Starting phenix.real_space_refine on Mon Mar 18 06:33:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6myy_9294/03_2024/6myy_9294_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6myy_9294/03_2024/6myy_9294.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6myy_9294/03_2024/6myy_9294.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6myy_9294/03_2024/6myy_9294.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6myy_9294/03_2024/6myy_9294_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6myy_9294/03_2024/6myy_9294_updated.pdb" } resolution = 3.8 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= 0.007 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 129 5.16 5 C 12564 2.51 5 N 3243 2.21 5 O 4203 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 172": "OE1" <-> "OE2" Residue "A TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 381": "OE1" <-> "OE2" Residue "A PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 504": "NH1" <-> "NH2" Residue "A TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 381": "OE1" <-> "OE2" Residue "B PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 504": "NH1" <-> "NH2" Residue "B TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 172": "OE1" <-> "OE2" Residue "E TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 381": "OE1" <-> "OE2" Residue "E PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 504": "NH1" <-> "NH2" Residue "E TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20139 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 4338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4338 Classifications: {'peptide': 550} Link IDs: {'PTRANS': 23, 'TRANS': 526} Chain breaks: 5 Chain: "L" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 767 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 93} Chain: "H" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 940 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PCA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 4338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4338 Classifications: {'peptide': 550} Link IDs: {'PTRANS': 23, 'TRANS': 526} Chain breaks: 5 Chain: "C" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 767 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 93} Chain: "D" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 940 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PCA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 4338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4338 Classifications: {'peptide': 550} Link IDs: {'PTRANS': 23, 'TRANS': 526} Chain breaks: 5 Chain: "F" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 767 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 93} Chain: "G" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 940 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PCA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "M" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "a" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "o" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "p" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "q" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "r" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "s" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "t" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "w" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "x" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 11.12, per 1000 atoms: 0.55 Number of scatterers: 20139 At special positions: 0 Unit cell: (149.6, 140.08, 125.12, 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 129 16.00 O 4203 8.00 N 3243 7.00 C 12564 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.13 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.05 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 459 " - pdb=" SG CYS H 60 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS A 605 " distance=2.20 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.17 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.13 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.04 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.02 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 433 " distance=2.02 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.05 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 459 " - pdb=" SG CYS D 60 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS B 605 " distance=2.20 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.17 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.13 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.02 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.02 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.05 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 459 " - pdb=" SG CYS G 60 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS E 605 " distance=2.20 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.17 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " 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 Links applied ALPHA1-2 " MAN O 4 " - " MAN O 5 " " MAN T 4 " - " MAN T 5 " " MAN c 4 " - " MAN c 5 " " MAN h 4 " - " MAN h 5 " " MAN q 4 " - " MAN q 5 " " MAN v 4 " - " MAN v 5 " ALPHA1-3 " BMA K 3 " - " MAN K 4 " " BMA M 3 " - " MAN M 6 " " MAN M 4 " - " MAN M 5 " " BMA O 3 " - " MAN O 4 " " MAN O 6 " - " MAN O 7 " " BMA R 3 " - " MAN R 4 " " BMA T 3 " - " MAN T 4 " " BMA Z 3 " - " MAN Z 4 " " BMA a 3 " - " MAN a 6 " " MAN a 4 " - " MAN a 5 " " BMA c 3 " - " MAN c 4 " " MAN c 6 " - " MAN c 7 " " BMA f 3 " - " MAN f 4 " " BMA h 3 " - " MAN h 4 " " BMA n 3 " - " MAN n 4 " " BMA o 3 " - " MAN o 6 " " MAN o 4 " - " MAN o 5 " " BMA q 3 " - " MAN q 4 " " MAN q 6 " - " MAN q 7 " " BMA t 3 " - " MAN t 4 " " BMA v 3 " - " MAN v 4 " ALPHA1-6 " BMA K 3 " - " MAN K 5 " " BMA M 3 " - " MAN M 4 " " BMA O 3 " - " MAN O 6 " " BMA Z 3 " - " MAN Z 5 " " BMA a 3 " - " MAN a 4 " " BMA c 3 " - " MAN c 6 " " BMA n 3 " - " MAN n 5 " " BMA o 3 " - " MAN o 4 " " BMA q 3 " - " MAN q 6 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " NAG-ASN " NAG A 738 " - " ASN A 357 " " NAG A 744 " - " ASN A 411 " " NAG A 747 " - " ASN A 611 " " NAG A 748 " - " ASN A 637 " " NAG B 738 " - " ASN B 357 " " NAG B 744 " - " ASN B 411 " " NAG B 747 " - " ASN B 611 " " NAG B 748 " - " ASN B 637 " " NAG E 738 " - " ASN E 357 " " NAG E 744 " - " ASN E 411 " " NAG E 747 " - " ASN E 611 " " NAG E 748 " - " ASN E 637 " " NAG I 1 " - " ASN A 88 " " NAG J 1 " - " ASN A 130 " " NAG K 1 " - " ASN A 156 " " NAG M 1 " - " ASN A 197 " " NAG N 1 " - " ASN A 241 " " NAG O 1 " - " ASN A 262 " " NAG P 1 " - " ASN A 289 " " NAG Q 1 " - " ASN A 301 " " NAG R 1 " - " ASN A 332 " " NAG S 1 " - " ASN A 337 " " NAG T 1 " - " ASN A 386 " " NAG U 1 " - " ASN A 442 " " NAG V 1 " - " ASN A 230 " " NAG W 1 " - " ASN A 392 " " NAG X 1 " - " ASN B 88 " " NAG Y 1 " - " ASN B 130 " " NAG Z 1 " - " ASN B 156 " " NAG a 1 " - " ASN B 197 " " NAG b 1 " - " ASN B 241 " " NAG c 1 " - " ASN B 262 " " NAG d 1 " - " ASN B 289 " " NAG e 1 " - " ASN B 301 " " NAG f 1 " - " ASN B 332 " " NAG g 1 " - " ASN B 337 " " NAG h 1 " - " ASN B 386 " " NAG i 1 " - " ASN B 442 " " NAG j 1 " - " ASN B 230 " " NAG k 1 " - " ASN B 392 " " NAG l 1 " - " ASN E 88 " " NAG m 1 " - " ASN E 130 " " NAG n 1 " - " ASN E 156 " " NAG o 1 " - " ASN E 197 " " NAG p 1 " - " ASN E 241 " " NAG q 1 " - " ASN E 262 " " NAG r 1 " - " ASN E 289 " " NAG s 1 " - " ASN E 301 " " NAG t 1 " - " ASN E 332 " " NAG u 1 " - " ASN E 337 " " NAG v 1 " - " ASN E 386 " " NAG w 1 " - " ASN E 442 " " NAG x 1 " - " ASN E 230 " " NAG y 1 " - " ASN E 392 " Time building additional restraints: 11.29 Conformation dependent library (CDL) restraints added in 3.4 seconds 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4290 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 51 helices and 42 sheets defined 19.8% alpha, 26.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.00 Creating SS restraints... Processing helix chain 'A' and resid 99 through 115 Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 194 through 197 removed outlier: 4.191A pdb=" N ASN A 197 " --> pdb=" O ILE A 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 194 through 197' Processing helix chain 'A' and resid 335 through 352 removed outlier: 3.769A pdb=" N HIS A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 372 No H-bonds generated for 'chain 'A' and resid 369 through 372' Processing helix chain 'A' and resid 475 through 480 removed outlier: 3.623A pdb=" N ARG A 480 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 485 No H-bonds generated for 'chain 'A' and resid 483 through 485' Processing helix chain 'A' and resid 524 through 527 Processing helix chain 'A' and resid 530 through 543 removed outlier: 4.276A pdb=" N MET A 535 " --> pdb=" O GLY A 531 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N THR A 536 " --> pdb=" O ALA A 532 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU A 537 " --> pdb=" O ALA A 533 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N THR A 538 " --> pdb=" O SER A 534 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N VAL A 539 " --> pdb=" O MET A 535 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ASN A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 595 Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 628 through 661 removed outlier: 3.612A pdb=" N GLU A 634 " --> pdb=" O GLN A 630 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ASN A 637 " --> pdb=" O LYS A 633 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N TYR A 638 " --> pdb=" O GLU A 634 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N THR A 639 " --> pdb=" O ILE A 635 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N GLN A 640 " --> pdb=" O SER A 636 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ILE A 641 " --> pdb=" O ASN A 637 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 82 No H-bonds generated for 'chain 'L' and resid 80 through 82' Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 61 through 63 No H-bonds generated for 'chain 'H' and resid 61 through 63' Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 84 through 86 No H-bonds generated for 'chain 'H' and resid 84 through 86' Processing helix chain 'B' and resid 99 through 115 Processing helix chain 'B' and resid 178 through 180 No H-bonds generated for 'chain 'B' and resid 178 through 180' Processing helix chain 'B' and resid 194 through 197 removed outlier: 4.190A pdb=" N ASN B 197 " --> pdb=" O ILE B 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 194 through 197' Processing helix chain 'B' and resid 335 through 352 removed outlier: 3.769A pdb=" N HIS B 352 " --> pdb=" O LYS B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 372 No H-bonds generated for 'chain 'B' and resid 369 through 372' Processing helix chain 'B' and resid 475 through 480 removed outlier: 3.623A pdb=" N ARG B 480 " --> pdb=" O ASP B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 485 No H-bonds generated for 'chain 'B' and resid 483 through 485' Processing helix chain 'B' and resid 524 through 527 Processing helix chain 'B' and resid 530 through 543 removed outlier: 4.276A pdb=" N MET B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N THR B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU B 537 " --> pdb=" O ALA B 533 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N THR B 538 " --> pdb=" O SER B 534 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N VAL B 539 " --> pdb=" O MET B 535 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 595 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 628 through 661 removed outlier: 3.612A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ASN B 637 " --> pdb=" O LYS B 633 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N TYR B 638 " --> pdb=" O GLU B 634 