30) REVERT: S 49 LYS cc_start: 0.8094 (mttm) cc_final: 0.7880 (mtpm) REVERT: S 62 GLU cc_start: 0.7488 (mm-30) cc_final: 0.7205 (mm-30) REVERT: S 68 LYS cc_start: 0.7914 (ttmp) cc_final: 0.7650 (ttmm) REVERT: S 92 ASP cc_start: 0.7717 (t0) cc_final: 0.7497 (t0) REVERT: S 162 GLU cc_start: 0.6599 (mp0) cc_final: 0.6327 (mm-30) REVERT: T 49 LYS cc_start: 0.8094 (mttm) cc_final: 0.7880 (mtpm) REVERT: T 62 GLU cc_start: 0.7487 (mm-30) cc_final: 0.7204 (mm-30) REVERT: T 92 ASP cc_start: 0.7704 (t0) cc_final: 0.7485 (t0) REVERT: T 162 GLU cc_start: 0.6599 (mp0) cc_final: 0.6328 (mm-30) REVERT: U 49 LYS cc_start: 0.8093 (mttm) cc_final: 0.7879 (mtpm) REVERT: U 62 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7210 (mm-30) REVERT: U 68 LYS cc_start: 0.7913 (ttmp) cc_final: 0.7648 (ttmm) REVERT: U 92 ASP cc_start: 0.7705 (t0) cc_final: 0.7486 (t0) REVERT: U 162 GLU cc_start: 0.6597 (mp0) cc_final: 0.6326 (mm-30) REVERT: V 49 LYS cc_start: 0.8091 (mttm) cc_final: 0.7876 (mtpm) REVERT: V 62 GLU cc_start: 0.7489 (mm-30) cc_final: 0.7207 (mm-30) REVERT: V 68 LYS cc_start: 0.7914 (ttmp) cc_final: 0.7651 (ttmm) REVERT: V 92 ASP cc_start: 0.7705 (t0) cc_final: 0.7486 (t0) REVERT: V 162 GLU cc_start: 0.6599 (mp0) cc_final: 0.6328 (mm-30) REVERT: W 49 LYS cc_start: 0.8092 (mttm) cc_final: 0.7877 (mtpm) REVERT: W 62 GLU cc_start: 0.7490 (mm-30) cc_final: 0.7208 (mm-30) REVERT: W 68 LYS cc_start: 0.7916 (ttmp) cc_final: 0.7650 (ttmm) REVERT: W 92 ASP cc_start: 0.7718 (t0) cc_final: 0.7498 (t0) REVERT: W 162 GLU cc_start: 0.6598 (mp0) cc_final: 0.6327 (mm-30) REVERT: X 49 LYS cc_start: 0.8093 (mttm) cc_final: 0.7879 (mtpm) REVERT: X 62 GLU cc_start: 0.7489 (mm-30) cc_final: 0.7207 (mm-30) REVERT: X 68 LYS cc_start: 0.7911 (ttmp) cc_final: 0.7647 (ttmm) REVERT: X 92 ASP cc_start: 0.7705 (t0) cc_final: 0.7486 (t0) REVERT: X 162 GLU cc_start: 0.6598 (mp0) cc_final: 0.6326 (mm-30) outliers start: 0 outliers final: 0 residues processed: 782 average time/residue: 1.8305 time to fit residues: 1631.2057 Evaluate side-chains 782 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 782 time to evaluate : 3.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 10.0000 chunk 344 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 chunk 298 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 chunk 89 optimal weight: 8.9990 chunk 324 optimal weight: 7.9990 chunk 135 optimal weight: 2.9990 chunk 332 optimal weight: 0.6980 chunk 41 optimal weight: 0.0970 chunk 59 optimal weight: 0.7980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN B 14 GLN C 14 GLN D 14 GLN E 14 GLN F 14 GLN G 14 GLN H 14 GLN I 14 GLN J 14 GLN K 14 GLN L 14 GLN M 14 GLN N 14 GLN O 14 GLN P 14 GLN Q 14 GLN R 14 GLN S 14 GLN T 14 GLN U 14 GLN V 14 GLN W 14 GLN X 14 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.149592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.135400 restraints weight = 77582.490| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 0.35 r_work: 0.3121 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 2.32 restraints_weight: 0.2500 r_work: 0.2841 rms_B_bonded: 3.58 restraints_weight: 0.1250 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2773 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2773 r_free = 0.2773 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2772 r_free = 0.2772 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2772 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 35616 Z= 0.150 Angle : 0.538 4.872 48072 Z= 0.293 Chirality : 0.037 0.133 4992 Planarity : 0.004 0.035 6384 Dihedral : 4.182 19.032 4752 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.45 (0.13), residues: 4440 helix: 4.16 (0.08), residues: 3552 sheet: None (None), residues: 0 loop : 0.98 (0.26), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP W 93 HIS 0.003 0.001 HIS D 128 PHE 0.016 0.002 PHE R 41 TYR 0.015 0.002 TYR R 137 ARG 0.002 0.000 ARG E 22 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21525.56 seconds wall clock time: 370 minutes 34.79 seconds (22234.79 seconds total)