Starting phenix.real_space_refine on Mon Apr 15 20:20:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bka_16094/04_2024/8bka_16094.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bka_16094/04_2024/8bka_16094.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bka_16094/04_2024/8bka_16094.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bka_16094/04_2024/8bka_16094.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bka_16094/04_2024/8bka_16094.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bka_16094/04_2024/8bka_16094.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 6 7.16 5 S 192 5.16 5 C 21216 2.51 5 N 5928 2.21 5 O 8751 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 15": "OD1" <-> "OD2" Residue "A ASP 42": "OD1" <-> "OD2" Residue "A PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 89": "OD1" <-> "OD2" Residue "A ASP 92": "OD1" <-> "OD2" Residue "A TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 64": "OE1" <-> "OE2" Residue "B GLU 107": "OE1" <-> "OE2" Residue "B GLU 140": "OE1" <-> "OE2" Residue "B GLU 162": "OE1" <-> "OE2" Residue "B TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 42": "OD1" <-> "OD2" Residue "C ASP 89": "OD1" <-> "OD2" Residue "C GLU 140": "OE1" <-> "OE2" Residue "C TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 92": "OD1" <-> "OD2" Residue "D ASP 123": "OD1" <-> "OD2" Residue "D ASP 131": "OD1" <-> "OD2" Residue "D TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 15": "OD1" <-> "OD2" Residue "E ASP 42": "OD1" <-> "OD2" Residue "E PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 92": "OD1" <-> "OD2" Residue "E ASP 131": "OD1" <-> "OD2" Residue "E ASP 150": "OD1" <-> "OD2" Residue "E TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 42": "OD1" <-> "OD2" Residue "F PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 116": "OE1" <-> "OE2" Residue "F GLU 140": "OE1" <-> "OE2" Residue "F TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 42": "OD1" <-> "OD2" Residue "G ASP 89": "OD1" <-> "OD2" Residue "G GLU 140": "OE1" <-> "OE2" Residue "G TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 42": "OD1" <-> "OD2" Residue "H PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 89": "OD1" <-> "OD2" Residue "H TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 89": "OD1" <-> "OD2" Residue "I GLU 140": "OE1" <-> "OE2" Residue "I TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 15": "OD1" <-> "OD2" Residue "J ASP 42": "OD1" <-> "OD2" Residue "J ASP 92": "OD1" <-> "OD2" Residue "J GLU 116": "OE1" <-> "OE2" Residue "J ASP 131": "OD1" <-> "OD2" Residue "J TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 42": "OD1" <-> "OD2" Residue "K ASP 89": "OD1" <-> "OD2" Residue "K GLU 116": "OE1" <-> "OE2" Residue "K GLU 140": "OE1" <-> "OE2" Residue "K TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 44": "OD1" <-> "OD2" Residue "L PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 89": "OD1" <-> "OD2" Residue "L TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 89": "OD1" <-> "OD2" Residue "M GLU 116": "OE1" <-> "OE2" Residue "M GLU 140": "OE1" <-> "OE2" Residue "M TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 42": "OD1" <-> "OD2" Residue "N ASP 44": "OD1" <-> "OD2" Residue "N PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 89": "OD1" <-> "OD2" Residue "N ASP 92": "OD1" <-> "OD2" Residue "N GLU 116": "OE1" <-> "OE2" Residue "N ASP 131": "OD1" <-> "OD2" Residue "N GLU 140": "OE1" <-> "OE2" Residue "N TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 15": "OD1" <-> "OD2" Residue "O PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 84": "OD1" <-> "OD2" Residue "O ASP 89": "OD1" <-> "OD2" Residue "O GLU 116": "OE1" <-> "OE2" Residue "O ASP 131": "OD1" <-> "OD2" Residue "O GLU 140": "OE1" <-> "OE2" Residue "O GLU 162": "OE1" <-> "OE2" Residue "O TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 15": "OD1" <-> "OD2" Residue "P ASP 42": "OD1" <-> "OD2" Residue "P PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 89": "OD1" <-> "OD2" Residue "P GLU 116": "OE1" <-> "OE2" Residue "P ASP 131": "OD1" <-> "OD2" Residue "P GLU 140": "OE1" <-> "OE2" Residue "P TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 42": "OD1" <-> "OD2" Residue "Q PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 89": "OD1" <-> "OD2" Residue "Q GLU 116": "OE1" <-> "OE2" Residue "Q GLU 140": "OE1" <-> "OE2" Residue "Q TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 89": "OD1" <-> "OD2" Residue "R ASP 92": "OD1" <-> "OD2" Residue "R GLU 140": "OE1" <-> "OE2" Residue "R TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 15": "OD1" <-> "OD2" Residue "S ASP 42": "OD1" <-> "OD2" Residue "S PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 89": "OD1" <-> "OD2" Residue "S GLU 116": "OE1" <-> "OE2" Residue "S GLU 140": "OE1" <-> "OE2" Residue "S ASP 150": "OD1" <-> "OD2" Residue "S TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 92": "OD1" <-> "OD2" Residue "T GLU 116": "OE1" <-> "OE2" Residue "T GLU 140": "OE1" <-> "OE2" Residue "T GLU 162": "OE1" <-> "OE2" Residue "T TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 42": "OD1" <-> "OD2" Residue "V PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 84": "OD1" <-> "OD2" Residue "V ASP 89": "OD1" <-> "OD2" Residue "V ASP 92": "OD1" <-> "OD2" Residue "V GLU 116": "OE1" <-> "OE2" Residue "V ASP 150": "OD1" <-> "OD2" Residue "V TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 42": "OD1" <-> "OD2" Residue "W PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 89": "OD1" <-> "OD2" Residue "W ASP 123": "OD1" <-> "OD2" Residue "W GLU 162": "OE1" <-> "OE2" Residue "W TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 89": "OD1" <-> "OD2" Residue "X GLU 162": "OE1" <-> "OE2" Residue "X TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 15": "OD1" <-> "OD2" Residue "Y ASP 42": "OD1" <-> "OD2" Residue "Y PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 84": "OD1" <-> "OD2" Residue "Y ASP 89": "OD1" <-> "OD2" Residue "Y ASP 92": "OD1" <-> "OD2" Residue "Y GLU 116": "OE1" <-> "OE2" Residue "Y GLU 140": "OE1" <-> "OE2" Residue "Y TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 36093 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "B" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "C" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "D" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "E" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "F" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "G" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "H" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "I" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "J" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "K" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "L" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "M" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "N" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "O" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "P" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "Q" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "R" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "S" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "T" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "V" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "W" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "X" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "Y" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 100 Classifications: {'water': 100} Link IDs: {None: 99} Chain: "B" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 96 Classifications: {'water': 96} Link IDs: {None: 95} Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 98 Classifications: {'water': 98} Link IDs: {None: 97} Chain: "D" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 91 Classifications: {'water': 91} Link IDs: {None: 90} Chain: "E" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 101 Classifications: {'water': 101} Link IDs: {None: 100} Chain: "F" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 93 Classifications: {'water': 93} Link IDs: {None: 92} Chain: "G" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 92 Classifications: {'water': 92} Link IDs: {None: 91} Chain: "H" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 98 Classifications: {'water': 98} Link IDs: {None: 97} Chain: "I" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 96 Classifications: {'water': 96} Link IDs: {None: 95} Chain: "J" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 99 Classifications: {'water': 99} Link IDs: {None: 98} Chain: "K" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 96 Classifications: {'water': 96} Link IDs: {None: 95} Chain: "L" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 98 Classifications: {'water': 98} Link IDs: {None: 97} Chain: "M" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 95 Classifications: {'water': 95} Link IDs: {None: 94} Chain: "N" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 86 Classifications: {'water': 86} Link IDs: {None: 85} Chain: "O" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 94 Classifications: {'water': 94} Link IDs: {None: 93} Chain: "P" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 87 Classifications: {'water': 87} Link IDs: {None: 86} Chain: "Q" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 89 Classifications: {'water': 89} Link IDs: {None: 88} Chain: "R" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 91 Classifications: {'water': 91} Link IDs: {None: 90} Chain: "S" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "T" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 93 Classifications: {'water': 93} Link IDs: {None: 92} Chain: "V" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 88 Classifications: {'water': 88} Link IDs: {None: 87} Chain: "W" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 101 Classifications: {'water': 101} Link IDs: {None: 100} Chain: "X" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 93 Classifications: {'water': 93} Link IDs: {None: 92} Chain: "Y" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 90 Classifications: {'water': 90} Link IDs: {None: 89} Time building chain proxies: 18.96, per 1000 atoms: 0.53 Number of scatterers: 36093 At special positions: 0 Unit cell: (134.25, 134.25, 134.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 6 26.01 S 192 16.00 O 8751 8.00 N 5928 7.00 C 21216 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 - 3.50 Amino acid : False - 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: 15.07 Conformation dependent library (CDL) restraints added in 5.9 seconds 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7920 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 79.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.91 Creating SS restraints... Processing helix chain 'A' and resid 13 through 42 Processing helix chain 'A' and resid 48 through 76 Processing helix chain 'A' and resid 95 through 124 Processing helix chain 'A' and resid 126 through 137 Processing helix chain 'A' and resid 137 through 159 Processing helix chain 'A' and resid 163 through 174 removed outlier: 4.118A pdb=" N GLU A 167 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TYR A 168 " --> pdb=" O GLY A 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 42 Processing helix chain 'B' and resid 48 through 76 Processing helix chain 'B' and resid 95 through 124 Processing helix chain 'B' and resid 126 through 137 Processing helix chain 'B' and resid 137 through 159 Processing helix chain 'B' and resid 163 through 174 removed outlier: 4.115A pdb=" N GLU B 167 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR B 168 " --> pdb=" O GLY B 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 42 Processing helix chain 'C' and resid 48 through 76 Processing helix chain 'C' and resid 95 through 124 Processing helix chain 'C' and resid 126 through 137 Processing helix chain 'C' and resid 137 through 159 Processing helix chain 'C' and resid 163 through 174 removed outlier: 4.142A pdb=" N GLU C 167 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR C 168 " --> pdb=" O GLY C 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 42 Processing helix chain 'D' and resid 48 through 76 Processing helix chain 'D' and resid 95 through 124 Processing helix chain 'D' and resid 126 through 137 Processing helix chain 'D' and resid 137 through 159 Processing helix chain 'D' and resid 163 through 174 removed outlier: 4.121A pdb=" N GLU D 167 " --> pdb=" O ALA D 163 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR D 168 " --> pdb=" O GLY D 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 42 Processing helix chain 'E' and resid 48 through 76 Processing helix chain 'E' and resid 95 through 124 Processing helix chain 'E' and resid 126 through 137 Processing helix chain 'E' and resid 137 through 159 Processing helix chain 'E' and resid 163 through 174 removed outlier: 4.111A pdb=" N GLU E 167 " --> pdb=" O ALA E 163 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TYR E 168 " --> pdb=" O GLY E 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 42 Processing helix chain 'F' and resid 48 through 76 Processing helix chain 'F' and resid 95 through 124 Processing helix chain 'F' and resid 126 through 137 Processing helix chain 'F' and resid 137 through 159 Processing helix chain 'F' and resid 163 through 174 removed outlier: 4.113A pdb=" N GLU F 167 " --> pdb=" O ALA F 163 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TYR F 168 " --> pdb=" O GLY F 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 42 Processing helix chain 'G' and resid 48 through 76 Processing helix chain 'G' and resid 95 through 124 Processing helix chain 'G' and resid 126 through 137 Processing helix chain 'G' and resid 137 through 159 Processing helix chain 'G' and resid 163 through 174 removed outlier: 4.134A pdb=" N GLU G 167 " --> pdb=" O ALA G 163 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TYR G 168 " --> pdb=" O GLY G 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 42 Processing helix chain 'H' and resid 48 through 76 Processing helix chain 'H' and resid 95 through 124 Processing helix chain 'H' and resid 126 through 137 Processing helix chain 'H' and resid 137 through 159 Processing helix chain 'H' and resid 163 through 174 removed outlier: 4.118A pdb=" N GLU H 167 " --> pdb=" O ALA H 163 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TYR H 168 " --> pdb=" O GLY H 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 42 Processing helix chain 'I' and resid 48 through 76 Processing helix chain 'I' and resid 95 through 124 Processing helix chain 'I' and resid 126 through 137 Processing helix chain 'I' and resid 137 through 159 Processing helix chain 'I' and resid 163 through 174 removed outlier: 4.136A pdb=" N GLU I 167 " --> pdb=" O ALA I 163 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR I 168 " --> pdb=" O GLY I 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 42 Processing helix chain 'J' and resid 48 through 76 Processing helix chain 'J' and resid 95 through 124 Processing helix chain 'J' and resid 126 through 137 Processing helix chain 'J' and resid 137 through 159 Processing helix chain 'J' and resid 163 through 174 removed outlier: 4.132A pdb=" N GLU J 167 " --> pdb=" O ALA J 163 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR J 168 " --> pdb=" O GLY J 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 13 through 42 Processing helix chain 'K' and resid 48 through 76 Processing helix chain 'K' and resid 95 through 124 Processing helix chain 'K' and resid 126 through 137 Processing helix chain 'K' and resid 137 through 159 Processing helix