Starting phenix.real_space_refine on Thu Apr 11 00:01:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6opq_20153/04_2024/6opq_20153.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6opq_20153/04_2024/6opq_20153.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6opq_20153/04_2024/6opq_20153.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6opq_20153/04_2024/6opq_20153.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6opq_20153/04_2024/6opq_20153.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6opq_20153/04_2024/6opq_20153.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.062 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 114 5.16 5 C 13074 2.51 5 N 3534 2.21 5 O 4155 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "H PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 91": "OE1" <-> "OE2" Residue "K PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 91": "OE1" <-> "OE2" Residue "M PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 20877 Number of models: 1 Model: "" Number of chains: 45 Chain: "A" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3014 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 22, 'TRANS': 362} Chain breaks: 2 Chain: "L" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 829 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 100} Chain: "B" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1027 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Chain: "C" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 775 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "H" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 987 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "D" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3014 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 22, 'TRANS': 362} Chain breaks: 2 Chain: "N" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 829 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 100} Chain: "F" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1027 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Chain: "I" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 775 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "K" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 987 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "E" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3014 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 22, 'TRANS': 362} Chain breaks: 2 Chain: "O" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 829 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 100} Chain: "G" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1027 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Chain: "J" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 775 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "M" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 987 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "R" 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: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 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: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "a" Number of atoms: 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: "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: 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: 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: "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: 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: "i" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 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: "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: "A" 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: "D" 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: "E" 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 Time building chain proxies: 11.09, per 1000 atoms: 0.53 Number of scatterers: 20877 At special positions: 0 Unit cell: (158.62, 157.59, 141.11, 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 114 16.00 O 4155 8.00 N 3534 7.00 C 13074 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.06 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.14 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.08 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 16 " - pdb=" SG CYS C 84 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.06 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.03 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.04 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.04 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.02 