Starting phenix.real_space_refine (version: dev) on Sat May 14 12:51:03 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qeq_13937/05_2022/7qeq_13937_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qeq_13937/05_2022/7qeq_13937.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qeq_13937/05_2022/7qeq_13937.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qeq_13937/05_2022/7qeq_13937.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qeq_13937/05_2022/7qeq_13937_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qeq_13937/05_2022/7qeq_13937_updated.pdb" } resolution = 1.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.001 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 187": "OE1" <-> "OE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 209": "OE1" <-> "OE2" Residue "B PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 187": "OE1" <-> "OE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 209": "OE1" <-> "OE2" Residue "C PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 187": "OE1" <-> "OE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 209": "OE1" <-> "OE2" Residue "D PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 187": "OE1" <-> "OE2" Residue "D PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 209": "OE1" <-> "OE2" Residue "E PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 187": "OE1" <-> "OE2" Residue "E PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 209": "OE1" <-> "OE2" Residue "F PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 187": "OE1" <-> "OE2" Residue "F PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 209": "OE1" <-> "OE2" Residue "G PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 187": "OE1" <-> "OE2" Residue "G PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 209": "OE1" <-> "OE2" Residue "H PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 187": "OE1" <-> "OE2" Residue "H PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 209": "OE1" <-> "OE2" Residue "I PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 187": "OE1" <-> "OE2" Residue "I PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 209": "OE1" <-> "OE2" Residue "J PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 187": "OE1" <-> "OE2" Residue "J PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 209": "OE1" <-> "OE2" Residue "K PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 187": "OE1" <-> "OE2" Residue "K PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 209": "OE1" <-> "OE2" Residue "L PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 187": "OE1" <-> "OE2" Residue "L PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 209": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 19313 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1536 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 5, 'TRANS': 182, 'PCIS': 1} Chain breaks: 1 Chain: "B" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1536 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 5, 'TRANS': 182, 'PCIS': 1} Chain breaks: 1 Chain: "C" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1536 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 5, 'TRANS': 182, 'PCIS': 1} Chain breaks: 1 Chain: "D" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1536 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 5, 'TRANS': 182, 'PCIS': 1} Chain breaks: 1 Chain: "E" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1536 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 5, 'TRANS': 182, 'PCIS': 1} Chain breaks: 1 Chain: "F" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1536 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 5, 'TRANS': 182, 'PCIS': 1} Chain breaks: 1 Chain: "G" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1536 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 5, 'TRANS': 182, 'PCIS': 1} Chain breaks: 1 Chain: "H" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1536 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 5, 'TRANS': 182, 'PCIS': 1} Chain breaks: 1 Chain: "I" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1536 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 5, 'TRANS': 182, 'PCIS': 1} Chain breaks: 1 Chain: "J" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1536 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 5, 'TRANS': 182, 'PCIS': 1} Chain breaks: 1 Chain: "K" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1536 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 5, 'TRANS': 182, 'PCIS': 1} Chain breaks: 1 Chain: "L" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1536 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 5, 'TRANS': 182, 'PCIS': 1} Chain breaks: 1 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "F" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "G" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "I" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "J" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "K" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "L" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "E" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "F" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "G" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "I" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "J" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Time building chain proxies: 10.99, per 1000 atoms: 0.57 Number of scatterers: 19313 At special positions: 0 Unit cell: (99.45, 109.65, 157.