Starting phenix.real_space_refine on Tue Feb 20 00:45:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8czz_27103/02_2024/8czz_27103_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8czz_27103/02_2024/8czz_27103.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8czz_27103/02_2024/8czz_27103_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8czz_27103/02_2024/8czz_27103_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8czz_27103/02_2024/8czz_27103_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8czz_27103/02_2024/8czz_27103.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8czz_27103/02_2024/8czz_27103.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8czz_27103/02_2024/8czz_27103_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8czz_27103/02_2024/8czz_27103_updated.pdb" } resolution = 3.14 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= 0.033 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 138 5.16 5 C 16491 2.51 5 N 4377 2.21 5 O 5282 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 49": "OD1" <-> "OD2" Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 192": "NH1" <-> "NH2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 409": "NH1" <-> "NH2" Residue "A ASP 477": "OD1" <-> "OD2" Residue "A ARG 504": "NH1" <-> "NH2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 49": "OD1" <-> "OD2" Residue "E TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 230": "OD1" <-> "OD2" Residue "E PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 477": "OD1" <-> "OD2" Residue "F PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 659": "OD1" <-> "OD2" Residue "G TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 49": "OD1" <-> "OD2" Residue "I GLU 164": "OE1" <-> "OE2" Residue "I ASP 211": "OD1" <-> "OD2" Residue "I TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 275": "OE1" <-> "OE2" Residue "I TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 381": "OE1" <-> "OE2" Residue "I PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 410": "OD1" <-> "OD2" Residue "J GLU 584": "OE1" <-> "OE2" Residue "J PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 634": "OE1" <-> "OE2" Residue "L PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26288 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 3479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3479 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 23, 'TRANS': 416} Chain breaks: 4 Chain: "B" Number of atoms: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 999 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "C" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1003 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "D" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 814 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "E" Number of atoms: 3462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3462 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 23, 'TRANS': 414} Chain breaks: 4 Chain: "F" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 956 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain breaks: 1 Chain: "G" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1003 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "H" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 823 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 102} Chain: "I" Number of atoms: 3455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3455 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 23, 'TRANS': 413} Chain breaks: 4 Chain: "J" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1034 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 2, 'TRANS': 125} Chain breaks: 1 Chain: "K" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1003 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "L" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 823 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 102} Chain: "M" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1030 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "N" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "O" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1030 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "P" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "Q" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1030 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "R" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "S" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "T" 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: "U" 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: "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: 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: "Z" 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: "a" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "b" 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: "c" 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: "d" 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: 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: "f" 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: "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: 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: "i" 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: "j" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "k" 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: "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: 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: "o" 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: "p" 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: "q" 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: "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: 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: "A" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 147 Unusual residues: {'83J': 1, 'NAG': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" 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: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 147 Unusual residues: {'83J': 1, 'NAG': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 133 Unusual residues: {'83J': 1, 'NAG': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "J" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 14.25, per 1000 atoms: 0.54 Number of scatterers: 26288 At special positions: 0 Unit cell: (164.521, 165.41, 151.181, 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 138 16.00 O 5282 8.00 N 4377 7.00 C 16491 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=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.05 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.63 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.06 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.02 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.00 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.05 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.04 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.06 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=2.05 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=1.98 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.52 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.05 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.04 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.42 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=1.95 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.06 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.02 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.02 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.02 Simple disulfide: pdb=" SG CYS I 501 " - pdb=" SG CYS J 605 " distance=2.01 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 92 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " 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 S 4 " - " MAN S 5 " " MAN S 5 " - " MAN S 6 " " MAN S 8 " - " MAN S 9 " " MAN T 4 " - " MAN T 5 " " MAN a 4 " - " MAN a 5 " " MAN a 5 " - " MAN a 6 " " MAN a 8 " - " MAN a 9 " " MAN b 4 " - " MAN b 5 " " MAN j 4 " - " MAN j 5 " " MAN j 5 " - " MAN j 6 " " MAN j 8 " - " MAN j 9 " " MAN k 4 " - " MAN k 5 " ALPHA1-3 " BMA S 3 " - " MAN S 4 " " BMA T 3 " - " MAN T 4 " " BMA a 3 " - " MAN a 4 " " MAN a 7 " - " MAN a 10 " " BMA b 3 " - " MAN b 4 " " BMA j 3 " - " MAN j 4 " " BMA k 3 " - " MAN k 4 " " BMA s 3 " - " MAN s 4 " ALPHA1-6 " BMA S 3 " - " MAN S 7 " " MAN S 7 " - " MAN S 8 " " BMA T 3 " - " MAN T 6 " " BMA a 3 " - " MAN a 7 " " MAN a 7 " - " MAN a 8 " " BMA b 3 " - " MAN b 6 " " BMA j 3 " - " MAN j 7 " " MAN j 7 " - " MAN j 8 " " BMA k 3 " - " MAN k 6 " BETA1-4 " 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 U 2 " - " NAG U 3 " " NAG U 3 " - " NAG U 4 " " 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 Y 2 " - " BMA Y 3 " " 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 d 1 " - " NAG d 2 " " NAG d 2 " - " NAG d 3 " " NAG d 3 " - " NAG d 4 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " 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 i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " NAG n 3 " " NAG n 3 " - " NAG n 4 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " 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-ASN " NAG A 602 " - " ASN A 160 " " NAG A 603 " - " ASN A 241 " " NAG A 604 " - " ASN A 295 " " NAG A 605 " - " ASN A 301 " " NAG A 606 " - " ASN A 448 " " NAG A 607 " - " ASN A 156 " " NAG A 608 " - " ASN A 289 " " NAG A 609 " - " ASN A 130 " " NAG B 701 " - " ASN B 616 " " NAG B 702 " - " ASN B 625 " " NAG C 301 " - " ASN C 82B" " NAG E 601 " - " ASN E 160 " " NAG E 602 " - " ASN E 241 " " NAG E 603 " - " ASN E 295 " " NAG E 604 " - " ASN E 301 " " NAG E 605 " - " ASN E 355 " " NAG E 606 " - " ASN E 448 " " NAG E 608 " - " ASN E 289 " " NAG E 609 " - " ASN E 130 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 616 " " NAG F 703 " - " ASN F 625 " " NAG G 301 " - " ASN G 82B" " NAG I 601 " - " ASN I 160 " " NAG I 602 " - " ASN I 241 " " NAG I 603 " - " ASN I 295 " " NAG I 604 " - " ASN I 301 " " NAG I 605 " - " ASN I 355 " " NAG I 606 " - " ASN I 448 " " NAG I 608 " - " ASN I 392 " " NAG J 701 " - " ASN J 611 " " NAG J 702 " - " ASN J 616 " " NAG J 703 " - " ASN J 625 " " NAG K 301 " - " ASN K 82B" " NAG S 1 " - " ASN A 234 " " NAG T 1 " - " ASN A 276 " " NAG U 1 " - " ASN A 332 " " NAG V 1 " - " ASN A 386 " " NAG W 1 " - " ASN A 392 " " NAG X 1 " - " ASN A 197 " " NAG Y 1 " - " ASN A 262 " " NAG Z 1 " - " ASN B 637 " " NAG a 1 " - " ASN E 234 " " NAG b 1 " - " ASN E 276 " " NAG c 1 " - " ASN E 156 " " NAG d 1 " - " ASN E 332 " " NAG e 1 " - " ASN E 386 " " NAG f 1 " - " ASN E 392 " " NAG g 1 " - " ASN E 197 " " NAG h 1 " - " ASN E 262 " " NAG i 1 " - " ASN F 637 " " NAG j 1 " - " ASN I 234 " " NAG k 1 " - " ASN I 276 " " NAG l 1 " - " ASN I 156 " " NAG m 1 " - " ASN I 289 " " NAG n 1 " - " ASN I 332 " " NAG o 1 " - " ASN I 386 " " NAG p 1 " - " ASN I 197 " " NAG q 1 " - " ASN I 130 " " NAG r 1 " - " ASN I 262 " " NAG s 1 " - " ASN J 637 " Time building additional restraints: 11.58 Conformation dependent library (CDL) restraints added in 4.3 seconds 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5712 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 49 helices and 61 sheets defined 13.3% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.84 Creating SS restraints... Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 122 through 125 Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 335 through 352 removed outlier: 3.549A 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: 4.213A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 542 removed outlier: 3.928A pdb=" N ILE B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N THR B 538 " --> pdb=" O SER B 534 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL B 539 " --> pdb=" O ILE B 535 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 596 removed outlier: 3.619A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N TRP B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 623 Processing helix chain 'B' and resid 628 through 634 Processing helix chain 'B' and resid 639 through 661 removed outlier: 3.596A pdb=" N ASP B 659 " --> pdb=" O LYS B 655 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU B 660 " --> pdb=" O ASN B 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 86 No H-bonds generated for 'chain 'C' and resid 84 through 86' Processing helix chain 'C' and resid 100 through 100B No H-bonds generated for 'chain 'C' and resid 100 through 100B' Processing helix chain 'D' and resid 80 through 82 No H-bonds generated for 'chain 'D' and resid 80 through 82' Processing helix chain 'E' and resid 95 through 97 No H-bonds generated for 'chain 'E' and resid 95 through 97' Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 123 through 125 No H-bonds generated for 'chain 'E' and resid 123 through 125' 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 337 through 352 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 427 through 429 No H-bonds generated for 'chain 'E' and resid 427 through 429' Processing helix chain 'E' and resid 477 through 480 No H-bonds generated for 'chain 'E' and resid 477 through 480' Processing helix chain 'F' and resid 530 through 535 Processing helix chain 'F' and resid 570 through 595 removed outlier: 3.675A pdb=" N LYS F 574 " --> pdb=" O VAL F 570 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 625 removed outlier: 3.526A pdb=" N ASN F 625 " --> pdb=" O GLU F 621 " (cutoff:3.500A) Processing helix chain 'F' and resid 628 through 634 removed outlier: 3.512A pdb=" N ARG F 633 " --> pdb=" O ILE F 629 " (cutoff:3.500A) Processing helix chain 'F' and resid 640 through 661 removed outlier: 3.878A pdb=" N LYS F 658 " --> pdb=" O GLU F 654 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP F 659 " --> pdb=" O LYS F 655 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 86 No H-bonds generated for 'chain 'G' and resid 84 through 86' Processing helix chain 'I' and resid 71 through 73 No H-bonds generated for 'chain 'I' and resid 71 through 73' Processing helix chain 'I' and resid 95 through 97 No H-bonds generated for 'chain 'I' and resid 95 through 97' Processing helix chain 'I' and resid 99 through 117 Processing helix chain 'I' and resid 123 through 125 No H-bonds generated for 'chain 'I' and resid 123 through 125' Processing helix chain 'I' and resid 178 through 180 No H-bonds generated for 'chain 'I' and resid 178 through 180' Processing helix chain 'I' and resid 194 through 197 removed outlier: 4.460A pdb=" N ASN I 197 " --> pdb=" O ILE I 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 194 through 197' Processing helix chain 'I' and resid 335 through 352 removed outlier: 3.530A pdb=" N HIS I 352 " --> pdb=" O LYS I 348 " (cutoff:3.500A) Processing helix chain 'I' and resid 369 through 372 No H-bonds generated for 'chain 'I' and resid 369 through 372' Processing helix chain 'J' and resid 530 through 534 Processing helix chain 'J' and resid 537 through 541 Processing helix chain 'J' and resid 570 through 596 removed outlier: 4.004A pdb=" N LYS J 574 " --> pdb=" O VAL J 570 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN J 575 " --> pdb=" O TRP J 571 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU J 576 " --> pdb=" O GLY J 572 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL J 580 " --> pdb=" O LEU J 576 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU J 595 " --> pdb=" O LYS J 591 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N TRP J 596 " --> pdb=" O PHE J 592 " (cutoff:3.500A) Processing helix chain 'J' and resid 619 through 623 Processing helix chain 'J' and resid 628 through 634 Processing helix chain 'J' and resid 640 through 661 removed outlier: 3.651A pdb=" N LYS J 658 " --> pdb=" O GLU J 654 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP J 659 " --> pdb=" O LYS J 655 " (cutoff:3.500A) Processing helix chain 'K' and resid 100 through 100B No H-bonds generated for 'chain 'K' and resid 100 through 100B' Processing helix chain 'M' and resid 84 through 86 No H-bonds generated for 'chain 'M' and resid 84 through 86' Processing helix chain 'N' and resid 80 through 83 Processing helix chain 'O' and resid 84 through 86 No H-bonds generated for 'chain 'O' and resid 84 through 86' Processing helix chain 'P' and resid 81 through 83 No H-bonds generated for 'chain 'P' and resid 81 through 83' Processing helix chain 'Q' and resid 100E through 100G No H-bonds generated for 'chain 'Q' and resid 100E through 100G' Processing helix chain 'R' and resid 81 through 83 No H-bonds generated for 'chain 'R' and resid 81 through 83' Processing sheet with id= A, first strand: chain 'A' and resid 35 through 40 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 93 Processing sheet with id= E, first strand: chain 'A' and resid 156 through 162 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 201 through 203 removed outlier: 7.139A pdb=" N ALA A 433 " --> pdb=" O LYS A 202 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.745A pdb=" N THR A 357 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N PHE A 468 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N LYS A 362 " --> pdb=" O PRO A 470 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 414 through 417 removed outlier: 3.519A pdb=" N VAL A 292 " --> pdb=" O ILE A 449 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 374 through 377 removed outlier: 3.854A pdb=" N ARG A 419 " --> pdb=" O TYR A 384 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.460A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 3 through 5 Processing sheet with id= M, first strand: chain 'C' and resid 91 through 96 removed outlier: 3.507A pdb=" N THR C 95 " --> pdb=" O ALA C 34 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA C 34 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ARG C 38 " --> pdb=" O TYR C 47 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N TYR C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 88 through 90 removed outlier: 3.589A pdb=" N ILE C 109 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR C 107 " --> pdb=" O TYR C 90 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.510A pdb=" N ILE D 75 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE D 21 " --> pdb=" O LEU D 73 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.734A pdb=" N LYS D 103 " --> pdb=" O LEU D 11 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY D 84 " --> pdb=" O VAL D 104 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 35 through 39 Processing sheet with id= R, first strand: chain 'E' and resid 45 through 47 Processing sheet with id= S, first strand: chain 'E' and resid 53 through 55 Processing sheet with id= T, first strand: chain 'E' and resid 91 through 94 Processing sheet with id= U, first strand: chain 'E' and resid 129 through 131 removed outlier: 3.542A pdb=" N SER E 189 " --> pdb=" O CYS E 131 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 156 through 162 removed outlier: 3.543A pdb=" N ALA E 174 " --> pdb=" O CYS E 157 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 201 through 203 removed outlier: 7.046A pdb=" N ALA E 433 " --> pdb=" O LYS E 202 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 271 through 273 removed outlier: 6.924A pdb=" N THR E 357 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N PHE E 468 " --> pdb=" O THR E 357 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N