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.02 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS F 605 " distance=2.14 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.08 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS I 16 " - pdb=" SG CYS I 84 " distance=2.02 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.06 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.02 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.02 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 G 605 " distance=2.14 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.08 Simple disulfide: pdb=" SG CYS G 598 " - pdb=" SG CYS G 604 " distance=2.02 Simple disulfide: pdb=" SG CYS J 16 " - pdb=" SG CYS J 84 " distance=2.02 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN Q 4 " - " MAN Q 5 " " MAN Z 4 " - " MAN Z 5 " " MAN i 4 " - " MAN i 5 " ALPHA1-3 " BMA Q 3 " - " MAN Q 4 " " BMA Z 3 " - " MAN Z 4 " " BMA i 3 " - " MAN i 4 " BETA1-4 " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " 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 i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " NAG-ASN " NAG A 601 " - " ASN A 234 " " NAG A 615 " - " ASN A 339 " " NAG A 624 " - " ASN A 448 " " NAG D 601 " - " ASN D 234 " " NAG D 615 " - " ASN D 339 " " NAG D 624 " - " ASN D 448 " " NAG E 601 " - " ASN E 234 " " NAG E 615 " - " ASN E 339 " " NAG E 624 " - " ASN E 448 " " NAG P 1 " - " ASN A 241 " " NAG Q 1 " - " ASN A 262 " " NAG R 1 " - " ASN A 276 " " NAG S 1 " - " ASN A 295 " " NAG T 1 " - " ASN A 332 " " NAG U 1 " - " ASN A 362 " " NAG V 1 " - " ASN A 386 " " NAG W 1 " - " ASN A 392 " " NAG X 1 " - " ASN A 413 " " NAG Y 1 " - " ASN D 241 " " NAG Z 1 " - " ASN D 262 " " NAG a 1 " - " ASN D 276 " " NAG b 1 " - " ASN D 295 " " NAG c 1 " - " ASN D 332 " " NAG d 1 " - " ASN D 362 " " NAG e 1 " - " ASN D 386 " " NAG f 1 " - " ASN D 392 " " NAG g 1 " - " ASN D 413 " " NAG h 1 " - " ASN E 241 " " NAG i 1 " - " ASN E 262 " " NAG j 1 " - " ASN E 276 " " NAG k 1 " - " ASN E 295 " " NAG l 1 " - " ASN E 332 " " NAG m 1 " - " ASN E 362 " " NAG n 1 " - " ASN E 386 " " NAG o 1 " - " ASN E 392 " " NAG p 1 " - " ASN E 413 " Time building additional restraints: 8.83 Conformation dependent library (CDL) restraints added in 3.5 seconds 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4698 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 42 sheets defined 23.8% alpha, 28.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.52 Creating SS restraints... Processing helix chain 'A' and resid 64 through 74 removed outlier: 3.824A pdb=" N HIS A 72 " --> pdb=" O VAL A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 114 Processing helix chain 'A' and resid 335 through 353 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 474 through 484 removed outlier: 3.854A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'B' and resid 522 through 526 Processing helix chain 'B' and resid 529 through 546 Processing helix chain 'B' and resid 565 through 593 removed outlier: 4.628A pdb=" N TRP B 571 " --> pdb=" O GLN B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 597 Processing helix chain 'B' and resid 618 through 626 removed outlier: 3.620A pdb=" N MET B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 661 Processing helix chain 'C' and resid 58 through 65 removed outlier: 4.571A pdb=" N ASP C 63 " --> pdb=" O SER C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 79 Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 99 through 100C Processing helix chain 'D' and resid 64 through 74 removed outlier: 3.824A pdb=" N HIS D 72 " --> pdb=" O VAL D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 114 Processing helix chain 'D' and resid 335 through 353 Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 387 through 391 Processing helix chain 'D' and resid 474 through 484 removed outlier: 3.854A pdb=" N GLU D 482 " --> pdb=" O ASN D 478 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'F' and resid 522 through 526 Processing helix chain 'F' and resid 529 through 546 Processing helix chain 'F' and resid 565 through 593 removed outlier: 4.628A pdb=" N TRP F 571 " --> pdb=" O GLN F 567 " (cutoff:3.500A) Processing helix chain 'F' and resid 594 through 597 Processing helix chain 'F' and resid 618 through 626 removed outlier: 3.619A pdb=" N MET F 626 " --> pdb=" O ILE F 622 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 661 Processing helix chain 'I' and resid 58 through 65 removed outlier: 4.571A pdb=" N ASP I 63 " --> pdb=" O SER I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 79 Processing helix chain 'K' and resid 28 through 30 No H-bonds generated for 'chain 'K' and