chain 'K' and resid 163 through 174 removed outlier: 4.151A pdb=" N GLU K 167 " --> pdb=" O ALA K 163 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR K 168 " --> pdb=" O GLY K 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 13 through 42 Processing helix chain 'L' and resid 48 through 76 Processing helix chain 'L' and resid 95 through 124 Processing helix chain 'L' and resid 126 through 137 Processing helix chain 'L' and resid 137 through 159 Processing helix chain 'L' and resid 163 through 174 removed outlier: 4.139A pdb=" N GLU L 167 " --> pdb=" O ALA L 163 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR L 168 " --> pdb=" O GLY L 164 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 42 Processing helix chain 'M' and resid 48 through 76 Processing helix chain 'M' and resid 95 through 124 Processing helix chain 'M' and resid 126 through 137 Processing helix chain 'M' and resid 137 through 159 Processing helix chain 'M' and resid 163 through 174 removed outlier: 4.131A pdb=" N GLU M 167 " --> pdb=" O ALA M 163 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TYR M 168 " --> pdb=" O GLY M 164 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 42 Processing helix chain 'N' and resid 48 through 76 Processing helix chain 'N' and resid 95 through 124 Processing helix chain 'N' and resid 126 through 137 Processing helix chain 'N' and resid 137 through 159 Processing helix chain 'N' and resid 163 through 174 removed outlier: 4.116A pdb=" N GLU N 167 " --> pdb=" O ALA N 163 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR N 168 " --> pdb=" O GLY N 164 " (cutoff:3.500A) Processing helix chain 'O' and resid 13 through 42 Processing helix chain 'O' and resid 48 through 76 Processing helix chain 'O' and resid 95 through 124 Processing helix chain 'O' and resid 126 through 137 Processing helix chain 'O' and resid 137 through 159 Processing helix chain 'O' and resid 163 through 174 removed outlier: 4.149A pdb=" N GLU O 167 " --> pdb=" O ALA O 163 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR O 168 " --> pdb=" O GLY O 164 " (cutoff:3.500A) Processing helix chain 'P' and resid 13 through 42 Processing helix chain 'P' and resid 48 through 76 Processing helix chain 'P' and resid 95 through 124 Processing helix chain 'P' and resid 126 through 137 Processing helix chain 'P' and resid 137 through 159 Processing helix chain 'P' and resid 163 through 174 removed outlier: 4.152A pdb=" N GLU P 167 " --> pdb=" O ALA P 163 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR P 168 " --> pdb=" O GLY P 164 " (cutoff:3.500A) Processing helix chain 'Q' and resid 13 through 42 Processing helix chain 'Q' and resid 48 through 76 Processing helix chain 'Q' and resid 95 through 124 Processing helix chain 'Q' and resid 126 through 137 Processing helix chain 'Q' and resid 137 through 159 Processing helix chain 'Q' and resid 163 through 174 removed outlier: 4.119A pdb=" N GLU Q 167 " --> pdb=" O ALA Q 163 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TYR Q 168 " --> pdb=" O GLY Q 164 " (cutoff:3.500A) Processing helix chain 'R' and resid 13 through 42 Processing helix chain 'R' and resid 48 through 76 Processing helix chain 'R' and resid 95 through 124 Processing helix chain 'R' and resid 126 through 137 Processing helix chain 'R' and resid 137 through 159 Processing helix chain 'R' and resid 163 through 174 removed outlier: 4.137A pdb=" N GLU R 167 " --> pdb=" O ALA R 163 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TYR R 168 " --> pdb=" O GLY R 164 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 42 Processing helix chain 'S' and resid 48 through 76 Processing helix chain 'S' and resid 95 through 124 Processing helix chain 'S' and resid 126 through 137 Processing helix chain 'S' and resid 137 through 159 Processing helix chain 'S' and resid 163 through 174 removed outlier: 4.114A pdb=" N GLU S 167 " --> pdb=" O ALA S 163 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR S 168 " --> pdb=" O GLY S 164 " (cutoff:3.500A) Processing helix chain 'T' and resid 13 through 42 Processing helix chain 'T' and resid 48 through 76 Processing helix chain 'T' and resid 95 through 124 Processing helix chain 'T' and resid 126 through 137 Processing helix chain 'T' and resid 137 through 159 Processing helix chain 'T' and resid 163 through 174 removed outlier: 4.136A pdb=" N GLU T 167 " --> pdb=" O ALA T 163 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR T 168 " --> pdb=" O GLY T 164 " (cutoff:3.500A) Processing helix chain 'V' and resid 13 through 42 Processing helix chain 'V' and resid 48 through 76 Processing helix chain 'V' and resid 95 through 124 Processing helix chain 'V' and resid 126 through 137 Processing helix chain 'V' and resid 137 through 159 Processing helix chain 'V' and resid 163 through 174 removed outlier: 4.109A pdb=" N GLU V 167 " --> pdb=" O ALA V 163 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TYR V 168 " --> pdb=" O GLY V 164 " (cutoff:3.500A) Processing helix chain 'W' and resid 13 through 42 Processing helix chain 'W' and resid 48 through 76 Processing helix chain 'W' and resid 95 through 124 Processing helix chain 'W' and resid 126 through 137 Processing helix chain 'W' and resid 137 through 159 Processing helix chain 'W' and resid 163 through 174 removed outlier: 4.141A pdb=" N GLU W 167 " --> pdb=" O ALA W 163 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR W 168 " --> pdb=" O GLY W 164 " (cutoff:3.500A) Processing helix chain 'X' and resid 13 through 42 Processing helix chain 'X' and resid 48 through 76 Processing helix chain 'X' and resid 95 through 124 Processing helix chain 'X' and resid 126 through 137 Processing helix chain 'X' and resid 137 through 159 Processing helix chain 'X' and resid 163 through 174 removed outlier: 4.134A pdb=" N GLU X 167 " --> pdb=" O ALA X 163 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TYR X 168 " --> pdb=" O GLY X 164 " (cutoff:3.500A) Processing helix chain 'Y' and resid 13 through 42 Processing helix chain 'Y' and resid 48 through 76 Processing helix chain 'Y' and resid 95 through 124 Processing helix chain 'Y' and resid 126 through 137 Processing helix chain 'Y' and resid 137 through 159 Processing helix chain 'Y' and resid 163 through 174 removed outlier: 4.116A pdb=" N GLU Y 167 " --> pdb=" O ALA Y 163 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR Y 168 " --> pdb=" O GLY Y 164 " (cutoff:3.500A) 2640 hydrogen bonds defined for protein. 7920 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: 11.58 Time building geometry restraints manager: 16.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11475 1.34 - 1.46: 4663 1.46 - 1.57: 18062 1.57 - 1.69: 0 1.69 - 1.81: 312 Bond restraints: 34512 Sorted by residual: bond pdb=" C TYR W 136 " pdb=" N TYR W 137 " ideal model delta sigma weight residual 1.332 1.319 0.014 1.40e-02 5.10e+03 9.71e-01 bond pdb=" C TYR H 136 " pdb=" N TYR H 137 " ideal model delta sigma weight residual 1.332 1.319 0.014 1.40e-02 5.10e+03 9.30e-01 bond pdb=" C TYR S 136 " pdb=" N TYR S 137 " ideal model delta sigma weight residual 1.332 1.319 0.013 1.40e-02 5.10e+03 9.16e-01 bond pdb=" C TYR B 136 " pdb=" N TYR B 137 " ideal model delta sigma weight residual 1.332 1.319 0.013 1.40e-02 5.10e+03 8.95e-01 bond pdb=" C TYR D 136 " pdb=" N TYR D 137 " ideal model delta sigma weight residual 1.332 1.319 0.013 1.40e-02 5.10e+03 8.87e-01 ... (remaining 34507 not shown) Histogram of bond angle deviations from ideal: 100.73 - 107.38: 1008 107.38 - 114.02: 18969 114.02 - 120.67: 15359 120.67 - 127.32: 10768 127.32 - 133.97: 312 Bond angle restraints: 46416 Sorted by residual: angle pdb=" C TYR I 136 " pdb=" N TYR I 137 " pdb=" CA TYR I 137 " ideal model delta sigma weight residual 122.08 117.05 5.03 1.53e+00 4.27e-01 1.08e+01 angle pdb=" C TYR G 136 " pdb=" N TYR G 137 " pdb=" CA TYR G 137 " ideal model delta sigma weight residual 122.08 117.13 4.95 1.53e+00 4.27e-01 1.05e+01 angle pdb=" C TYR M 136 " pdb=" N TYR M 137 " pdb=" CA TYR M 137 " ideal model delta sigma weight residual 122.08 117.23 4.85 1.53e+00 4.27e-01 1.01e+01 angle pdb=" C TRP H 93 " pdb=" N GLU H 94 " pdb=" CA GLU H 94 " ideal model delta sigma weight residual 121.54 127.02 -5.48 1.91e+00 2.74e-01 8.22e+00 angle pdb=" C TRP O 93 " pdb=" N GLU O 94 " pdb=" CA GLU O 94 " ideal model delta sigma weight residual 121.54 126.94 -5.40 1.91e+00 2.74e-01 8.01e+00 ... (remaining 46411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 18064 17.81 - 35.62: 1998 35.62 - 53.42: 537 53.42 - 71.23: 287 71.23 - 89.04: 114 Dihedral angle restraints: 21000 sinusoidal: 8760 harmonic: 12240 Sorted by residual: dihedral pdb=" CA ASP V 92 " pdb=" CB ASP V 92 " pdb=" CG ASP V 92 " pdb=" OD1 ASP V 92 " ideal model delta sinusoidal sigma weight residual -30.00 -89.85 59.85 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CA ASP T 92 " pdb=" CB ASP T 92 " pdb=" CG ASP T 92 " pdb=" OD1 ASP T 92 " ideal model delta sinusoidal sigma weight residual -30.00 -89.81 59.81 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CA ASP R 92 " pdb=" CB ASP R 92 " pdb=" CG ASP R 92 " pdb=" OD1 ASP R 92 " ideal model delta sinusoidal sigma weight residual -30.00 -89.79 59.79 1 2.00e+01 2.50e-03 1.19e+01 ... (remaining 20997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 2975 0.027 - 0.055: 1289 0.055 - 0.082: 340 0.082 - 0.110: 172 0.110 - 0.137: 72 Chirality restraints: 4848 Sorted by residual: chirality pdb=" CG LEU M 72 " pdb=" CB LEU M 72 " pdb=" CD1 LEU M 72 " pdb=" CD2 LEU M 72 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.71e-01 chirality pdb=" CG LEU S 72 " pdb=" CB LEU S 72 " pdb=" CD1 LEU S 72 " pdb=" CD2 LEU S 72 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.66e-01 chirality pdb=" CG LEU Y 72 " pdb=" CB LEU Y 72 " pdb=" CD1 LEU Y 72 " pdb=" CD2 LEU Y 72 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.60e-01 ... (remaining 4845 not shown) Planarity restraints: 6096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS Y 87 " 0.023 5.00e-02 4.00e+02 3.45e-02 1.90e+00 pdb=" N PRO Y 88 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO Y 88 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO Y 88 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLN F 83 " 0.007 2.00e-02 2.50e+03 1.38e-02 1.90e+00 pdb=" CD GLN F 83 " -0.024 2.00e-02 2.50e+03 pdb=" OE1 GLN F 83 " 0.009 2.00e-02 2.50e+03 pdb=" NE2 GLN F 83 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS F 87 " -0.023 5.00e-02 4.00e+02 3.44e-02 1.89e+00 pdb=" N PRO F 88 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO F 88 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO F 88 " -0.019 5.00e-02 4.00e+02 ... (remaining 6093 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1588 2.73 - 3.27: 35825 3.27 - 3.81: 70662 3.81 - 4.36: 85364 4.36 - 4.90: 135607 Nonbonded interactions: 329046 Sorted by model distance: nonbonded pdb=" OH TYR H 34 " pdb=" OE1 GLU H 107 " model vdw 2.186 2.440 nonbonded pdb=" OH TYR A 34 " pdb=" OE1 GLU A 107 " model vdw 2.187 2.440 nonbonded pdb=" OH TYR S 34 " pdb=" OE1 GLU S 107 " model vdw 2.187 2.440 nonbonded pdb=" OH TYR C 34 " pdb=" OE1 GLU C 107 " model vdw 2.187 2.440 nonbonded pdb=" OH TYR L 34 " pdb=" OE1 GLU L 107 " model vdw 2.188 2.440 ... (remaining 329041 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 5 through 176) selection = (chain 'B' and resid 5 through 176) selection = (chain 'C' and resid 5 through 176) selection = (chain 'D' and resid 5 through 176) selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = (chain 'H' and resid 5 through 176) selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = (chain 'N' and resid 5 through 176) selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 12.040 Check model and map are aligned: 0.530 Set scattering table: 0.350 Process input model: 90.980 Find NCS groups from input model: 3.020 Set up NCS constraints: 0.370 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:12.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 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 : 0.003 0.022 34512 Z= 0.192 Angle : 0.565 7.094 46416 Z= 0.296 Chirality : 0.037 0.137 4848 Planarity : 0.004 0.034 6096 Dihedral : 18.734 89.041 13080 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.64 % Allowed : 20.34 % Favored : 78.02 % 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: 4.05 (0.13), residues: 4080 helix: 3.41 (0.08), residues: 3168 sheet: None (None), residues: 0 loop : -0.17 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP S 93 HIS 0.003 0.001 HIS K 173 PHE 0.015 0.002 PHE J 41 TYR 0.013 0.001 TYR B 137 ARG 0.004 0.000 ARG X 156 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 763 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 703 time to evaluate : 4.229 Fit side-chains REVERT: A 89 ASP cc_start: 0.7509 (m-30) cc_final: 0.7277 (m-30) REVERT: C 89 ASP cc_start: 0.7501 (m-30) cc_final: 0.7260 (m-30) REVERT: C 92 ASP cc_start: 0.8355 (t70) cc_final: 0.8133 (t70) REVERT: C 131 ASP cc_start: 0.8570 (t70) cc_final: 0.8354 (t70) REVERT: G 63 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7651 (ttm170) REVERT: G 89 ASP cc_start: 0.7542 (m-30) cc_final: 0.7294 (m-30) REVERT: G 92 ASP cc_start: 0.8374 (t70) cc_final: 0.8149 (t70) REVERT: H 89 ASP cc_start: 0.7565 (m-30) cc_final: 0.7331 (m-30) REVERT: H 92 ASP cc_start: 0.8311 (t70) cc_final: 0.8088 (t70) REVERT: H 131 ASP cc_start: 0.8566 (t70) cc_final: 0.8359 (t70) REVERT: I 89 ASP cc_start: 0.7496 (m-30) cc_final: 0.7252 (m-30) REVERT: I 92 ASP cc_start: 0.8378 (t70) cc_final: 0.8142 (t70) REVERT: J 83 GLN cc_start: 0.8842 (mm-40) cc_final: 0.8620 (mm-40) REVERT: K 83 GLN cc_start: 0.8837 (mm-40) cc_final: 0.8617 (mm-40) REVERT: K 89 ASP cc_start: 0.7576 (m-30) cc_final: 0.7338 (m-30) REVERT: K 92 ASP cc_start: 0.8302 (t70) cc_final: 0.8068 (t70) REVERT: L 89 ASP cc_start: 0.7491 (m-30) cc_final: 0.7258 (m-30) REVERT: M 89 ASP cc_start: 0.7539 (m-30) cc_final: 0.7306 (m-30) REVERT: M 92 ASP cc_start: 0.8329 (t70) cc_final: 0.8099 (t70) REVERT: N 89 ASP cc_start: 0.7498 (m-30) cc_final: 0.7237 (m-30) REVERT: N 92 ASP cc_start: 0.8282 (t70) cc_final: 0.7851 (t0) REVERT: O 89 ASP cc_start: 0.7518 (m-30) cc_final: 0.7280 (m-30) REVERT: P 89 ASP cc_start: 0.7442 (m-30) cc_final: 0.7180 (m-30) REVERT: Q 89 ASP cc_start: 0.7492 (m-30) cc_final: 0.7239 (m-30) REVERT: R 89 ASP cc_start: 0.7436 (m-30) cc_final: 0.7173 (m-30) REVERT: S 89 ASP cc_start: 0.7383 (m-30) cc_final: 0.7139 (m-30) REVERT: V 89 ASP cc_start: 0.7508 (m-30) cc_final: 0.7279 (m-30) REVERT: W 89 ASP cc_start: 0.7408 (m-30) cc_final: 0.7158 (m-30) REVERT: W 92 ASP cc_start: 0.8308 (t70) cc_final: 0.8073 (t70) REVERT: W 131 ASP cc_start: 0.8604 (t70) cc_final: 0.8398 (t70) REVERT: X 83 GLN cc_start: 0.8872 (mm-40) cc_final: 0.8651 (mm-40) REVERT: X 89 ASP cc_start: 0.7479 (m-30) cc_final: 0.7236 (m-30) REVERT: Y 89 ASP cc_start: 0.7457 (m-30) cc_final: 0.7189 (m-30) outliers start: 60 outliers final: 30 residues processed: 751 average time/residue: 1.9697 time to fit residues: 1709.8439 Evaluate side-chains 667 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 636 time to evaluate : 4.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain F residue 126 ASP Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain J residue 126 ASP Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain K residue 126 ASP Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain L residue 126 ASP Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 ASP Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain O residue 139 SER Chi-restraints excluded: chain P residue 126 ASP Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain T residue 126 ASP Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain V residue 126 ASP Chi-restraints excluded: chain V residue 139 SER Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain Y residue 139 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 5.9990 chunk 309 optimal weight: 6.9990 chunk 171 optimal weight: 0.7980 chunk 105 optimal weight: 4.9990 chunk 208 optimal weight: 9.9990 chunk 165 optimal weight: 5.9990 chunk 319 optimal weight: 9.9990 chunk 123 optimal weight: 9.9990 chunk 194 optimal weight: 5.9990 chunk 238 optimal weight: 7.9990 chunk 370 optimal weight: 9.