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 168 16.00 O 3377 8.00 N 2976 7.00 C 12792 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS A 180 " distance=2.04 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 174 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 169 " distance=2.03 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 180 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 174 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 169 " distance=2.03 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS C 180 " distance=2.03 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 174 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 169 " distance=2.03 Simple disulfide: pdb=" SG CYS D 53 " - pdb=" SG CYS D 180 " distance=2.04 Simple disulfide: pdb=" SG CYS D 60 " - pdb=" SG CYS D 174 " distance=2.03 Simple disulfide: pdb=" SG CYS D 64 " - pdb=" SG CYS D 169 " distance=2.03 Simple disulfide: pdb=" SG CYS E 53 " - pdb=" SG CYS E 180 " distance=2.03 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS E 174 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 169 " distance=2.03 Simple disulfide: pdb=" SG CYS F 53 " - pdb=" SG CYS F 180 " distance=2.03 Simple disulfide: pdb=" SG CYS F 60 " - pdb=" SG CYS F 174 " distance=2.03 Simple disulfide: pdb=" SG CYS F 64 " - pdb=" SG CYS F 169 " distance=2.03 Simple disulfide: pdb=" SG CYS G 53 " - pdb=" SG CYS G 180 " distance=2.03 Simple disulfide: pdb=" SG CYS G 60 " - pdb=" SG CYS G 174 " distance=2.03 Simple disulfide: pdb=" SG CYS G 64 " - pdb=" SG CYS G 169 " distance=2.03 Simple disulfide: pdb=" SG CYS H 53 " - pdb=" SG CYS H 180 " distance=2.03 Simple disulfide: pdb=" SG CYS H 60 " - pdb=" SG CYS H 174 " distance=2.03 Simple disulfide: pdb=" SG CYS H 64 " - pdb=" SG CYS H 169 " distance=2.03 Simple disulfide: pdb=" SG CYS I 53 " - pdb=" SG CYS I 180 " distance=2.03 Simple disulfide: pdb=" SG CYS I 60 " - pdb=" SG CYS I 174 " distance=2.03 Simple disulfide: pdb=" SG CYS I 64 " - pdb=" SG CYS I 169 " distance=2.03 Simple disulfide: pdb=" SG CYS J 53 " - pdb=" SG CYS J 180 " distance=2.04 Simple disulfide: pdb=" SG CYS J 60 " - pdb=" SG CYS J 174 " distance=2.03 Simple disulfide: pdb=" SG CYS J 64 " - pdb=" SG CYS J 169 " distance=2.03 Simple disulfide: pdb=" SG CYS K 53 " - pdb=" SG CYS K 180 " distance=2.03 Simple disulfide: pdb=" SG CYS K 60 " - pdb=" SG CYS K 174 " distance=2.03 Simple disulfide: pdb=" SG CYS K 64 " - pdb=" SG CYS K 169 " distance=2.03 Simple disulfide: pdb=" SG CYS L 53 " - pdb=" SG CYS L 180 " distance=2.03 Simple disulfide: pdb=" SG CYS L 60 " - pdb=" SG CYS L 174 " distance=2.03 Simple disulfide: pdb=" SG CYS L 64 " - pdb=" SG CYS L 169 " distance=2.03 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: 8.13 Conformation dependent library (CDL) restraints added in 2.8 seconds 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4320 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 84 helices and 12 sheets defined 70.4% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 5 through 14 Processing helix chain 'A' and resid 19 through 38 removed outlier: 4.323A pdb=" N LEU A 25 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR A 26 " --> pdb=" O LYS A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 42 No H-bonds generated for 'chain 'A' and resid 40 through 42' Processing helix chain 'A' and resid 60 through 68 Processing helix chain 'A' and resid 73 through 102 Proline residue: A 87 - end of helix Processing helix chain 'A' and resid 130 through 158 removed outlier: 3.579A pdb=" N VAL A 144 " --> pdb=" O ILE A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 216 Processing helix chain 'B' and resid 5 through 14 Processing helix chain 'B' and resid 19 through 38 removed outlier: 4.322A pdb=" N LEU B 25 " --> pdb=" O GLY B 21 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N THR B 26 " --> pdb=" O LYS B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 42 No H-bonds generated for 'chain 'B' and resid 40 through 42' Processing helix chain 'B' and resid 60 through 68 Processing helix chain 'B' and resid 73 through 102 Proline residue: B 