Starting phenix.real_space_refine on Sat Dec 16 18:14:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bka_16094/12_2023/8bka_16094.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bka_16094/12_2023/8bka_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_16094/12_2023/8bka_16094.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bka_16094/12_2023/8bka_16094.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bka_16094/12_2023/8bka_16094.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bka_16094/12_2023/8bka_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: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 18.64, per 1000 atoms: 0.52 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: 14.75 Conformation dependent library (CDL) restraints added in 6.0 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: 3.37 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: 11.15 Time building geometry restraints manager: 15.54 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: 2.280 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: 0.020 Extract box with map and model: 12.300 Check model and map are aligned: 0.550 Set scattering table: 0.320 Process input model: 88.460 Find NCS groups from input model: 2.710 Set up NCS constraints: 0.320 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: 0.000 Load rotamer database and sin/cos tables:12.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.770 ------------------------------------------------------------------------------- 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 : 4.589 Fit side-chains outliers start: 60 outliers final: 30 residues processed: 751 average time/residue: 1.9260 time to fit residues: 1673.8179 Evaluate side-chains 695 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 665 time to evaluate : 4.139 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 30 residues processed: 0 time to fit residues: 5.5163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 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: 10.0000 overall best weight: 4.5588 ------------------------------------------------------------------------------- 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 J 83 GLN K 14 GLN K 83 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 83 GLN X 154 ASN Y 14 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.0796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 34512 Z= 0.331 Angle : 0.564 6.860 46416 Z= 0.289 Chirality : 0.040 0.132 4848 Planarity : 0.004 0.033 6096 Dihedral : 4.147 16.300 4512 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 5.81 % Allowed : 16.89 % Favored : 77.30 % 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: 4.56 (0.13), residues: 4080 helix: 3.74 (0.09), residues: 3168 sheet: None (None), residues: 0 loop : 0.17 (0.23), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP N 93 HIS 0.004 0.001 HIS Q 173 PHE 0.017 0.002 PHE W 41 TYR 0.016 0.002 TYR W 137 ARG 0.004 0.001 ARG G 63 *********************** 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 907 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 695 time to evaluate : 4.493 Fit side-chains outliers start: 212 outliers final: 45 residues processed: 850 average time/residue: 1.9249 time to fit residues: 1903.6629 Evaluate side-chains 708 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 663 time to evaluate : 4.535 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 44 residues processed: 1 average time/residue: 2.1275 time to fit residues: 8.7026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 10.0000 chunk 114 optimal weight: 6.9990 chunk 308 optimal weight: 6.9990 chunk 252 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 chunk 371 optimal weight: 7.9990 chunk 400 optimal weight: 0.9990 chunk 330 optimal weight: 10.0000 chunk 368 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 297 optimal weight: 9.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 Q 75 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: 0.8709 moved from start: 0.0723 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= 0.138 Angle : 0.435 5.483 46416 Z= 0.229 Chirality : 0.033 0.112 4848 Planarity : 0.003 0.029 6096 Dihedral : 3.751 16.789 4512 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.10 % Allowed : 19.02 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 5.19 (0.13), residues: 4080 helix: 4.27 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : -0.12 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP N 93 HIS 0.002 0.001 HIS O 173 PHE 0.013 0.002 PHE W 41 TYR 0.012 0.001 TYR N 137 ARG 0.002 0.000 ARG T 63 *********************** 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 828 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 715 time to evaluate : 4.234 Fit side-chains outliers start: 113 