resid 28 through 30' Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'K' and resid 99 through 100C Processing helix chain 'E' and resid 64 through 74 removed outlier: 3.824A pdb=" N HIS E 72 " --> pdb=" O VAL E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 114 Processing helix chain 'E' and resid 335 through 353 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 391 Processing helix chain 'E' and resid 474 through 484 removed outlier: 3.854A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 83 Processing helix chain 'G' and resid 522 through 526 Processing helix chain 'G' and resid 529 through 546 Processing helix chain 'G' and resid 565 through 593 removed outlier: 4.628A pdb=" N TRP G 571 " --> pdb=" O GLN G 567 " (cutoff:3.500A) Processing helix chain 'G' and resid 594 through 597 Processing helix chain 'G' and resid 618 through 626 removed outlier: 3.619A pdb=" N MET G 626 " --> pdb=" O ILE G 622 " (cutoff:3.500A) Processing helix chain 'G' and resid 627 through 635 Processing helix chain 'G' and resid 638 through 661 Processing helix chain 'J' and resid 58 through 65 removed outlier: 4.571A pdb=" N ASP J 63 " --> pdb=" O SER J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 75 through 79 Processing helix chain 'M' and resid 28 through 30 No H-bonds generated for 'chain 'M' and resid 28 through 30' Processing helix chain 'M' and resid 61 through 64 Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'M' and resid 99 through 100C Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 93 Processing sheet with id=AA5, first strand: chain 'A' and resid 197 through 202 Processing sheet with id=AA6, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.694A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.411A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 394 through 395 removed outlier: 6.162A pdb=" N THR A 357 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N PHE A 468 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE A 359 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 4 through 6 removed outlier: 5.595A pdb=" N ALA L 69 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 9.681A pdb=" N GLU L 27 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 9.676A pdb=" N SER L 67 " --> pdb=" O GLU L 27 " (cutoff:3.500A) removed outlier: 11.556A pdb=" N VAL L 29 " --> pdb=" O SER L 65 " (cutoff:3.500A) removed outlier: 11.681A pdb=" N SER L 65 " --> pdb=" O VAL L 29 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 12 removed outlier: 5.938A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG L 45 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 2 through 5 removed outlier: 6.590A pdb=" N LYS C 2 " --> pdb=" O GLN C 94 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N LEU C 96 " --> pdb=" O LYS C 2 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL C 4 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N PHE C 26 " --> pdb=" O ASN C 39 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 12 through 14 Processing sheet with id=AB3, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AB4, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.571A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 8.851A pdb=" N TYR H 32 " --> pdb=" O ILE H 52 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE H 52 " --> pdb=" O TYR H 32 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N PHE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG H 50 " --> pdb=" O PHE H 34 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU H 46 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL H 56 " --> pdb=" O ILE H 52 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.571A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 494 through 499 Processing sheet with id=AB7, first strand: chain 'D' and resid 45 through 47 Processing sheet with id=AB8, first strand: chain 'D' and resid 53 through 56 Processing sheet with id=AB9, first strand: chain 'D' and resid 91 through 93 Processing sheet with id=AC1, first strand: chain 'D' and resid 197 through 202 Processing sheet with id=AC2, first strand: chain 'D' and resid 259 through 261 removed outlier: 6.694A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLY D 451 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 10.411A pdb=" N GLU D 290 " --> pdb=" O GLY D 451 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N GLU D 293 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N SER D 334 " --> pdb=" O GLU D 293 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N PHE D 382 " --> pdb=" O LYS D 421 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 394 through 395 removed