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N THR B 639 " --> pdb=" O ILE B 635 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N GLN B 640 " --> pdb=" O SER B 636 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ILE B 641 " --> pdb=" O ASN B 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 82 No H-bonds generated for 'chain 'C' and resid 80 through 82' Processing helix chain 'D' and resid 29 through 31 No H-bonds generated for 'chain 'D' and resid 29 through 31' Processing helix chain 'D' and resid 61 through 63 No H-bonds generated for 'chain 'D' and resid 61 through 63' Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'D' and resid 84 through 86 No H-bonds generated for 'chain 'D' and resid 84 through 86' Processing helix chain 'E' and resid 99 through 115 Processing helix chain 'E' and resid 178 through 180 No H-bonds generated for 'chain 'E' and resid 178 through 180' Processing helix chain 'E' and resid 194 through 197 removed outlier: 4.190A pdb=" N ASN E 197 " --> pdb=" O ILE E 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 194 through 197' Processing helix chain 'E' and resid 335 through 352 removed outlier: 3.769A pdb=" N HIS E 352 " --> pdb=" O LYS E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 372 No H-bonds generated for 'chain 'E' and resid 369 through 372' Processing helix chain 'E' and resid 475 through 480 removed outlier: 3.623A pdb=" N ARG E 480 " --> pdb=" O ASP E 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 483 through 485 No H-bonds generated for 'chain 'E' and resid 483 through 485' Processing helix chain 'E' and resid 524 through 527 Processing helix chain 'E' and resid 530 through 543 removed outlier: 4.276A pdb=" N MET E 535 " --> pdb=" O GLY E 531 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N THR E 536 " --> pdb=" O ALA E 532 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU E 537 " --> pdb=" O ALA E 533 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N THR E 538 " --> pdb=" O SER E 534 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N VAL E 539 " --> pdb=" O MET E 535 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ASN E 543 " --> pdb=" O VAL E 539 " (cutoff:3.500A) Processing helix chain 'E' and resid 572 through 595 Processing helix chain 'E' and resid 619 through 624 Processing helix chain 'E' and resid 628 through 661 removed outlier: 3.612A pdb=" N GLU E 634 " --> pdb=" O GLN E 630 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ASN E 637 " --> pdb=" O LYS E 633 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N TYR E 638 " --> pdb=" O GLU E 634 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N THR E 639 " --> pdb=" O ILE E 635 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N GLN E 640 " --> pdb=" O SER E 636 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ILE E 641 " --> pdb=" O ASN E 637 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 82 No H-bonds generated for 'chain 'F' and resid 80 through 82' Processing helix chain 'G' and resid 29 through 31 No H-bonds generated for 'chain 'G' and resid 29 through 31' Processing helix chain 'G' and resid 61 through 63 No H-bonds generated for 'chain 'G' and resid 61 through 63' Processing helix chain 'G' and resid 73 through 75 No H-bonds generated for 'chain 'G' and resid 73 through 75' Processing helix chain 'G' and resid 84 through 86 No H-bonds generated for 'chain 'G' and resid 84 through 86' Processing sheet with id= A, first strand: chain 'A' and resid 494 through 499 Processing sheet with id= B, first strand: chain 'A' and resid 45 through 47 Processing sheet with id= C, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= D, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.831A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 130 through 132 Processing sheet with id= F, first strand: chain 'A' and resid 181 through 183 Processing sheet with id= G, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.315A pdb=" N ASN A 357 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N PHE A 468 " --> pdb=" O ASN A 357 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N SER A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N GLN A 362 " --> pdb=" O PRO A 470 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 414 through 417 removed outlier: 6.919A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 374 through 377 removed outlier: 3.576A pdb=" N PHE A 383 " --> pdb=" O PHE A 376 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 302 through 312 removed outlier: 6.390A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.777A pdb=" N SER L 7 " --> pdb=" O SER L 22 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'L' and resid 85 through 89 removed outlier: 5.915A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'H' and resid 3 through 6 Processing sheet with id= N, first strand: chain 'H' and resid 107 through 109 removed outlier: 6.177A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ALA H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU H 45 " --> pdb=" O ALA H 40 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 494 through 499 Processing sheet with id= P, first strand: chain 'B' and resid 45 through 47 Processing sheet with id= Q, first strand: chain 'B' and resid 53 through 55 Processing sheet with id= R, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.832A pdb=" N GLU B 91 " --> pdb=" O CYS B 239 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 130 through 132 Processing sheet with id= T, first strand: chain 'B' and resid 181 through 183 Processing sheet with id= U, first strand: chain 'B' and resid 271 through 273 removed outlier: 6.315A pdb=" N ASN B 357 " --> pdb=" O GLU B 466 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N PHE B 468 " --> pdb=" O ASN B 357 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N SER B 360 " --> pdb=" O PHE B 468 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N GLN