Starting phenix.real_space_refine on Sun Mar 17 23:11:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qeq_13937/03_2024/7qeq_13937_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qeq_13937/03_2024/7qeq_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_13937/03_2024/7qeq_13937.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qeq_13937/03_2024/7qeq_13937.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qeq_13937/03_2024/7qeq_13937_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qeq_13937/03_2024/7qeq_13937_updated.pdb" } resolution = 1.9 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= 0.001 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 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. 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 182} 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: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 182} 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: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 182} 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: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 182} 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: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 182} 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: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 182} 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: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 182} 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: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 182} 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: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 182} 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: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 182} 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: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 182} 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: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 182} 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: 256 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: 256 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: 256 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: 256 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: 256 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: 256 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: 256 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: 256 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: 256 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: 256 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: 256 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: 256 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: 10.71, per 1000 atoms: 0.55 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: 7.54 Conformation dependent library (CDL) restraints added in 3.1 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: 3.18 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: 5.41 Time building geometry restraints manager: 8.22 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=" C1 LMT H 305 " pdb=" C2 LMT H 305 " ideal model delta sigma weight residual 1.516 1.566 -0.050 2.00e-02 2.50e+03 6.16e+00 bond pdb=" C1 LMT L 303 " pdb=" C2 LMT L 303 " ideal model delta sigma weight residual 1.516 1.566 -0.050 2.00e-02 2.50e+03 6.16e+00 bond pdb=" C1 LMT K 303 " pdb=" C2 LMT K 303 " ideal model delta sigma weight residual 1.516 1.566 -0.050 2.00e-02 2.50e+03 6.15e+00 bond pdb=" C1 LMT A 305 " pdb=" C2 LMT A 305 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.00e-02 2.50e+03 6.10e+00 bond pdb=" C1 LMT J 303 " pdb=" C2 LMT J 303 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.00e-02 2.50e+03 6.06e+00 ... (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: 618 32.31 - 48.47: 211 48.47 - 64.63: 41 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 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: 3.880 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: 17.620 Check model and map are aligned: 0.310 Set scattering table: 0.170 Process input model: 50.290 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.170 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:11.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 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 : 0.005 0.050 19464 Z= 0.323 Angle : 0.867 7.892 26220 Z= 0.374 Chirality : 0.037 0.130 2952 Planarity : 0.002 0.022 3096 Dihedral : 12.392 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 % Allowed : 6.51 % Favored : 92.31 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 24 HIS 0.001 0.000 HIS A 94 PHE 0.013 0.001 PHE E 51 TYR 0.008 0.001 TYR I 65 ARG 0.002 0.000 ARG F 165 *********************** 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 : 2.396 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 354 average time/residue: 1.1009 time to fit residues: 447.6111 Evaluate side-chains 290 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 290 time to evaluate : 2.175 ------------------------------------------------------------------------------- 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: 0.8809 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 19464 Z= 0.177 Angle : 