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- 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 B 141 GLN B 154 ASN 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 11 ASN N 14 GLN O 14 GLN P 14 GLN Q 14 GLN Q 75 GLN Q 154 ASN R 14 GLN S 14 GLN T 14 GLN V 14 GLN W 14 GLN X 14 GLN X 154 ASN Y 14 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.0795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 34512 Z= 0.345 Angle : 0.572 6.929 46416 Z= 0.294 Chirality : 0.040 0.134 4848 Planarity : 0.004 0.033 6096 Dihedral : 4.813 58.206 4556 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 4.71 % Allowed : 17.21 % Favored : 78.07 % 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: 4.53 (0.13), residues: 4080 helix: 3.70 (0.09), residues: 3168 sheet: None (None), residues: 0 loop : 0.24 (0.23), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP R 93 HIS 0.004 0.001 HIS O 173 PHE 0.018 0.002 PHE W 41 TYR 0.016 0.002 TYR S 137 ARG 0.003 0.001 ARG Q 76 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 887 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 715 time to evaluate : 4.604 Fit side-chains REVERT: A 63 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7765 (ttm170) REVERT: A 89 ASP cc_start: 0.7504 (m-30) cc_final: 0.7197 (m-30) REVERT: A 143 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8070 (ttmt) REVERT: A 147 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7900 (tt0) REVERT: B 63 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7758 (ttm170) REVERT: B 83 GLN cc_start: 0.8899 (mm-40) cc_final: 0.8628 (mm110) REVERT: B 89 ASP cc_start: 0.7445 (m-30) cc_final: 0.7159 (m-30) REVERT: B 143 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8102 (ttmt) REVERT: C 63 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7776 (ttm170) REVERT: C 89 ASP cc_start: 0.7460 (m-30) cc_final: 0.7129 (m-30) REVERT: C 92 ASP cc_start: 0.8401 (t70) cc_final: 0.8188 (t70) REVERT: C 147 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7862 (tt0) REVERT: D 63 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7757 (ttm170) REVERT: D 89 ASP cc_start: 0.7401 (m-30) cc_final: 0.7079 (m-30) REVERT: D 143 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8083 (ttmt) REVERT: E 63 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7725 (ttm170) REVERT: E 89 ASP cc_start: 0.7379 (m-30) cc_final: 0.7072 (m-30) REVERT: E 143 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8088 (ttmt) REVERT: E 147 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7904 (tt0) REVERT: F 63 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7723 (ttm170) REVERT: F 89 ASP cc_start: 0.7461 (m-30) cc_final: 0.7166 (m-30) REVERT: F 143 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8072 (ttmt) REVERT: F 147 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7885 (tt0) REVERT: G 89 ASP cc_start: 0.7501 (m-30) cc_final: 0.7178 (m-30) REVERT: G 92 ASP cc_start: 0.8409 (t70) cc_final: 0.8194 (t70) REVERT: G 143 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8084 (ttmt) REVERT: G 147 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7900 (tt0) REVERT: H 63 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7750 (ttm170) REVERT: H 89 ASP cc_start: 0.7526 (m-30) cc_final: 0.7218 (m-30) REVERT: H 92 ASP cc_start: 0.8343 (t70) cc_final: 0.8132 (t70) REVERT: H 147 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7862 (tt0) REVERT: I 63 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7767 (ttm170) REVERT: I 89 ASP cc_start: 0.7452 (m-30) cc_final: 0.7122 (m-30) REVERT: I 92 ASP cc_start: 0.8409 (t70) cc_final: 0.8183 (t70) REVERT: I 143 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8070 (ttmt) REVERT: J 63 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7750 (ttm170) REVERT: J 83 GLN cc_start: 0.8903 (mm-40) cc_final: 0.8628 (mm110) REVERT: J 143 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8056 (ttmt) REVERT: J 147 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7875 (tt0) REVERT: K 83 GLN cc_start: 0.8908 (mm-40) cc_final: 0.8627 (mm110) REVERT: K 89 ASP cc_start: 0.7548 (m-30) cc_final: 0.7224 (m-30) REVERT: K 92 ASP cc_start: 0.8352 (t70) cc_final: 0.8133 (t70) REVERT: K 143 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8055 (ttmt) REVERT: L 63 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7777 (ttm170) REVERT: L 89 ASP cc_start: 0.7492 (m-30) cc_final: 0.7189 (m-30) REVERT: L 143 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8087 (ttmt) REVERT: M 63 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7806 (ttm170) REVERT: M 89 ASP cc_start: 0.7509 (m-30) cc_final: 0.7192 (m-30) REVERT: M 92 ASP cc_start: 0.8374 (t70) cc_final: 0.8156 (t70) REVERT: M 143 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8073 (ttmt) REVERT: M 147 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7884 (tt0) REVERT: N 89 ASP cc_start: 0.7502 (m-30) cc_final: 0.7170 (m-30) REVERT: N 143 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8058 (ttmt) REVERT: O 83 GLN cc_start: 0.8902 (mm-40) cc_final: 0.8678 (mm110) REVERT: O 89 ASP cc_start: 0.7513 (m-30) cc_final: 0.7202 (m-30) REVERT: O 143 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8073 (ttmt) REVERT: O 147 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7875 (tt0) REVERT: P 89 ASP cc_start: 0.7428 (m-30) cc_final: 0.7080 (m-30) REVERT: P 143 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8065 (ttmt) REVERT: P 147 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8092 (tt0) REVERT: Q 89 ASP cc_start: 0.7514 (m-30) cc_final: 0.7184 (m-30) REVERT: Q 143 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8096 (ttmt) REVERT: Q 147 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7941 (tt0) REVERT: R 89 ASP cc_start: 0.7445 (m-30) cc_final: 0.7077 (m-30) REVERT: R 143 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8050 (ttmt) REVERT: S 89 ASP cc_start: 0.7375 (m-30) cc_final: 0.7040 (m-30) REVERT: S 143 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8082 (ttmt) REVERT: T 89 ASP cc_start: 0.7460 (m-30) cc_final: 0.7162 (m-30) REVERT: T 92 ASP cc_start: 0.8366 (t70) cc_final: 0.8165 (t70) REVERT: T 143 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8074 (ttmt) REVERT: V 89 ASP cc_start: 0.7514 (m-30) cc_final: 0.7194 (m-30) REVERT: V 143 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8050 (ttmt) REVERT: V 147 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8061 (tt0) REVERT: W 89 ASP cc_start: 0.7372 (m-30) cc_final: 0.7043 (m-30) REVERT: W 92 ASP cc_start: 0.8360 (t70) cc_final: 0.8148 (t70) REVERT: W 143 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8066 (ttmt) REVERT: X 83 GLN cc_start: 0.8905 (mm-40) cc_final: 0.8624 (mm110) REVERT: X 89 ASP cc_start: 0.7477 (m-30) cc_final: 0.7150 (m-30) REVERT: X 141 GLN cc_start: 0.9098 (tp-100) cc_final: 0.8885 (tp40) REVERT: X 143 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8041 (ttmt) REVERT: X 147 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7896 (tt0) REVERT: Y 89 ASP cc_start: 0.7465 (m-30) cc_final: 0.7105 (m-30) REVERT: Y 143 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8064 (ttmt) outliers start: 172 outliers final: 27 residues processed: 846 average time/residue: 1.9875 time to fit residues: 1941.7329 Evaluate side-chains 748 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 675 time to evaluate : 4.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain B residue 63 ARG Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain C residue 63 ARG Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain F residue 63 ARG Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 143 LYS Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 143 LYS Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain H residue 63 ARG Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 147 GLU Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 122 THR Chi-restraints excluded: chain I residue 143 LYS Chi-restraints excluded: chain J residue 63 ARG Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain J residue 143 LYS Chi-restraints excluded: chain J residue 147 GLU Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 143 LYS Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 143 LYS Chi-restraints excluded: chain M residue 63 ARG Chi-restraints excluded: chain M residue 64 GLU Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 143 LYS Chi-restraints excluded: chain M residue 147 GLU Chi-restraints excluded: chain N residue 143 LYS Chi-restraints excluded: chain O residue 122 THR Chi-restraints excluded: chain O residue 143 LYS Chi-restraints excluded: chain O residue 147 GLU Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain P residue 143 LYS Chi-restraints excluded: chain P residue 147 GLU Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain Q residue 143 LYS Chi-restraints excluded: chain Q residue 147 GLU Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 126 ASP Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain S residue 122 THR Chi-restraints excluded: chain S residue 126 ASP Chi-restraints excluded: chain S residue 143 LYS Chi-restraints excluded: chain T residue 122 THR Chi-restraints excluded: chain T residue 143 LYS Chi-restraints excluded: chain V residue 122 THR Chi-restraints excluded: chain V residue 143 LYS Chi-restraints excluded: chain V residue 147 GLU Chi-restraints excluded: chain W residue 122 THR Chi-restraints excluded: chain W residue 143 LYS Chi-restraints excluded: chain X residue 122 THR Chi-restraints excluded: chain X residue 143 LYS Chi-restraints excluded: chain X residue 147 GLU Chi-restraints excluded: chain Y residue 122 THR Chi-restraints excluded: chain Y residue 126 ASP Chi-restraints excluded: chain Y residue 143 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 9.9990 chunk 114 optimal weight: 6.9990 chunk 308 optimal weight: 6.9990 chunk 252 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 371 optimal weight: 6.9990 chunk 400 optimal weight: 0.6980 chunk 330 optimal weight: 7.9990 chunk 368 optimal weight: 6.9990 chunk 126 optimal weight: 5.9990 chunk 297 optimal weight: 6.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- 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 V 14 GLN W 14 GLN X 14 GLN Y 14 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.0802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 34512 Z= 0.267 Angle : 0.528 6.516 46416 Z= 0.272 Chirality : 0.038 0.127 4848 Planarity : 0.004 0.032 6096 Dihedral : 4.062 16.317 4512 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 5.15 % Allowed : 17.96 % Favored : 76.89 % 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 (0.13), residues: 4080 helix: 3.91 (0.08), residues: 3168 sheet: None (None), residues: 0 loop : 0.33 (0.24), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP V 93 HIS 0.003 0.001 HIS O 173 PHE 0.017 0.002 PHE W 41 TYR 0.015 0.002 TYR C 137 ARG 0.002 0.000 ARG Y 76 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 886 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 698 time to evaluate : 4.205 Fit side-chains REVERT: A 63 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7756 (ttm170) REVERT: A 89 ASP cc_start: 0.7520 (m-30) cc_final: 0.7183 (m-30) REVERT: A 143 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8047 (ttmt) REVERT: A 147 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7820 (tt0) REVERT: B 63 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7771 (ttm170) REVERT: B 89 ASP cc_start: 0.7446 (m-30) cc_final: 0.7116 (m-30) REVERT: B 143 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8076 (ttmt) REVERT: B 147 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7809 (tt0) REVERT: C 63 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7768 (ttm170) REVERT: C 89 ASP cc_start: 0.7457 (m-30) cc_final: 0.7096 (m-30) REVERT: C 147 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7804 (tt0) REVERT: D 63 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7702 (ttm170) REVERT: D 89 ASP cc_start: 0.7394 (m-30) cc_final: 0.7040 (m-30) REVERT: D 143 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8050 (ttmt) REVERT: D 147 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7869 (tt0) REVERT: E 63 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7671 (ttm170) REVERT: E 89 ASP cc_start: 0.7374 (m-30) cc_final: 0.7033 (m-30) REVERT: E 143 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8057 (ttmt) REVERT: E 147 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7822 (tt0) REVERT: F 63 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7761 (ttm170) REVERT: F 89 ASP cc_start: 0.7466 (m-30) cc_final: 0.7147 (m-30) REVERT: F 143 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8042 (ttmt) REVERT: F 147 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7836 (tt0) REVERT: G 63 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7671 (ttm170) REVERT: G 89 ASP cc_start: 0.7513 (m-30) cc_final: 0.7156 (m-30) REVERT: G 143 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8050 (ttmt) REVERT: G 147 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7821 (tt0) REVERT: H 63 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7685 (ttm170) REVERT: H 89 ASP cc_start: 0.7537 (m-30) cc_final: 0.7194 (m-30) REVERT: H 147 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7800 (tt0) REVERT: I 63 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7760 (ttm170) REVERT: I 89 ASP cc_start: 0.7452 (m-30) cc_final: 0.7088 (m-30) REVERT: I 92 ASP cc_start: 0.8394 (t70) cc_final: 0.8190 (t70) REVERT: I 143 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8029 (ttmt) REVERT: I 147 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7819 (tt0) REVERT: J 63 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7694 (ttm170) REVERT: J 143 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8030 (ttmt) REVERT: J 147 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7824 (tt0) REVERT: K 89 ASP cc_start: 0.7557 (m-30) cc_final: 0.7203 (m-30) REVERT: K 143 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8025 (ttmt) REVERT: L 63 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7756 (ttm170) REVERT: L 89 ASP cc_start: 0.7509 (m-30) cc_final: 0.7172 (m-30) REVERT: L 143 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8055 (ttmt) REVERT: L 147 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7826 (tt0) REVERT: M 63 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7799 (ttm170) REVERT: M 89 ASP cc_start: 0.7515 (m-30) cc_final: 0.7170 (m-30) REVERT: M 143 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8063 (ttmt) REVERT: M 147 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7826 (tt0) REVERT: N 70 MET cc_start: 0.9281 (OUTLIER) cc_final: 0.9037 (mtm) REVERT: N 89 ASP cc_start: 0.7499 (m-30) cc_final: 0.7136 (m-30) REVERT: N 143 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8035 (ttmt) REVERT: N 147 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7843 (tt0) REVERT: O 89 ASP cc_start: 0.7525 (m-30) cc_final: 0.7178 (m-30) REVERT: O 143 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8042 (ttmt) REVERT: O 147 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7828 (tt0) REVERT: P 70 MET cc_start: 0.9285 (OUTLIER) cc_final: 0.9036 (mtm) REVERT: P 89 ASP cc_start: 0.7430 (m-30) cc_final: 0.7056 (m-30) REVERT: P 143 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8044 (ttmt) REVERT: P 147 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.8034 (tt0) REVERT: Q 89 ASP cc_start: 0.7533 (m-30) cc_final: 0.7166 (m-30) REVERT: Q 143 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8077 (ttmt) REVERT: Q 147 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7858 (tt0) REVERT: R 89 ASP cc_start: 0.7470 (m-30) cc_final: 0.7087 (m-30) REVERT: R 143 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8038 (ttmt) REVERT: S 89 ASP cc_start: 0.7389 (m-30) cc_final: 0.7025 (m-30) REVERT: S 143 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8067 (ttmt) REVERT: T 70 MET cc_start: 0.9296 (OUTLIER) cc_final: 0.9050 (mtm) REVERT: T 89 ASP cc_start: 0.7449 (m-30) cc_final: 0.7111 (m-30) REVERT: T 143 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8039 (ttmt) REVERT: T 147 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7844 (tt0) REVERT: V 70 MET cc_start: 0.9292 (OUTLIER) cc_final: 0.9050 (mtm) REVERT: V 89 ASP cc_start: 0.7524 (m-30) cc_final: 0.7182 (m-30) REVERT: V 143 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8027 (ttmt) REVERT: V 147 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.8032 (tt0) REVERT: W 89 ASP cc_start: 0.7396 (m-30) cc_final: 0.7027 (m-30) REVERT: W 143 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8048 (ttmt) REVERT: X 89 ASP cc_start: 0.7491 (m-30) cc_final: 0.7134 (m-30) REVERT: X 141 GLN cc_start: 0.9090 (tp-100) cc_final: 0.8876 (tp40) REVERT: X 143 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8037 (ttmt) REVERT: X 147 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7849 (tt0) REVERT: Y 89 ASP cc_start: 0.7486 (m-30) cc_final: 0.7103 (m-30) REVERT: Y 143 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8044 (ttmt) outliers start: 188 outliers final: 77 residues processed: 827 average time/residue: 2.0567 time to fit residues: 1955.9802 Evaluate side-chains 801 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 667 time to evaluate : 4.