B 362 " --> pdb=" O PRO B 470 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 414 through 417 removed outlier: 6.919A pdb=" N LEU B 260 " --> pdb=" O THR B 450 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'B' and resid 374 through 377 removed outlier: 3.576A pdb=" N PHE B 383 " --> pdb=" O PHE B 376 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 302 through 312 removed outlier: 6.390A pdb=" N GLN B 315 " --> pdb=" O ILE B 309 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 5 through 7 removed outlier: 3.777A pdb=" N SER C 7 " --> pdb=" O SER C 22 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'C' and resid 85 through 89 removed outlier: 5.917A pdb=" N GLN C 37 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N LEU C 46 " --> pdb=" O GLN C 37 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'D' and resid 3 through 6 Processing sheet with id= AB, first strand: chain 'D' and resid 107 through 109 removed outlier: 6.177A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ALA D 40 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU D 45 " --> pdb=" O ALA D 40 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 494 through 499 Processing sheet with id= AD, first strand: chain 'E' and resid 45 through 47 Processing sheet with id= AE, first strand: chain 'E' and resid 53 through 55 Processing sheet with id= AF, first strand: chain 'E' and resid 91 through 94 removed outlier: 3.832A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'E' and resid 130 through 132 Processing sheet with id= AH, first strand: chain 'E' and resid 181 through 183 Processing sheet with id= AI, first strand: chain 'E' and resid 271 through 273 removed outlier: 6.315A pdb=" N ASN E 357 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N PHE E 468 " --> pdb=" O ASN E 357 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N SER E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N GLN E 362 " --> pdb=" O PRO E 470 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'E' and resid 414 through 417 removed outlier: 6.919A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'E' and resid 374 through 377 removed outlier: 3.576A pdb=" N PHE E 383 " --> pdb=" O PHE E 376 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'E' and resid 302 through 312 removed outlier: 6.390A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'F' and resid 5 through 7 removed outlier: 3.777A pdb=" N SER F 7 " --> pdb=" O SER F 22 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'F' and resid 85 through 89 removed outlier: 5.916A pdb=" N GLN F 37 " --> pdb=" O LEU F 46 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N LEU F 46 " --> pdb=" O GLN F 37 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'G' and resid 3 through 6 Processing sheet with id= AP, first strand: chain 'G' and resid 107 through 109 removed outlier: 6.178A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ALA G 40 " --> pdb=" O LEU G 45 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU G 45 " --> pdb=" O ALA G 40 " (cutoff:3.500A) 642 hydrogen bonds defined for protein. 1692 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: 6.56 Time building geometry restraints manager: 11.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4680 1.33 - 1.45: 4605 1.45 - 1.57: 11013 1.57 - 1.70: 60 1.70 - 1.82: 168 Bond restraints: 20526 Sorted by residual: bond pdb=" C5 BMA c 3 " pdb=" C6 BMA c 3 " ideal model delta sigma weight residual 1.526 1.610 -0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" C5 BMA O 3 " pdb=" C6 BMA O 3 " ideal model delta sigma weight residual 1.526 1.610 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C5 BMA q 3 " pdb=" C6 BMA q 3 " ideal model delta sigma weight residual 1.526 1.609 -0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" C5 BMA M 3 " pdb=" C6 BMA M 3 " ideal model delta sigma weight residual 1.526 1.607 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" C5 BMA o 3 " pdb=" C6 BMA o 3 " ideal model delta sigma weight residual 1.526 1.607 -0.081 2.00e-02 2.50e+03 1.62e+01 ... (remaining 20521 not shown) Histogram of bond angle deviations from ideal: 100.35 - 107.08: 819 107.08 - 113.81: 12219 113.81 - 120.54: 6667 120.54 - 127.27: 7973 127.27 - 134.00: 189 Bond angle restraints: 27867 Sorted by residual: angle pdb=" C ALA B 436 " pdb=" N PRO B 437 " pdb=" CA PRO B 437 " ideal model delta sigma weight residual 119.66 126.41 -6.75 7.20e-01 1.93e+00 8.78e+01 angle pdb=" C ALA E 436 " pdb=" N PRO E 437 " pdb=" CA PRO E 437 " ideal model delta sigma weight residual 119.66 126.40 -6.74 7.20e-01 1.93e+00 8.77e+01 angle pdb=" C ALA A 436 " pdb=" N PRO A 437 " pdb=" CA PRO A 437 " ideal model delta sigma weight residual 119.66 126.39 -6.73 7.20e-01 1.93e+00 8.74e+01 angle pdb=" C PHE E 353 " pdb=" N PRO E 354 " pdb=" CA PRO E 354 " ideal model delta sigma weight residual 119.56 128.13 -8.57 1.01e+00 9.80e-01 7.20e+01 angle pdb=" C PHE A 353 " pdb=" N PRO A 354 " pdb=" CA PRO A 354 " ideal model delta sigma weight residual 119.56 128.12 -8.56 1.01e+00 9.80e-01 7.18e+01 ... (remaining 27862 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.74: 13389 21.74 - 43.48: 531 43.48 - 65.23: 159 65.23 - 86.97: 144 86.97 - 108.71: 96 Dihedral angle restraints: 14319 sinusoidal: 7656 harmonic: 6663 Sorted by residual: dihedral pdb=" CA PHE E 353 " pdb=" C PHE E 353 " pdb=" N PRO E 354 " pdb=" CA PRO E 354 " ideal model delta harmonic sigma weight residual -180.00 -154.39 -25.61 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA PHE B 353 " pdb=" C PHE B 353 " pdb=" N PRO B 354 " pdb=" CA PRO B 354 " ideal model delta harmonic sigma weight residual -180.00 -154.43 -25.57 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA PHE A 353 " pdb=" C PHE A 353 " pdb=" N PRO A 354 " pdb=" CA PRO A 354 " ideal model delta harmonic sigma weight residual -180.00 -154.48 -25.52 0 5.00e+00 4.00e-02 2.61e+01 ... (remaining 14316 