0.539 7.078 26220 Z= 0.289 Chirality : 0.041 0.144 2952 Planarity : 0.003 0.019 3096 Dihedral : 8.807 49.082 2808 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.07 % Allowed : 11.83 % Favored : 86.09 % 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: 3.14 (0.17), residues: 2220 helix: 3.17 (0.12), residues: 1524 sheet: 2.78 (0.40), residues: 132 loop : -1.46 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 134 HIS 0.002 0.000 HIS E 73 PHE 0.012 0.002 PHE G 51 TYR 0.012 0.002 TYR G 65 ARG 0.002 0.000 ARG B 165 *********************** 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 353 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 311 time to evaluate : 2.214 Fit side-chains outliers start: 42 outliers final: 23 residues processed: 333 average time/residue: 1.0979 time to fit residues: 418.8177 Evaluate side-chains 324 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 301 time to evaluate : 1.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 138 SER Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 151 MET Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 162 SER Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 138 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 109 optimal weight: 4.9990 chunk 60 optimal weight: 0.0870 chunk 163 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 196 optimal weight: 0.6980 chunk 212 optimal weight: 0.0270 chunk 175 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 overall best weight: 0.9620 ------------------------------------------------------------------------------- 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: 0.8827 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19464 Z= 0.202 Angle : 0.535 6.710 26220 Z= 0.288 Chirality : 0.042 0.216 2952 Planarity : 0.003 0.019 3096 Dihedral : 8.024 45.600 2808 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.86 % Allowed : 11.93 % Favored : 85.21 % 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: 3.28 (0.17), residues: 2220 helix: 3.38 (0.12), residues: 1536 sheet: 1.50 (0.40), residues: 204 loop : -1.92 (0.22), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 133 HIS 0.002 0.000 HIS E 73 PHE 0.015 0.002 PHE C 51 TYR 0.016 0.002 TYR E 65 ARG 0.003 0.000 ARG D 75 *********************** 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 392 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 334 time to evaluate : 2.152 Fit side-chains REVERT: A 159 ASP cc_start: 0.7947 (p0) cc_final: 0.7736 (p0) REVERT: G 159 ASP cc_start: 0.7979 (p0) cc_final: 0.7746 (p0) REVERT: G 217 TYR cc_start: 0.6549 (m-80) cc_final: 0.6286 (m-80) REVERT: I 94 HIS cc_start: 0.6771 (OUTLIER) cc_final: 0.6487 (t-90) REVERT: I 132 LEU cc_start: 0.7498 (tt) cc_final: 0.7167 (mm) REVERT: J 25 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8741 (mm) outliers start: 58 outliers final: 22 residues processed: 362 average time/residue: 1.0844 time to fit residues: 449.2495 Evaluate side-chains 335 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 311 time to evaluate : 2.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 213 LEU Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 94 HIS Chi-restraints excluded: chain I residue 162 SER Chi-restraints excluded: chain I residue 215 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain K residue 213 LEU Chi-restraints excluded: chain K residue 215 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 0.4980 chunk 147 optimal weight: 0.6980 chunk 101 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 93 optimal weight: 0.0010 chunk 131 optimal weight: 0.2980 chunk 197 optimal weight: 0.9990 chunk 208 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 186 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 overall best weight: 0.4386 ------------------------------------------------------------------------------- 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: 0.8786 moved from start: 0.2044 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= 0.139 Angle : 0.505 7.514 26220 Z= 0.258 Chirality : 0.040 0.187 2952 Planarity : 0.002 0.018 3096 Dihedral : 6.989 42.206 2808 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.27 % Allowed : 13.91 % Favored : 83.83 % 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: 3.65 (0.18), residues: 2220 helix: 3.69 (0.12), residues: 1536 sheet: 1.67 (0.40), residues: 204 loop : -1.94 (0.22), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 133 HIS 0.002 0.000 HIS I 73 PHE 0.011 0.001 PHE K 31 TYR 0.009 0.001 TYR B 158 ARG 0.002 0.000 ARG D 216 *********************** 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: 46 poor density : 340 time to evaluate : 2.284 Fit side-chains REVERT: B 132 LEU cc_start: 0.7384 (tt) cc_final: 0.7110 (mm) REVERT: D 159 ASP cc_start: 0.7882 (p0) cc_final: 0.7642 (p0) REVERT: D 208 THR cc_start: 0.8899 (OUTLIER) cc_final: 0.8665 (p) REVERT: D 217 TYR cc_start: 0.6495 (m-80) cc_final: 0.6280 (m-80) REVERT: E 132 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.7259 (mm) REVERT: G 159 ASP cc_start: 0.7995 (p0) cc_final: 0.7765 (p0) REVERT: H 140 ILE cc_start: 0.8612 (pt) cc_final: 0.8300 (mp) REVERT: I 132 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.7125 (mm) REVERT: K 132 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.7267 (mm) REVERT: L 132 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.7273 (mm) outliers start: 46 outliers final: 18 residues processed: 361 average time/residue: 1.1416 time to fit residues: 469.1254 Evaluate side-chains 340 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 317 time to evaluate : 1.