outliers final: 65 residues processed: 804 average time/residue: 1.9724 time to fit residues: 1833.3774 Evaluate side-chains 782 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 717 time to evaluate : 4.073 Switching outliers to nearest non-outliers outliers start: 65 outliers final: 59 residues processed: 6 average time/residue: 0.7256 time to fit residues: 11.8788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 0.6980 chunk 279 optimal weight: 3.9990 chunk 192 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 177 optimal weight: 8.9990 chunk 249 optimal weight: 0.9990 chunk 372 optimal weight: 7.9990 chunk 394 optimal weight: 8.9990 chunk 194 optimal weight: 5.9990 chunk 353 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 overall best weight: 3.1388 ------------------------------------------------------------------------------- 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 F 75 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: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.0878 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= 0.243 Angle : 0.509 6.300 46416 Z= 0.262 Chirality : 0.037 0.125 4848 Planarity : 0.003 0.031 6096 Dihedral : 3.949 16.258 4512 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 5.24 % Allowed : 17.93 % Favored : 76.84 % 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: 5.17 (0.13), residues: 4080 helix: 4.17 (0.08), residues: 3168 sheet: None (None), residues: 0 loop : 0.36 (0.23), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 93 HIS 0.002 0.001 HIS R 173 PHE 0.016 0.002 PHE J 41 TYR 0.013 0.002 TYR K 137 ARG 0.002 0.000 ARG G 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 887 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 696 time to evaluate : 4.691 Fit side-chains outliers start: 191 outliers final: 75 residues processed: 823 average time/residue: 2.0079 time to fit residues: 1905.5398 Evaluate side-chains 744 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 669 time to evaluate : 4.103 Switching outliers to nearest non-outliers outliers start: 75 outliers final: 74 residues processed: 1 average time/residue: 0.5237 time to fit residues: 6.9805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 4.9990 chunk 223 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 293 optimal weight: 9.9990 chunk 162 optimal weight: 0.7980 chunk 336 optimal weight: 1.9990 chunk 272 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 201 optimal weight: 0.8980 chunk 353 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 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: 0.8721 moved from start: 0.0851 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 : 0.456 5.713 46416 Z= 0.239 Chirality : 0.034 0.117 4848 Planarity : 0.003 0.030 6096 Dihedral : 3.800 16.384 4512 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 4.88 % Allowed : 17.49 % Favored : 77.63 % 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: 5.24 (0.13), residues: 4080 helix: 4.28 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.03 (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 R 173 PHE 0.014 0.002 PHE J 41 TYR 0.012 0.001 TYR H 137 ARG 0.001 0.000 ARG G 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 865 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 687 time to evaluate : 4.390 Fit side-chains outliers start: 178 outliers final: 86 residues processed: 811 average time/residue: 2.0596 time to fit residues: 1932.6140 Evaluate side-chains 774 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 688 time to evaluate : 4.683 Switching outliers to nearest non-outliers outliers start: 86 outliers final: 79 residues processed: 7 average time/residue: 1.9204 time to fit residues: 21.4676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 8.9990 chunk 355 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 231 optimal weight: 4.9990 chunk 97 optimal weight: 0.7980 chunk 394 optimal weight: 0.6980 chunk 327 optimal weight: 10.0000 chunk 182 optimal weight: 0.6980 chunk 32 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 207 optimal weight: 4.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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: 0.8697 moved from start: 0.0866 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= 0.131 Angle : 0.423 5.301 46416 Z= 0.224 Chirality : 0.033 0.111 4848 Planarity : 0.003 0.029 6096 Dihedral : 3.658 16.133 4512 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 4.55 % Allowed : 18.20 % 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: 5.45 (0.13), residues: 4080 helix: 4.46 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : -0.03 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP H 93 HIS 0.001 0.000 HIS P 105 PHE 0.014 0.002 PHE W 41 TYR 0.011 0.001 TYR H 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 