87 - end of helix Processing helix chain 'B' and resid 130 through 158 removed outlier: 3.579A pdb=" N VAL B 144 " --> pdb=" O ILE B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 216 Processing helix chain 'C' and resid 5 through 14 Processing helix chain 'C' and resid 19 through 38 removed outlier: 4.322A pdb=" N LEU C 25 " --> pdb=" O GLY C 21 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR C 26 " --> pdb=" O LYS C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 42 No H-bonds generated for 'chain 'C' and resid 40 through 42' Processing helix chain 'C' and resid 60 through 68 Processing helix chain 'C' and resid 73 through 102 Proline residue: C 87 - end of helix Processing helix chain 'C' and resid 130 through 158 removed outlier: 3.579A pdb=" N VAL C 144 " --> pdb=" O ILE C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 216 Processing helix chain 'D' and resid 5 through 14 Processing helix chain 'D' and resid 19 through 38 removed outlier: 4.322A pdb=" N LEU D 25 " --> pdb=" O GLY D 21 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR D 26 " --> pdb=" O LYS D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 42 No H-bonds generated for 'chain 'D' and resid 40 through 42' Processing helix chain 'D' and resid 60 through 68 Processing helix chain 'D' and resid 73 through 102 Proline residue: D 87 - end of helix Processing helix chain 'D' and resid 130 through 158 removed outlier: 3.580A pdb=" N VAL D 144 " --> pdb=" O ILE D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 216 Processing helix chain 'E' and resid 5 through 14 Processing helix chain 'E' and resid 19 through 38 removed outlier: 4.323A pdb=" N LEU E 25 " --> pdb=" O GLY E 21 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR E 26 " --> pdb=" O LYS E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 42 No H-bonds generated for 'chain 'E' and resid 40 through 42' Processing helix chain 'E' and resid 60 through 68 Processing helix chain 'E' and resid 73 through 102 Proline residue: E 87 - end of helix Processing helix chain 'E' and resid 130 through 158 removed outlier: 3.579A pdb=" N VAL E 144 " --> pdb=" O ILE E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 216 Processing helix chain 'F' and resid 5 through 14 Processing helix chain 'F' and resid 19 through 38 removed outlier: 4.322A pdb=" N LEU F 25 " --> pdb=" O GLY F 21 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR F 26 " --> pdb=" O LYS F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 42 No H-bonds generated for 'chain 'F' and resid 40 through 42' Processing helix chain 'F' and resid 60 through 68 Processing helix chain 'F' and resid 73 through 102 Proline residue: F 87 - end of helix Processing helix chain 'F' and resid 130 through 158 removed outlier: 3.580A pdb=" N VAL F 144 " --> pdb=" O ILE F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 216 Processing helix chain 'G' and resid 5 through 14 Processing helix chain 'G' and resid 19 through 38 removed outlier: 4.322A pdb=" N LEU G 25 " --> pdb=" O GLY G 21 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR G 26 " --> pdb=" O LYS G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 42 No H-bonds generated for 'chain 'G' and resid 40 through 42' Processing helix chain 'G' and resid 60 through 68 Processing helix chain 'G' and resid 73 through 102 Proline residue: G 87 - end of helix Processing helix chain 'G' and resid 130 through 158 removed outlier: 3.580A pdb=" N VAL G 144 " --> pdb=" O ILE G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 216 Processing helix chain 'H' and resid 5 through 14 Processing helix chain 'H' and resid 19 through 38 removed outlier: 4.322A pdb=" N LEU H 25 " --> pdb=" O GLY H 21 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR H 26 " --> pdb=" O LYS H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 42 No H-bonds generated for 'chain 'H' and resid 40 through 42' Processing helix chain 'H' and resid 60 through 68 Processing helix chain 'H' and resid 73 through 102 Proline residue: H 87 - end of helix Processing helix chain 'H' and resid 130 through 158 removed outlier: 3.579A pdb=" N VAL H 144 " --> pdb=" O ILE H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 185 through 216 Processing helix chain 'I' and resid 5 through 14 Processing helix chain 'I' and resid 19 through 38 removed outlier: 4.322A pdb=" N LEU I 25 " --> pdb=" O GLY I 21 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N THR I 26 " --> pdb=" O LYS I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 42 No H-bonds generated for 'chain 'I' and resid 40 through 42' Processing helix chain 'I' and resid 60 through 68 Processing helix chain 'I' and resid 73 through 102 Proline residue: I 87 - end of helix Processing helix chain 'I' and resid 130 through 158 removed outlier: 3.579A pdb=" N VAL I 