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 3300 0.130 - 0.261: 238 0.261 - 0.391: 20 0.391 - 0.521: 0 0.521 - 0.651: 24 Chirality restraints: 3582 Sorted by residual: chirality pdb=" C1 BMA c 3 " pdb=" O4 NAG c 2 " pdb=" C2 BMA c 3 " pdb=" O5 BMA c 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.68 0.28 2.00e-02 2.50e+03 1.90e+02 chirality pdb=" C1 BMA q 3 " pdb=" O4 NAG q 2 " pdb=" C2 BMA q 3 " pdb=" O5 BMA q 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.67 0.27 2.00e-02 2.50e+03 1.89e+02 chirality pdb=" C1 BMA O 3 " pdb=" O4 NAG O 2 " pdb=" C2 BMA O 3 " pdb=" O5 BMA O 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.67 0.27 2.00e-02 2.50e+03 1.89e+02 ... (remaining 3579 not shown) Planarity restraints: 3366 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 301 " -0.026 2.00e-02 2.50e+03 2.78e-02 9.67e+00 pdb=" CG ASN E 301 " 0.008 2.00e-02 2.50e+03 pdb=" OD1 ASN E 301 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN E 301 " 0.044 2.00e-02 2.50e+03 pdb=" C1 NAG s 1 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 301 " -0.026 2.00e-02 2.50e+03 2.78e-02 9.66e+00 pdb=" CG ASN A 301 " 0.008 2.00e-02 2.50e+03 pdb=" OD1 ASN A 301 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN A 301 " 0.044 2.00e-02 2.50e+03 pdb=" C1 NAG Q 1 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 301 " -0.026 2.00e-02 2.50e+03 2.78e-02 9.65e+00 pdb=" CG ASN B 301 " 0.008 2.00e-02 2.50e+03 pdb=" OD1 ASN B 301 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN B 301 " 0.044 2.00e-02 2.50e+03 pdb=" C1 NAG e 1 " -0.034 2.00e-02 2.50e+03 ... (remaining 3363 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 6354 2.82 - 3.34: 17816 3.34 - 3.86: 33385 3.86 - 4.38: 38507 4.38 - 4.90: 62463 Nonbonded interactions: 158525 Sorted by model distance: nonbonded pdb=" OD1 ASP B 107 " pdb=" NZ LYS B 574 " model vdw 2.302 2.520 nonbonded pdb=" OD1 ASP E 107 " pdb=" NZ LYS E 574 " model vdw 2.303 2.520 nonbonded pdb=" OD1 ASP A 107 " pdb=" NZ LYS A 574 " model vdw 2.303 2.520 nonbonded pdb=" OG1 THR A 37 " pdb=" OG1 THR A 499 " model vdw 2.328 2.440 nonbonded pdb=" OG1 THR E 37 " pdb=" OG1 THR E 499 " model vdw 2.329 2.440 ... (remaining 158520 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' selection = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'L' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'g' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'u' selection = chain 'w' selection = chain 'x' selection = chain 'y' } ncs_group { reference = chain 'K' selection = chain 'T' selection = chain 'Z' selection = chain 'h' selection = chain 'n' selection = chain 'v' } ncs_group { reference = (chain 'M' and (resid 1 or resid 4 through 6)) selection = (chain 'O' and (resid 2 or resid 5 through 7)) selection = (chain 'a' and (resid 1 or resid 4 through 6)) selection = (chain 'c' and (resid 2 or resid 5 through 7)) selection = (chain 'o' and (resid 1 or resid 4 through 6)) selection = (chain 'q' and (resid 2 or resid 5 through 7)) } ncs_group { reference = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'b' selection = chain 'd' selection = chain 'e' selection = chain 'p' selection = chain 'r' selection = chain 's' } ncs_group { reference = chain 'R' selection = chain 'f' selection = chain 't' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.150 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: 0.010 Extract box with map and model: 7.950 Check model and map are aligned: 0.290 Set scattering table: 0.170 Process input model: 58.160 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.410 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 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 : 0.015 0.084 20526 Z= 0.947 Angle : 1.366 8.568 27867 Z= 0.801 Chirality : 0.089 0.651 3582 Planarity : 0.003 0.013 3312 Dihedral : 18.198 108.711 9894 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 1.19 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.32 % Favored : 96.54 % Rotamer: Outliers : 0.30 % Allowed : 1.34 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.23 (0.17), residues: 2256 helix: -0.17 (0.25), residues: 411 sheet: 0.08 (0.19), residues: 717 loop : -0.16 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 47 HIS 0.002 0.000 HIS A 374 PHE 0.014 0.002 PHE E 383 TYR 0.016 0.002 TYR B 484 ARG 0.002 0.000 ARG E 298 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 301 time to evaluate : 2.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 ASN cc_start: 0.8159 (t0) cc_final: 0.7833 (t0) REVERT: A 464 ASN cc_start: 0.7894 (m-40) cc_final: 0.7377 (t0) REVERT: H 48 MET cc_start: 0.7465 (mmm) cc_final: 0.7076 (mmt) REVERT: B 125 LEU cc_start: 0.9103 (mm) cc_final: 0.8878 (mt) REVERT: B 377 ASN cc_start: 0.8297 (t0) cc_final: 0.7691 (t0) REVERT: B 464 ASN cc_start: 0.7696 (m-40) cc_final: 0.7390 (t0) REVERT: C 32 TYR cc_start: 0.7653 (m-80) cc_final: 0.6765 (m-10) REVERT: D 51 ILE cc_start: 0.9263 (tt) cc_final: 0.9059 (tt) REVERT: D 75 ILE cc_start: 0.8894 (pt) cc_final: 0.8674 (mt) REVERT: D 85 ASP cc_start: 0.8313 (p0) cc_final: 0.8099 (p0) REVERT: E 69 TRP cc_start: 0.8257 (m-90) cc_final: 0.7338 (m-10) REVERT: E 377 ASN cc_start: 0.8376 (t0) cc_final: 0.7932 (t0) REVERT: E 464 ASN cc_start: 0.7592 (m-40) cc_final: 0.7088 (t0) REVERT: G 75 ILE cc_start: 0.8906 (pt) cc_final: 0.8662 (mt) REVERT: G 85 ASP cc_start: 0.8538 (p0) cc_final: 0.8266 (p0) outliers start: 6 outliers final: 0 residues processed: 307 average time/residue: 0.2956 time to fit residues: 142.0727 Evaluate side-chains 116 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 2.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 0.5980 chunk 172 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 207 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 HIS A 355 HIS L 37 GLN B 216 HIS B 229 ASN B 355 HIS B 543 ASN C 37 GLN E 216 HIS E 355 HIS F 37 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 20526 Z= 0.249 Angle : 0.717 10.626 27867 Z= 0.340 Chirality : 0.050 0.671 3582 Planarity : 0.004 0.033 3312 Dihedral : 14.037 89.697 5640 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.08 % Favored : 97.78 % Rotamer: Outliers : 1.44 % Allowed : 6.32 % Favored : 92.