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 215 ILE Chi-restraints excluded: chain H residue 215 ILE Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 162 SER Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 215 ILE Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 215 ILE Chi-restraints excluded: chain K residue 132 LEU Chi-restraints excluded: chain K residue 215 ILE Chi-restraints excluded: chain L residue 132 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 0.8980 chunk 118 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 86 optimal weight: 0.0040 chunk 178 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 106 optimal weight: 0.8980 chunk 187 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.6992 ------------------------------------------------------------------------------- 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: 0.8808 moved from start: 0.2207 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= 0.165 Angle : 0.525 6.887 26220 Z= 0.269 Chirality : 0.040 0.200 2952 Planarity : 0.002 0.019 3096 Dihedral : 6.655 40.243 2808 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.12 % Allowed : 15.29 % Favored : 82.59 % 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: 3.76 (0.12), residues: 1536 sheet: 1.67 (0.40), residues: 204 loop : -1.93 (0.22), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 133 HIS 0.002 0.000 HIS I 73 PHE 0.012 0.001 PHE B 51 TYR 0.013 0.002 TYR J 65 ARG 0.003 0.000 ARG B 216 *********************** 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 379 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 336 time to evaluate : 2.047 Fit side-chains REVERT: A 159 ASP cc_start: 0.7949 (p0) cc_final: 0.7735 (p0) REVERT: B 132 LEU cc_start: 0.7380 (tt) cc_final: 0.7134 (mm) REVERT: C 159 ASP cc_start: 0.8090 (p0) cc_final: 0.7875 (p0) REVERT: D 208 THR cc_start: 0.8925 (OUTLIER) cc_final: 0.8623 (p) REVERT: E 132 LEU cc_start: 0.7486 (tt) cc_final: 0.7282 (mm) REVERT: G 159 ASP cc_start: 0.8044 (p0) cc_final: 0.7824 (p0) REVERT: I 132 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7135 (mm) REVERT: L 132 LEU cc_start: 0.7473 (tt) cc_final: 0.7266 (mm) outliers start: 43 outliers final: 14 residues processed: 358 average time/residue: 1.1483 time to fit residues: 469.3103 Evaluate side-chains 347 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 331 time to evaluate : 2.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain F residue 215 ILE Chi-restraints excluded: chain H residue 213 LEU Chi-restraints excluded: chain H residue 215 ILE Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 162 SER Chi-restraints excluded: chain J residue 215 ILE Chi-restraints excluded: chain K residue 215 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 0.9980 chunk 188 optimal weight: 4.9990 chunk 41 optimal weight: 0.2980 chunk 122 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 208 optimal weight: 10.0000 chunk 173 optimal weight: 0.9980 chunk 96 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.8806 moved from start: 0.2329 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 : 0.520 7.154 26220 Z= 0.266 Chirality : 0.040 0.192 2952 Planarity : 0.002 0.020 3096 Dihedral : 6.322 39.432 2808 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.92 % Allowed : 16.07 % Favored : 82.00 % 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: 3.81 (0.18), residues: 2220 helix: 3.83 (0.12), residues: 1536 sheet: 1.68 (0.40), residues: 204 loop : -1.94 (0.22), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 133 HIS 0.002 0.000 HIS C 73 PHE 0.012 0.001 PHE D 31 TYR 0.012 0.002 TYR F 65 ARG 0.001 0.000 ARG H 216 *********************** 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 390 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 351 time to evaluate : 2.079 Fit side-chains REVERT: A 140 ILE cc_start: 0.8608 (pt) cc_final: 0.8355 (mp) REVERT: B 132 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.7107 (mm) REVERT: C 159 ASP cc_start: 0.8088 (p0) cc_final: 0.7886 (p0) REVERT: D 159 ASP cc_start: 0.7933 (p0) cc_final: 0.7718 (p0) REVERT: D 208 THR cc_start: 0.8942 (OUTLIER) cc_final: 0.8627 (p) REVERT: G 159 ASP cc_start: 0.8052 (p0) cc_final: 0.7850 (p0) REVERT: H 140 ILE cc_start: 0.8616 (pt) cc_final: 0.8368 (mp) REVERT: H 159 ASP cc_start: 0.7978 (p0) cc_final: 0.7778 (p0) REVERT: H 208 THR cc_start: 0.8891 (OUTLIER) cc_final: 0.8647 (p) REVERT: I 132 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.7095 (mm) REVERT: I 140 ILE cc_start: 0.8452 (pt) cc_final: 0.8172 (mp) REVERT: K 159 ASP cc_start: 0.7996 (p0) cc_final: 0.7779 (p0) outliers start: 39 outliers final: 13 residues processed: 369 average time/residue: 1.0680 time to fit residues: 451.2226 Evaluate side-chains 360 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 343 time to evaluate : 1.