outlier: 6.162A pdb=" N THR D 357 " --> pdb=" O GLU D 466 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N PHE D 468 " --> pdb=" O THR D 357 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE D 359 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 4 through 6 removed outlier: 5.594A pdb=" N ALA N 69 " --> pdb=" O ALA N 25 " (cutoff:3.500A) removed outlier: 9.681A pdb=" N GLU N 27 " --> pdb=" O SER N 67 " (cutoff:3.500A) removed outlier: 9.676A pdb=" N SER N 67 " --> pdb=" O GLU N 27 " (cutoff:3.500A) removed outlier: 11.557A pdb=" N VAL N 29 " --> pdb=" O SER N 65 " (cutoff:3.500A) removed outlier: 11.681A pdb=" N SER N 65 " --> pdb=" O VAL N 29 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'N' and resid 10 through 12 removed outlier: 5.938A pdb=" N LEU N 11 " --> pdb=" O GLU N 105 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG N 45 " --> pdb=" O GLN N 37 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 2 through 5 removed outlier: 6.590A pdb=" N LYS I 2 " --> pdb=" O GLN I 94 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N LEU I 96 " --> pdb=" O LYS I 2 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL I 4 " --> pdb=" O LEU I 96 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N PHE I 26 " --> pdb=" O ASN I 39 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 12 through 14 Processing sheet with id=AC8, first strand: chain 'K' and resid 5 through 6 Processing sheet with id=AC9, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.571A pdb=" N GLU K 10 " --> pdb=" O THR K 110 " (cutoff:3.500A) removed outlier: 8.851A pdb=" N TYR K 32 " --> pdb=" O ILE K 52 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE K 52 " --> pdb=" O TYR K 32 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N PHE K 34 " --> pdb=" O ARG K 50 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ARG K 50 " --> pdb=" O PHE K 34 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TRP K 36 " --> pdb=" O MET K 48 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU K 46 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL K 56 " --> pdb=" O ILE K 52 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.571A pdb=" N GLU K 10 " --> pdb=" O THR K 110 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 494 through 499 Processing sheet with id=AD3, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AD4, first strand: chain 'E' and resid 53 through 56 Processing sheet with id=AD5, first strand: chain 'E' and resid 91 through 93 Processing sheet with id=AD6, first strand: chain 'E' and resid 197 through 202 Processing sheet with id=AD7, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.694A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.411A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N GLU E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N SER E 334 " --> pdb=" O GLU E 293 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 394 through 395 removed outlier: 6.162A pdb=" N THR E 357 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N PHE E 468 " --> pdb=" O THR E 357 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE E 359 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 4 through 6 removed outlier: 5.595A pdb=" N ALA O 69 " --> pdb=" O ALA O 25 " (cutoff:3.500A) removed outlier: 9.680A pdb=" N GLU O 27 " --> pdb=" O SER O 67 " (cutoff:3.500A) removed outlier: 9.675A pdb=" N SER O 67 " --> pdb=" O GLU O 27 " (cutoff:3.500A) removed outlier: 11.556A pdb=" N VAL O 29 " --> pdb=" O SER O 65 " (cutoff:3.500A) removed outlier: 11.681A pdb=" N SER O 65 " --> pdb=" O VAL O 29 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'O' and resid 10 through 12 removed outlier: 5.938A pdb=" N LEU O 11 " --> pdb=" O GLU O 105 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU O 33 " --> pdb=" O TYR O 49 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N TYR O 49 " --> pdb=" O LEU O 33 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TRP O 35 " --> pdb=" O LEU O 47 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG O 45 " --> pdb=" O GLN O 37 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 2 through 5 removed outlier: 6.590A pdb=" N LYS J 2 " --> pdb=" O GLN J 94 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N LEU J 96 " --> pdb=" O LYS J 2 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL J 4 " --> pdb=" O LEU J 96 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N PHE J 26 " --> pdb=" O ASN J 39 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 12 through 14 Processing sheet with id=AE4, first strand: chain 'M' and resid 5 through 6 Processing sheet with id=AE5, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.570A