LYS E 362 " --> pdb=" O PRO E 470 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER E 393 " --> pdb=" O PHE E 361 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 443 through 449 removed outlier: 3.931A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL E 292 " --> pdb=" O ILE E 449 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR E 330 " --> pdb=" O THR E 297 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 374 through 377 removed outlier: 3.503A pdb=" N PHE E 376 " --> pdb=" O PHE E 383 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 304 through 312 removed outlier: 3.647A pdb=" N THR E 305 " --> pdb=" O LYS E 319 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'G' and resid 3 through 5 removed outlier: 3.743A pdb=" N VAL G 18 " --> pdb=" O ILE G 82 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'G' and resid 88 through 96 removed outlier: 3.568A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ARG G 38 " --> pdb=" O TYR G 47 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N TYR G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ALA G 40 " --> pdb=" O LEU G 45 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU G 45 " --> pdb=" O ALA G 40 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'H' and resid 4 through 7 Processing sheet with id= AE, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.463A pdb=" N LYS H 103 " --> pdb=" O LEU H 11 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N ALA H 13 " --> pdb=" O LYS H 103 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLU H 105 " --> pdb=" O ALA H 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'H' and resid 85 through 90 removed outlier: 3.603A pdb=" N ILE H 48 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLN H 37 " --> pdb=" O LEU H 46 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N LEU H 46 " --> pdb=" O GLN H 37 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'I' and resid 35 through 40 Processing sheet with id= AH, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.694A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'I' and resid 53 through 55 Processing sheet with id= AJ, first strand: chain 'I' and resid 91 through 94 Processing sheet with id= AK, first strand: chain 'I' and resid 156 through 162 Processing sheet with id= AL, first strand: chain 'I' and resid 181 through 183 Processing sheet with id= AM, first strand: chain 'I' and resid 201 through 203 removed outlier: 6.963A pdb=" N ALA I 433 " --> pdb=" O LYS I 202 " (cutoff:3.500A) No H-bonds generated for sheet with id= AM Processing sheet with id= AN, first strand: chain 'I' and resid 271 through 273 removed outlier: 3.573A pdb=" N ILE I 271 " --> pdb=" O HIS I 287 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE I 452 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR I 467 " --> pdb=" O ASP I 457 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N THR I 357 " --> pdb=" O GLU I 466 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N PHE I 468 " --> pdb=" O THR I 357 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N VAL I 360 " --> pdb=" O PHE I 468 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N LYS I 362 " --> pdb=" O PRO I 470 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'I' and resid 414 through 417 removed outlier: 3.603A pdb=" N ILE I 414 " --> pdb=" O ILE I 333 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR I 330 " --> pdb=" O THR I 297 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG I 298 " --> pdb=" O ILE I 443 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE I 443 " --> pdb=" O ARG I 298 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU I 260 " --> pdb=" O THR I 450 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'I' and resid 374 through 377 removed outlier: 3.900A pdb=" N PHE I 376 " --> pdb=" O PHE I 383 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG I 419 " --> pdb=" O TYR I 384 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'I' and resid 304 through 312 removed outlier: 6.488A pdb=" N GLN I 315 " --> pdb=" O ILE I 309 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'K' and resid 3 through 5 removed outlier: 3.950A pdb=" N VAL K 18 " --> pdb=" O ILE K 82 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU K 81 " --> pdb=" O LEU K 68 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'K' and resid 107 through 109 removed outlier: 3.622A pdb=" N ILE K 109 " --> pdb=" O ALA K 88 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL K 37 " --> pdb=" O PHE K 91 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL K 35 " --> pdb=" O ILE K 51 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE K 51 " --> pdb=" O VAL K 35 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY K 49 " --> pdb=" O TRP K 36 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ARG K 38 " --> pdb=" O TYR K 47 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N TYR K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.701A pdb=" N SER L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.777A pdb=" N LYS L 103 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ALA L 13 " --> pdb=" O LYS L 103 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLU L 105 " --> pdb=" O ALA L 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= AU Processing sheet with id= AV, first strand: chain 'L' and resid 85 through 90 removed outlier: 3.583A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'M' and resid 4 through 8 removed outlier: 3.502A pdb=" N THR M 21 " --> pdb=" O SER M 7 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'M' and resid 33 through 36 removed outlier: 3.811A pdb=" N ARG M 100 " --> pdb=" O PHE M 100K" (cutoff:3.500A) removed outlier: 4.074A pdb=" N PHE M 100K" --> pdb=" O ARG M 100 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'M' and resid 37 through 39 Processing sheet with id= AZ, first strand: chain 'M' and resid 68 through 71 Processing sheet with id= BA, first strand: chain 'N' and resid 31 through 34 Processing sheet with id= BB, first strand: chain 'O' and resid 20 through 23 Processing sheet with id= BC, first strand: chain 'O' and resid 33 through 39 removed outlier: 3.672A pdb=" N GLN O 39 " --> pdb=" O VAL O 89 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG O 96 " --> pdb=" O SER O 100O" (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'O' and resid 49 through 51 Processing sheet with id= BE, first strand: chain 'P' and resid 31 through 34 Processing sheet with id= BF, first strand: chain 'Q' and resid 3 through 7 Processing sheet with id= BG, first strand: chain 'Q' and resid 35 through 37 Processing sheet with id= BH, first strand: chain 'Q' and resid 96 through 100A removed outlier: 3.637A pdb=" N PHE Q 100K" --> pdb=" O ARG Q 100 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'R' and resid 86 through 89 removed outlier: 3.554A pdb=" N TYR R 87 " --> pdb=" O TYR R 36 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR R 36 " --> pdb=" O TYR R 87 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE R 48 " --> pdb=" O TRP R 35 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N GLN R 37 " --> pdb=" O LEU R 46 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N LEU R 46 " --> pdb=" O GLN R 37 " (cutoff:3.500A) 633 hydrogen bonds defined for protein. 1701 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: 9.08 Time building geometry restraints manager: 12.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 4061 1.30 - 1.44: 7989 1.44 - 1.57: 14627 1.57 - 1.71: 0 1.71 - 1.84: 186 Bond restraints: 26863 Sorted by residual: bond pdb=" C ASN E 156 " pdb=" N CYS E 157 " ideal model delta sigma weight residual 1.330 1.481 -0.151 1.41e-02 5.03e+03 1.15e+02 bond pdb=" C ASN E 130 " pdb=" N CYS E 131 " ideal model delta sigma weight residual 1.330 1.437 -0.108 1.36e-02 5.41e+03 6.28e+01 bond pdb=" C CYS I 331 " pdb=" N ASN I 332 " ideal model delta sigma weight residual 1.330 1.244 0.085 1.32e-02 5.74e+03 4.18e+01 bond pdb=" C ASN E 301 " pdb=" N ASN E 302 " ideal model delta sigma weight residual 1.331 1.237 0.094 1.51e-02 4.39e+03 3.85e+01 bond pdb=" CA CYS I 74 " pdb=" C CYS I 74 " ideal model delta sigma weight residual 1.530 1.469 0.061 1.10e-02 8.26e+03 3.07e+01 ... (remaining 26858 not shown) Histogram of bond angle deviations from ideal: 93.31 - 103.56: 369 103.56 - 113.80: 15978 113.80 - 124.05: 19247 124.05 - 134.29: 880 134.29 - 144.54: 14 Bond angle restraints: 36488 Sorted by residual: angle pdb=" C13 83J E 607 " pdb=" C15 83J E 607 " pdb=" C21 83J E 607 " ideal model delta sigma weight residual 82.04 142.53 -60.49 3.00e+00 1.11e-01 4.07e+02 angle pdb=" C13 83J A 601 " pdb=" C15 83J A 601 " pdb=" C21 83J A 601 " ideal model delta sigma weight residual 82.04 141.08 -59.04 3.00e+00 1.11e-01 3.87e+02 angle pdb=" C13 83J E 607 " pdb=" C15 83J E 607 " pdb=" C20 83J E 607 " ideal model delta sigma weight residual 155.13 97.06 58.07 3.00e+00 1.11e-01 3.75e+02 angle pdb=" C13 83J I 607 " pdb=" C15 83J I 607 " pdb=" C21 83J I 607 " ideal model delta sigma weight residual 82.04 139.62 -57.58 3.00e+00 1.11e-01 3.68e+02 angle pdb=" C13 83J A 601 " pdb=" C15 83J A 601 " pdb=" C20 83J A 601 " ideal model delta sigma weight residual 155.13 98.16 56.97 3.00e+00 1.11e-01 3.61e+02 ... (remaining 36483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.90: 16290 24.90 - 49.81: 922 49.81 - 74.71: 188 74.71 - 99.61: 112 99.61 - 124.52: 94 Dihedral angle restraints: 17606 sinusoidal: 8690 harmonic: 8916 Sorted by residual: dihedral pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " pdb=" SG CYS A 74 " pdb=" CB CYS A 74 " ideal model delta sinusoidal sigma weight residual -86.00 1.99 -87.99 1 1.00e+01 1.00e-02 9.26e+01 dihedral pdb=" C CYS