829 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 663 time to evaluate : 4.076 Fit side-chains outliers start: 166 outliers final: 89 residues processed: 771 average time/residue: 1.9438 time to fit residues: 1735.5466 Evaluate side-chains 745 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 656 time to evaluate : 4.351 Switching outliers to nearest non-outliers outliers start: 89 outliers final: 68 residues processed: 21 average time/residue: 1.2917 time to fit residues: 38.9868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 224 optimal weight: 10.0000 chunk 288 optimal weight: 9.9990 chunk 223 optimal weight: 4.9990 chunk 332 optimal weight: 0.9990 chunk 220 optimal weight: 7.9990 chunk 393 optimal weight: 10.0000 chunk 246 optimal weight: 5.9990 chunk 239 optimal weight: 4.9990 chunk 181 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 D 14 GLN E 14 GLN F 14 GLN G 14 GLN H 14 GLN I 14 GLN J 14 GLN J 75 GLN K 14 GLN L 14 GLN L 75 GLN M 14 GLN N 14 GLN N 75 GLN O 14 GLN P 14 GLN P 75 GLN P 125 ASN Q 14 GLN R 14 GLN S 14 GLN S 75 GLN T 14 GLN V 14 GLN V 75 GLN W 14 GLN X 14 GLN Y 14 GLN Y 125 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.0936 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= 0.273 Angle : 0.525 6.322 46416 Z= 0.271 Chirality : 0.038 0.128 4848 Planarity : 0.004 0.031 6096 Dihedral : 3.971 16.022 4512 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 4.50 % Allowed : 17.82 % Favored : 77.69 % 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: 5.14 (0.13), residues: 4080 helix: 4.13 (0.08), residues: 3168 sheet: None (None), residues: 0 loop : 0.48 (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 R 65 PHE 0.016 0.002 PHE W 41 TYR 0.015 0.002 TYR E 137 ARG 0.003 0.001 ARG F 76 *********************** 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 834 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 670 time to evaluate : 4.350 Fit side-chains outliers start: 164 outliers final: 65 residues processed: 793 average time/residue: 2.0235 time to fit residues: 1853.2381 Evaluate side-chains 748 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 683 time to evaluate : 4.260 Switching outliers to nearest non-outliers outliers start: 65 outliers final: 65 residues processed: 0 time to fit residues: 5.7246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 0.8980 chunk 157 optimal weight: 7.9990 chunk 234 optimal weight: 9.9990 chunk 118 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 250 optimal weight: 8.9990 chunk 267 optimal weight: 10.0000 chunk 194 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 309 optimal weight: 4.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- 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 G 75 GLN H 14 GLN I 14 GLN ** J 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 14 GLN L 14 GLN M 14 GLN N 14 GLN O 14 GLN O 75 GLN P 14 GLN Q 14 GLN R 14 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: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 34512 Z= 0.172 Angle : 0.464 5.634 46416 Z= 0.243 Chirality : 0.035 0.118 4848 Planarity : 0.003 0.031 6096 Dihedral : 3.819 16.553 4512 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 4.11 % Allowed : 18.50 % Favored : 77.38 % 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: 5.38 (0.13), residues: 4080 helix: 4.32 (0.08), residues: 3168 sheet: None (None), residues: 0 loop : 0.43 (0.23), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP N 93 HIS 0.001 0.001 HIS K 173 PHE 0.014 0.002 PHE J 41 TYR 0.012 0.001 TYR M 137 ARG 0.002 0.000 ARG H 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 813 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 663 time to evaluate : 4.642 Fit side-chains outliers start: 150 outliers final: 67 residues processed: 779 average time/residue: 1.9991 time to fit residues: 1812.5712 Evaluate side-chains 718 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 651 time to evaluate : 4.132 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 65 residues processed: 2 average time/residue: 1.9593 time to fit residues: 10.1336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 1.9990 chunk 376 optimal weight: 3.9990 chunk 343 optimal weight: 0.9980 chunk 366 optimal weight: 0.6980 chunk 220 optimal weight: 5.9990 chunk 159 optimal weight: 7.9990 chunk 287 optimal weight: 0.5980 chunk 112 optimal weight: 5.9990 chunk 331 optimal weight: 6.9990 chunk 346 optimal weight: 8.9990 chunk 365 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 14 GLN G 14 GLN G 75 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 75 GLN P 14 GLN Q 14 GLN R 14 GLN S 14 GLN T 14 GLN T 75 GLN V 14 GLN W 14 GLN W 75 GLN X 14 GLN Y 14 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.0901 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= 0.127 Angle : 0.425 5.267 46416 Z= 0.226 Chirality : 0.033 0.111 4848 Planarity : 0.003 0.030 6096 Dihedral : 3.651 15.840 4512 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.15 % Allowed : 19.08 % Favored : 77.77 % 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: 5.52 (0.13), residues: 4080 helix: 4.49 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.07 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP O 93 HIS 0.001 0.000 HIS X 151 PHE 0.013 0.002 PHE W 41 TYR 0.011 0.001 TYR R 137 ARG 0.003 0.000 ARG Q 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 779 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 664 time to evaluate : 4.161 Fit side-chains outliers start: 115 outliers final: 64 residues processed: 754 average time/residue: 1.9378 time to fit residues: 1694.9952 Evaluate side-chains 706 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 642 time to evaluate : 4.247 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 61 residues processed: 3 average time/residue: 0.4745 time to fit residues: 7.9919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 9.9990 chunk 387 optimal weight: 9.9990 chunk 236 optimal weight: 0.0980 chunk 183 optimal weight: 4.9990 chunk 269 optimal weight: 3.9990 chunk 406 optimal weight: 6.9990 chunk 374 optimal weight: 7.9990 chunk 323 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 250 optimal weight: 2.9990 chunk 198 optimal weight: 9.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- 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 F 75 GLN G 14 GLN G 75 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 75 GLN P 14 GLN P 125 ASN Q 14 GLN R 14 GLN S 14 GLN S 75 GLN T 14 GLN T 75 GLN V 14 GLN W 14 GLN W 75 GLN X 14 GLN Y 14 GLN Y 125 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.0895 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= 0.224 Angle : 0.508 5.929 46416 Z= 0.264 Chirality : 0.036 0.123 4848 Planarity : 0.004 0.033 6096 Dihedral : 3.910 16.079 4512 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.56 % Allowed : 19.13 % Favored : 77.30 % 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: 5.32 (0.13), residues: 4080 helix: 4.25 (0.08), residues: 3168 sheet: None (None), residues: 0 loop : 0.56 (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 O 105 PHE 0.016 0.002 PHE J 41 TYR 0.013 0.001 TYR D 137 ARG 0.004 0.000 ARG M 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 781 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 651 time to evaluate : 4.546 Fit side-chains outliers start: 130 outliers final: 69 residues processed: 744 average time/residue: 2.0357 time to fit residues: 1752.4679 Evaluate side-chains 733 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 664 time to evaluate : 4.122 Switching outliers to nearest non-outliers outliers start: 69 outliers final: 61 residues processed: 8 average time/residue: 1.2607 time to fit residues: 17.8879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 8.9990 chunk 344 optimal weight: 7.9990 chunk 99 optimal weight: 4.9990 chunk 298 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 89 optimal weight: 9.9990 chunk 324 optimal weight: 9.9990 chunk 135 optimal weight: 8.9990 chunk 332 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 59 optimal weight: 7.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN C 14 GLN D 14 GLN ** E 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 14 GLN F 75 GLN G 14 GLN G 75 GLN H 14 GLN I 14 GLN ** J 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 14 GLN L 14 GLN M 14 GLN N 14 GLN O 14 GLN O 75 GLN ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 125 ASN Q 14 GLN R 14 GLN S 14 GLN S 75 GLN ** T 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 75 GLN V 14 GLN ** W 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 75 GLN X 14 GLN ** Y 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.110663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.101133 restraints weight = 38665.326| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.22 r_work: 0.2890 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.0886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 34512 Z= 0.171 Angle : 0.472 5.548 46416 Z= 0.249 Chirality : 0.035 0.117 4848 Planarity : 0.003 0.030 6096 Dihedral : 3.820 16.197 4512 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.34 % Allowed : 19.02 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.45 (0.13), residues: 4080 helix: 4.36 (0.08), residues: 3168 sheet: None (None), residues: 0 loop : 0.53 (0.23), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP H 93 HIS 0.002 0.001 HIS H 105 PHE 0.014 0.002 PHE J 41 TYR 0.012 0.001 TYR D 137 ARG 0.004 0.000 ARG M 156 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22109.83 seconds wall clock time: 390 minutes 1.11 seconds (23401.11 seconds total)