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 215 ILE Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 162 SER Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain K residue 215 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 0.9980 chunk 23 optimal weight: 0.0770 chunk 119 optimal weight: 4.9990 chunk 152 optimal weight: 0.7980 chunk 118 optimal weight: 0.7980 chunk 175 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 208 optimal weight: 0.0470 chunk 130 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 overall best weight: 0.5436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 94 HIS K 94 HIS L 94 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 19464 Z= 0.150 Angle : 0.514 7.626 26220 Z= 0.261 Chirality : 0.040 0.191 2952 Planarity : 0.002 0.020 3096 Dihedral : 5.921 36.722 2808 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.13 % Allowed : 17.11 % Favored : 81.76 % 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: 3.87 (0.18), residues: 2220 helix: 3.87 (0.12), residues: 1536 sheet: 1.73 (0.41), residues: 204 loop : -1.95 (0.22), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 133 HIS 0.002 0.000 HIS C 73 PHE 0.012 0.001 PHE D 31 TYR 0.010 0.001 TYR F 65 ARG 0.001 0.000 ARG E 75 *********************** 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 385 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 362 time to evaluate : 2.479 Fit side-chains REVERT: A 159 ASP cc_start: 0.7968 (p0) cc_final: 0.7765 (p0) REVERT: B 132 LEU cc_start: 0.7347 (tt) cc_final: 0.7135 (mm) REVERT: B 140 ILE cc_start: 0.8471 (pt) cc_final: 0.8179 (mp) REVERT: C 159 ASP cc_start: 0.8084 (p0) cc_final: 0.7877 (p0) REVERT: D 159 ASP cc_start: 0.7928 (p0) cc_final: 0.7722 (p0) REVERT: D 208 THR cc_start: 0.8941 (OUTLIER) cc_final: 0.8633 (p) REVERT: E 140 ILE cc_start: 0.8523 (pt) cc_final: 0.8275 (mp) REVERT: G 159 ASP cc_start: 0.8057 (p0) cc_final: 0.7854 (p0) REVERT: H 159 ASP cc_start: 0.7981 (p0) cc_final: 0.7758 (p0) REVERT: H 208 THR cc_start: 0.8914 (OUTLIER) cc_final: 0.8626 (p) REVERT: I 132 LEU cc_start: 0.7337 (tt) cc_final: 0.7063 (mm) REVERT: K 159 ASP cc_start: 0.8000 (p0) cc_final: 0.7787 (p0) outliers start: 23 outliers final: 14 residues processed: 370 average time/residue: 1.0711 time to fit residues: 454.1466 Evaluate side-chains 364 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 348 time to evaluate : 2.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 212 TYR Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 209 GLU Chi-restraints excluded: chain H residue 215 ILE Chi-restraints excluded: chain I residue 162 SER Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain K residue 138 SER Chi-restraints excluded: chain K residue 212 TYR Chi-restraints excluded: chain K residue 215 ILE Chi-restraints excluded: chain L residue 85 SER 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: 2.9990 chunk 124 optimal weight: 0.5980 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: 0.9990 chunk 19 optimal weight: 0.9990 chunk 163 optimal weight: 0.9990 chunk 189 optimal weight: 9.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- 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: 0.8814 moved from start: 0.2477 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= 0.190 Angle : 0.544 7.494 26220 Z= 0.278 Chirality : 0.041 0.193 2952 Planarity : 0.003 0.020 3096 Dihedral : 5.943 37.656 2808 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.38 % Allowed : 16.96 % Favored : 81.66 % 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: 3.86 (0.18), residues: 2220 helix: 3.87 (0.12), residues: 1536 sheet: 1.63 (0.40), residues: 204 loop : -1.91 (0.22), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 133 HIS 0.002 0.000 HIS C 73 PHE 0.012 0.001 PHE E 51 TYR 0.014 0.002 TYR L 65 ARG 0.002 0.000 ARG D 216 *********************** 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 372 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 344 time to evaluate : 2.111 Fit side-chains REVERT: B 132 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.7171 (mm) REVERT: C 159 ASP cc_start: 0.8107 (p0) cc_final: 0.7903 (p0) REVERT: D 159 ASP cc_start: 0.7953 (p0) cc_final: 0.7713 (p0) REVERT: D 208 THR cc_start: 0.8952 (OUTLIER) cc_final: 0.8622 (p) REVERT: G 159 ASP cc_start: 0.8076 (p0) cc_final: 0.7876 (p0) REVERT: H 208 THR cc_start: 0.8930 (OUTLIER) cc_final: 0.8635 (p) REVERT: I 132 LEU cc_start: 0.7357 (OUTLIER) cc_final: 0.7111 (mm) outliers start: 28 outliers final: 17 residues processed: 352 average time/residue: 1.1494 time to fit residues: 460.6311 Evaluate side-chains 360 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 339 time to evaluate : 1.