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.75 (0.18), residues: 2256 helix: 1.90 (0.27), residues: 381 sheet: 0.25 (0.19), residues: 717 loop : 0.32 (0.19), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 47 HIS 0.004 0.001 HIS H 35 PHE 0.017 0.002 PHE B 382 TYR 0.020 0.002 TYR C 91 ARG 0.005 0.001 ARG A 585 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 144 time to evaluate : 2.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 ASN cc_start: 0.8279 (t0) cc_final: 0.8065 (t0) REVERT: A 464 ASN cc_start: 0.7874 (m-40) cc_final: 0.7363 (t0) REVERT: L 29 VAL cc_start: 0.7325 (t) cc_final: 0.6647 (t) REVERT: B 69 TRP cc_start: 0.8268 (m-10) cc_final: 0.7367 (m-10) REVERT: B 86 LEU cc_start: 0.8614 (mp) cc_final: 0.8368 (mp) REVERT: B 377 ASN cc_start: 0.8350 (t0) cc_final: 0.8041 (t0) REVERT: B 464 ASN cc_start: 0.7320 (m-40) cc_final: 0.7102 (t0) REVERT: D 85 ASP cc_start: 0.8605 (p0) cc_final: 0.8344 (p0) REVERT: E 377 ASN cc_start: 0.8375 (t0) cc_final: 0.8097 (t0) REVERT: E 464 ASN cc_start: 0.7160 (m-40) cc_final: 0.6819 (t0) REVERT: G 85 ASP cc_start: 0.8935 (p0) cc_final: 0.8623 (p0) outliers start: 29 outliers final: 17 residues processed: 166 average time/residue: 0.2610 time to fit residues: 72.0116 Evaluate side-chains 131 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 114 time to evaluate : 2.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain D residue 69 MET Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain G residue 73 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 172 optimal weight: 7.9990 chunk 140 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 207 optimal weight: 10.0000 chunk 224 optimal weight: 0.6980 chunk 184 optimal weight: 3.9990 chunk 205 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 166 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN B 422 GLN E 229 ASN E 374 HIS E 422 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 20526 Z= 0.228 Angle : 0.621 7.773 27867 Z= 0.296 Chirality : 0.046 0.356 3582 Planarity : 0.004 0.039 3312 Dihedral : 11.354 81.504 5640 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.84 % Favored : 97.03 % Rotamer: Outliers : 1.14 % Allowed : 7.21 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.98 (0.18), residues: 2256 helix: 2.33 (0.28), residues: 381 sheet: 0.42 (0.19), residues: 696 loop : 0.35 (0.19), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 69 HIS 0.003 0.001 HIS A 249 PHE 0.016 0.001 PHE E 53 TYR 0.019 0.002 TYR F 91 ARG 0.006 0.000 ARG C 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 120 time to evaluate : 2.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 ASN cc_start: 0.8391 (t0) cc_final: 0.8191 (t0) REVERT: B 377 ASN cc_start: 0.8332 (t0) cc_final: 0.7943 (t0) REVERT: B 464 ASN cc_start: 0.7569 (m-40) cc_final: 0.7311 (t0) REVERT: D 85 ASP cc_start: 0.8721 (p0) cc_final: 0.8420 (p0) REVERT: E 377 ASN cc_start: 0.8428 (t0) cc_final: 0.8163 (t0) REVERT: E 475 MET cc_start: 0.8062 (mmt) cc_final: 0.7804 (mmt) REVERT: F 20 THR cc_start: 0.8176 (p) cc_final: 0.7955 (t) REVERT: G 85 ASP cc_start: 0.8783 (p0) cc_final: 0.8432 (p0) outliers start: 23 outliers final: 14 residues processed: 137 average time/residue: 0.2838 time to fit residues: 64.3575 Evaluate side-chains 119 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 105 time to evaluate : 2.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain H residue 12 LYS Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain D residue 69 MET Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 75 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 5.9990 chunk 155 optimal weight: 0.1980 chunk 107 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 139 optimal weight: 6.9990 chunk 208 optimal weight: 7.9990 chunk 220 optimal weight: 4.9990 chunk 108 optimal weight: 0.6980 chunk 197 optimal weight: 0.0980 chunk 59 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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: 0.8064 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20526 Z= 0.181 Angle : 0.584 8.812 27867 Z= 0.272 Chirality : 0.045 0.317 3582 Planarity : 0.004 0.035 3312 Dihedral : 9.079 61.474 5640 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.57 % Favored : 97.30 % Rotamer: Outliers : 1.34 % Allowed : 7.51 % Favored : 91.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.84 (0.18), residues: 2256 helix: 2.46 (0.27), residues: 381 sheet: 0.39 (0.19), residues: 735 loop : 0.11 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 50 HIS 0.002 0.001 HIS B 72 PHE 0.016 0.001 PHE B 522 TYR 0.014 0.001 TYR F 91 ARG 0.002 0.000 ARG E 273 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 113 time to evaluate : 2.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 377 ASN cc_start: 0.8251 (t0) cc_final: 0.7951 (t0) REVERT: B 464 ASN cc_start: 0.7592 (m-40) cc_final: 0.7329 (t0) REVERT: D 85 ASP cc_start: 0.8802 (p0) cc_final: 0.8583 (p0) REVERT: E 69 TRP cc_start: 0.8329 (m-90) cc_final: 0.7489 (m-10) REVERT: E 475 MET cc_start: 0.8163 (mmt) cc_final: 0.7956 (mmt) REVERT: G 85 ASP cc_start: 0.8933 (p0) cc_final: 0.8642 (p0) outliers start: 27 outliers final: 21 residues processed: 133 average time/residue: 0.2563 time to fit residues: 58.5037 Evaluate side-chains 125 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 104 time to evaluate : 2.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 69 MET Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 75 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 7.9990 chunk 125 optimal weight: 1.9990 chunk 3 optimal weight: 0.2980 chunk 164 optimal weight: 0.3980 chunk 90 optimal weight: 4.9990 chunk 188 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 chunk 197 optimal weight: 4.9990 chunk 55 optimal weight: 8.