I 501 " pdb=" N CYS I 501 " pdb=" CA CYS I 501 " pdb=" CB CYS I 501 " ideal model delta harmonic sigma weight residual -122.60 -145.37 22.77 0 2.50e+00 1.60e-01 8.29e+01 dihedral pdb=" CB CYS I 126 " pdb=" SG CYS I 126 " pdb=" SG CYS I 196 " pdb=" CB CYS I 196 " ideal model delta sinusoidal sigma weight residual -86.00 -165.21 79.21 1 1.00e+01 1.00e-02 7.80e+01 ... (remaining 17603 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.285: 4317 0.285 - 0.571: 95 0.571 - 0.856: 6 0.856 - 1.141: 3 1.141 - 1.427: 1 Chirality restraints: 4422 Sorted by residual: chirality pdb=" C1 MAN S 9 " pdb=" O2 MAN S 8 " pdb=" C2 MAN S 9 " pdb=" O5 MAN S 9 " both_signs ideal model delta sigma weight residual False 2.40 2.61 -0.21 2.00e-02 2.50e+03 1.10e+02 chirality pdb=" C1 NAG A 609 " pdb=" ND2 ASN A 130 " pdb=" C2 NAG A 609 " pdb=" O5 NAG A 609 " both_signs ideal model delta sigma weight residual False -2.40 -0.97 -1.43 2.00e-01 2.50e+01 5.09e+01 chirality pdb=" CA ASN F 625 " pdb=" N ASN F 625 " pdb=" C ASN F 625 " pdb=" CB ASN F 625 " both_signs ideal model delta sigma weight residual False 2.51 1.54 0.97 2.00e-01 2.50e+01 2.36e+01 ... (remaining 4419 not shown) Planarity restraints: 4500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 609 " -0.337 2.00e-02 2.50e+03 2.93e-01 1.07e+03 pdb=" C7 NAG A 609 " 0.076 2.00e-02 2.50e+03 pdb=" C8 NAG A 609 " -0.100 2.00e-02 2.50e+03 pdb=" N2 NAG A 609 " 0.523 2.00e-02 2.50e+03 pdb=" O7 NAG A 609 " -0.162 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 607 " 0.283 2.00e-02 2.50e+03 2.33e-01 6.81e+02 pdb=" C7 NAG A 607 " -0.079 2.00e-02 2.50e+03 pdb=" C8 NAG A 607 " 0.192 2.00e-02 2.50e+03 pdb=" N2 NAG A 607 " -0.386 2.00e-02 2.50e+03 pdb=" O7 NAG A 607 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 130 " -0.104 2.00e-02 2.50e+03 1.78e-01 3.97e+02 pdb=" CG ASN A 130 " 0.049 2.00e-02 2.50e+03 pdb=" OD1 ASN A 130 " -0.060 2.00e-02 2.50e+03 pdb=" ND2 ASN A 130 " 0.318 2.00e-02 2.50e+03 pdb=" C1 NAG A 609 " -0.203 2.00e-02 2.50e+03 ... (remaining 4497 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 222 2.54 - 3.13: 19700 3.13 - 3.72: 36748 3.72 - 4.31: 53438 4.31 - 4.90: 89376 Nonbonded interactions: 199484 Sorted by model distance: nonbonded pdb=" O VAL I 154 " pdb=" O ARG I 155 " model vdw 1.950 3.040 nonbonded pdb=" O THR A 198 " pdb=" OG SER A 199 " model vdw 1.955 2.440 nonbonded pdb=" N ASN A 302 " pdb=" OD1 ASN A 302 " model vdw 2.163 2.520 nonbonded pdb=" O ARG R 61 " pdb=" OG1 THR R 74 " model vdw 2.218 2.440 nonbonded pdb=" O SER F 612 " pdb=" O SER F 615 " model vdw 2.221 3.040 ... (remaining 199479 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 134 or resid 152 through 396 or resid 408 throu \ gh 504 or resid 602 through 606 or resid 608)) selection = (chain 'E' and (resid 33 through 134 or resid 152 through 504 or resid 602 throu \ gh 606 or resid 608)) selection = (chain 'I' and (resid 33 through 504 or resid 602 through 606 or resid 608)) } ncs_group { reference = (chain 'B' and (resid 522 through 542 or resid 566 through 662 or resid 701 thro \ ugh 702)) selection = (chain 'F' and (resid 522 through 662 or resid 701 through 702)) selection = (chain 'J' and (resid 522 through 542 or resid 566 through 662 or resid 701 thro \ ugh 702)) } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 1 through 106) selection = (chain 'L' and resid 1 through 106) } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'Q' } ncs_group { reference = chain 'N' selection = chain 'P' selection = chain 'R' } ncs_group { reference = (chain 'S' and (resid 1 or resid 4 through 9)) selection = (chain 'a' and (resid 2 or resid 5 through 10)) selection = (chain 'j' and (resid 1 or resid 4 through 9)) } ncs_group { reference = chain 'T' selection = chain 'b' selection = chain 'k' } ncs_group { reference = (chain 'U' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'n' and resid 1 through 2) selection = (chain 's' and resid 1 through 2) } ncs_group { reference = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'c' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'l' selection = chain 'm' selection = chain 'o' selection = chain 'p' selection = chain 'q' } ncs_group { reference = chain 'Y' selection = chain 'Z' selection = chain 'h' selection = chain 'i' selection = chain 'r' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.690 Check model and map are aligned: 0.410 Set scattering table: 0.250 Process input model: 69.850 Find NCS groups from input model: 1.860 Set up NCS constraints: 0.450 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.151 26863 Z= 0.578 Angle : 1.530 60.487 36488 Z= 0.871 Chirality : 0.102 1.427 4422 Planarity : 0.009 0.293 4439 Dihedral : 19.010 124.517 11759 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.90 % Favored : 95.96 % Rotamer: Outliers : 2.12 % Allowed : 4.92 % Favored : 92.96 % Cbeta Deviations : 0.67 % Peptide Plane: Cis-proline : 4.55 % 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: -0.42 (0.15), residues: 3048 helix: 1.39 (0.26), residues: 396 sheet: 0.19 (0.18), residues: 893 loop : -0.93 (0.14), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP P 35 HIS 0.007 0.001 HIS I 216 PHE 0.029 0.002 PHE I 391 TYR 0.040 0.002 TYR D 91 ARG 0.006 0.001 ARG B 579 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 2684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 431 time to evaluate : 2.650 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 211 ASP cc_start: 0.7758 (t0) cc_final: 0.7413 (m-30) REVERT: A 229 ASN cc_start: 0.6901 (m110) cc_final: 0.6297 (m110) REVERT: A 303 THR cc_start: 0.8611 (p) cc_final: 0.8235 (t) REVERT: A 304 ARG cc_start: 0.7815 (ptm160) cc_final: 0.7518 (ptp-170) REVERT: A 354 ASN cc_start: 0.7857 (t0) cc_final: 0.7271 (t0) REVERT: A 413 THR cc_start: 0.8889 (m) cc_final: 0.8685 (p) REVERT: A 466 GLU cc_start: 0.7508 (mm-30) cc_final: 0.7062 (mm-30) REVERT: A 492 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7847 (mt-10) REVERT: A 496 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8243 (mp) REVERT: B 656 ASN cc_start: 0.7872 (t0) cc_final: 0.7445 (t0) REVERT: C 23 LYS cc_start: 0.6937 (mtpt) cc_final: 0.6547 (mttt) REVERT: C 38 ARG cc_start: 0.6932 (OUTLIER) cc_final: 0.6679 (ttt180) REVERT: D 3 GLN cc_start: 0.7365 (mp10) cc_final: 0.6919 (mp10) REVERT: E 117 LYS cc_start: 0.7195 (mttt) cc_final: 0.6965 (mmtp) REVERT: F 577 GLN cc_start: 0.7753 (tp-100) cc_final: 0.7552 (tp-100) REVERT: F 632 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8355 (mm-30) REVERT: G 35 ASN cc_start: 0.8196 (m-40) cc_final: 0.7839 (m110) REVERT: G 56 LYS cc_start: 0.7530 (mmmt) cc_final: 0.7060 (tttp) REVERT: H 33 VAL cc_start: 0.6639 (m) cc_final: 0.6416 (t) REVERT: H 65 SER cc_start: 0.8747 (t) cc_final: 0.8448 (p) REVERT: I 211 ASP cc_start: 0.7165 (t70) cc_final: 0.6768 (m-30) REVERT: I 246 GLN cc_start: 0.7196 (tp40) cc_final: 0.6861 (tp-100) REVERT: I 303 THR cc_start: 0.8587 (p) cc_final: 0.8336 (t) REVERT: I 354 ASN cc_start: 0.7932 (m110) cc_final: 0.7722 (m110) REVERT: I 377 ASN cc_start: 0.8096 (p0) cc_final: 0.7731 (p0) REVERT: I 440 LYS cc_start: 0.7671 (tmtt) cc_final: 0.7306 (tptp) REVERT: K 23 LYS cc_start: 0.6859 (mtpt) cc_final: 0.6528 (mttt) REVERT: M 100 ILE cc_start: 0.7157 (pt) cc_final: 0.6909 (pt) REVERT: Q 100 MET cc_start: 0.3907 (mmm) cc_final: 0.3427 (mtm) outliers start: 57 outliers final: 24 residues processed: 480 average time/residue: 0.3469 time to fit residues: 260.6194 Evaluate side-chains 325 residues out of total 2684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 299 time to evaluate : 2.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 275 GLU Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain F residue 617 LYS Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain I residue 61 TYR Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 277 LEU Chi-restraints excluded: chain I residue 302 ASN Chi-restraints excluded: chain I residue 323 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 255 optimal weight: 20.0000 chunk 229 optimal weight: 4.9990 chunk 127 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 154 optimal weight: 0.5980 chunk 122 optimal weight: 0.9990 chunk 237 optimal weight: 30.0000 chunk 91 optimal weight: 0.8980 chunk 144 optimal weight: 0.9980 chunk 176 optimal weight: 1.9990 chunk 275 optimal weight: 0.0980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN A 195 ASN A 203 GLN A 339 HIS A 425 ASN A 478 ASN D 27 GLN D 38 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN E 72 HIS E 99 ASN E 203 GLN G 6 GLN I 99 ASN I 195 ASN I 302 ASN K 35AASN L 31 ASN L 37 GLN ** O 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 50 ASN ** R 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26863 Z= 0.189 Angle : 0.669 10.971 36488 Z= 0.331 Chirality : 0.050 0.460 4422 Planarity : 0.005 0.047 4439 Dihedral : 16.256 101.491 6188 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.12 % Allowed : 11.48 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.76 % 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 (0.15), residues: 3048 helix: 1.46 (0.27), residues: 394 sheet: 0.27 (0.18), residues: 869 loop : -0.80 (0.14), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP O 47 HIS 0.005 0.001 HIS E 72 PHE 0.022 0.001 PHE Q 100K TYR 0.018 0.001 TYR D 91 ARG 0.008 0.000 ARG A 469 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 306 time to evaluate : 2.542 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: symmetry clash REVERT: A 107 ASP cc_start: 0.7959 (m-30) cc_final: 0.7717 (m-30) REVERT: A 110 SER cc_start: 0.8160 (t) cc_final: 0.7716 (m) REVERT: A 193 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7950 (mp) REVERT: A 211 ASP cc_start: 0.7825 (t0) cc_final: 0.7412 (m-30) REVERT: A 348 LYS cc_start: 0.7240 (tppt) cc_final: 0.6905 (tptp) REVERT: A 354 ASN cc_start: 0.7616 (t0) cc_final: 0.7072 (t0) REVERT: A 444 LYS cc_start: 0.8202 (ttmt) cc_final: 0.7901 (tttp) REVERT: A 492 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7697 (mt-10) REVERT: C 23 LYS cc_start: 0.6494 (mtpt) cc_final: 0.6157 (mttt) REVERT: C 99 ASP cc_start: 0.7280 (p0) cc_final: 0.6988 (p0) REVERT: E 84 MET cc_start: 0.6992 (ptp) cc_final: 0.6719 (ptp) REVERT: E 110 SER cc_start: 0.8237 (t) cc_final: 0.7748 (m) REVERT: E 444 LYS cc_start: 0.8571 (ttmt) cc_final: 0.8248 (tttp) REVERT: G 28 ASN cc_start: 0.8411 (p0) cc_final: 0.8151 (p0) REVERT: G 35 ASN cc_start: 0.7677 (m-40) cc_final: 0.7209 (m110) REVERT: H 33 VAL cc_start: 0.6553 (m) cc_final: 0.6339 (t) REVERT: I 61 TYR cc_start: 0.4352 (OUTLIER) cc_final: 0.2275 (t80) REVERT: I 110 SER cc_start: 0.8392 (t) cc_final: 0.7965 (m) REVERT: I 211 ASP cc_start: 0.7195 (t70) cc_final: 0.6693 (m-30) REVERT: I 229 ASN cc_start: 0.7410 (m-40) cc_final: 0.7166 (m-40) REVERT: K 56 LYS cc_start: 0.7221 (mmmt) cc_final: 0.6604 (tttp) REVERT: K 99 ASP cc_start: 0.7378 (p0) cc_final: 0.7088 (p0) REVERT: M 29 MET cc_start: 0.3377 (tpp) cc_final: 0.2168 (ttt) outliers start: 57 outliers final: 37 residues processed: 347 average time/residue: 0.3469 time to fit residues: 196.0865 Evaluate side-chains 308 residues out of total 2684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 269 time to evaluate : 2.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 475 MET Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain I residue 61 TYR Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 320 THR Chi-restraints excluded: chain I residue 322 ILE Chi-restraints excluded: chain I residue 323 ILE Chi-restraints excluded: chain I residue 448 ASN Chi-restraints excluded: chain K residue 61 HIS Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain Q residue 25 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 152 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 229 optimal weight: 7.9990 chunk 187 optimal weight: 0.8980 chunk 75 optimal weight: 7.9990 chunk 275 optimal weight: 0.0570 chunk 297 optimal weight: 8.9990 chunk 245 optimal weight: 6.9990 chunk 273 optimal weight: 30.0000 chunk 93 optimal weight: 2.9990 chunk 221 optimal weight: 6.9990 overall best weight: 2.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN C 61 HIS C 105 GLN D 6 GLN D 27 GLN E 33 ASN E 67 ASN E 229 ASN E 352 HIS K 61 HIS ** O 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 26863 Z= 0.357 Angle : 0.727 9.645 36488 Z= 0.358 Chirality : 0.053 0.524 4422 Planarity : 0.005 0.046 4439 Dihedral : 14.295 110.926 6162 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.91 % Allowed : 13.97 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.76 % 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: -0.55 (0.15), residues: 3048 helix: 0.99 (0.27), residues: 386 sheet: 0.20 (0.18), residues: 851 loop : -0.96 (0.14), residues: 1811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP O 47 HIS 0.006 0.001 HIS A 249 PHE 0.029 0.002 PHE E 382 TYR 0.032 0.002 TYR D 91 ARG 0.006 0.001 ARG A 469 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 278 time to evaluate : 2.697 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: A 104 MET cc_start: 0.8406 (ttt) cc_final: 0.8007 (ttt) REVERT: A 107 ASP cc_start: 0.8234 (m-30) cc_final: 0.7527 (m-30) REVERT: A 110 SER cc_start: 0.8273 (t) cc_final: 0.7747 (m) REVERT: A 166 ARG cc_start: 0.7896 (ttp80) cc_final: 0.7693 (ttp80) REVERT: A 211 ASP cc_start: 0.8074 (t0) cc_final: 0.7608 (m-30) REVERT: A 348 LYS cc_start: 0.7296 (tppt) cc_final: 0.7004 (tptp) REVERT: A 354 ASN cc_start: 0.7688 (t0) cc_final: 0.7197 (t0) REVERT: A 444 LYS cc_start: 0.8236 (ttmt) cc_final: 0.7898 (tttp) REVERT: B 577 GLN cc_start: 0.7713 (tp-100) cc_final: 0.7127 (tp40) REVERT: C 23 LYS cc_start: 0.6526 (mtpt) cc_final: 0.6122 (mttt) REVERT: C 38 ARG cc_start: 0.6520 (OUTLIER) cc_final: 0.5883 (ttt180) REVERT: C 99 ASP cc_start: 0.7692 (p0) cc_final: 0.7429 (p0) REVERT: C 100 MET cc_start: 0.8117 (ptp) cc_final: 0.7913 (ptp) REVERT: D 3 GLN cc_start: 0.7311 (mp10) cc_final: 0.6961 (mp10) REVERT: E 110 SER cc_start: 0.8261 (t) cc_final: 0.7750 (m) REVERT: E 316 VAL cc_start: 0.8756 (p) cc_final: 0.8439 (t) REVERT: E 444 LYS cc_start: 0.8442 (ttmt) cc_final: 0.8065 (ttmm) REVERT: F 626 MET cc_start: 0.8916 (ttm) cc_final: 0.8675 (mtp) REVERT: G 13 LYS cc_start: 0.7456 (mmmt) cc_final: 0.7136 (mmmt) REVERT: I 61 TYR cc_start: 0.4769 (OUTLIER) cc_final: 0.2872 (t80) REVERT: I 65 VAL cc_start: 0.8352 (t) cc_final: 0.7305 (p) REVERT: I 110 SER cc_start: 0.8463 (t) cc_final: 0.7988 (m) REVERT: I 275 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7327 (tp30) REVERT: K 56 LYS cc_start: 0.7369 (mmmt) cc_final: 0.6715 (tttp) REVERT: K 64 ARG cc_start: 0.7841 (mtm110) cc_final: 0.7322 (ttm-80) REVERT: K 99 ASP cc_start: 0.7829 (p0) cc_final: 0.7599 (p0) REVERT: M 29 MET cc_start: 0.3614 (tpp) cc_final: 0.2616 (ttt) outliers start: 78 outliers final: 56 residues processed: 334 average time/residue: 0.3484 time to fit residues: 189.0938 Evaluate side-chains 317 residues out of total 2684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 258 time to evaluate : 3.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 27 GLN Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain E residue 413 THR Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain I residue 61 TYR Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 251 ILE Chi-restraints excluded: chain I residue 274 SER Chi-restraints excluded: chain I residue 275 GLU Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 320 THR Chi-restraints excluded: chain I residue 321 ASP Chi-restraints excluded: chain I residue 322 ILE Chi-restraints excluded: chain I residue 448 ASN Chi-restraints excluded: chain I residue 500 LYS Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain K residue 61 HIS Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain Q residue 25 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 272 optimal weight: 10.0000 chunk 207 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 185 optimal weight: 1.9990 chunk 276 optimal weight: 9.9990 chunk 292 optimal weight: 9.9990 chunk 144 optimal weight: 3.9990 chunk 262 optimal weight: 20.0000 chunk 78 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 229 ASN D 6 GLN G 105 GLN I 82 GLN I 432 GLN ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 26863 Z= 0.408 Angle : 0.742 9.879 36488 Z= 0.366 Chirality : 0.053 0.413 4422 Planarity : 0.005 0.045 4439 Dihedral : 13.053 103.868 6155 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.54 % Allowed : 15.61 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.81 (0.15), residues: 3048 helix: 0.61 (0.26), residues: 386 sheet: 0.10 (0.18), residues: 849 loop : -1.14 (0.14), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP O 47 HIS 0.013 0.001 HIS K 61 PHE 0.028 0.002 PHE I 383 TYR 0.029 0.002 TYR D 91 ARG 0.005 0.000 ARG H 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 270 time to evaluate : 2.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8403 (ttt) cc_final: 0.8147 (ttt) REVERT: A 110 SER cc_start: 0.8297 (t) cc_final: 0.7747 (m) REVERT: A 166 ARG cc_start: 0.7981 (ttp80) cc_final: 0.7768 (ttp80) REVERT: A 211 ASP cc_start: 0.8056 (t0) cc_final: 0.7621 (m-30) REVERT: A 348 LYS cc_start: 0.7327 (tppt) cc_final: 0.7033 (tptp) REVERT: A 354 ASN cc_start: 0.7789 (t0) cc_final: 0.7282 (t0) REVERT: A 444 LYS cc_start: 0.8259 (ttmt) cc_final: 0.7901 (ttmm) REVERT: A 465 ASN cc_start: 0.7862 (p0) cc_final: 0.7603 (p0) REVERT: A 466 GLU cc_start: 0.7579 (mm-30) cc_final: 0.6997 (mm-30) REVERT: B 530 MET cc_start: 0.7763 (OUTLIER) cc_final: 0.7413 (mtt) REVERT: B 577 GLN cc_start: 0.7748 (tp-100) cc_final: 0.7155 (tp40) REVERT: B 584 GLU cc_start: 0.7431 (mm-30) cc_final: 0.7201 (mm-30) REVERT: B 656 ASN cc_start: 0.7849 (t0) cc_final: 0.7368 (t0) REVERT: B 662 GLU cc_start: 0.5923 (OUTLIER) cc_final: 0.5009 (mt-10) REVERT: C 23 LYS cc_start: 0.6421 (mtpt) cc_final: 0.5948 (mttt) REVERT: C 38 ARG cc_start: 0.6587 (OUTLIER) cc_final: 0.5870 (ttt180) REVERT: C 82 LEU cc_start: 0.7965 (tt) cc_final: 0.7755 (tt) REVERT: C 99 ASP cc_start: 0.8008 (p0) cc_final: 0.7786 (p0) REVERT: E 110 SER cc_start: 0.8264 (t) cc_final: 0.7738 (m) REVERT: E 444 LYS cc_start: 0.8470 (ttmt) cc_final: 0.8129 (ttmm) REVERT: F 626 MET cc_start: 0.8951 (ttm) cc_final: 0.8694 (mtp) REVERT: G 13 LYS cc_start: 0.7585 (mmmt) cc_final: 0.7209 (mmmt) REVERT: I 61 TYR cc_start: 0.5027 (OUTLIER) cc_final: 0.3004 (t80) REVERT: I 65 VAL cc_start: 0.8369 (t) cc_final: 0.7151 (p) REVERT: I 110 SER cc_start: 0.8492 (t) cc_final: 0.7991 (m) REVERT: J 656 ASN cc_start: 0.7980 (t0) cc_final: 0.7598 (t0) REVERT: K 56 LYS cc_start: 0.7509 (mmmt) cc_final: 0.6872 (tttp) REVERT: K 64 ARG cc_start: 0.7838 (mtm110) cc_final: 0.7337 (ttm-80) REVERT: M 29 MET cc_start: 0.4007 (tpp) cc_final: 0.3187 (ttt) REVERT: O 100 MET cc_start: 0.4133 (tpt) cc_final: 0.3739 (mtt) outliers start: 95 outliers final: 74 residues processed: 340 average time/residue: 0.3533 time to fit residues: 195.1790 Evaluate side-chains 330 residues out of total 2684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 252 time to evaluate : 2.