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain B residue 63 ARG Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain C residue 63 ARG Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain D residue 87 LYS Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain F residue 63 ARG Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 126 ASP Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 143 LYS Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 143 LYS Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain H residue 63 ARG Chi-restraints excluded: chain H residue 87 LYS Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 147 GLU Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 87 LYS Chi-restraints excluded: chain I residue 122 THR Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 143 LYS Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain J residue 63 ARG Chi-restraints excluded: chain J residue 87 LYS Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain J residue 143 LYS Chi-restraints excluded: chain J residue 147 GLU Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 143 LYS Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain L residue 87 LYS Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 126 ASP Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain L residue 143 LYS Chi-restraints excluded: chain L residue 147 GLU Chi-restraints excluded: chain M residue 63 ARG Chi-restraints excluded: chain M residue 87 LYS Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain M residue 143 LYS Chi-restraints excluded: chain M residue 147 GLU Chi-restraints excluded: chain N residue 70 MET Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 126 ASP Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain N residue 143 LYS Chi-restraints excluded: chain N residue 147 GLU Chi-restraints excluded: chain O residue 122 THR Chi-restraints excluded: chain O residue 139 SER Chi-restraints excluded: chain O residue 143 LYS Chi-restraints excluded: chain O residue 147 GLU Chi-restraints excluded: chain P residue 70 MET Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain P residue 126 ASP Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain P residue 143 LYS Chi-restraints excluded: chain P residue 147 GLU Chi-restraints excluded: chain Q residue 87 LYS Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain Q residue 143 LYS Chi-restraints excluded: chain Q residue 147 GLU Chi-restraints excluded: chain R residue 87 LYS Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 126 ASP Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain R residue 147 GLU Chi-restraints excluded: chain S residue 87 LYS Chi-restraints excluded: chain S residue 122 THR Chi-restraints excluded: chain S residue 126 ASP Chi-restraints excluded: chain S residue 139 SER Chi-restraints excluded: chain S residue 143 LYS Chi-restraints excluded: chain T residue 70 MET Chi-restraints excluded: chain T residue 87 LYS Chi-restraints excluded: chain T residue 122 THR Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain T residue 143 LYS Chi-restraints excluded: chain T residue 147 GLU Chi-restraints excluded: chain V residue 70 MET Chi-restraints excluded: chain V residue 87 LYS Chi-restraints excluded: chain V residue 122 THR Chi-restraints excluded: chain V residue 126 ASP Chi-restraints excluded: chain V residue 139 SER Chi-restraints excluded: chain V residue 143 LYS Chi-restraints excluded: chain V residue 147 GLU Chi-restraints excluded: chain W residue 87 LYS Chi-restraints excluded: chain W residue 122 THR Chi-restraints excluded: chain W residue 139 SER Chi-restraints excluded: chain W residue 143 LYS Chi-restraints excluded: chain X residue 64 GLU Chi-restraints excluded: chain X residue 87 LYS Chi-restraints excluded: chain X residue 122 THR Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain X residue 143 LYS Chi-restraints excluded: chain X residue 147 GLU Chi-restraints excluded: chain Y residue 87 LYS Chi-restraints excluded: chain Y residue 122 THR Chi-restraints excluded: chain Y residue 126 ASP Chi-restraints excluded: chain Y residue 139 SER Chi-restraints excluded: chain Y residue 143 LYS Chi-restraints excluded: chain Y residue 147 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 9.9990 chunk 279 optimal weight: 5.9990 chunk 192 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 177 optimal weight: 2.9990 chunk 249 optimal weight: 4.9990 chunk 372 optimal weight: 4.9990 chunk 394 optimal weight: 4.9990 chunk 194 optimal weight: 0.7980 chunk 353 optimal weight: 2.9990 chunk 106 optimal weight: 9.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 V 14 GLN W 14 GLN X 14 GLN Y 14 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.0724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 34512 Z= 0.171 Angle : 0.459 5.858 46416 Z= 0.240 Chirality : 0.034 0.118 4848 Planarity : 0.003 0.030 6096 Dihedral : 3.842 16.371 4512 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.80 % Allowed : 17.96 % Favored : 77.25 % 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: 5.10 (0.13), residues: 4080 helix: 4.16 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.06 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 93 HIS 0.002 0.001 HIS J 173 PHE 0.015 0.002 PHE W 41 TYR 0.012 0.001 TYR M 137 ARG 0.001 0.000 ARG A 76 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 843 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 668 time to evaluate : 4.401 Fit side-chains REVERT: A 63 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7763 (ttm170) REVERT: A 89 ASP cc_start: 0.7547 (m-30) cc_final: 0.7208 (m-30) REVERT: A 143 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8015 (ttmt) REVERT: A 147 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7812 (tt0) REVERT: B 63 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7740 (ttm170) REVERT: B 89 ASP cc_start: 0.7450 (m-30) cc_final: 0.7123 (m-30) REVERT: B 143 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8033 (ttmt) REVERT: C 63 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7735 (ttm170) REVERT: C 89 ASP cc_start: 0.7461 (m-30) cc_final: 0.7091 (m-30) REVERT: C 147 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7801 (tt0) REVERT: D 63 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7673 (ttm170) REVERT: D 89 ASP cc_start: 0.7406 (m-30) cc_final: 0.7052 (m-30) REVERT: D 143 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8023 (ttmt) REVERT: D 147 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.7889 (tt0) REVERT: E 63 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7643 (ttm170) REVERT: E 89 ASP cc_start: 0.7381 (m-30) cc_final: 0.7039 (m-30) REVERT: E 143 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8030 (ttmt) REVERT: E 147 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7814 (tt0) REVERT: F 63 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7640 (ttm170) REVERT: F 89 ASP cc_start: 0.7476 (m-30) cc_final: 0.7156 (m-30) REVERT: F 143 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8017 (ttmt) REVERT: F 147 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7830 (tt0) REVERT: G 63 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7672 (ttm170) REVERT: G 89 ASP cc_start: 0.7530 (m-30) cc_final: 0.7160 (m-30) REVERT: G 143 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8027 (ttmt) REVERT: G 147 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7811 (tt0) REVERT: H 63 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7657 (ttm170) REVERT: H 89 ASP cc_start: 0.7541 (m-30) cc_final: 0.7189 (m-30) REVERT: H 147 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7798 (tt0) REVERT: I 63 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7724 (ttm170) REVERT: I 89 ASP cc_start: 0.7454 (m-30) cc_final: 0.7081 (m-30) REVERT: I 92 ASP cc_start: 0.8384 (t70) cc_final: 0.8181 (t70) REVERT: I 143 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8008 (ttmt) REVERT: I 147 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7828 (tt0) REVERT: J 63 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7664 (ttm170) REVERT: J 143 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.7993 (ttmt) REVERT: J 147 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7819 (tt0) REVERT: K 89 ASP cc_start: 0.7557 (m-30) cc_final: 0.7194 (m-30) REVERT: K 143 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8001 (ttmt) REVERT: L 63 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7773 (ttm170) REVERT: L 89 ASP cc_start: 0.7539 (m-30) cc_final: 0.7195 (m-30) REVERT: L 143 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8020 (ttmt) REVERT: L 147 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.7825 (tt0) REVERT: M 63 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7766 (ttm170) REVERT: M 89 ASP cc_start: 0.7526 (m-30) cc_final: 0.7170 (m-30) REVERT: M 143 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8016 (ttmt) REVERT: M 147 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7807 (tt0) REVERT: N 89 ASP cc_start: 0.7516 (m-30) cc_final: 0.7149 (m-30) REVERT: N 143 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.7994 (ttmt) REVERT: N 147 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7836 (tt0) REVERT: O 89 ASP cc_start: 0.7559 (m-30) cc_final: 0.7210 (m-30) REVERT: O 143 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8009 (ttmt) REVERT: O 147 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7817 (tt0) REVERT: P 89 ASP cc_start: 0.7446 (m-30) cc_final: 0.7064 (m-30) REVERT: P 143 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8013 (ttmt) REVERT: Q 89 ASP cc_start: 0.7536 (m-30) cc_final: 0.7164 (m-30) REVERT: Q 143 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8036 (ttmt) REVERT: Q 147 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7851 (tt0) REVERT: R 89 ASP cc_start: 0.7495 (m-30) cc_final: 0.7102 (m-30) REVERT: R 143 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8014 (ttmt) REVERT: S 89 ASP cc_start: 0.7416 (m-30) cc_final: 0.7053 (m-30) REVERT: S 143 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8038 (ttmt) REVERT: T 89 ASP cc_start: 0.7467 (m-30) cc_final: 0.7139 (m-30) REVERT: T 143 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8010 (ttmt) REVERT: T 147 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7847 (tt0) REVERT: V 89 ASP cc_start: 0.7538 (m-30) cc_final: 0.7192 (m-30) REVERT: V 143 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8003 (ttmt) REVERT: W 89 ASP cc_start: 0.7405 (m-30) cc_final: 0.7032 (m-30) REVERT: W 143 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8024 (ttmt) REVERT: X 89 ASP cc_start: 0.7514 (m-30) cc_final: 0.7155 (m-30) REVERT: X 143 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8007 (ttmt) REVERT: X 147 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7847 (tt0) REVERT: Y 89 ASP cc_start: 0.7506 (m-30) cc_final: 0.7118 (m-30) REVERT: Y 143 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8010 (ttmt) outliers start: 175 outliers final: 69 residues processed: 802 average time/residue: 2.0532 time to fit residues: 1896.0732 Evaluate side-chains 765 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 646 time to evaluate : 4.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain B residue 63 ARG Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain C residue 63 ARG Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain F residue 63 ARG Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 143 LYS Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 143 LYS Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain H residue 63 ARG Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 126 ASP Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 147 GLU Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 122 THR Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 143 LYS Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain J residue 63 ARG Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain J residue 126 ASP Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain J residue 143 LYS Chi-restraints excluded: chain J residue 147 GLU Chi-restraints excluded: chain K residue 87 LYS Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 126 ASP Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 143 LYS Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 126 ASP Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain L residue 143 LYS Chi-restraints excluded: chain L residue 147 GLU Chi-restraints excluded: chain M residue 63 ARG Chi-restraints excluded: chain M residue 64 GLU Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain M residue 143 LYS Chi-restraints excluded: chain M residue 147 GLU Chi-restraints excluded: chain N residue 126 ASP Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain N residue 143 LYS Chi-restraints excluded: chain N residue 147 GLU Chi-restraints excluded: chain O residue 87 LYS Chi-restraints excluded: chain O residue 122 THR Chi-restraints excluded: chain O residue 139 SER Chi-restraints excluded: chain O residue 143 LYS Chi-restraints excluded: chain O residue 147 GLU Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain P residue 126 ASP Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain P residue 143 LYS Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain Q residue 143 LYS Chi-restraints excluded: chain Q residue 147 GLU Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 126 ASP Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain S residue 122 THR Chi-restraints excluded: chain S residue 126 ASP Chi-restraints excluded: chain S residue 139 SER Chi-restraints excluded: chain S residue 143 LYS Chi-restraints excluded: chain T residue 122 THR Chi-restraints excluded: chain T residue 126 ASP Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain T residue 143 LYS Chi-restraints excluded: chain T residue 147 GLU Chi-restraints excluded: chain V residue 87 LYS Chi-restraints excluded: chain V residue 122 THR Chi-restraints excluded: chain V residue 126 ASP Chi-restraints excluded: chain V residue 139 SER Chi-restraints excluded: chain V residue 143 LYS Chi-restraints excluded: chain W residue 122 THR Chi-restraints excluded: chain W residue 126 ASP Chi-restraints excluded: chain W residue 139 SER Chi-restraints excluded: chain W residue 143 LYS Chi-restraints excluded: chain X residue 64 GLU Chi-restraints excluded: chain X residue 122 THR Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain X residue 143 LYS Chi-restraints excluded: chain X residue 147 GLU Chi-restraints excluded: chain Y residue 87 LYS Chi-restraints excluded: chain Y residue 122 THR Chi-restraints excluded: chain Y residue 126 ASP Chi-restraints excluded: chain Y residue 139 SER Chi-restraints excluded: chain Y residue 143 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 5.9990 chunk 223 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 293 optimal weight: 9.9990 chunk 162 optimal weight: 0.5980 chunk 336 optimal weight: 3.9990 chunk 272 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 chunk 201 optimal weight: 6.9990 chunk 353 optimal weight: 4.9990 chunk 99 optimal weight: 9.