pdb=" N GLU M 10 " --> pdb=" O THR M 110 " (cutoff:3.500A) removed outlier: 8.851A pdb=" N TYR M 32 " --> pdb=" O ILE M 52 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE M 52 " --> pdb=" O TYR M 32 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N PHE M 34 " --> pdb=" O ARG M 50 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ARG M 50 " --> pdb=" O PHE M 34 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU M 46 " --> pdb=" O ARG M 38 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL M 56 " --> pdb=" O ILE M 52 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.570A pdb=" N GLU M 10 " --> pdb=" O THR M 110 " (cutoff:3.500A) 837 hydrogen bonds defined for protein. 2079 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: 7.07 Time building geometry restraints manager: 9.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4095 1.32 - 1.44: 5730 1.44 - 1.57: 11253 1.57 - 1.70: 63 1.70 - 1.83: 147 Bond restraints: 21288 Sorted by residual: bond pdb=" CB HIS A 374 " pdb=" CG HIS A 374 " ideal model delta sigma weight residual 1.497 1.380 0.117 1.40e-02 5.10e+03 6.98e+01 bond pdb=" CB HIS D 374 " pdb=" CG HIS D 374 " ideal model delta sigma weight residual 1.497 1.380 0.117 1.40e-02 5.10e+03 6.96e+01 bond pdb=" CB HIS E 374 " pdb=" CG HIS E 374 " ideal model delta sigma weight residual 1.497 1.380 0.117 1.40e-02 5.10e+03 6.94e+01 bond pdb=" C1 NAG f 2 " pdb=" O5 NAG f 2 " ideal model delta sigma weight residual 1.406 1.549 -0.143 2.00e-02 2.50e+03 5.12e+01 bond pdb=" C1 NAG o 2 " pdb=" O5 NAG o 2 " ideal model delta sigma weight residual 1.406 1.549 -0.143 2.00e-02 2.50e+03 5.11e+01 ... (remaining 21283 not shown) Histogram of bond angle deviations from ideal: 98.12 - 105.35: 555 105.35 - 112.58: 10868 112.58 - 119.80: 8143 119.80 - 127.03: 9037 127.03 - 134.26: 290 Bond angle restraints: 28893 Sorted by residual: angle pdb=" C PRO D 437 " pdb=" N PRO D 438 " pdb=" CA PRO D 438 " ideal model delta sigma weight residual 119.78 128.94 -9.16 1.03e+00 9.43e-01 7.91e+01 angle pdb=" C PRO A 437 " pdb=" N PRO A 438 " pdb=" CA PRO A 438 " ideal model delta sigma weight residual 119.78 128.93 -9.15 1.03e+00 9.43e-01 7.89e+01 angle pdb=" C PRO E 437 " pdb=" N PRO E 438 " pdb=" CA PRO E 438 " ideal model delta sigma weight residual 119.78 128.92 -9.14 1.03e+00 9.43e-01 7.88e+01 angle pdb=" C PHE E 353 " pdb=" N PRO E 354 " pdb=" CA PRO E 354 " ideal model delta sigma weight residual 119.56 127.71 -8.15 1.02e+00 9.61e-01 6.38e+01 angle pdb=" C PHE A 353 " pdb=" N PRO A 354 " pdb=" CA PRO A 354 " ideal model delta sigma weight residual 119.56 127.69 -8.13 1.02e+00 9.61e-01 6.36e+01 ... (remaining 28888 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.93: 13152 21.93 - 43.86: 417 43.86 - 65.79: 105 65.79 - 87.72: 36 87.72 - 109.65: 12 Dihedral angle restraints: 13722 sinusoidal: 6438 harmonic: 7284 Sorted by residual: dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual 93.00 152.17 -59.17 1 1.00e+01 1.00e-02 4.68e+01 dihedral pdb=" CB CYS D 119 " pdb=" SG CYS D 119 " pdb=" SG CYS D 205 " pdb=" CB CYS D 205 " ideal model delta sinusoidal sigma weight residual 93.00 152.17 -59.17 1 1.00e+01 1.00e-02 4.68e+01 dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 205 " pdb=" CB CYS E 205 " ideal model delta sinusoidal sigma weight residual 93.00 152.17 -59.17 1 1.00e+01 1.00e-02 4.68e+01 ... (remaining 13719 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 2607 0.114 - 0.228: 763 0.228 - 0.342: 50 0.342 - 0.456: 18 0.456 - 0.570: 9 Chirality restraints: 3447 Sorted by residual: chirality pdb=" C1 NAG b 2 " pdb=" O4 NAG b 1 " pdb=" C2 NAG b 2 " pdb=" O5 NAG b 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 7.90e+01 chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 7.86e+01 chirality pdb=" C1 NAG k 2 " pdb=" O4 NAG k 1 " pdb=" C2 NAG k 2 " pdb=" O5 NAG k 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 7.77e+01 ... (remaining 3444 not shown) Planarity restraints: 3642 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 234 " -0.062 2.00e-02 2.50e+03 6.60e-02 5.44e+01 pdb=" CG ASN A 234 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN A 234 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN A 234 " 0.102 2.00e-02 2.50e+03 pdb=" C1 NAG A 601 " -0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 234 " -0.062 2.00e-02 2.50e+03 6.59e-02 5.43e+01 pdb=" CG ASN E 234 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN E 234 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN E 234 " 0.102 2.00e-02 2.50e+03 pdb=" C1 NAG E 601 " -0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 234 " 0.062 2.00e-02 