144 " --> pdb=" O ILE I 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 185 through 216 Processing helix chain 'J' and resid 5 through 14 Processing helix chain 'J' and resid 19 through 38 removed outlier: 4.322A pdb=" N LEU J 25 " --> pdb=" O GLY J 21 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR J 26 " --> pdb=" O LYS J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 40 through 42 No H-bonds generated for 'chain 'J' and resid 40 through 42' Processing helix chain 'J' and resid 60 through 68 Processing helix chain 'J' and resid 73 through 102 Proline residue: J 87 - end of helix Processing helix chain 'J' and resid 130 through 158 removed outlier: 3.580A pdb=" N VAL J 144 " --> pdb=" O ILE J 140 " (cutoff:3.500A) Processing helix chain 'J' and resid 185 through 216 Processing helix chain 'K' and resid 5 through 14 Processing helix chain 'K' and resid 19 through 38 removed outlier: 4.322A pdb=" N LEU K 25 " --> pdb=" O GLY K 21 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N THR K 26 " --> pdb=" O LYS K 22 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 42 No H-bonds generated for 'chain 'K' and resid 40 through 42' Processing helix chain 'K' and resid 60 through 68 Processing helix chain 'K' and resid 73 through 102 Proline residue: K 87 - end of helix Processing helix chain 'K' and resid 130 through 158 removed outlier: 3.580A pdb=" N VAL K 144 " --> pdb=" O ILE K 140 " (cutoff:3.500A) Processing helix chain 'K' and resid 185 through 216 Processing helix chain 'L' and resid 5 through 14 Processing helix chain 'L' and resid 19 through 38 removed outlier: 4.322A pdb=" N LEU L 25 " --> pdb=" O GLY L 21 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N THR L 26 " --> pdb=" O LYS L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 42 No H-bonds generated for 'chain 'L' and resid 40 through 42' Processing helix chain 'L' and resid 60 through 68 Processing helix chain 'L' and resid 73 through 102 Proline residue: L 87 - end of helix Processing helix chain 'L' and resid 130 through 158 removed outlier: 3.580A pdb=" N VAL L 144 " --> pdb=" O ILE L 140 " (cutoff:3.500A) Processing helix chain 'L' and resid 185 through 216 Processing sheet with id= A, first strand: chain 'A' and resid 166 through 169 Processing sheet with id= B, first strand: chain 'B' and resid 166 through 169 Processing sheet with id= C, first strand: chain 'C' and resid 166 through 169 Processing sheet with id= D, first strand: chain 'D' and resid 166 through 169 Processing sheet with id= E, first strand: chain 'E' and resid 166 through 169 Processing sheet with id= F, first strand: chain 'F' and resid 166 through 169 Processing sheet with id= G, first strand: chain 'G' and resid 166 through 169 Processing sheet with id= H, first strand: chain 'H' and resid 166 through 169 Processing sheet with id= I, first strand: chain 'I' and resid 166 through 169 Processing sheet with id= J, first strand: chain 'J' and resid 166 through 169 Processing sheet with id= K, first strand: chain 'K' and resid 166 through 169 Processing sheet with id= L, first strand: chain 'L' and resid 166 through 169 1248 hydrogen bonds defined for protein. 3708 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: 5.61 Time building geometry restraints manager: 8.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5463 1.34 - 1.46: 5103 1.46 - 1.58: 8658 1.58 - 1.70: 0 1.70 - 1.81: 240 Bond restraints: 19464 Sorted by residual: bond pdb=" C7 LMT K 301 " pdb=" C8 LMT K 301 " ideal model delta sigma weight residual 1.489 1.569 -0.080 2.50e-02 1.60e+03 1.02e+01 bond pdb=" C7 LMT F 304 " pdb=" C8 LMT F 304 " ideal model delta sigma weight residual 1.489 1.568 -0.079 2.50e-02 1.60e+03 1.01e+01 bond pdb=" C7 LMT I 305 " pdb=" C8 LMT I 305 " ideal model delta sigma weight residual 1.489 1.568 -0.079 2.50e-02 1.60e+03 1.01e+01 bond pdb=" C7 LMT H 301 " pdb=" C8 LMT H 301 " ideal model delta sigma weight residual 1.489 1.568 -0.079 2.50e-02 1.60e+03 1.01e+01 bond pdb=" C7 LMT J 304 " pdb=" C8 LMT J 304 " ideal model delta sigma weight residual 1.489 1.568 -0.079 2.50e-02 1.60e+03 1.01e+01 ... (remaining 19459 not shown) Histogram of bond angle deviations from ideal: 100.55 - 107.24: 596 107.24 - 113.93: 11281 113.93 - 120.61: 8121 120.61 - 127.30: 5946 127.30 - 133.99: 276 Bond angle restraints: 26220 Sorted by residual: angle pdb=" C ASN K 176 " pdb=" CA ASN K 176 " pdb=" CB ASN K 176 " ideal model delta sigma weight residual 116.63 111.76 4.87 1.16e+00 7.43e-01 1.76e+01 angle pdb=" C ASN I 176 " pdb=" CA ASN I 176 " pdb=" CB ASN I 176 " ideal model delta sigma weight residual 116.63 111.76 4.87 1.16e+00 7.43e-01 1.76e+01 angle pdb=" C ASN H 176 " pdb=" CA ASN H 176 " pdb=" CB ASN H 176 " ideal model delta sigma weight residual 116.63 111.76 4.87 1.16e+00 7.43e-01 1.76e+01 angle pdb=" C ASN A 