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- 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 V 14 GLN W 14 GLN X 14 GLN Y 14 GLN Y 125 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.0844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 34512 Z= 0.233 Angle : 0.504 6.297 46416 Z= 0.260 Chirality : 0.036 0.125 4848 Planarity : 0.003 0.031 6096 Dihedral : 3.948 16.368 4512 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 5.37 % Allowed : 17.11 % Favored : 77.52 % 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: 5.15 (0.13), residues: 4080 helix: 4.14 (0.08), residues: 3168 sheet: None (None), residues: 0 loop : 0.44 (0.24), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 93 HIS 0.002 0.001 HIS S 173 PHE 0.016 0.002 PHE W 41 TYR 0.013 0.001 TYR A 137 ARG 0.002 0.000 ARG W 76 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 858 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 662 time to evaluate : 4.470 Fit side-chains REVERT: A 63 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7765 (ttm170) REVERT: A 89 ASP cc_start: 0.7533 (m-30) cc_final: 0.7166 (m-30) REVERT: A 143 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8015 (ttmt) REVERT: A 147 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7820 (tt0) REVERT: B 63 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7770 (ttm170) REVERT: B 83 GLN cc_start: 0.8884 (mm-40) cc_final: 0.8628 (mm110) REVERT: B 89 ASP cc_start: 0.7479 (m-30) cc_final: 0.7130 (m-30) REVERT: B 143 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8029 (ttmt) REVERT: B 147 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7842 (tt0) REVERT: C 63 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7766 (ttm170) REVERT: C 89 ASP cc_start: 0.7464 (m-30) cc_final: 0.7070 (m-30) REVERT: C 147 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7814 (tt0) REVERT: D 63 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7689 (ttm170) REVERT: D 89 ASP cc_start: 0.7429 (m-30) cc_final: 0.7047 (m-30) REVERT: D 143 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8020 (ttmt) REVERT: D 147 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7874 (tt0) REVERT: E 63 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7659 (ttm170) REVERT: E 89 ASP cc_start: 0.7408 (m-30) cc_final: 0.7039 (m-30) REVERT: E 143 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8032 (ttmt) REVERT: E 147 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7825 (tt0) REVERT: F 63 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7652 (ttm170) REVERT: F 89 ASP cc_start: 0.7500 (m-30) cc_final: 0.7147 (m-30) REVERT: F 143 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8004 (ttmt) REVERT: F 147 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7835 (tt0) REVERT: G 63 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7697 (ttm170) REVERT: G 89 ASP cc_start: 0.7525 (m-30) cc_final: 0.7143 (m-30) REVERT: G 143 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8026 (ttmt) REVERT: G 147 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7819 (tt0) REVERT: H 63 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7679 (ttm170) REVERT: H 89 ASP cc_start: 0.7541 (m-30) cc_final: 0.7163 (m-30) REVERT: H 147 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7809 (tt0) REVERT: I 63 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7747 (ttm170) REVERT: I 89 ASP cc_start: 0.7459 (m-30) cc_final: 0.7067 (m-30) REVERT: I 92 ASP cc_start: 0.8392 (OUTLIER) cc_final: 0.8190 (t70) REVERT: I 143 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8009 (ttmt) REVERT: I 147 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7845 (tt0) REVERT: J 63 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7682 (ttm170) REVERT: J 89 ASP cc_start: 0.7437 (m-30) cc_final: 0.7193 (m-30) REVERT: J 143 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8001 (ttmt) REVERT: J 147 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7826 (tt0) REVERT: K 83 GLN cc_start: 0.8878 (mm-40) cc_final: 0.8608 (mm110) REVERT: K 89 ASP cc_start: 0.7559 (m-30) cc_final: 0.7173 (m-30) REVERT: K 143 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.7994 (ttmt) REVERT: L 63 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7779 (ttm170) REVERT: L 89 ASP cc_start: 0.7523 (m-30) cc_final: 0.7162 (m-30) REVERT: L 143 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8034 (ttmt) REVERT: L 147 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7835 (tt0) REVERT: M 63 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7784 (ttm170) REVERT: M 89 ASP cc_start: 0.7519 (m-30) cc_final: 0.7141 (m-30) REVERT: M 143 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8027 (ttmt) REVERT: M 147 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7837 (tt0) REVERT: N 70 MET cc_start: 0.9273 (OUTLIER) cc_final: 0.9058 (mtp) REVERT: N 89 ASP cc_start: 0.7512 (m-30) cc_final: 0.7121 (m-30) REVERT: N 143 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.7994 (ttmt) REVERT: N 147 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7849 (tt0) REVERT: O 89 ASP cc_start: 0.7542 (m-30) cc_final: 0.7172 (m-30) REVERT: O 143 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8018 (ttmt) REVERT: O 147 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7825 (tt0) REVERT: P 70 MET cc_start: 0.9277 (OUTLIER) cc_final: 0.9059 (mtp) REVERT: P 89 ASP cc_start: 0.7437 (m-30) cc_final: 0.7034 (m-30) REVERT: P 143 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8004 (ttmt) REVERT: Q 89 ASP cc_start: 0.7527 (m-30) cc_final: 0.7137 (m-30) REVERT: Q 143 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8038 (ttmt) REVERT: Q 147 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7861 (tt0) REVERT: R 89 ASP cc_start: 0.7482 (m-30) cc_final: 0.7062 (m-30) REVERT: R 143 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8018 (ttmt) REVERT: S 89 ASP cc_start: 0.7411 (m-30) cc_final: 0.7016 (m-30) REVERT: S 143 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8043 (ttmt) REVERT: T 70 MET cc_start: 0.9290 (OUTLIER) cc_final: 0.9074 (mtp) REVERT: T 89 ASP cc_start: 0.7496 (m-30) cc_final: 0.7138 (m-30) REVERT: T 143 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8004 (ttmt) REVERT: T 147 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7860 (tt0) REVERT: V 70 MET cc_start: 0.9284 (OUTLIER) cc_final: 0.9075 (mtp) REVERT: V 89 ASP cc_start: 0.7537 (m-30) cc_final: 0.7184 (m-30) REVERT: V 143 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.7998 (ttmt) REVERT: W 89 ASP cc_start: 0.7412 (m-30) cc_final: 0.7008 (m-30) REVERT: W 143 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8023 (ttmt) REVERT: X 83 GLN cc_start: 0.8895 (mm-40) cc_final: 0.8629 (mm110) REVERT: X 89 ASP cc_start: 0.7496 (m-30) cc_final: 0.7113 (m-30) REVERT: X 141 GLN cc_start: 0.9085 (tp-100) cc_final: 0.8880 (tp40) REVERT: X 143 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8015 (ttmt) REVERT: X 147 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7853 (tt0) REVERT: Y 89 ASP cc_start: 0.7502 (m-30) cc_final: 0.7103 (m-30) REVERT: Y 143 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8014 (ttmt) outliers start: 196 outliers final: 85 residues processed: 814 average time/residue: 2.1025 time to fit residues: 1971.1083 Evaluate side-chains 784 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 643 time to evaluate : 4.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain B residue 63 ARG Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain C residue 63 ARG Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain D residue 87 LYS Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain F residue 63 ARG Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 143 LYS Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 143 LYS Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain H residue 63 ARG Chi-restraints excluded: chain H residue 87 LYS Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain H residue 147 GLU Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 87 LYS Chi-restraints excluded: chain I residue 92 ASP Chi-restraints excluded: chain I residue 122 THR Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 143 LYS Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain J residue 63 ARG Chi-restraints excluded: chain J residue 87 LYS Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain J residue 126 ASP Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain J residue 143 LYS Chi-restraints excluded: chain J residue 147 GLU Chi-restraints excluded: chain K residue 87 LYS Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 126 ASP Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 143 LYS Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 126 ASP Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain L residue 143 LYS Chi-restraints excluded: chain L residue 147 GLU Chi-restraints excluded: chain M residue 63 ARG Chi-restraints excluded: chain M residue 64 GLU Chi-restraints excluded: chain M residue 87 LYS Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain M residue 143 LYS Chi-restraints excluded: chain M residue 147 GLU Chi-restraints excluded: chain N residue 70 MET Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 126 ASP Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain N residue 143 LYS Chi-restraints excluded: chain N residue 147 GLU Chi-restraints excluded: chain O residue 87 LYS Chi-restraints excluded: chain O residue 122 THR Chi-restraints excluded: chain O residue 139 SER Chi-restraints excluded: chain O residue 143 LYS Chi-restraints excluded: chain O residue 147 GLU Chi-restraints excluded: chain P residue 70 MET Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain P residue 126 ASP Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain P residue 143 LYS Chi-restraints excluded: chain Q residue 87 LYS Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain Q residue 143 LYS Chi-restraints excluded: chain Q residue 147 GLU Chi-restraints excluded: chain R residue 87 LYS Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 126 ASP Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain S residue 64 GLU Chi-restraints excluded: chain S residue 87 LYS Chi-restraints excluded: chain S residue 122 THR Chi-restraints excluded: chain S residue 126 ASP Chi-restraints excluded: chain S residue 139 SER Chi-restraints excluded: chain S residue 143 LYS Chi-restraints excluded: chain T residue 64 GLU Chi-restraints excluded: chain T residue 70 MET Chi-restraints excluded: chain T residue 87 LYS Chi-restraints excluded: chain T residue 122 THR Chi-restraints excluded: chain T residue 126 ASP Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain T residue 143 LYS Chi-restraints excluded: chain T residue 147 GLU Chi-restraints excluded: chain V residue 70 MET Chi-restraints excluded: chain V residue 87 LYS Chi-restraints excluded: chain V residue 122 THR Chi-restraints excluded: chain V residue 126 ASP Chi-restraints excluded: chain V residue 139 SER Chi-restraints excluded: chain V residue 143 LYS Chi-restraints excluded: chain W residue 87 LYS Chi-restraints excluded: chain W residue 122 THR Chi-restraints excluded: chain W residue 139 SER Chi-restraints excluded: chain W residue 143 LYS Chi-restraints excluded: chain X residue 87 LYS Chi-restraints excluded: chain X residue 122 THR Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain X residue 143 LYS Chi-restraints excluded: chain X residue 147 GLU Chi-restraints excluded: chain Y residue 87 LYS Chi-restraints excluded: chain Y residue 122 THR Chi-restraints excluded: chain Y residue 126 ASP Chi-restraints excluded: chain Y residue 139 SER Chi-restraints excluded: chain Y residue 143 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 0.9980 chunk 355 optimal weight: 7.9990 chunk 77 optimal weight: 9.9990 chunk 231 optimal weight: 10.0000 chunk 97 optimal weight: 0.6980 chunk 394 optimal weight: 7.9990 chunk 327 optimal weight: 10.0000 chunk 182 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 130 optimal weight: 0.9980 chunk 207 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 O 83 GLN P 14 GLN Q 14 GLN R 14 GLN S 14 GLN T 14 GLN V 14 GLN W 14 GLN X 14 GLN Y 14 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.0855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 34512 Z= 0.117 Angle : 0.411 5.223 46416 Z= 0.218 Chirality : 0.032 0.113 4848 Planarity : 0.003 0.028 6096 Dihedral : 3.606 15.878 4512 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.10 % Allowed : 19.30 % Favored : 77.60 % 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: 5.54 (0.13), residues: 4080 helix: 4.52 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.02 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP W 93 HIS 0.001 0.000 HIS X 105 PHE 0.013 0.002 PHE W 41 TYR 0.011 0.001 TYR K 137 ARG 0.002 0.000 ARG B 156 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 805 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 692 time to evaluate : 4.791 Fit side-chains REVERT: A 63 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7651 (ttm170) REVERT: A 89 ASP cc_start: 0.7534 (m-30) cc_final: 0.7202 (m-30) REVERT: A 143 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8043 (ttmt) REVERT: A 147 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7872 (tt0) REVERT: B 63 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7710 (ttm170) REVERT: B 89 ASP cc_start: 0.7457 (m-30) cc_final: 0.7135 (m-30) REVERT: B 143 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8068 (ttmt) REVERT: C 63 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7708 (ttm170) REVERT: C 89 ASP cc_start: 0.7451 (m-30) cc_final: 0.7083 (m-30) REVERT: C 147 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7825 (tt0) REVERT: D 89 ASP cc_start: 0.7410 (m-30) cc_final: 0.7053 (m-30) REVERT: D 143 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8057 (ttmt) REVERT: E 89 ASP cc_start: 0.7399 (m-30) cc_final: 0.7057 (m-30) REVERT: E 143 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8053 (ttmt) REVERT: E 147 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7876 (tt0) REVERT: F 89 ASP cc_start: 0.7473 (m-30) cc_final: 0.7140 (m-30) REVERT: F 143 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8035 (ttmt) REVERT: F 147 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7889 (tt0) REVERT: G 63 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7623 (ttm170) REVERT: G 89 ASP cc_start: 0.7489 (m-30) cc_final: 0.7132 (m-30) REVERT: G 143 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8049 (ttmt) REVERT: G 147 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7873 (tt0) REVERT: H 89 ASP cc_start: 0.7533 (m-30) cc_final: 0.7180 (m-30) REVERT: H 147 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7821 (tt0) REVERT: I 63 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7699 (ttm170) REVERT: I 89 ASP cc_start: 0.7430 (m-30) cc_final: 0.7065 (m-30) REVERT: I 143 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8043 (ttmt) REVERT: J 89 ASP cc_start: 0.7391 (m-30) cc_final: 0.7147 (m-30) REVERT: J 143 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8021 (ttmt) REVERT: J 147 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7881 (tt0) REVERT: K 89 ASP cc_start: 0.7531 (m-30) cc_final: 0.7170 (m-30) REVERT: K 143 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8019 (ttmt) REVERT: L 63 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7664 (ttm170) REVERT: L 89 ASP cc_start: 0.7499 (m-30) cc_final: 0.7170 (m-30) REVERT: L 143 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8051 (ttmt) REVERT: M 63 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7643 (ttm170) REVERT: M 89 ASP cc_start: 0.7483 (m-30) cc_final: 0.7139 (m-30) REVERT: M 143 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8036 (ttmt) REVERT: M 147 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7889 (tt0) REVERT: N 89 ASP cc_start: 0.7487 (m-30) cc_final: 0.7125 (m-30) REVERT: N 143 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8035 (ttmt) REVERT: O 89 ASP cc_start: 0.7544 (m-30) cc_final: 0.7204 (m-30) REVERT: O 143 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8041 (ttmt) REVERT: O 147 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7882 (tt0) REVERT: P 89 ASP cc_start: 0.7424 (m-30) cc_final: 0.7056 (m-30) REVERT: P 143 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8037 (ttmt) REVERT: Q 89 ASP cc_start: 0.7516 (m-30) cc_final: 0.7160 (m-30) REVERT: Q 143 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8068 (ttmt) REVERT: Q 147 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7913 (tt0) REVERT: R 89 ASP cc_start: 0.7482 (m-30) cc_final: 0.7096 (m-30) REVERT: R 143 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8032 (ttmt) REVERT: S 89 ASP cc_start: 0.7409 (m-30) cc_final: 0.7047 (m-30) REVERT: S 143 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8064 (ttmt) REVERT: T 89 ASP cc_start: 0.7471 (m-30) cc_final: 0.7134 (m-30) REVERT: T 143 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8044 (ttmt) REVERT: V 89 ASP cc_start: 0.7510 (m-30) cc_final: 0.7168 (m-30) REVERT: V 143 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8011 (ttmt) REVERT: W 89 ASP cc_start: 0.7423 (m-30) cc_final: 0.7052 (m-30) REVERT: W 143 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8039 (ttmt) REVERT: X 89 ASP cc_start: 0.7469 (m-30) cc_final: 0.7123 (m-30) REVERT: X 143 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8025 (ttmt) REVERT: X 147 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7879 (tt0) REVERT: Y 89 ASP cc_start: 0.7483 (m-30) cc_final: 0.7102 (m-30) REVERT: Y 143 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8040 (ttmt) outliers start: 113 outliers final: 14 residues processed: 754 average time/residue: 2.0567 time to fit residues: 1785.2917 Evaluate side-chains 719 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 665 time to evaluate : 4.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain B residue 63 ARG Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain C residue 63 ARG Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain F residue 126 ASP Chi-restraints excluded: chain F residue 143 LYS Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 143 LYS Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain H residue 147 GLU Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 143 LYS Chi-restraints excluded: chain J residue 143 LYS Chi-restraints excluded: chain J residue 147 GLU Chi-restraints excluded: chain K residue 143 LYS Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain L residue 143 LYS Chi-restraints excluded: chain M residue 63 ARG Chi-restraints excluded: chain M residue 64 GLU Chi-restraints excluded: chain M residue 143 LYS Chi-restraints excluded: chain M residue 147 GLU Chi-restraints excluded: chain N residue 64 GLU Chi-restraints excluded: chain N residue 143 LYS Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain O residue 143 LYS Chi-restraints excluded: chain O residue 147 GLU Chi-restraints excluded: chain P residue 64 GLU Chi-restraints excluded: chain P residue 143 LYS Chi-restraints excluded: chain Q residue 64 GLU Chi-restraints excluded: chain Q residue 143 LYS Chi-restraints excluded: chain Q residue 147 GLU Chi-restraints excluded: chain R residue 126 ASP Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain S residue 64 GLU Chi-restraints excluded: chain S residue 126 ASP Chi-restraints excluded: chain S residue 143 LYS Chi-restraints excluded: chain T residue 64 GLU Chi-restraints excluded: chain T residue 143 LYS Chi-restraints excluded: chain V residue 64 GLU Chi-restraints excluded: chain V residue 143 LYS Chi-restraints excluded: chain W residue 143 LYS Chi-restraints excluded: chain X residue 64 GLU Chi-restraints excluded: chain X residue 143 LYS Chi-restraints excluded: chain X residue 147 GLU Chi-restraints excluded: chain Y residue 64 GLU Chi-restraints excluded: chain Y residue 126 ASP Chi-restraints excluded: chain Y residue 143 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 chunk 224 optimal weight: 0.8980 chunk 288 optimal weight: 9.9990 chunk 223 optimal weight: 3.9990 chunk 332 optimal weight: 0.9990 chunk 220 optimal weight: 6.9990 chunk 393 optimal weight: 6.9990 chunk 246 optimal weight: 1.9990 chunk 239 optimal weight: 4.9990 chunk 181 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 D 75 GLN E 14 GLN E 75 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 P 125 ASN Q 14 GLN R 14 GLN S 14 GLN T 14 GLN V 14 GLN W 14 GLN X 14 GLN Y 14 GLN Y 125 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.0779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 34512 Z= 0.159 Angle : 0.452 5.496 46416 Z= 0.237 Chirality : 0.034 0.115 4848 Planarity : 0.003 0.029 6096 Dihedral : 3.717 15.937 4512 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.56 % Allowed : 18.78 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 5.49 (0.13), residues: 4080 helix: 4.43 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.21 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP H 93 HIS 0.002 0.001 HIS X 105 PHE 0.014 0.002 PHE W 41 TYR 0.011 0.001 TYR V 137 ARG 0.002 0.000 ARG V 156 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 795 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 665 time to evaluate : 4.424 Fit side-chains REVERT: A 63 ARG cc_start: 0.8143 (OUTLIER) cc_final: 0.7705 (ttm170) REVERT: A 89 ASP cc_start: 0.7538 (m-30) cc_final: 0.7189 (m-30) REVERT: A 143 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8050 (ttmt) REVERT: A 147 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7838 (tt0) REVERT: B 63 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7720 (ttm170) REVERT: B 89 ASP cc_start: 0.7465 (m-30) cc_final: 0.7130 (m-30) REVERT: B 143 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8068 (ttmt) REVERT: B 147 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7847 (tt0) REVERT: C 63 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7720 (ttm170) REVERT: C 89 ASP cc_start: 0.7445 (m-30) cc_final: 0.7063 (m-30) REVERT: C 131 ASP cc_start: 0.8552 (t70) cc_final: 0.8342 (t70) REVERT: C 143 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8044 (ttmt) REVERT: C 147 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7823 (tt0) REVERT: D 89 ASP cc_start: 0.7430 (m-30) cc_final: 0.7064 (m-30) REVERT: D 143 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8069 (ttmt) REVERT: E 89 ASP cc_start: 0.7431 (m-30) cc_final: 0.7076 (m-30) REVERT: E 143 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8063 (ttmt) REVERT: E 147 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7829 (tt0) REVERT: F 63 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7626 (ttm170) REVERT: F 89 ASP cc_start: 0.7500 (m-30) cc_final: 0.7162 (m-30) REVERT: F 143 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8043 (ttmt) REVERT: F 147 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7849 (tt0) REVERT: G 63 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7670 (ttm170) REVERT: G 89 ASP cc_start: 0.7506 (m-30) cc_final: 0.7124 (m-30) REVERT: G 143 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8058 (ttmt) REVERT: G 147 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7825 (tt0) REVERT: H 63 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7665 (ttm170) REVERT: H 89 ASP cc_start: 0.7521 (m-30) cc_final: 0.7160 (m-30) REVERT: H 143 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8026 (ttmt) REVERT: H 147 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7816 (tt0) REVERT: I 63 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7730 (ttm170) REVERT: I 89 ASP cc_start: 0.7444 (m-30) cc_final: 0.7065 (m-30) REVERT: I 131 ASP cc_start: 0.8543 (t70) cc_final: 0.8311 (t70) REVERT: I 143 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8054 (ttmt) REVERT: J 89 ASP cc_start: 0.7348 (m-30) cc_final: 0.7112 (m-30) REVERT: J 143 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8031 (ttmt) REVERT: J 147 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7831 (tt0) REVERT: K 89 ASP cc_start: 0.7539 (m-30) cc_final: 0.7161 (m-30) REVERT: K 143 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8024 (ttmt) REVERT: K 147 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7847 (tt0) REVERT: L 63 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7723 (ttm170) REVERT: L 89 ASP cc_start: 0.7528 (m-30) cc_final: 0.7175 (m-30) REVERT: L 131 ASP cc_start: 0.8568 (t70) cc_final: 0.8324 (t70) REVERT: L 143 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8064 (ttmt) REVERT: M 63 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7702 (ttm170) REVERT: M 89 ASP cc_start: 0.7501 (m-30) cc_final: 0.7135 (m-30) REVERT: M 131 ASP cc_start: 0.8557 (t70) cc_final: 0.8326 (t70) REVERT: M 143 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8054 (ttmt) REVERT: M 147 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7831 (tt0) REVERT: N 89 ASP cc_start: 0.7497 (m-30) cc_final: 0.7119 (m-30) REVERT: N 143 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8042 (ttmt) REVERT: O 89 ASP cc_start: 0.7549 (m-30) cc_final: 0.7191 (m-30) REVERT: O 143 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8045 (ttmt) REVERT: O 147 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7839 (tt0) REVERT: P 89 ASP cc_start: 0.7431 (m-30) cc_final: 0.7038 (m-30) REVERT: P 131 ASP cc_start: 0.8540 (t70) cc_final: 0.8310 (t70) REVERT: P 143 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8036 (ttmt) REVERT: P 147 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7840 (tt0) REVERT: Q 89 ASP cc_start: 0.7522 (m-30) cc_final: 0.7157 (m-30) REVERT: Q 143 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8070 (ttmt) REVERT: Q 147 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7867 (tt0) REVERT: R 89 ASP cc_start: 0.7493 (m-30) cc_final: 0.7102 (m-30) REVERT: R 143 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8038 (ttmt) REVERT: R 147 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7861 (tt0) REVERT: S 89 ASP cc_start: 0.7439 (m-30) cc_final: 0.7069 (m-30) REVERT: S 143 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8060 (ttmt) REVERT: S 147 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7851 (tt0) REVERT: T 89 ASP cc_start: 0.7469 (m-30) cc_final: 0.7125 (m-30) REVERT: T 143 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8051 (ttmt) REVERT: V 89 ASP cc_start: 0.7529 (m-30) cc_final: 0.7167 (m-30) REVERT: V 143 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8018 (ttmt) REVERT: V 147 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7841 (tt0) REVERT: W 89 ASP cc_start: 0.7417 (m-30) cc_final: 0.7033 (m-30) REVERT: W 131 ASP cc_start: 0.8588 (t70) cc_final: 0.8379 (t70) REVERT: W 143 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8046 (ttmt) REVERT: W 147 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7850 (tt0) REVERT: X 89 ASP cc_start: 0.7501 (m-30) cc_final: 0.7136 (m-30) REVERT: X 143 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8040 (ttmt) REVERT: X 147 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7817 (tt0) REVERT: Y 89 ASP cc_start: 0.7507 (m-30) cc_final: 0.7114 (m-30) REVERT: Y 143 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8040 (ttmt) REVERT: Y 147 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7845 (tt0) outliers start: 130 outliers final: 42 residues processed: 756 average time/residue: 2.0407 time to fit residues: 1778.8226 Evaluate side-chains 737 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 643 time to evaluate : 4.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain B residue 63 ARG Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain C residue 63 ARG Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain D residue 87 LYS Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain F residue 63 ARG Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain F residue 126 ASP Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 143 LYS Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 143 LYS Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain H residue 63 ARG Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain H residue 147 GLU Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 143 LYS Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain J residue 143 LYS Chi-restraints excluded: chain J residue 147 GLU Chi-restraints excluded: chain K residue 87 LYS Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 143 LYS Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain L residue 143 LYS Chi-restraints excluded: chain M residue 63 ARG Chi-restraints excluded: chain M residue 64 GLU Chi-restraints excluded: chain M residue 87 LYS Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain M residue 143 LYS Chi-restraints excluded: chain M residue 147 GLU Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain N residue 143 LYS Chi-restraints excluded: chain O residue 139 SER Chi-restraints excluded: chain O residue 143 LYS Chi-restraints excluded: chain O residue 147 GLU Chi-restraints excluded: chain P residue 87 LYS Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain P residue 143 LYS Chi-restraints excluded: chain P residue 147 GLU Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain Q residue 143 LYS Chi-restraints excluded: chain Q residue 147 GLU Chi-restraints excluded: chain R residue 87 LYS Chi-restraints excluded: chain R residue 126 ASP Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain R residue 147 GLU Chi-restraints excluded: chain S residue 64 GLU Chi-restraints excluded: chain S residue 87 LYS Chi-restraints excluded: chain S residue 126 ASP Chi-restraints excluded: chain S residue 139 SER Chi-restraints excluded: chain S residue 143 LYS Chi-restraints excluded: chain S residue 147 GLU Chi-restraints excluded: chain T residue 64 GLU Chi-restraints excluded: chain T residue 87 LYS Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain T residue 143 LYS Chi-restraints excluded: chain V residue 139 SER Chi-restraints excluded: chain V residue 143 LYS Chi-restraints excluded: chain V residue 147 GLU Chi-restraints excluded: chain W residue 139 SER Chi-restraints excluded: chain W residue 143 LYS Chi-restraints excluded: chain W residue 147 GLU Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain X residue 143 LYS Chi-restraints excluded: chain X residue 147 GLU Chi-restraints excluded: chain Y residue 64 GLU Chi-restraints excluded: chain Y residue 126 ASP Chi-restraints excluded: chain Y residue 139 SER Chi-restraints excluded: chain Y residue 143 LYS Chi-restraints excluded: chain Y residue 147 GLU 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: 0.9990 chunk 234 optimal weight: 7.9990 chunk 118 optimal weight: 10.0000 chunk 77 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 250 optimal weight: 6.9990 chunk 267 optimal weight: 1.9990 chunk 194 optimal weight: 8.9990 chunk 36 optimal weight: 8.9990 chunk 309 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 P 125 ASN Q 14 GLN R 14 GLN S 14 GLN T 14 GLN V 14 GLN W 14 GLN X 14 GLN Y 14 GLN Y 125 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.0815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 34512 Z= 0.183 Angle : 0.477 5.643 46416 Z= 0.249 Chirality : 0.035 0.119 4848 Planarity : 0.003 0.030 6096 Dihedral : 3.818 16.215 4512 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.78 % Allowed : 18.64 % Favored : 77.58 % 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: 4080 helix: 4.31 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.31 (0.24), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP H 93 HIS 0.002 0.001 HIS F 105 PHE 0.014 0.002 PHE V 41 TYR 0.012 0.001 TYR V 137 ARG 0.002 0.000 ARG F 156 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 656 time to evaluate : 4.553 Fit side-chains REVERT: A 63 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7655 (ttm170) REVERT: A 143 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8064 (ttmt) REVERT: A 147 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7850 (tt0) REVERT: B 63 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7739 (ttm170) REVERT: B 83 GLN cc_start: 0.8864 (mm-40) cc_final: 0.8625 (mm-40) REVERT: B 89 ASP cc_start: 0.7509 (m-30) cc_final: 0.7141 (m-30) REVERT: B 143 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8077 (ttmt) REVERT: B 147 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7843 (tt0) REVERT: C 63 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7742 (ttm170) REVERT: C 89 ASP cc_start: 0.7488 (m-30) cc_final: 0.7072 (m-30) REVERT: C 143 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8032 (ttmt) REVERT: C 147 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7833 (tt0) REVERT: D 63 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7712 (ttm170) REVERT: D 89 ASP cc_start: 0.7429 (m-30) cc_final: 0.7073 (m-30) REVERT: D 143 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8079 (ttmt) REVERT: E 63 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7683 (ttm170) REVERT: E 89 ASP cc_start: 0.7428 (m-30) cc_final: 0.7077 (m-30) REVERT: E 143 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8079 (ttmt) REVERT: E 147 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7850 (tt0) REVERT: F 63 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7649 (ttm170) REVERT: F 89 ASP cc_start: 0.7485 (m-30) cc_final: 0.7151 (m-30) REVERT: F 143 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8056 (ttmt) REVERT: F 147 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7861 (tt0) REVERT: G 63 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7693 (ttm170) REVERT: G 89 ASP cc_start: 0.7552 (m-30) cc_final: 0.7145 (m-30) REVERT: G 143 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8074 (ttmt) REVERT: G 147 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7845 (tt0) REVERT: H 63 ARG cc_start: 0.8143 (OUTLIER) cc_final: 0.7679 (ttm170) REVERT: H 89 ASP cc_start: 0.7570 (m-30) cc_final: 0.7173 (m-30) REVERT: H 143 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8009 (ttmt) REVERT: H 147 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7806 (tt0) REVERT: I 63 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7731 (ttm170) REVERT: I 89 ASP cc_start: 0.7476 (m-30) cc_final: 0.7060 (m-30) REVERT: I 143 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8052 (ttmt) REVERT: J 63 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7704 (ttm170) REVERT: J 83 GLN cc_start: 0.8859 (mm-40) cc_final: 0.8610 (mm-40) REVERT: J 89 ASP cc_start: 0.7399 (m-30) cc_final: 0.7143 (m-30) REVERT: J 143 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8045 (ttmt) REVERT: J 147 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.7851 (tt0) REVERT: K 83 GLN cc_start: 0.8862 (mm-40) cc_final: 0.8608 (mm-40) REVERT: K 89 ASP cc_start: 0.7580 (m-30) cc_final: 0.7171 (m-30) REVERT: K 143 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8041 (ttmt) REVERT: K 147 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7821 (tt0) REVERT: L 63 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7669 (ttm170) REVERT: L 89 ASP cc_start: 0.7567 (m-30) cc_final: 0.7186 (m-30) REVERT: L 143 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8070 (ttmt) REVERT: M 63 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7733 (ttm170) REVERT: M 89 ASP cc_start: 0.7546 (m-30) cc_final: 0.7149 (m-30) REVERT: M 143 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8031 (ttmt) REVERT: M 147 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7864 (tt0) REVERT: N 89 ASP cc_start: 0.7526 (m-30) cc_final: 0.7117 (m-30) REVERT: N 143 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8054 (ttmt) REVERT: O 143 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8061 (ttmt) REVERT: O 147 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7853 (tt0) REVERT: P 89 ASP cc_start: 0.7470 (m-30) cc_final: 0.7055 (m-30) REVERT: P 143 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8045 (ttmt) REVERT: P 147 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7827 (tt0) REVERT: Q 89 ASP cc_start: 0.7562 (m-30) cc_final: 0.7154 (m-30) REVERT: Q 143 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8087 (ttmt) REVERT: Q 147 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7883 (tt0) REVERT: R 89 ASP cc_start: 0.7529 (m-30) cc_final: 0.7106 (m-30) REVERT: R 143 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8049 (ttmt) REVERT: R 147 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.7818 (tt0) REVERT: S 89 ASP cc_start: 0.7483 (m-30) cc_final: 0.7086 (m-30) REVERT: S 143 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8077 (ttmt) REVERT: S 147 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7830 (tt0) REVERT: T 89 ASP cc_start: 0.7479 (m-30) cc_final: 0.7150 (m-30) REVERT: T 143 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8057 (ttmt) REVERT: T 147 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.7864 (tt0) REVERT: V 89 ASP cc_start: 0.7567 (m-30) cc_final: 0.7178 (m-30) REVERT: V 143 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8048 (ttmt) REVERT: V 147 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7825 (tt0) REVERT: W 89 ASP cc_start: 0.7455 (m-30) cc_final: 0.7046 (m-30) REVERT: W 143 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8058 (ttmt) REVERT: W 147 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7800 (tt0) REVERT: X 83 GLN cc_start: 0.8877 (mm-40) cc_final: 0.8631 (mm-40) REVERT: X 89 ASP cc_start: 0.7540 (m-30) cc_final: 0.7139 (m-30) REVERT: X 143 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8015 (ttmt) REVERT: X 147 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7850 (tt0) REVERT: Y 89 ASP cc_start: 0.7545 (m-30) cc_final: 0.7124 (m-30) REVERT: Y 143 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8041 (ttmt) REVERT: Y 147 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.7840 (tt0) outliers start: 138 outliers final: 36 residues processed: 754 average time/residue: 2.1369 time to fit residues: 1845.6693 Evaluate side-chains 751 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 659 time to evaluate : 4.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain B residue 63 ARG Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain C residue 63 ARG Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain F residue 63 ARG Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain F residue 126 ASP Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 143 LYS Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 143 LYS Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain H residue 63 ARG Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain H residue 147 GLU Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 143 LYS Chi-restraints excluded: chain J residue 63 ARG Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain J residue 143 LYS Chi-restraints excluded: chain J residue 147 GLU Chi-restraints excluded: chain K residue 126 ASP Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 143 LYS Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain L residue 143 LYS Chi-restraints excluded: chain M residue 63 ARG Chi-restraints excluded: chain M residue 64 GLU Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain M residue 143 LYS Chi-restraints excluded: chain M residue 147 GLU Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain N residue 143 LYS Chi-restraints excluded: chain O residue 139 SER Chi-restraints excluded: chain O residue 143 LYS Chi-restraints excluded: chain O residue 147 GLU Chi-restraints excluded: chain P residue 126 ASP Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain P residue 143 LYS Chi-restraints excluded: chain P residue 147 GLU Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain Q residue 143 LYS Chi-restraints excluded: chain Q residue 147 GLU Chi-restraints excluded: chain R residue 126 ASP Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain R residue 147 GLU Chi-restraints excluded: chain S residue 64 GLU Chi-restraints excluded: chain S residue 126 ASP Chi-restraints excluded: chain S residue 139 SER Chi-restraints excluded: chain S residue 143 LYS Chi-restraints excluded: chain S residue 147 GLU Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain T residue 143 LYS Chi-restraints excluded: chain T residue 147 GLU Chi-restraints excluded: chain V residue 139 SER Chi-restraints excluded: chain V residue 143 LYS Chi-restraints excluded: chain V residue 147 GLU Chi-restraints excluded: chain W residue 64 GLU Chi-restraints excluded: chain W residue 139 SER Chi-restraints excluded: chain W residue 143 LYS Chi-restraints excluded: chain W residue 147 GLU Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain X residue 143 LYS Chi-restraints excluded: chain X residue 147 GLU Chi-restraints excluded: chain Y residue 87 LYS Chi-restraints excluded: chain Y residue 126 ASP Chi-restraints excluded: chain Y residue 139 SER Chi-restraints excluded: chain Y residue 143 LYS Chi-restraints excluded: chain Y residue 147 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 3.9990 chunk 376 optimal weight: 9.9990 chunk 343 optimal weight: 0.8980 chunk 366 optimal weight: 10.0000 chunk 220 optimal weight: 6.9990 chunk 159 optimal weight: 1.9990 chunk 287 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 331 optimal weight: 0.4980 chunk 346 optimal weight: 10.0000 chunk 365 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 75 GLN B 14 GLN C 14 GLN C 75 GLN D 14 GLN D 75 GLN E 14 GLN E 75 GLN F 14 GLN F 75 GLN G 14 GLN H 14 GLN H 75 GLN I 14 GLN J 14 GLN J 75 GLN K 14 GLN L 14 GLN L 75 GLN M 14 GLN M 75 GLN N 14 GLN N 75 GLN O 14 GLN O 75 GLN P 14 GLN P 75 GLN Q 14 GLN R 14 GLN R 75 GLN S 14 GLN T 14 GLN T 75 GLN V 14 GLN ** W 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 75 GLN X 14 GLN Y 14 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.0820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 34512 Z= 0.147 Angle : 0.451 5.402 46416 Z= 0.237 Chirality : 0.034 0.114 4848 Planarity : 0.003 0.029 6096 Dihedral : 3.718 16.062 4512 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.91 % Allowed : 19.52 % Favored : 77.58 % 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: 4080 helix: 4.42 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.28 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP H 93 HIS 0.001 0.000 HIS X 105 PHE 0.013 0.002 PHE J 41 TYR 0.011 0.001 TYR V 137 ARG 0.004 0.000 ARG M 156 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 758 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 652 time to evaluate : 4.238 Fit side-chains REVERT: A 63 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7634 (ttm170) REVERT: A 143 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8060 (ttmt) REVERT: A 147 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7851 (tt0) REVERT: B 63 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7730 (ttm170) REVERT: B 89 ASP cc_start: 0.7506 (m-30) cc_final: 0.7142 (m-30) REVERT: B 143 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8065 (ttmt) REVERT: B 147 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7852 (tt0) REVERT: C 63 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7734 (ttm170) REVERT: C 89 ASP cc_start: 0.7487 (m-30) cc_final: 0.7076 (m-30) REVERT: C 143 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8047 (ttmt) REVERT: C 147 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7815 (tt0) REVERT: D 63 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7678 (ttm170) REVERT: D 89 ASP cc_start: 0.7424 (m-30) cc_final: 0.7072 (m-30) REVERT: D 143 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8069 (ttmt) REVERT: E 63 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7652 (ttm170) REVERT: E 89 ASP cc_start: 0.7439 (m-30) cc_final: 0.7089 (m-30) REVERT: E 143 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8070 (ttmt) REVERT: E 147 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7841 (tt0) REVERT: F 63 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7641 (ttm170) REVERT: F 89 ASP cc_start: 0.7474 (m-30) cc_final: 0.7144 (m-30) REVERT: F 143 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8057 (ttmt) REVERT: F 147 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7862 (tt0) REVERT: G 63 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7670 (ttm170) REVERT: G 89 ASP cc_start: 0.7509 (m-30) cc_final: 0.7109 (m-30) REVERT: G 143 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8062 (ttmt) REVERT: G 147 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7837 (tt0) REVERT: H 63 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7673 (ttm170) REVERT: H 89 ASP cc_start: 0.7565 (m-30) cc_final: 0.7169 (m-30) REVERT: H 143 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8033 (ttmt) REVERT: H 147 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7842 (tt0) REVERT: I 63 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7725 (ttm170) REVERT: I 89 ASP cc_start: 0.7466 (m-30) cc_final: 0.7058 (m-30) REVERT: I 131 ASP cc_start: 0.8544 (t70) cc_final: 0.8300 (t70) REVERT: I 143 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8062 (ttmt) REVERT: J 63 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7668 (ttm170) REVERT: J 89 ASP cc_start: 0.7381 (m-30) cc_final: 0.7128 (m-30) REVERT: J 143 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8044 (ttmt) REVERT: J 147 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7848 (tt0) REVERT: K 89 ASP cc_start: 0.7581 (m-30) cc_final: 0.7176 (m-30) REVERT: K 143 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8025 (ttmt) REVERT: K 147 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7835 (tt0) REVERT: L 63 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7732 (ttm170) REVERT: L 89 ASP cc_start: 0.7564 (m-30) cc_final: 0.7184 (m-30) REVERT: L 143 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8072 (ttmt) REVERT: M 63 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7703 (ttm170) REVERT: M 89 ASP cc_start: 0.7505 (m-30) cc_final: 0.7123 (m-30) REVERT: M 143 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8046 (ttmt) REVERT: M 147 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7849 (tt0) REVERT: N 89 ASP cc_start: 0.7490 (m-30) cc_final: 0.7092 (m-30) REVERT: N 143 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8046 (ttmt) REVERT: O 143 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8051 (ttmt) REVERT: O 147 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7844 (tt0) REVERT: P 89 ASP cc_start: 0.7463 (m-30) cc_final: 0.7048 (m-30) REVERT: P 143 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8043 (ttmt) REVERT: P 147 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7830 (tt0) REVERT: Q 89 ASP cc_start: 0.7557 (m-30) cc_final: 0.7151 (m-30) REVERT: Q 143 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8086 (ttmt) REVERT: Q 147 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7867 (tt0) REVERT: R 89 ASP cc_start: 0.7523 (m-30) cc_final: 0.7103 (m-30) REVERT: R 143 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8040 (ttmt) REVERT: S 89 ASP cc_start: 0.7478 (m-30) cc_final: 0.7086 (m-30) REVERT: S 143 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8072 (ttmt) REVERT: S 147 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7851 (tt0) REVERT: T 89 ASP cc_start: 0.7486 (m-30) cc_final: 0.7152 (m-30) REVERT: T 143 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8057 (ttmt) REVERT: V 89 ASP cc_start: 0.7565 (m-30) cc_final: 0.7177 (m-30) REVERT: V 143 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8029 (ttmt) REVERT: V 147 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7826 (tt0) REVERT: W 89 ASP cc_start: 0.7440 (m-30) cc_final: 0.7032 (m-30) REVERT: W 143 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8049 (ttmt) REVERT: W 147 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7825 (tt0) REVERT: X 89 ASP cc_start: 0.7536 (m-30) cc_final: 0.7139 (m-30) REVERT: X 143 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8033 (ttmt) REVERT: X 147 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7832 (tt0) REVERT: Y 89 ASP cc_start: 0.7539 (m-30) cc_final: 0.7121 (m-30) REVERT: Y 143 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8052 (ttmt) outliers start: 106 outliers final: 27 residues processed: 718 average time/residue: 2.1016 time to fit residues: 1731.8814 Evaluate side-chains 720 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 640 time to evaluate : 4.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain B residue 63 ARG Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain C residue 63 ARG Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain D residue 87 LYS Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain F residue 63 ARG Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain F residue 126 ASP Chi-restraints excluded: chain F residue 143 LYS Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 143 LYS Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain H residue 63 ARG Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain H residue 147 GLU Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 143 LYS Chi-restraints excluded: chain J residue 63 ARG Chi-restraints excluded: chain J residue 143 LYS Chi-restraints excluded: chain J residue 147 GLU Chi-restraints excluded: chain K residue 87 LYS Chi-restraints excluded: chain K residue 143 LYS Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain L residue 87 LYS Chi-restraints excluded: chain L residue 126 ASP Chi-restraints excluded: chain L residue 143 LYS Chi-restraints excluded: chain M residue 63 ARG Chi-restraints excluded: chain M residue 64 GLU Chi-restraints excluded: chain M residue 87 LYS Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain M residue 143 LYS Chi-restraints excluded: chain M residue 147 GLU Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 126 ASP Chi-restraints excluded: chain N residue 143 LYS Chi-restraints excluded: chain O residue 143 LYS Chi-restraints excluded: chain O residue 147 GLU Chi-restraints excluded: chain P residue 87 LYS Chi-restraints excluded: chain P residue 143 LYS Chi-restraints excluded: chain P residue 147 GLU Chi-restraints excluded: chain Q residue 143 LYS Chi-restraints excluded: chain Q residue 147 GLU Chi-restraints excluded: chain R residue 87 LYS Chi-restraints excluded: chain R residue 126 ASP Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain S residue 64 GLU Chi-restraints excluded: chain S residue 87 LYS Chi-restraints excluded: chain S residue 126 ASP Chi-restraints excluded: chain S residue 143 LYS Chi-restraints excluded: chain S residue 147 GLU Chi-restraints excluded: chain T residue 87 LYS Chi-restraints excluded: chain T residue 126 ASP Chi-restraints excluded: chain T residue 143 LYS Chi-restraints excluded: chain V residue 126 ASP Chi-restraints excluded: chain V residue 143 LYS Chi-restraints excluded: chain V residue 147 GLU Chi-restraints excluded: chain W residue 143 LYS Chi-restraints excluded: chain W residue 147 GLU Chi-restraints excluded: chain X residue 143 LYS Chi-restraints excluded: chain X residue 147 GLU Chi-restraints excluded: chain Y residue 126 ASP Chi-restraints excluded: chain Y residue 143 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 10.0000 chunk 387 optimal weight: 4.9990 chunk 236 optimal weight: 0.0010 chunk 183 optimal weight: 3.9990 chunk 269 optimal weight: 5.9990 chunk 406 optimal weight: 0.8980 chunk 374 optimal weight: 5.9990 chunk 323 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 250 optimal weight: 0.7980 chunk 198 optimal weight: 0.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 75 GLN B 14 GLN B 75 GLN C 14 GLN C 75 GLN D 14 GLN D 75 GLN E 14 GLN E 75 GLN F 14 GLN F 75 GLN G 14 GLN G 75 GLN H 14 GLN H 75 GLN I 14 GLN I 75 GLN J 14 GLN J 75 GLN K 14 GLN K 75 GLN L 14 GLN L 75 GLN M 14 GLN M 75 GLN N 14 GLN N 75 GLN O 14 GLN O 75 GLN P 14 GLN P 75 GLN Q 14 GLN R 14 GLN R 75 GLN S 14 GLN S 75 GLN T 14 GLN T 75 GLN V 14 GLN V 75 GLN ** W 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 75 GLN X 14 GLN X 75 GLN Y 14 GLN Y 75 GLN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.0964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 34512 Z= 0.115 Angle : 0.423 5.025 46416 Z= 0.225 Chirality : 0.033 0.112 4848 Planarity : 0.003 0.028 6096 Dihedral : 3.585 15.272 4512 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.80 % Allowed : 19.65 % Favored : 77.55 % 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: 5.71 (0.13), residues: 4080 helix: 4.60 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.24 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP W 93 HIS 0.001 0.000 HIS K 105 PHE 0.013 0.002 PHE V 41 TYR 0.010 0.001 TYR W 137 ARG 0.003 0.000 ARG A 156 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 780 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 678 time to evaluate : 4.278 Fit side-chains REVERT: A 89 ASP cc_start: 0.7651 (m-30) cc_final: 0.7263 (m-30) REVERT: A 143 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.8087 (ttmt) REVERT: A 147 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7836 (tt0) REVERT: B 63 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7679 (ttm170) REVERT: B 89 ASP cc_start: 0.7439 (m-30) cc_final: 0.7085 (m-30) REVERT: B 143 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8021 (ttmt) REVERT: C 63 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7596 (ttm170) REVERT: C 89 ASP cc_start: 0.7424 (m-30) cc_final: 0.7080 (m-30) REVERT: D 89 ASP cc_start: 0.7377 (m-30) cc_final: 0.7048 (m-30) REVERT: D 143 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.8106 (ttmt) REVERT: E 89 ASP cc_start: 0.7389 (m-30) cc_final: 0.7067 (m-30) REVERT: E 143 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8099 (ttmt) REVERT: E 147 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7837 (tt0) REVERT: F 63 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7572 (ttm170) REVERT: F 89 ASP cc_start: 0.7448 (m-30) cc_final: 0.7094 (m-30) REVERT: F 143 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8070 (ttmt) REVERT: F 147 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7858 (tt0) REVERT: G 89 ASP cc_start: 0.7483 (m-30) cc_final: 0.7085 (m-30) REVERT: G 143 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.8028 (ttmm) REVERT: G 147 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7829 (tt0) REVERT: H 63 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7602 (ttm170) REVERT: H 89 ASP cc_start: 0.7507 (m-30) cc_final: 0.7132 (m-30) REVERT: I 63 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7678 (ttm170) REVERT: I 89 ASP cc_start: 0.7457 (m-30) cc_final: 0.7070 (m-30) REVERT: I 131 ASP cc_start: 0.8536 (t70) cc_final: 0.8320 (t70) REVERT: I 143 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8010 (ttmt) REVERT: J 89 ASP cc_start: 0.7365 (m-30) cc_final: 0.7123 (m-30) REVERT: J 143 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8056 (ttmt) REVERT: J 147 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7841 (tt0) REVERT: K 89 ASP cc_start: 0.7531 (m-30) cc_final: 0.7148 (m-30) REVERT: K 143 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.7957 (ttmt) REVERT: L 89 ASP cc_start: 0.7519 (m-30) cc_final: 0.7150 (m-30) REVERT: L 143 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.8086 (ttmt) REVERT: M 89 ASP cc_start: 0.7480 (m-30) cc_final: 0.7101 (m-30) REVERT: M 131 ASP cc_start: 0.8544 (t70) cc_final: 0.8335 (t70) REVERT: M 143 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.8076 (ttmt) REVERT: M 147 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7866 (tt0) REVERT: N 89 ASP cc_start: 0.7466 (m-30) cc_final: 0.7077 (m-30) REVERT: N 143 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8072 (ttmt) REVERT: O 89 ASP cc_start: 0.7655 (m-30) cc_final: 0.7289 (m-30) REVERT: O 143 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.8085 (ttmt) REVERT: O 147 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7842 (tt0) REVERT: P 89 ASP cc_start: 0.7438 (m-30) cc_final: 0.7028 (m-30) REVERT: P 143 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.8019 (ttmm) REVERT: Q 89 ASP cc_start: 0.7492 (m-30) cc_final: 0.7113 (m-30) REVERT: Q 143 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.8098 (ttmt) REVERT: Q 147 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7894 (tt0) REVERT: R 89 ASP cc_start: 0.7483 (m-30) cc_final: 0.7101 (m-30) REVERT: R 143 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.8060 (ttmt) REVERT: S 89 ASP cc_start: 0.7433 (m-30) cc_final: 0.7056 (m-30) REVERT: S 143 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8084 (ttmt) REVERT: T 89 ASP cc_start: 0.7416 (m-30) cc_final: 0.7089 (m-30) REVERT: T 143 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.8083 (ttmt) REVERT: V 89 ASP cc_start: 0.7509 (m-30) cc_final: 0.7142 (m-30) REVERT: V 143 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8004 (ttmm) REVERT: W 89 ASP cc_start: 0.7403 (m-30) cc_final: 0.7008 (m-30) REVERT: W 143 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8083 (ttmt) REVERT: X 89 ASP cc_start: 0.7480 (m-30) cc_final: 0.7106 (m-30) REVERT: X 143 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8021 (ttmt) REVERT: X 147 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7875 (tt0) REVERT: Y 89 ASP cc_start: 0.7490 (m-30) cc_final: 0.7106 (m-30) REVERT: Y 143 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.8072 (ttmt) REVERT: Y 147 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7870 (tt0) outliers start: 102 outliers final: 12 residues processed: 721 average time/residue: 2.0506 time to fit residues: 1704.4844 Evaluate side-chains 738 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 689 time to evaluate : 4.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain B residue 63 ARG Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain C residue 63 ARG Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain F residue 63 ARG Chi-restraints excluded: chain F residue 126 ASP Chi-restraints excluded: chain F residue 143 LYS Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain G residue 143 LYS Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain H residue 63 ARG Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 143 LYS Chi-restraints excluded: chain J residue 126 ASP Chi-restraints excluded: chain J residue 143 LYS Chi-restraints excluded: chain J residue 147 GLU Chi-restraints excluded: chain K residue 143 LYS Chi-restraints excluded: chain L residue 87 LYS Chi-restraints excluded: chain L residue 143 LYS Chi-restraints excluded: chain M residue 64 GLU Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain M residue 143 LYS Chi-restraints excluded: chain M residue 147 GLU Chi-restraints excluded: chain N residue 143 LYS Chi-restraints excluded: chain O residue 143 LYS Chi-restraints excluded: chain O residue 147 GLU Chi-restraints excluded: chain P residue 143 LYS Chi-restraints excluded: chain Q residue 143 LYS Chi-restraints excluded: chain Q residue 147 GLU Chi-restraints excluded: chain R residue 126 ASP Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain S residue 64 GLU Chi-restraints excluded: chain S residue 126 ASP Chi-restraints excluded: chain S residue 143 LYS Chi-restraints excluded: chain T residue 87 LYS Chi-restraints excluded: chain T residue 143 LYS Chi-restraints excluded: chain V residue 143 LYS Chi-restraints excluded: chain W residue 143 LYS Chi-restraints excluded: chain X residue 143 LYS Chi-restraints excluded: chain X residue 147 GLU Chi-restraints excluded: chain Y residue 126 ASP Chi-restraints excluded: chain Y residue 143 LYS Chi-restraints excluded: chain Y residue 147 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 5.9990 chunk 344 optimal weight: 9.9990 chunk 99 optimal weight: 4.9990 chunk 298 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 89 optimal weight: 9.9990 chunk 324 optimal weight: 4.9990 chunk 135 optimal weight: 10.0000 chunk 332 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 75 GLN B 14 GLN B 75 GLN C 14 GLN C 75 GLN D 14 GLN D 75 GLN E 14 GLN E 75 GLN F 14 GLN F 75 GLN G 14 GLN G 75 GLN H 14 GLN H 75 GLN I 14 GLN I 75 GLN J 14 GLN J 75 GLN K 14 GLN K 75 GLN L 14 GLN L 75 GLN M 14 GLN M 75 GLN N 14 GLN N 75 GLN O 14 GLN O 75 GLN P 14 GLN P 75 GLN P 125 ASN Q 14 GLN R 14 GLN R 75 GLN S 14 GLN S 75 GLN T 14 GLN T 75 GLN V 14 GLN V 75 GLN ** W 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 75 GLN X 14 GLN X 75 GLN Y 14 GLN Y 75 GLN Y 125 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.107006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.097598 restraints weight = 39072.547| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 1.20 r_work: 0.2832 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 34512 Z= 0.390 Angle : 0.624 6.710 46416 Z= 0.320 Chirality : 0.043 0.139 4848 Planarity : 0.004 0.042 6096 Dihedral : 4.183 16.102 4512 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.97 % Allowed : 17.90 % Favored : 78.12 % 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: 4.96 (0.13), residues: 4080 helix: 3.89 (0.09), residues: 3168 sheet: None (None), residues: 0 loop : 0.85 (0.25), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP I 93 HIS 0.003 0.001 HIS L 105 PHE 0.017 0.003 PHE S 41 TYR 0.016 0.002 TYR V 137 ARG 0.005 0.001 ARG C 156 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22312.90 seconds wall clock time: 395 minutes 58.67 seconds (23758.67 seconds total)