2.50e+03 6.58e-02 5.42e+01 pdb=" CG ASN D 234 " -0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN D 234 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN D 234 " -0.102 2.00e-02 2.50e+03 pdb=" C1 NAG D 601 " 0.080 2.00e-02 2.50e+03 ... (remaining 3639 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 5950 2.81 - 3.33: 18783 3.33 - 3.85: 35573 3.85 - 4.38: 42095 4.38 - 4.90: 67442 Nonbonded interactions: 169843 Sorted by model distance: nonbonded pdb=" O3 NAG D 601 " pdb=" O7 NAG D 601 " model vdw 2.284 2.440 nonbonded pdb=" O3 NAG A 601 " pdb=" O7 NAG A 601 " model vdw 2.284 2.440 nonbonded pdb=" O3 NAG E 601 " pdb=" O7 NAG E 601 " model vdw 2.284 2.440 nonbonded pdb=" O5 NAG f 1 " pdb=" O6 NAG f 1 " model vdw 2.336 2.432 nonbonded pdb=" O5 NAG o 1 " pdb=" O6 NAG o 1 " model vdw 2.336 2.432 ... (remaining 169838 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'C' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'M' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' } ncs_group { reference = chain 'Q' selection = chain 'Z' selection = chain 'i' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.160 Check model and map are aligned: 0.330 Set scattering table: 0.200 Process input model: 55.250 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.400 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:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 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 : 0.022 0.177 21288 Z= 1.423 Angle : 1.762 10.837 28893 Z= 1.149 Chirality : 0.103 0.570 3447 Planarity : 0.009 0.052 3606 Dihedral : 12.051 109.654 8907 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.17 % Favored : 97.71 % Rotamer: Outliers : 0.14 % Allowed : 0.82 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.54 (0.16), residues: 2487 helix: 1.22 (0.23), residues: 423 sheet: 0.91 (0.20), residues: 654 loop : -0.12 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.010 TRP L 94 HIS 0.014 0.003 HIS E 308 PHE 0.028 0.007 PHE E 233 TYR 0.060 0.008 TYR N 91 ARG 0.009 0.001 ARG D 327 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 817 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 814 time to evaluate : 2.277 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 TRP cc_start: 0.8232 (t-100) cc_final: 0.7996 (t-100) REVERT: A 358 ILE cc_start: 0.8464 (mm) cc_final: 0.8226 (tp) REVERT: A 449 ILE cc_start: 0.8854 (mt) cc_final: 0.8585 (pt) REVERT: A 475 MET cc_start: 0.7355 (mmm) cc_final: 0.6651 (mmp) REVERT: L 58 VAL cc_start: 0.7915 (t) cc_final: 0.7626 (t) REVERT: L 102 THR cc_start: 0.4727 (p) cc_final: 0.4159 (t) REVERT: B 537 LEU cc_start: 0.8792 (tp) cc_final: 0.8561 (tt) REVERT: B 629 MET cc_start: 0.7807 (mtp) cc_final: 0.7085 (mtm) REVERT: B 647 GLU cc_start: 0.8511 (tt0) cc_final: 0.8186 (tt0) REVERT: C 67 PHE cc_start: 0.8639 (m-80) cc_final: 0.8420 (m-80) REVERT: H 72 ASP cc_start: 0.8132 (t0) cc_final: 0.7925 (t0) REVERT: H 100 PHE cc_start: 0.7540 (m-80) cc_final: 0.7131 (m-80) REVERT: D 119 CYS cc_start: 0.6793 (m) cc_final: 0.6521 (m) REVERT: D 358 ILE cc_start: 0.8466 (mm) cc_final: 0.8160 (tp) REVERT: D 395 TRP cc_start: 0.8311 (m100) cc_final: 0.8101 (m100) REVERT: D 449 ILE cc_start: 0.8897 (mt) cc_final: 0.8589 (pt) REVERT: D 475 MET cc_start: 0.7403 (mmm) cc_final: 0.6799 (mmp) REVERT: D 478 ASN cc_start: 0.8596 (m-40) cc_final: 0.8117 (m110) REVERT: N 40 PRO cc_start: 0.7359 (Cg_exo) cc_final: 0.6990 (Cg_endo) REVERT: N 102 THR cc_start: 0.5024 (p) cc_final: 0.4421 (t) REVERT: F 537 LEU cc_start: 0.8930 (tp) cc_final: 0.8630 (tt) REVERT: F 647 GLU cc_start: 0.8658 (tt0) cc_final: 0.8224 (tt0) REVERT: I 34 ILE cc_start: 0.8133 (mm) cc_final: 0.7851 (mt) REVERT: E 258 GLN cc_start: 0.8401 (mt0) cc_final: 0.8197 (mt0) REVERT: E 338 TRP cc_start: 0.8297 (t-100) cc_final: 0.7830 (t-100) REVERT: E 358 ILE cc_start: 0.8380 (mm) cc_final: 0.8170 (tp) REVERT: E 395 TRP cc_start: 0.8251 (m100) cc_final: 0.7401 (m100) REVERT: E 449 ILE cc_start: 0.8801 (mt) cc_final: 0.8196 (tt) REVERT: E 475 MET cc_start: 0.7336 (mmm) cc_final: 0.6717 (mmp) REVERT: O 40 PRO cc_start: 0.7558 (Cg_exo) cc_final: 0.7174 (Cg_endo) REVERT: O 49 TYR cc_start: 0.7311 (t80) cc_final: 0.7051 (t80) REVERT: G 537 LEU cc_start: 0.8807 (tp) cc_final: 0.8556 (tt) REVERT: G 647 GLU cc_start: 0.8643 (tt0) cc_final: 0.8021 (tt0) REVERT: J 69 LEU cc_start: 0.9052 (tp) cc_final: 0.8740 (tt) REVERT: M 100 PHE cc_start: 0.7772 (m-80) cc_final: 0.7186 (m-80) outliers start: 3 outliers final: 0 residues processed: 817 average time/residue: 0.3657 time to fit residues: 438.1876 Evaluate side-chains 428 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 428 time to evaluate : 2.