176 " pdb=" CA ASN A 176 " pdb=" CB ASN A 176 " ideal model delta sigma weight residual 116.63 111.77 4.86 1.16e+00 7.43e-01 1.76e+01 angle pdb=" C ASN E 176 " pdb=" CA ASN E 176 " pdb=" CB ASN E 176 " ideal model delta sigma weight residual 116.63 111.77 4.86 1.16e+00 7.43e-01 1.75e+01 ... (remaining 26215 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.16: 10470 16.16 - 32.31: 594 32.31 - 48.47: 223 48.47 - 64.63: 53 64.63 - 80.79: 12 Dihedral angle restraints: 11352 sinusoidal: 4680 harmonic: 6672 Sorted by residual: dihedral pdb=" CB GLU J 209 " pdb=" CG GLU J 209 " pdb=" CD GLU J 209 " pdb=" OE1 GLU J 209 " ideal model delta sinusoidal sigma weight residual 0.00 -80.79 80.79 1 3.00e+01 1.11e-03 8.96e+00 dihedral pdb=" CB GLU F 209 " pdb=" CG GLU F 209 " pdb=" CD GLU F 209 " pdb=" OE1 GLU F 209 " ideal model delta sinusoidal sigma weight residual 0.00 -80.79 80.79 1 3.00e+01 1.11e-03 8.96e+00 dihedral pdb=" CB GLU I 209 " pdb=" CG GLU I 209 " pdb=" CD GLU I 209 " pdb=" OE1 GLU I 209 " ideal model delta sinusoidal sigma weight residual 0.00 -80.78 80.78 1 3.00e+01 1.11e-03 8.96e+00 ... (remaining 11349 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1776 0.026 - 0.052: 701 0.052 - 0.078: 339 0.078 - 0.104: 112 0.104 - 0.130: 24 Chirality restraints: 2952 Sorted by residual: chirality pdb=" CA THR K 86 " pdb=" N THR K 86 " pdb=" C THR K 86 " pdb=" CB THR K 86 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 4.24e-01 chirality pdb=" CA THR I 86 " pdb=" N THR I 86 " pdb=" C THR I 86 " pdb=" CB THR I 86 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 4.22e-01 chirality pdb=" CA THR C 86 " pdb=" N THR C 86 " pdb=" C THR C 86 " pdb=" CB THR C 86 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 4.17e-01 ... (remaining 2949 not shown) Planarity restraints: 3096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP F 172 " -0.014 5.00e-02 4.00e+02 2.17e-02 7.56e-01 pdb=" N PRO F 173 " 0.038 5.00e-02 4.00e+02 pdb=" CA PRO F 173 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO F 173 " -0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP G 172 " -0.014 5.00e-02 4.00e+02 2.16e-02 7.49e-01 pdb=" N PRO G 173 " 0.037 5.00e-02 4.00e+02 pdb=" CA PRO G 173 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO G 173 " -0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP D 172 " 0.014 5.00e-02 4.00e+02 2.16e-02 7.49e-01 pdb=" N PRO D 173 " -0.037 5.00e-02 4.00e+02 pdb=" CA PRO D 173 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO D 173 " 0.011 5.00e-02 4.00e+02 ... (remaining 3093 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 608 2.72 - 3.27: 19807 3.27 - 3.81: 31395 3.81 - 4.36: 38633 4.36 - 4.90: 65140 Nonbonded interactions: 155583 Sorted by model distance: nonbonded pdb=" O ILE H 71 " pdb=" OH TYR H 158 " model vdw 2.181 2.440 nonbonded pdb=" O ILE C 71 " pdb=" OH TYR C 158 " model vdw 2.181 2.440 nonbonded pdb=" O ILE I 71 " pdb=" OH TYR I 158 " model vdw 2.181 2.440 nonbonded pdb=" O ILE F 71 " pdb=" OH TYR F 158 " model vdw 2.181 2.440 nonbonded pdb=" O ILE A 71 " pdb=" OH TYR A 158 " model vdw 2.181 2.440 ... (remaining 155578 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 4 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'B' and (resid 4 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'C' and (resid 4 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'D' and (resid 4 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'E' and (resid 4 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'F' and (resid 4 through 217 or (resid 301 and (name C2 or name C3 or nam \ e C4 or name C5 or name C6 or name C7 or name C8 )) or resid 303 through 304)) selection = (chain 'G' and (resid 4 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'H' and (resid 4 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'I' and (resid 4 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'J' and (resid 4 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'K' and (resid 4 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'L' and (resid 4 through 217 or (resid 301 and (name C2 or name C3 or nam \ e C4 or name C5 or name C6 or name C7 or name C8 )) or resid 303 through 304)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 168 5.16 5 C 12792 2.51 5 N 2976 2.21 5 O 3377 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 10.330 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: 18.330 Check model and map are aligned: 0.290 Convert atoms to be neutral: 0.150 Process input model: 51.850 Find NCS groups from input model: 1.590 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:14.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9047 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 : 0.009 0.080 19464 Z= 0.574 Angle : 0.613 7.030 26220 Z= 0.324 Chirality : 0.037 0.130 2952 Planarity : 0.002 0.022 3096 Dihedral : 12.539 80.787 6924 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer Outliers : 1.