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 215 ILE Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain K residue 138 SER Chi-restraints excluded: chain K residue 212 TYR Chi-restraints excluded: chain K residue 215 ILE Chi-restraints excluded: chain L residue 85 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 8.9990 chunk 181 optimal weight: 0.9980 chunk 194 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 152 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 175 optimal weight: 4.9990 chunk 183 optimal weight: 0.8980 chunk 193 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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: 0.8816 moved from start: 0.2514 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= 0.187 Angle : 0.554 8.629 26220 Z= 0.281 Chirality : 0.041 0.194 2952 Planarity : 0.003 0.020 3096 Dihedral : 5.902 38.343 2808 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.38 % Allowed : 17.06 % Favored : 81.56 % 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: 3.91 (0.18), residues: 2220 helix: 3.91 (0.12), residues: 1536 sheet: 1.59 (0.40), residues: 204 loop : -1.86 (0.22), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 133 HIS 0.002 0.000 HIS C 73 PHE 0.013 0.001 PHE E 51 TYR 0.014 0.002 TYR L 65 ARG 0.002 0.000 ARG B 165 *********************** 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 375 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 347 time to evaluate : 2.150 Fit side-chains REVERT: B 132 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.7174 (mm) REVERT: C 159 ASP cc_start: 0.8103 (p0) cc_final: 0.7895 (p0) REVERT: D 159 ASP cc_start: 0.7969 (p0) cc_final: 0.7725 (p0) REVERT: D 208 THR cc_start: 0.8963 (OUTLIER) cc_final: 0.8647 (p) REVERT: G 159 ASP cc_start: 0.8084 (p0) cc_final: 0.7883 (p0) REVERT: H 208 THR cc_start: 0.8943 (OUTLIER) cc_final: 0.8638 (p) REVERT: I 132 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.7131 (mm) outliers start: 28 outliers final: 22 residues processed: 356 average time/residue: 1.0795 time to fit residues: 440.0940 Evaluate side-chains 368 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 342 time to evaluate : 2.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 212 TYR Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain G residue 212 TYR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 215 ILE Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain K residue 138 SER Chi-restraints excluded: chain K residue 212 TYR Chi-restraints excluded: chain K residue 215 ILE Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 93 MET Chi-restraints excluded: chain L residue 212 TYR 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: 2.9990 chunk 97 optimal weight: 3.9990 chunk 142 optimal weight: 0.6980 chunk 215 optimal weight: 1.9990 chunk 198 optimal weight: 20.0000 chunk 171 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 136 optimal weight: 9.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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: 0.8851 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 19464 Z= 0.343 Angle : 0.639 10.176 26220 Z= 0.331 Chirality : 0.046 0.200 2952 Planarity : 0.003 0.028 3096 Dihedral : 6.612 46.827 2808 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.13 % Allowed : 17.65 % Favored : 81.21 % 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: 3.86 (0.17), residues: 2220 helix: 3.75 (0.12), residues: 1536 sheet: 2.34 (0.42), residues: 132 loop : -1.22 (0.22), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 133 HIS 0.002 0.000 HIS I 73 PHE 0.018 0.002 PHE G 51 TYR 0.037 0.003 TYR G 212 ARG 0.005 0.001 ARG G 216 ********************** 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 356 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 333 time to evaluate : 2.208 Fit side-chains REVERT: B 94 HIS cc_start: 0.6635 (OUTLIER) cc_final: 0.6328 (t-90) REVERT: C 159 ASP cc_start: 0.8121 (p0) cc_final: 0.7913 (p0) REVERT: H 208 THR cc_start: 0.8964 (OUTLIER) cc_final: 0.8637 (p) REVERT: I 94 HIS cc_start: 0.6713 (OUTLIER) cc_final: 0.6460 (t-90) REVERT: I 132 LEU cc_start: 0.7446 (tt) cc_final: 0.7168 (mm) outliers start: 23 outliers final: 17 residues processed: 342 average time/residue: 1.1609 time to fit residues: 451.5824 Evaluate side-chains 344 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 324 time to evaluate : 2.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 94 HIS Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 215 ILE Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 94 HIS Chi-restraints excluded: chain K residue 138 SER Chi-restraints excluded: chain K residue 215 ILE Chi-restraints excluded: chain L residue 85 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 158 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 171 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 176 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 150 optimal weight: 0.6980 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 = 0.4052 r_free = 0.4052 target = 0.144606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.086441 restraints weight = 23700.670| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 1.65 r_work: 0.2843 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9049 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19464 Z= 0.171 Angle : 0.558 10.401 26220 Z= 0.281 Chirality : 0.041 0.192 2952 Planarity : 0.003 0.021 3096 Dihedral : 6.128 45.386 2808 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.13 % Allowed : 17.65 % Favored : 81.21 % 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: 3.96 (0.17), residues: 2220 helix: 3.96 (0.12), residues: 1536 sheet: 1.49 (0.40), residues: 204 loop : -1.84 (0.22), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 133 HIS 0.002 0.000 HIS C 73 PHE 0.012 0.001 PHE B 51 TYR 0.011 0.002 TYR J 65 ARG 0.002 0.000 ARG B 165 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8477.36 seconds wall clock time: 150 minutes 13.98 seconds (9013.98 seconds total)