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 658 LYS Chi-restraints excluded: chain B residue 662 GLU Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain E residue 61 TYR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 61 TYR Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 236 THR Chi-restraints excluded: chain I residue 251 ILE Chi-restraints excluded: chain I residue 274 SER Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain I residue 320 THR Chi-restraints excluded: chain I residue 321 ASP Chi-restraints excluded: chain I residue 322 ILE Chi-restraints excluded: chain I residue 372 THR Chi-restraints excluded: chain I residue 448 ASN Chi-restraints excluded: chain I residue 500 LYS Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain K residue 57 SER Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain Q residue 25 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 243 optimal weight: 7.9990 chunk 166 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 218 optimal weight: 0.9990 chunk 120 optimal weight: 0.9980 chunk 249 optimal weight: 7.9990 chunk 202 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 chunk 262 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN I 82 GLN I 432 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 HIS ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 26863 Z= 0.348 Angle : 0.700 10.581 36488 Z= 0.344 Chirality : 0.052 0.406 4422 Planarity : 0.005 0.046 4439 Dihedral : 12.115 103.402 6153 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 4.06 % Allowed : 16.73 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.95 (0.15), residues: 3048 helix: 0.58 (0.27), residues: 386 sheet: 0.01 (0.18), residues: 829 loop : -1.24 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP O 47 HIS 0.006 0.001 HIS A 249 PHE 0.028 0.002 PHE I 383 TYR 0.028 0.002 TYR D 91 ARG 0.012 0.000 ARG R 31 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 269 time to evaluate : 2.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8383 (ttt) cc_final: 0.8128 (ttt) REVERT: A 110 SER cc_start: 0.8219 (t) cc_final: 0.7683 (m) REVERT: A 211 ASP cc_start: 0.8054 (t0) cc_final: 0.7596 (m-30) REVERT: A 348 LYS cc_start: 0.7327 (tppt) cc_final: 0.7034 (tptp) REVERT: A 354 ASN cc_start: 0.7840 (t0) cc_final: 0.7344 (t0) REVERT: A 444 LYS cc_start: 0.8252 (ttmt) cc_final: 0.7872 (ttmm) REVERT: A 465 ASN cc_start: 0.7868 (p0) cc_final: 0.7629 (p0) REVERT: A 466 GLU cc_start: 0.7631 (mm-30) cc_final: 0.6919 (mm-30) REVERT: A 492 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7901 (mt-10) REVERT: B 530 MET cc_start: 0.7740 (OUTLIER) cc_final: 0.7257 (mtt) REVERT: B 577 GLN cc_start: 0.7724 (tp-100) cc_final: 0.7124 (tp40) REVERT: B 656 ASN cc_start: 0.7865 (t0) cc_final: 0.7368 (t0) REVERT: B 658 LYS cc_start: 0.6610 (OUTLIER) cc_final: 0.6191 (ttpt) REVERT: B 662 GLU cc_start: 0.5960 (OUTLIER) cc_final: 0.5042 (mt-10) REVERT: C 23 LYS cc_start: 0.6326 (mtpt) cc_final: 0.5881 (mttt) REVERT: C 38 ARG cc_start: 0.6668 (OUTLIER) cc_final: 0.6009 (ttt180) REVERT: C 64 ARG cc_start: 0.7864 (mtm110) cc_final: 0.7537 (mtm-85) REVERT: D 3 GLN cc_start: 0.7339 (mp10) cc_final: 0.7068 (mp10) REVERT: D 38 GLN cc_start: 0.7169 (pt0) cc_final: 0.6885 (tt0) REVERT: D 79 GLN cc_start: 0.6826 (mp10) cc_final: 0.6181 (mp10) REVERT: E 110 SER cc_start: 0.8246 (t) cc_final: 0.7731 (m) REVERT: E 444 LYS cc_start: 0.8435 (ttmt) cc_final: 0.8080 (ttmm) REVERT: G 97 THR cc_start: 0.8972 (m) cc_final: 0.8645 (p) REVERT: I 61 TYR cc_start: 0.5123 (OUTLIER) cc_final: 0.2951 (t80) REVERT: I 65 VAL cc_start: 0.8332 (t) cc_final: 0.6997 (p) REVERT: I 110 SER cc_start: 0.8468 (t) cc_final: 0.7986 (m) REVERT: I 193 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7871 (mp) REVERT: I 275 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7852 (tp30) REVERT: J 656 ASN cc_start: 0.8024 (t0) cc_final: 0.7634 (t0) REVERT: K 32 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7725 (pp) REVERT: K 56 LYS cc_start: 0.7495 (mmmt) cc_final: 0.6860 (tttp) REVERT: M 29 MET cc_start: 0.3778 (tpp) cc_final: 0.2963 (ttt) REVERT: O 100 MET cc_start: 0.4218 (tpt) cc_final: 0.3820 (mtt) REVERT: R 66 ILE cc_start: 0.5833 (OUTLIER) cc_final: 0.5545 (mp) outliers start: 109 outliers final: 79 residues processed: 353 average time/residue: 0.3558 time to fit residues: 204.7854 Evaluate side-chains 344 residues out of total 2684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 256 time to evaluate : 2.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 658 LYS Chi-restraints excluded: chain B residue 662 GLU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain E residue 61 TYR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 61 TYR Chi-restraints excluded: chain I residue 108 ILE Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 193 LEU Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 236 THR Chi-restraints excluded: chain I residue 251 ILE Chi-restraints excluded: chain I residue 270 ILE Chi-restraints excluded: chain I residue 274 SER Chi-restraints excluded: chain I residue 275 GLU Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain I residue 320 THR Chi-restraints excluded: chain I residue 321 ASP Chi-restraints excluded: chain I residue 322 ILE Chi-restraints excluded: chain I residue 372 THR Chi-restraints excluded: chain I residue 448 ASN Chi-restraints excluded: chain I residue 500 LYS Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 61 HIS Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain Q residue 25 SER Chi-restraints excluded: chain R residue 66 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 98 optimal weight: 0.5980 chunk 263 optimal weight: 0.0570 chunk 57 optimal weight: 4.9990 chunk 171 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 293 optimal weight: 3.9990 chunk 243 optimal weight: 9.9990 chunk 135 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 153 optimal weight: 1.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN E 114 GLN I 82 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 HIS ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 89 HIS R 50 ASN ** R 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 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 : 0.002 0.061 26863 Z= 0.163 Angle : 0.596 10.825 36488 Z= 0.292 Chirality : 0.047 0.366 4422 Planarity : 0.004 0.046 4439 Dihedral : 11.273 99.772 6153 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.57 % Allowed : 18.63 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 (0.15), residues: 3048 helix: 0.98 (0.27), residues: 385 sheet: 0.05 (0.18), residues: 822 loop : -1.11 (0.14), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 36 HIS 0.035 0.001 HIS K 61 PHE 0.023 0.001 PHE Q 100K TYR 0.017 0.001 TYR E 330 ARG 0.007 0.000 ARG H 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 270 time to evaluate : 3.685 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: A 107 ASP cc_start: 0.8311 (m-30) cc_final: 0.7904 (m-30) REVERT: A 110 SER cc_start: 0.8252 (t) cc_final: 0.7776 (m) REVERT: A 155 ARG cc_start: 0.5261 (OUTLIER) cc_final: 0.4958 (ttm170) REVERT: A 211 ASP cc_start: 0.7979 (t0) cc_final: 0.7358 (m-30) REVERT: A 348 LYS cc_start: 0.7224 (tppt) cc_final: 0.6778 (tptp) REVERT: A 354 ASN cc_start: 0.7874 (t0) cc_final: 0.7359 (t0) REVERT: A 425 ASN cc_start: 0.7871 (OUTLIER) cc_final: 0.7643 (m110) REVERT: A 444 LYS cc_start: 0.8180 (ttmt) cc_final: 0.7763 (ttmm) REVERT: A 465 ASN cc_start: 0.7897 (p0) cc_final: 0.7647 (p0) REVERT: A 466 GLU cc_start: 0.7513 (mm-30) cc_final: 0.7012 (mm-30) REVERT: A 492 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7790 (mt-10) REVERT: B 577 GLN cc_start: 0.7452 (tp-100) cc_final: 0.7154 (tp-100) REVERT: B 656 ASN cc_start: 0.7731 (t0) cc_final: 0.7266 (t0) REVERT: C 64 ARG cc_start: 0.7896 (mtm110) cc_final: 0.7566 (mtm-85) REVERT: D 3 GLN cc_start: 0.7285 (mp10) cc_final: 0.7006 (mp10) REVERT: D 38 GLN cc_start: 0.7042 (pt0) cc_final: 0.6838 (tt0) REVERT: E 110 SER cc_start: 0.8251 (t) cc_final: 0.7778 (m) REVERT: E 444 LYS cc_start: 0.8322 (ttmt) cc_final: 0.7976 (ttmm) REVERT: F 621 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7500 (mt-10) REVERT: F 656 ASN cc_start: 0.7934 (t0) cc_final: 0.7383 (t0) REVERT: G 23 LYS cc_start: 0.6461 (mtpt) cc_final: 0.5977 (mttt) REVERT: I 61 TYR cc_start: 0.4965 (OUTLIER) cc_final: 0.2878 (t80) REVERT: I 65 VAL cc_start: 0.8331 (t) cc_final: 0.7124 (p) REVERT: I 110 SER cc_start: 0.8450 (t) cc_final: 0.8026 (m) REVERT: I 275 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7860 (tp30) REVERT: I 449 ILE cc_start: 0.7887 (OUTLIER) cc_final: 0.7633 (mt) REVERT: J 621 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7575 (mp0) REVERT: J 656 ASN cc_start: 0.8021 (t0) cc_final: 0.7640 (t0) REVERT: K 56 LYS cc_start: 0.7429 (mmmt) cc_final: 0.6704 (tttp) REVERT: M 29 MET cc_start: 0.3771 (tpp) cc_final: 0.2939 (ttt) REVERT: O 100 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.7444 (mt-10) REVERT: O 100 MET cc_start: 0.4237 (tpt) cc_final: 0.3761 (mtt) outliers start: 69 outliers final: 48 residues processed: 320 average time/residue: 0.3617 time to fit residues: 187.3673 Evaluate side-chains 315 residues out of total 2684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 261 time to evaluate : 2.