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.60 (0.17), residues: 2220 helix: 2.03 (0.12), residues: 1500 sheet: 1.45 (0.39), residues: 204 loop : -2.18 (0.21), residues: 516 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 332 time to evaluate : 2.404 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 354 average time/residue: 1.0362 time to fit residues: 424.4197 Evaluate side-chains 290 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 290 time to evaluate : 2.466 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.7980 chunk 163 optimal weight: 0.7980 chunk 90 optimal weight: 0.0020 chunk 55 optimal weight: 0.9990 chunk 110 optimal weight: 0.6980 chunk 87 optimal weight: 6.9990 chunk 169 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 196 optimal weight: 0.6980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN B 57 GLN D 206 ASN E 57 GLN F 206 ASN G 57 GLN H 206 ASN J 57 GLN K 206 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9034 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 19464 Z= 0.178 Angle : 0.528 6.798 26220 Z= 0.286 Chirality : 0.041 0.151 2952 Planarity : 0.003 0.019 3096 Dihedral : 8.982 52.735 2808 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer Outliers : 1.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.18 (0.17), residues: 2220 helix: 3.21 (0.12), residues: 1524 sheet: 2.80 (0.40), residues: 132 loop : -1.46 (0.23), residues: 564 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 311 time to evaluate : 2.455 Fit side-chains outliers start: 38 outliers final: 21 residues processed: 333 average time/residue: 1.0225 time to fit residues: 393.2599 Evaluate side-chains 321 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 300 time to evaluate : 2.218 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 10 residues processed: 12 average time/residue: 0.4979 time to fit residues: 10.7684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 109 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 163 optimal weight: 5.9990 chunk 133 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 196 optimal weight: 0.7980 chunk 212 optimal weight: 0.7980 chunk 175 optimal weight: 4.9990 chunk 194 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 157 optimal weight: 0.0570 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 HIS B 73 HIS C 73 HIS D 73 HIS H 73 HIS K 73 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9044 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 19464 Z= 0.189 Angle : 0.526 6.544 26220 Z= 0.282 Chirality : 0.042 0.208 2952 Planarity : 0.003 0.018 3096 Dihedral : 7.924 46.002 2808 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer Outliers : 3.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.31 (0.17), residues: 2220 helix: 3.47 (0.12), residues: 1524 sheet: 1.50 (0.39), residues: 204 loop : -2.03 (0.22), residues: 492 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 336 time to evaluate : 2.347 Fit side-chains outliers start: 62 outliers final: 27 residues processed: 365 average time/residue: 1.0838 time to fit residues: 455.3261 Evaluate side-chains 344 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 317 time to evaluate : 2.339 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 14 residues processed: 13 average time/residue: 0.3644 time to fit residues: 9.7251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 0.1980 chunk 147 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 131 optimal weight: 0.1980 chunk 197 optimal weight: 0.8980 chunk 208 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 186 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 94 HIS I 94 HIS L 94 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9027 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 19464 Z= 0.156 Angle : 0.511 7.161 26220 Z= 0.265 Chirality : 0.041 0.190 2952 Planarity : 0.002 0.017 3096 Dihedral : 7.061 42.343 2808 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer Outliers : 2.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.62 (0.18), residues: 2220 helix: 3.66 (0.12), residues: 1536 sheet: 1.59 (0.40), residues: 204 loop : -1.92 (0.22), residues: 480 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 341 time to evaluate : 2.391 Fit side-chains outliers start: 45 outliers final: 24 residues processed: 364 average time/residue: 1.0696 time to fit residues: 448.2544 Evaluate side-chains 344 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 320 time to evaluate : 2.457 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 17 residues processed: 7 average time/residue: 0.2005 time to fit residues: 5.5756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 3.9990 chunk 118 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 86 optimal weight: 0.0270 chunk 178 optimal weight: 0.8980 chunk 144 optimal weight: 0.7980 chunk 0 optimal weight: 30.0000 chunk 106 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 94 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9030 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 19464 Z= 0.162 Angle : 0.518 7.029 26220 Z= 0.268 Chirality : 0.040 0.197 2952 Planarity : 0.002 0.019 3096 Dihedral : 6.528 40.015 2808 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer Outliers : 2.