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 8.9990 chunk 184 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 124 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 190 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 115 optimal weight: 0.3980 chunk 141 optimal weight: 20.0000 chunk 220 optimal weight: 2.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 HIS A 325 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 92 ASN C 25 GLN C 27 HIS C 66 ASN C 73 ASN H 82BASN ** D 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 HIS D 325 ASN N 92 ASN I 25 GLN I 27 HIS I 73 ASN ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 HIS E 325 ASN ** E 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 92 ASN J 25 GLN J 27 HIS M 82BASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 21288 Z= 0.278 Angle : 0.760 8.895 28893 Z= 0.403 Chirality : 0.049 0.280 3447 Planarity : 0.005 0.043 3606 Dihedral : 8.815 65.434 4191 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.61 % Favored : 97.27 % Rotamer: Outliers : 3.82 % Allowed : 11.78 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.22 (0.16), residues: 2487 helix: 2.00 (0.25), residues: 408 sheet: 0.68 (0.20), residues: 687 loop : -0.70 (0.15), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 395 HIS 0.005 0.001 HIS A 374 PHE 0.025 0.003 PHE K 100J TYR 0.030 0.002 TYR M 100E ARG 0.009 0.001 ARG L 103 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 513 time to evaluate : 2.380 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 LEU cc_start: 0.8493 (tt) cc_final: 0.8284 (tp) REVERT: A 258 GLN cc_start: 0.8238 (mt0) cc_final: 0.7863 (mt0) REVERT: A 338 TRP cc_start: 0.8108 (t-100) cc_final: 0.7591 (t-100) REVERT: A 358 ILE cc_start: 0.8360 (mm) cc_final: 0.8131 (mm) REVERT: A 428 GLN cc_start: 0.8447 (mp10) cc_final: 0.8190 (mp10) REVERT: A 475 MET cc_start: 0.6687 (mmm) cc_final: 0.6373 (mmm) REVERT: A 479 TRP cc_start: 0.6385 (m-90) cc_final: 0.5875 (m-90) REVERT: L 38 GLN cc_start: 0.8598 (tm-30) cc_final: 0.8223 (tm-30) REVERT: L 58 VAL cc_start: 0.6958 (t) cc_final: 0.6729 (t) REVERT: L 85 VAL cc_start: 0.7277 (t) cc_final: 0.6907 (t) REVERT: B 629 MET cc_start: 0.7805 (mtp) cc_final: 0.7193 (mtm) REVERT: B 647 GLU cc_start: 0.8299 (tt0) cc_final: 0.7944 (tt0) REVERT: C 67 PHE cc_start: 0.8752 (m-80) cc_final: 0.8453 (m-80) REVERT: C 73 ASN cc_start: 0.8212 (t0) cc_final: 0.7796 (p0) REVERT: H 23 LYS cc_start: 0.8484 (tmmt) cc_final: 0.8206 (tmmt) REVERT: H 72 ASP cc_start: 0.7960 (t0) cc_final: 0.7608 (t0) REVERT: H 83 ARG cc_start: 0.7675 (ptt180) cc_final: 0.7474 (ptp-170) REVERT: D 107 ASP cc_start: 0.7673 (OUTLIER) cc_final: 0.7452 (t70) REVERT: D 358 ILE cc_start: 0.8255 (mm) cc_final: 0.7948 (mm) REVERT: D 475 MET cc_start: 0.6893 (mmm) cc_final: 0.5506 (mmm) REVERT: D 479 TRP cc_start: 0.6299 (m-90) cc_final: 0.5885 (m-90) REVERT: D 482 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7281 (mt-10) REVERT: N 38 GLN cc_start: 0.8619 (tm-30) cc_final: 0.8244 (tm-30) REVERT: N 40 PRO cc_start: 0.7602 (Cg_exo) cc_final: 0.7399 (Cg_endo) REVERT: N 58 VAL cc_start: 0.7820 (t) cc_final: 0.6959 (t) REVERT: N 85 VAL cc_start: 0.7544 (t) cc_final: 0.7159 (t) REVERT: I 34 ILE cc_start: 0.8451 (mm) cc_final: 0.8163 (mt) REVERT: I 82 TYR cc_start: 0.7554 (m-10) cc_final: 0.7265 (m-10) REVERT: K 23 LYS cc_start: 0.8679 (tmmt) cc_final: 0.8410 (tmmt) REVERT: E 201 ILE cc_start: 0.8600 (mp) cc_final: 0.8340 (mt) REVERT: E 338 TRP cc_start: 0.8170 (t-100) cc_final: 0.7793 (t-100) REVERT: E 475 MET cc_start: 0.6366 (mmm) cc_final: 0.6150 (mmm) REVERT: E 479 TRP cc_start: 0.6482 (m-90) cc_final: 0.5999 (m-90) REVERT: O 38 GLN cc_start: 0.8534 (tm-30) cc_final: 0.8151 (tm-30) REVERT: O 49 TYR cc_start: 0.6982 (t80) cc_final: 0.6659 (t80) REVERT: O 58 VAL cc_start: 0.7698 (t) cc_final: 0.7234 (t) REVERT: O 70 GLU cc_start: 0.8452 (mm-30) cc_final: 0.7985 (mm-30) REVERT: O 85 VAL cc_start: 0.7381 (t) cc_final: 0.6968 (t) REVERT: G 540 GLN cc_start: 0.8741 (mm110) cc_final: 0.8184 (tt0) REVERT: J 5 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8618 (tp) REVERT: M 23 LYS cc_start: 0.8595 (tmmt) cc_final: 0.8255 (tmmt) REVERT: M 100 PHE cc_start: 0.7206 (m-80) cc_final: 0.6369 (m-80) outliers start: 84 outliers final: 51 residues processed: 551 average time/residue: 0.3395 time to fit residues: 284.7723 Evaluate side-chains 473 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 419 time to evaluate : 2.