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain D residue 27 GLN Chi-restraints excluded: chain E residue 61 TYR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 89 GLN Chi-restraints excluded: chain I residue 61 TYR Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 274 SER Chi-restraints excluded: chain I residue 275 GLU Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain I residue 320 THR Chi-restraints excluded: chain I residue 321 ASP Chi-restraints excluded: chain I residue 322 ILE Chi-restraints excluded: chain I residue 448 ASN Chi-restraints excluded: chain I residue 449 ILE Chi-restraints excluded: chain I residue 500 LYS Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain J residue 523 LEU Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain O residue 100 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 282 optimal weight: 30.0000 chunk 33 optimal weight: 0.9980 chunk 167 optimal weight: 0.5980 chunk 214 optimal weight: 0.9990 chunk 165 optimal weight: 0.5980 chunk 246 optimal weight: 9.9990 chunk 163 optimal weight: 1.9990 chunk 292 optimal weight: 8.9990 chunk 182 optimal weight: 2.9990 chunk 178 optimal weight: 0.4980 chunk 134 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 82 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN ** O 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 89 HIS ** R 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 26863 Z= 0.163 Angle : 0.584 10.812 36488 Z= 0.283 Chirality : 0.047 0.363 4422 Planarity : 0.004 0.047 4439 Dihedral : 10.835 101.370 6150 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.87 % Allowed : 18.44 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.65 (0.15), residues: 3048 helix: 1.10 (0.27), residues: 388 sheet: 0.11 (0.18), residues: 832 loop : -1.06 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP G 36 HIS 0.003 0.000 HIS E 374 PHE 0.022 0.001 PHE Q 100K TYR 0.017 0.001 TYR D 91 ARG 0.007 0.000 ARG H 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 268 time to evaluate : 2.816 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: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8253 (m-30) cc_final: 0.7832 (m-30) REVERT: A 110 SER cc_start: 0.8314 (t) cc_final: 0.7846 (m) REVERT: A 155 ARG cc_start: 0.5195 (OUTLIER) cc_final: 0.4887 (ttm170) REVERT: A 211 ASP cc_start: 0.7972 (t0) cc_final: 0.7347 (m-30) REVERT: A 230 ASP cc_start: 0.8451 (OUTLIER) cc_final: 0.8033 (m-30) REVERT: A 348 LYS cc_start: 0.7216 (tppt) cc_final: 0.6781 (tptp) REVERT: A 354 ASN cc_start: 0.7906 (t0) cc_final: 0.7389 (t0) REVERT: A 425 ASN cc_start: 0.7870 (OUTLIER) cc_final: 0.7654 (m110) REVERT: A 444 LYS cc_start: 0.8189 (ttmt) cc_final: 0.7746 (ttmm) REVERT: A 465 ASN cc_start: 0.7889 (p0) cc_final: 0.7666 (p0) REVERT: A 492 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7738 (mt-10) REVERT: B 577 GLN cc_start: 0.7431 (tp-100) cc_final: 0.7107 (tp40) REVERT: B 656 ASN cc_start: 0.7701 (t0) cc_final: 0.7252 (t0) REVERT: B 662 GLU cc_start: 0.5760 (OUTLIER) cc_final: 0.4845 (mt-10) REVERT: C 64 ARG cc_start: 0.7896 (mtm110) cc_final: 0.7580 (mtm-85) REVERT: D 38 GLN cc_start: 0.7021 (pt0) cc_final: 0.6821 (tt0) REVERT: E 110 SER cc_start: 0.8208 (t) cc_final: 0.7800 (m) REVERT: E 198 THR cc_start: 0.9015 (m) cc_final: 0.8672 (p) REVERT: E 444 LYS cc_start: 0.8251 (ttmt) cc_final: 0.7897 (ttmm) REVERT: F 656 ASN cc_start: 0.7932 (t0) cc_final: 0.7386 (t0) REVERT: I 61 TYR cc_start: 0.4948 (OUTLIER) cc_final: 0.2884 (t80) REVERT: I 65 VAL cc_start: 0.8313 (t) cc_final: 0.7093 (p) REVERT: I 67 ASN cc_start: 0.7815 (OUTLIER) cc_final: 0.7601 (m-40) REVERT: I 110 SER cc_start: 0.8441 (t) cc_final: 0.8034 (m) REVERT: I 193 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7552 (mp) REVERT: I 275 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7863 (tp30) REVERT: I 449 ILE cc_start: 0.7896 (OUTLIER) cc_final: 0.7676 (mt) REVERT: J 656 ASN cc_start: 0.7967 (t0) cc_final: 0.7611 (t0) REVERT: K 56 LYS cc_start: 0.7476 (mmmt) cc_final: 0.6800 (tttp) REVERT: K 100 MET cc_start: 0.7989 (ptp) cc_final: 0.7714 (ptp) REVERT: M 29 MET cc_start: 0.3659 (tpp) cc_final: 0.3019 (ttt) REVERT: O 100 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7377 (mt-10) REVERT: O 100 MET cc_start: 0.4252 (tpt) cc_final: 0.3848 (mtt) REVERT: R 66 ILE cc_start: 0.5794 (OUTLIER) cc_final: 0.5506 (mp) outliers start: 77 outliers final: 47 residues processed: 330 average time/residue: 0.3506 time to fit residues: 189.0853 Evaluate side-chains 320 residues out of total 2684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 262 time to evaluate : 2.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 662 GLU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain E residue 61 TYR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 89 GLN Chi-restraints excluded: chain I residue 61 TYR Chi-restraints excluded: chain I residue 67 ASN Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 193 LEU Chi-restraints excluded: chain I residue 234 ASN Chi-restraints excluded: chain I residue 274 SER Chi-restraints excluded: chain I residue 275 GLU Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 320 THR Chi-restraints excluded: chain I residue 321 ASP Chi-restraints excluded: chain I residue 322 ILE Chi-restraints excluded: chain I residue 448 ASN Chi-restraints excluded: chain I residue 449 ILE Chi-restraints excluded: chain I residue 500 LYS Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain L residue 3 GLN Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain R residue 66 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 180 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 174 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 57 optimal weight: 0.3980 chunk 56 optimal weight: 5.9990 chunk 185 optimal weight: 4.9990 chunk 198 optimal weight: 4.9990 chunk 144 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 229 optimal weight: 1.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 82 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 89 HIS ** R 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 26863 Z= 0.290 Angle : 0.647 10.422 36488 Z= 0.315 Chirality : 0.049 0.385 4422 Planarity : 0.004 0.048 4439 Dihedral : 10.716 102.008 6147 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.13 % Allowed : 18.07 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.78 (0.15), residues: 3048 helix: 0.95 (0.27), residues: 385 sheet: 0.02 (0.18), residues: 834 loop : -1.12 (0.14), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP G 36 HIS 0.004 0.001 HIS I 105 PHE 0.026 0.002 PHE I 383 TYR 0.027 0.001 TYR D 91 ARG 0.007 0.000 ARG H 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 257 time to evaluate : 2.980 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: A 104 MET cc_start: 0.8371 (ttt) cc_final: 0.8124 (ttt) REVERT: A 110 SER cc_start: 0.8249 (t) cc_final: 0.7730 (m) REVERT: A 211 ASP cc_start: 0.8069 (t0) cc_final: 0.7522 (m-30) REVERT: A 348 LYS cc_start: 0.7247 (tppt) cc_final: 0.6966 (tptp) REVERT: A 354 ASN cc_start: 0.7997 (t0) cc_final: 0.7443 (t0) REVERT: A 444 LYS cc_start: 0.8258 (ttmt) cc_final: 0.7852 (ttmm) REVERT: A 465 ASN cc_start: 0.7967 (p0) cc_final: 0.7753 (p0) REVERT: A 492 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7817 (mt-10) REVERT: B 577 GLN cc_start: 0.7637 (tp-100) cc_final: 0.7254 (tp-100) REVERT: B 656 ASN cc_start: 0.7779 (t0) cc_final: 0.7330 (t0) REVERT: B 662 GLU cc_start: 0.5942 (OUTLIER) cc_final: 0.4992 (mt-10) REVERT: C 64 ARG cc_start: 0.7865 (mtm110) cc_final: 0.7646 (mtm-85) REVERT: D 3 GLN cc_start: 0.7424 (mp10) cc_final: 0.7137 (mp10) REVERT: D 79 GLN cc_start: 0.6925 (mp10) cc_final: 0.6269 (mp10) REVERT: E 110 SER cc_start: 0.8279 (t) cc_final: 0.7783 (m) REVERT: E 444 LYS cc_start: 0.8356 (ttmt) cc_final: 0.8011 (ttmm) REVERT: F 621 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7541 (mt-10) REVERT: I 61 TYR cc_start: 0.5052 (OUTLIER) cc_final: 0.2917 (t80) REVERT: I 65 VAL cc_start: 0.8358 (t) cc_final: 0.7093 (p) REVERT: I 110 SER cc_start: 0.8478 (t) cc_final: 0.8009 (m) REVERT: I 193 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7772 (mp) REVERT: I 275 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7896 (tp30) REVERT: I 449 ILE cc_start: 0.8014 (OUTLIER) cc_final: 0.7666 (mt) REVERT: J 621 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7564 (mp0) REVERT: J 656 ASN cc_start: 0.8091 (t0) cc_final: 0.7682 (t0) REVERT: K 56 LYS cc_start: 0.7529 (mmmt) cc_final: 0.6865 (tttp) REVERT: K 64 ARG cc_start: 0.7534 (mtm-85) cc_final: 0.7295 (mtm-85) REVERT: M 29 MET cc_start: 0.3807 (tpp) cc_final: 0.3181 (ttt) REVERT: O 100 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.7517 (mt-10) REVERT: O 100 MET cc_start: 0.4232 (tpt) cc_final: 0.3712 (mtt) REVERT: R 66 ILE cc_start: 0.5896 (OUTLIER) cc_final: 0.5597 (mt) outliers start: 84 outliers final: 71 residues processed: 324 average time/residue: 0.3504 time to fit residues: 185.5932 Evaluate side-chains 330 residues out of total 2684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 252 time to evaluate : 2.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 662 GLU Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain E residue 61 TYR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 89 GLN Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 61 TYR Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 193 LEU Chi-restraints excluded: chain I residue 234 ASN Chi-restraints excluded: chain I residue 274 SER Chi-restraints excluded: chain I residue 275 GLU Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain I residue 320 THR Chi-restraints excluded: chain I residue 321 ASP Chi-restraints excluded: chain I residue 322 ILE Chi-restraints excluded: chain I residue 383 PHE Chi-restraints excluded: chain I residue 448 ASN Chi-restraints excluded: chain I residue 449 ILE Chi-restraints excluded: chain I residue 500 LYS Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain R residue 66 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 265 optimal weight: 30.0000 chunk 279 optimal weight: 0.9980 chunk 255 optimal weight: 30.0000 chunk 272 optimal weight: 20.0000 chunk 163 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 213 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 chunk 245 optimal weight: 10.0000 chunk 257 optimal weight: 50.0000 chunk 271 optimal weight: 20.