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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: 0.8112 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20526 Z= 0.226 Angle : 0.603 7.649 27867 Z= 0.283 Chirality : 0.045 0.297 3582 Planarity : 0.004 0.041 3312 Dihedral : 7.953 56.485 5640 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.59 % Favored : 96.28 % Rotamer: Outliers : 1.74 % Allowed : 8.46 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.79 (0.18), residues: 2256 helix: 2.53 (0.27), residues: 381 sheet: 0.31 (0.19), residues: 711 loop : 0.07 (0.19), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 571 HIS 0.003 0.001 HIS B 72 PHE 0.015 0.001 PHE B 383 TYR 0.016 0.002 TYR A 217 ARG 0.004 0.000 ARG D 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 107 time to evaluate : 2.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 TRP cc_start: 0.8223 (m-10) cc_final: 0.7391 (m-10) REVERT: B 377 ASN cc_start: 0.8338 (t0) cc_final: 0.8023 (t0) REVERT: E 69 TRP cc_start: 0.8330 (m-90) cc_final: 0.7492 (m-10) REVERT: G 85 ASP cc_start: 0.8896 (p0) cc_final: 0.8667 (p0) outliers start: 35 outliers final: 27 residues processed: 133 average time/residue: 0.2600 time to fit residues: 58.9515 Evaluate side-chains 126 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 99 time to evaluate : 2.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain D residue 69 MET Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 75 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 5.9990 chunk 198 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 chunk 129 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 220 optimal weight: 3.9990 chunk 183 optimal weight: 7.9990 chunk 102 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20526 Z= 0.265 Angle : 0.626 8.106 27867 Z= 0.295 Chirality : 0.045 0.284 3582 Planarity : 0.004 0.036 3312 Dihedral : 7.865 58.711 5640 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.50 % Favored : 96.37 % Rotamer: Outliers : 1.94 % Allowed : 8.76 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.59 (0.18), residues: 2256 helix: 2.43 (0.27), residues: 381 sheet: 0.11 (0.20), residues: 672 loop : -0.02 (0.18), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 571 HIS 0.004 0.001 HIS E 72 PHE 0.016 0.001 PHE B 383 TYR 0.016 0.002 TYR F 36 ARG 0.003 0.000 ARG E 476 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 91 time to evaluate : 2.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 377 ASN cc_start: 0.8377 (t0) cc_final: 0.8157 (t0) REVERT: E 69 TRP cc_start: 0.8342 (m-90) cc_final: 0.7471 (m-10) REVERT: E 475 MET cc_start: 0.8215 (mmt) cc_final: 0.7827 (mmt) outliers start: 39 outliers final: 31 residues processed: 123 average time/residue: 0.2606 time to fit residues: 54.1400 Evaluate side-chains 118 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 87 time to evaluate : 2.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain E residue 409 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 75 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 125 optimal weight: 6.9990 chunk 161 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 185 optimal weight: 9.9990 chunk 123 optimal weight: 0.6980 chunk 219 optimal weight: 5.9990 chunk 137 optimal weight: 10.0000 chunk 133 optimal weight: 0.7980 chunk 101 optimal weight: 5.9990 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 ASN E 460 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 20526 Z= 0.375 Angle : 0.719 7.137 27867 Z= 0.340 Chirality : 0.048 0.287 3582 Planarity : 0.005 0.049 3312 Dihedral : 8.667 59.014 5640 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.70 % Favored : 95.17 % Rotamer: Outliers : 2.39 % Allowed : 8.91 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.28 (0.18), residues: 2256 helix: 1.94 (0.26), residues: 399 sheet: -0.17 (0.20), residues: 630 loop : -0.12 (0.18), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 427 HIS 0.005 0.001 HIS E 72 PHE 0.018 0.002 PHE B 383 TYR 0.026 0.002 TYR B 217 ARG 0.007 0.001 ARG C 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 88 time to evaluate : 2.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 THR cc_start: 0.7560 (m) cc_final: 0.7357 (p) REVERT: A 535 MET cc_start: 0.8883 (mmm) cc_final: 0.8676 (mmm) REVERT: B 209 THR cc_start: 0.7227 (m) cc_final: 0.6999 (p) REVERT: E 69 TRP cc_start: 0.8374 (m-90) cc_final: 0.7408 (m-10) REVERT: E 475 MET cc_start: 0.8159 (mmt) cc_final: 0.7889 (mmt) outliers start: 48 outliers final: 35 residues processed: 127 average time/residue: 0.2584 time to fit residues: 56.2324 Evaluate side-chains 117 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 82 time to evaluate : 2.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain E residue 409 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain E residue 660 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 75 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 131 optimal weight: 9.9990 chunk 66 optimal weight: 20.0000 chunk 43 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 chunk 139 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 chunk 20 optimal weight: 5.9990 chunk 172 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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: 0.8185 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20526 Z= 0.269 Angle : 0.646 8.929 27867 Z= 0.301 Chirality : 0.046 0.262 3582 Planarity : 0.004 0.042 3312 Dihedral : 8.348 59.948 5640 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.68 % Favored : 96.19 % Rotamer: Outliers : 1.94 % Allowed : 9.50 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.24 (0.18), residues: 2256 helix: 2.24 (0.26), residues: 381 sheet: -0.28 (0.19), residues: 732 loop : -0.16 (0.19), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 628 HIS 0.004 0.001 HIS A 72 PHE 0.015 0.001 PHE B 383 TYR 0.018 0.002 TYR B 217 ARG 0.003 0.000 ARG G 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 90 time to evaluate : 2.