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.74 (0.18), residues: 2220 helix: 3.78 (0.12), residues: 1536 sheet: 1.59 (0.40), residues: 204 loop : -1.93 (0.22), residues: 480 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 345 time to evaluate : 2.327 Fit side-chains outliers start: 50 outliers final: 25 residues processed: 371 average time/residue: 1.0679 time to fit residues: 456.2037 Evaluate side-chains 363 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 338 time to evaluate : 2.308 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 13 residues processed: 12 average time/residue: 0.1919 time to fit residues: 7.0913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 0.8980 chunk 188 optimal weight: 4.9990 chunk 41 optimal weight: 0.1980 chunk 122 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 208 optimal weight: 9.9990 chunk 173 optimal weight: 4.9990 chunk 96 optimal weight: 0.4980 chunk 17 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 94 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9037 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 19464 Z= 0.178 Angle : 0.531 8.277 26220 Z= 0.275 Chirality : 0.041 0.195 2952 Planarity : 0.003 0.020 3096 Dihedral : 6.275 37.500 2808 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer Outliers : 1.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.80 (0.18), residues: 2220 helix: 3.83 (0.12), residues: 1536 sheet: 1.56 (0.40), residues: 204 loop : -1.93 (0.22), residues: 480 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 334 time to evaluate : 2.305 Fit side-chains outliers start: 39 outliers final: 18 residues processed: 357 average time/residue: 1.0678 time to fit residues: 439.0626 Evaluate side-chains 349 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 331 time to evaluate : 2.225 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 14 residues processed: 4 average time/residue: 0.4017 time to fit residues: 5.2510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 0.0870 chunk 23 optimal weight: 0.9990 chunk 119 optimal weight: 4.9990 chunk 152 optimal weight: 0.9980 chunk 118 optimal weight: 4.9990 chunk 175 optimal weight: 3.9990 chunk 116 optimal weight: 0.3980 chunk 208 optimal weight: 9.9990 chunk 130 optimal weight: 3.9990 chunk 126 optimal weight: 6.9990 chunk 96 optimal weight: 0.7980 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9027 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 19464 Z= 0.158 Angle : 0.518 7.429 26220 Z= 0.265 Chirality : 0.040 0.191 2952 Planarity : 0.002 0.020 3096 Dihedral : 5.946 34.361 2808 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer Outliers : 1.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.88 (0.18), residues: 2220 helix: 3.89 (0.12), residues: 1536 sheet: 1.61 (0.40), residues: 204 loop : -1.91 (0.22), residues: 480 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 351 time to evaluate : 2.483 Fit side-chains outliers start: 30 outliers final: 18 residues processed: 371 average time/residue: 1.0257 time to fit residues: 439.9839 Evaluate side-chains 362 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 344 time to evaluate : 2.221 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 16 residues processed: 5 average time/residue: 0.5154 time to fit residues: 6.2858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 124 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 141 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 163 optimal weight: 2.9990 chunk 189 optimal weight: 7.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9044 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 19464 Z= 0.209 Angle : 0.559 7.655 26220 Z= 0.288 Chirality : 0.042 0.195 2952 Planarity : 0.003 0.021 3096 Dihedral : 5.987 32.588 2808 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer Outliers : 1.