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 GLN E 114 GLN G 61 HIS I 67 ASN I 82 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN M 39 GLN ** M 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 89 HIS ** R 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 26863 Z= 0.484 Angle : 0.780 10.510 36488 Z= 0.382 Chirality : 0.055 0.442 4422 Planarity : 0.005 0.055 4439 Dihedral : 10.890 108.997 6147 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 3.61 % Allowed : 17.92 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.15), residues: 3048 helix: 0.27 (0.26), residues: 387 sheet: -0.06 (0.18), residues: 823 loop : -1.35 (0.14), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP G 36 HIS 0.006 0.001 HIS I 105 PHE 0.031 0.003 PHE I 383 TYR 0.035 0.002 TYR D 91 ARG 0.006 0.001 ARG H 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 251 time to evaluate : 2.729 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 104 MET cc_start: 0.8423 (ttt) cc_final: 0.8156 (ttt) REVERT: A 110 SER cc_start: 0.8281 (t) cc_final: 0.7697 (m) REVERT: A 211 ASP cc_start: 0.8114 (t0) cc_final: 0.7560 (m-30) REVERT: A 348 LYS cc_start: 0.7353 (tppt) cc_final: 0.7070 (tptp) REVERT: A 354 ASN cc_start: 0.8017 (t0) cc_final: 0.7548 (t0) REVERT: A 444 LYS cc_start: 0.8338 (ttmt) cc_final: 0.7961 (tttp) REVERT: A 465 ASN cc_start: 0.7983 (p0) cc_final: 0.7775 (p0) REVERT: A 492 GLU cc_start: 0.8273 (mt-10) cc_final: 0.8006 (mt-10) REVERT: B 662 GLU cc_start: 0.6000 (OUTLIER) cc_final: 0.5024 (mt-10) REVERT: C 23 LYS cc_start: 0.6450 (mtpt) cc_final: 0.5916 (mttt) REVERT: C 64 ARG cc_start: 0.7799 (mtm110) cc_final: 0.7561 (mtm-85) REVERT: D 3 GLN cc_start: 0.7492 (mp10) cc_final: 0.7179 (mp10) REVERT: D 79 GLN cc_start: 0.6870 (mp10) cc_final: 0.6373 (mp10) REVERT: E 110 SER cc_start: 0.8255 (t) cc_final: 0.7688 (m) REVERT: E 246 GLN cc_start: 0.7348 (pm20) cc_final: 0.6905 (tt0) REVERT: F 621 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7607 (mt-10) REVERT: G 13 LYS cc_start: 0.7570 (mmmt) cc_final: 0.6839 (mmmt) REVERT: I 61 TYR cc_start: 0.5362 (OUTLIER) cc_final: 0.3160 (t80) REVERT: I 65 VAL cc_start: 0.8361 (t) cc_final: 0.6946 (p) REVERT: I 110 SER cc_start: 0.8529 (t) cc_final: 0.8001 (m) REVERT: I 193 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7957 (mp) REVERT: I 275 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7419 (tp30) REVERT: I 426 MET cc_start: 0.8753 (ttt) cc_final: 0.8441 (ttt) REVERT: J 656 ASN cc_start: 0.8164 (t0) cc_final: 0.7774 (t0) REVERT: K 56 LYS cc_start: 0.7583 (mmmt) cc_final: 0.6982 (tttp) REVERT: K 64 ARG cc_start: 0.7620 (mtm-85) cc_final: 0.7408 (mtm-85) REVERT: M 29 MET cc_start: 0.3848 (tpp) cc_final: 0.3241 (ttt) REVERT: O 28 SER cc_start: 0.5420 (t) cc_final: 0.4919 (p) REVERT: O 100 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.7634 (mt-10) REVERT: O 100 MET cc_start: 0.4254 (tpt) cc_final: 0.3761 (mtt) REVERT: R 66 ILE cc_start: 0.6181 (OUTLIER) cc_final: 0.5978 (mm) outliers start: 97 outliers final: 79 residues processed: 328 average time/residue: 0.3584 time to fit residues: 192.4952 Evaluate side-chains 330 residues out of total 2684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 245 time to evaluate : 2.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 662 GLU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain E residue 61 TYR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 61 HIS Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 61 TYR Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 193 LEU Chi-restraints excluded: chain I residue 234 ASN Chi-restraints excluded: chain I residue 251 ILE Chi-restraints excluded: chain I residue 274 SER Chi-restraints excluded: chain I residue 275 GLU Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain I residue 320 THR Chi-restraints excluded: chain I residue 321 ASP Chi-restraints excluded: chain I residue 322 ILE Chi-restraints excluded: chain I residue 383 PHE Chi-restraints excluded: chain I residue 448 ASN Chi-restraints excluded: chain I residue 500 LYS Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain R residue 66 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 178 optimal weight: 1.9990 chunk 287 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 chunk 200 optimal weight: 0.5980 chunk 301 optimal weight: 30.0000 chunk 277 optimal weight: 40.0000 chunk 240 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 185 optimal weight: 3.9990 chunk 147 optimal weight: 20.0000 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 588 GLN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 89 HIS ** R 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 26863 Z= 0.226 Angle : 0.635 11.125 36488 Z= 0.311 Chirality : 0.048 0.372 4422 Planarity : 0.004 0.050 4439 Dihedral : 10.346 101.786 6147 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.68 % Allowed : 19.34 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.97 (0.15), residues: 3048 helix: 0.66 (0.27), residues: 385 sheet: 0.01 (0.18), residues: 804 loop : -1.26 (0.14), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP G 36 HIS 0.012 0.001 HIS G 62 PHE 0.022 0.001 PHE I 383 TYR 0.022 0.001 TYR D 91 ARG 0.007 0.000 ARG H 20 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 257 time to evaluate : 2.890 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: A 110 SER cc_start: 0.8233 (t) cc_final: 0.7707 (m) REVERT: A 211 ASP cc_start: 0.8062 (t0) cc_final: 0.7528 (m-30) REVERT: A 348 LYS cc_start: 0.7284 (tppt) cc_final: 0.7000 (tptp) REVERT: A 354 ASN cc_start: 0.7988 (t0) cc_final: 0.7485 (t0) REVERT: A 444 LYS cc_start: 0.8339 (ttmt) cc_final: 0.7880 (ttmm) REVERT: A 465 ASN cc_start: 0.7894 (p0) cc_final: 0.7668 (p0) REVERT: A 492 GLU cc_start: 0.8256 (mt-10) cc_final: 0.8008 (mt-10) REVERT: B 577 GLN cc_start: 0.7623 (tp-100) cc_final: 0.7274 (tp-100) REVERT: B 656 ASN cc_start: 0.7972 (t0) cc_final: 0.7555 (t0) REVERT: B 662 GLU cc_start: 0.5929 (OUTLIER) cc_final: 0.4963 (mt-10) REVERT: C 64 ARG cc_start: 0.7801 (mtm110) cc_final: 0.7563 (mtm-85) REVERT: D 3 GLN cc_start: 0.7370 (mp10) cc_final: 0.7045 (mp10) REVERT: D 79 GLN cc_start: 0.6850 (mp10) cc_final: 0.6219 (mp10) REVERT: E 110 SER cc_start: 0.8205 (t) cc_final: 0.7718 (m) REVERT: E 444 LYS cc_start: 0.8430 (ttmt) cc_final: 0.8072 (ttmm) REVERT: F 621 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7483 (mt-10) REVERT: I 61 TYR cc_start: 0.5092 (OUTLIER) cc_final: 0.2872 (t80) REVERT: I 65 VAL cc_start: 0.8349 (t) cc_final: 0.7015 (p) REVERT: I 110 SER cc_start: 0.8441 (t) cc_final: 0.7962 (m) REVERT: I 275 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7854 (tp30) REVERT: J 621 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7614 (mp0) REVERT: J 656 ASN cc_start: 0.8166 (t0) cc_final: 0.7778 (t0) REVERT: K 56 LYS cc_start: 0.7529 (mmmt) cc_final: 0.6880 (tttp) REVERT: K 64 ARG cc_start: 0.7629 (mtm-85) cc_final: 0.7253 (mtm-85) REVERT: M 29 MET cc_start: 0.3762 (tpp) cc_final: 0.3073 (ttt) REVERT: O 28 SER cc_start: 0.5488 (t) cc_final: 0.4760 (p) REVERT: O 29 MET cc_start: 0.2846 (mmt) cc_final: 0.2618 (ttm) REVERT: O 100 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.7455 (mt-10) REVERT: O 100 MET cc_start: 0.4322 (tpt) cc_final: 0.3792 (mtt) REVERT: R 66 ILE cc_start: 0.6078 (OUTLIER) cc_final: 0.5873 (mm) outliers start: 72 outliers final: 58 residues processed: 313 average time/residue: 0.3517 time to fit residues: 179.2782 Evaluate side-chains 313 residues out of total 2684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 250 time to evaluate : 2.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 662 GLU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain D residue 91 TYR Chi-restraints excluded: chain E residue 61 TYR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 61 HIS Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 61 TYR Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 234 ASN Chi-restraints excluded: chain I residue 274 SER Chi-restraints excluded: chain I residue 275 GLU Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain I residue 320 THR Chi-restraints excluded: chain I residue 321 ASP Chi-restraints excluded: chain I residue 322 ILE Chi-restraints excluded: chain I residue 383 PHE Chi-restraints excluded: chain I residue 448 ASN Chi-restraints excluded: chain I residue 500 LYS Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain R residue 66 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 190 optimal weight: 3.9990 chunk 256 optimal weight: 30.0000 chunk 73 optimal weight: 4.9990 chunk 221 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 240 optimal weight: 10.0000 chunk 100 optimal weight: 0.8980 chunk 247 optimal weight: 0.0970 chunk 30 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 588 GLN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 652 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 89 HIS ** R 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.222272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.171165 restraints weight = 30901.455| |-----------------------------------------------------------------------------| r_work (start): 0.4052 rms_B_bonded: 3.29 r_work: 0.3753 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 26863 Z= 0.231 Angle : 0.627 11.018 36488 Z= 0.306 Chirality : 0.048 0.372 4422 Planarity : 0.004 0.049 4439 Dihedral : 10.073 101.048 6147 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.76 % Allowed : 19.56 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.90 (0.15), residues: 3048 helix: 0.80 (0.27), residues: 386 sheet: 0.03 (0.18), residues: 812 loop : -1.23 (0.14), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP G 36 HIS 0.006 0.001 HIS G 62 PHE 0.022 0.001 PHE I 383 TYR 0.023 0.001 TYR D 91 ARG 0.007 0.000 ARG H 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5469.97 seconds wall clock time: 102 minutes 53.01 seconds (6173.01 seconds total)