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 THR cc_start: 0.7528 (m) cc_final: 0.7325 (p) REVERT: L 47 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8157 (mm) REVERT: B 209 THR cc_start: 0.7196 (m) cc_final: 0.6987 (p) REVERT: E 69 TRP cc_start: 0.8395 (m-90) cc_final: 0.7556 (m-10) REVERT: E 104 MET cc_start: 0.8242 (tpp) cc_final: 0.7807 (ttm) REVERT: E 475 MET cc_start: 0.8035 (mmt) cc_final: 0.7715 (mmt) outliers start: 39 outliers final: 34 residues processed: 120 average time/residue: 0.2641 time to fit residues: 53.9743 Evaluate side-chains 118 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 83 time to evaluate : 2.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 409 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 75 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 2.9990 chunk 210 optimal weight: 4.9990 chunk 192 optimal weight: 0.9980 chunk 204 optimal weight: 4.9990 chunk 123 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 160 optimal weight: 0.9990 chunk 62 optimal weight: 9.9990 chunk 185 optimal weight: 4.9990 chunk 193 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 20526 Z= 0.201 Angle : 0.604 9.358 27867 Z= 0.279 Chirality : 0.045 0.248 3582 Planarity : 0.004 0.042 3312 Dihedral : 7.880 59.788 5640 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.55 % Favored : 96.32 % Rotamer: Outliers : 1.74 % Allowed : 9.85 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.39 (0.18), residues: 2256 helix: 2.27 (0.26), residues: 399 sheet: -0.08 (0.19), residues: 678 loop : -0.16 (0.19), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 36 HIS 0.003 0.001 HIS E 72 PHE 0.014 0.001 PHE A 383 TYR 0.025 0.001 TYR E 638 ARG 0.003 0.000 ARG D 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 94 time to evaluate : 2.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 47 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8139 (mm) REVERT: B 530 MET cc_start: 0.8103 (tpp) cc_final: 0.7816 (tpp) REVERT: E 104 MET cc_start: 0.8147 (tpp) cc_final: 0.7785 (ttm) REVERT: E 475 MET cc_start: 0.7978 (mmt) cc_final: 0.7716 (mmt) outliers start: 35 outliers final: 31 residues processed: 122 average time/residue: 0.2647 time to fit residues: 55.0989 Evaluate side-chains 115 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 83 time to evaluate : 2.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 409 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 73 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 150 optimal weight: 4.9990 chunk 227 optimal weight: 3.9990 chunk 209 optimal weight: 0.4980 chunk 180 optimal weight: 0.0970 chunk 18 optimal weight: 1.9990 chunk 139 optimal weight: 8.9990 chunk 110 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20526 Z= 0.219 Angle : 0.613 9.139 27867 Z= 0.282 Chirality : 0.045 0.268 3582 Planarity : 0.004 0.042 3312 Dihedral : 7.777 59.926 5640 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.55 % Favored : 96.32 % Rotamer: Outliers : 1.64 % Allowed : 10.15 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.40 (0.18), residues: 2256 helix: 2.49 (0.27), residues: 381 sheet: -0.07 (0.19), residues: 678 loop : -0.20 (0.19), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 69 HIS 0.004 0.001 HIS A 72 PHE 0.014 0.001 PHE A 383 TYR 0.016 0.001 TYR B 217 ARG 0.003 0.000 ARG B 480 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 91 time to evaluate : 2.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 TRP cc_start: 0.8124 (m-10) cc_final: 0.7827 (m-10) REVERT: B 209 THR cc_start: 0.7403 (m) cc_final: 0.7139 (p) REVERT: E 69 TRP cc_start: 0.8179 (m-90) cc_final: 0.7484 (m-10) REVERT: E 104 MET cc_start: 0.8134 (tpp) cc_final: 0.7789 (ttm) REVERT: E 475 MET cc_start: 0.7987 (mmt) cc_final: 0.7742 (mmt) outliers start: 33 outliers final: 31 residues processed: 118 average time/residue: 0.2650 time to fit residues: 55.0195 Evaluate side-chains 117 residues out of total 2010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 86 time to evaluate : 2.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 409 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 73 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 0.4980 chunk 55 optimal weight: 8.9990 chunk 166 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 chunk 181 optimal weight: 0.8980 chunk 75 optimal weight: 0.5980 chunk 186 optimal weight: 1.9990 chunk 22 optimal weight: 0.0670 chunk 33 optimal weight: 7.9990 chunk 159 optimal weight: 6.9990 overall best weight: 0.8120 ------------------------------------------------------------------------------- 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 = 0.3405 r_free = 0.3405 target = 0.066952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.056172 restraints weight = 89191.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.057572 restraints weight = 50674.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.058507 restraints weight = 35539.488| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 20526 Z= 0.160 Angle : 0.581 9.278 27867 Z= 0.266 Chirality : 0.044 0.230 3582 Planarity : 0.004 0.041 3312 Dihedral : 7.315 58.908 5640 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.15 % Favored : 96.76 % Rotamer: Outliers : 1.64 % Allowed : 10.55 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.49 (0.18), residues: 2256 helix: 2.30 (0.27), residues: 405 sheet: -0.02 (0.19), residues: 678 loop : -0.09 (0.19), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 69 HIS 0.002 0.001 HIS E 72 PHE 0.013 0.001 PHE A 383 TYR 0.013 0.001 TYR L 36 ARG 0.005 0.000 ARG A 542 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2924.61 seconds wall clock time: 55 minutes 12.97 seconds (3312.97 seconds total)