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.83 (0.18), residues: 2220 helix: 3.85 (0.12), residues: 1536 sheet: 1.51 (0.40), residues: 204 loop : -1.86 (0.22), residues: 480 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 345 time to evaluate : 2.364 Fit side-chains outliers start: 24 outliers final: 20 residues processed: 358 average time/residue: 1.0520 time to fit residues: 433.6147 Evaluate side-chains 361 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 341 time to evaluate : 2.287 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 16 residues processed: 7 average time/residue: 0.5411 time to fit residues: 7.9344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 6.9990 chunk 181 optimal weight: 0.9990 chunk 194 optimal weight: 0.9990 chunk 116 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 152 optimal weight: 0.9980 chunk 59 optimal weight: 0.0170 chunk 175 optimal weight: 0.0570 chunk 183 optimal weight: 0.9990 chunk 193 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 overall best weight: 0.5336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9016 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 19464 Z= 0.150 Angle : 0.528 8.344 26220 Z= 0.266 Chirality : 0.040 0.191 2952 Planarity : 0.002 0.020 3096 Dihedral : 5.503 28.840 2808 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer Outliers : 1.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 4.02 (0.18), residues: 2220 helix: 3.99 (0.12), residues: 1536 sheet: 1.66 (0.41), residues: 204 loop : -1.86 (0.22), residues: 480 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 358 time to evaluate : 2.225 Fit side-chains outliers start: 25 outliers final: 18 residues processed: 375 average time/residue: 1.0583 time to fit residues: 462.3802 Evaluate side-chains 366 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 348 time to evaluate : 2.416 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 18 residues processed: 6 average time/residue: 0.4374 time to fit residues: 6.6899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 205 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 142 optimal weight: 0.6980 chunk 215 optimal weight: 2.9990 chunk 198 optimal weight: 30.0000 chunk 171 optimal weight: 0.0770 chunk 17 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 chunk 136 optimal weight: 8.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 94 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9036 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 19464 Z= 0.195 Angle : 0.567 9.944 26220 Z= 0.287 Chirality : 0.042 0.194 2952 Planarity : 0.003 0.020 3096 Dihedral : 5.509 27.421 2808 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer Outliers : 0.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.97 (0.17), residues: 2220 helix: 3.96 (0.12), residues: 1536 sheet: 1.58 (0.40), residues: 204 loop : -1.83 (0.22), residues: 480 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 342 time to evaluate : 2.118 Fit side-chains outliers start: 20 outliers final: 20 residues processed: 355 average time/residue: 1.0691 time to fit residues: 437.0960 Evaluate side-chains 351 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 331 time to evaluate : 2.462 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 20 residues processed: 7 average time/residue: 0.3629 time to fit residues: 6.8378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 158 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 171 optimal weight: 0.2980 chunk 71 optimal weight: 0.6980 chunk 176 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.145548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.086469 restraints weight = 23555.454| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.68 r_work: 0.2975 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 1.47 restraints_weight: 0.2500 r_work: 0.2935 rms_B_bonded: 1.50 restraints_weight: 0.1250 r_work: 0.2916 rms_B_bonded: 1.57 restraints_weight: 0.0625 r_work: 0.2895 rms_B_bonded: 1.68 restraints_weight: 0.0312 r_work: 0.2874 rms_B_bonded: 1.82 restraints_weight: 0.0156 r_work: 0.2853 rms_B_bonded: 2.00 restraints_weight: 0.0078 r_work: 0.2830 rms_B_bonded: 2.22 restraints_weight: 0.0039 r_work: 0.2806 rms_B_bonded: 2.49 restraints_weight: 0.0020 r_work: 0.2783 rms_B_bonded: 2.81 restraints_weight: 0.0010 r_work: 0.2759 rms_B_bonded: 3.18 restraints_weight: 0.0005 r_work: 0.2737 rms_B_bonded: 3.63 restraints_weight: 0.0002 r_work: 0.2717 rms_B_bonded: 4.15 restraints_weight: 0.0001 r_work: 0.2702 rms_B_bonded: 4.76 restraints_weight: 0.0001 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9226 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 19464 Z= 0.171 Angle : 0.556 10.319 26220 Z= 0.278 Chirality : 0.041 0.192 2952 Planarity : 0.002 0.020 3096 Dihedral : 5.310 25.375 2808 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer Outliers : 1.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 4.07 (0.17), residues: 2220 helix: 4.04 (0.12), residues: 1536 sheet: 1.61 (0.40), residues: 204 loop : -1.84 (0.22), residues: 480 =============================================================================== Job complete usr+sys time: 7091.80 seconds wall clock time: 126 minutes 26.99 seconds (7586.99 seconds total)