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 325 ASN Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 482 GLU Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 97 THR Chi-restraints excluded: chain N residue 104 LEU Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain I residue 76 ILE Chi-restraints excluded: chain K residue 85 ASP Chi-restraints excluded: chain K residue 91 PHE Chi-restraints excluded: chain K residue 105 GLN Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 325 ASN Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 402 ASP Chi-restraints excluded: chain O residue 31 SER Chi-restraints excluded: chain O residue 93 ASN Chi-restraints excluded: chain O residue 104 LEU Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 603 ILE Chi-restraints excluded: chain G residue 646 LEU Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 85 ASP Chi-restraints excluded: chain M residue 91 PHE Chi-restraints excluded: chain M residue 105 GLN Chi-restraints excluded: chain M residue 107 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 122 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 183 optimal weight: 9.9990 chunk 150 optimal weight: 10.0000 chunk 60 optimal weight: 8.9990 chunk 221 optimal weight: 0.7980 chunk 238 optimal weight: 10.0000 chunk 196 optimal weight: 5.9990 chunk 219 optimal weight: 6.9990 chunk 75 optimal weight: 9.9990 chunk 177 optimal weight: 6.9990 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 ASN ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 GLN B 607 ASN C 20 GLN ** C 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 58 HIS ** D 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 ASN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 590 GLN F 607 ASN I 20 GLN ** I 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 66 ASN I 73 ASN ** E 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 ASN O 89 GLN ** O 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 590 GLN G 607 ASN G 656 ASN J 20 GLN ** J 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 66 ASN M 58 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.4827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.115 21288 Z= 0.578 Angle : 0.915 9.549 28893 Z= 0.479 Chirality : 0.055 0.272 3447 Planarity : 0.006 0.070 3606 Dihedral : 8.219 50.263 4191 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 20.92 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.47 % Favored : 94.41 % Rotamer: Outliers : 6.18 % Allowed : 13.55 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.87 (0.16), residues: 2487 helix: 0.72 (0.24), residues: 438 sheet: 0.39 (0.21), residues: 690 loop : -1.60 (0.15), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP D 395 HIS 0.020 0.003 HIS E 374 PHE 0.027 0.004 PHE E 383 TYR 0.031 0.004 TYR K 100E ARG 0.008 0.001 ARG I 59 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 405 time to evaluate : 2.434 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 SER cc_start: 0.7657 (t) cc_final: 0.7446 (p) REVERT: A 475 MET cc_start: 0.7486 (mmm) cc_final: 0.6964 (mmm) REVERT: L 94 TRP cc_start: 0.7379 (t60) cc_final: 0.7116 (t60) REVERT: B 540 GLN cc_start: 0.8823 (mm110) cc_final: 0.8158 (tt0) REVERT: B 629 MET cc_start: 0.8200 (mtp) cc_final: 0.7677 (mtm) REVERT: H 23 LYS cc_start: 0.8969 (tmmt) cc_final: 0.8113 (mmtm) REVERT: H 72 ASP cc_start: 0.7773 (t0) cc_final: 0.7391 (t0) REVERT: D 475 MET cc_start: 0.7572 (mmm) cc_final: 0.6764 (tpp) REVERT: D 479 TRP cc_start: 0.6836 (m-90) cc_final: 0.6317 (m-90) REVERT: N 58 VAL cc_start: 0.7216 (t) cc_final: 0.6991 (t) REVERT: N 83 PHE cc_start: 0.8566 (m-10) cc_final: 0.8315 (m-10) REVERT: F 565 MET cc_start: 0.6956 (ttp) cc_final: 0.6697 (ttp) REVERT: F 629 MET cc_start: 0.8021 (OUTLIER) cc_final: 0.7283 (mtt) REVERT: K 23 LYS cc_start: 0.9071 (tmmt) cc_final: 0.8257 (mmtm) REVERT: K 30 ILE cc_start: 0.8665 (OUTLIER) cc_final: 0.8226 (tt) REVERT: E 107 ASP cc_start: 0.8531 (OUTLIER) cc_final: 0.8263 (t0) REVERT: E 217 TYR cc_start: 0.7111 (OUTLIER) cc_final: 0.5819 (m-80) REVERT: E 258 GLN cc_start: 0.8484 (mt0) cc_final: 0.8203 (mt0) REVERT: E 338 TRP cc_start: 0.8129 (t-100) cc_final: 0.7827 (t-100) REVERT: E 475 MET cc_start: 0.7328 (mmm) cc_final: 0.6779 (mmm) REVERT: O 58 VAL cc_start: 0.7846 (t) cc_final: 0.7471 (t) REVERT: O 83 PHE cc_start: 0.8511 (m-10) cc_final: 0.8252 (m-10) REVERT: G 540 GLN cc_start: 0.8810 (mm110) cc_final: 0.8290 (tt0) REVERT: G 629 MET cc_start: 0.7995 (OUTLIER) cc_final: 0.7395 (mtm) REVERT: J 5 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8685 (tp) REVERT: J 13 GLU cc_start: 0.7229 (tt0) cc_final: 0.6919 (tm-30) REVERT: M 23 LYS cc_start: 0.9080 (tmmt) cc_final: 0.8182 (mmtm) REVERT: M 36 TRP cc_start: 0.7759 (m100) cc_final: 0.7286 (m100) outliers start: 136 outliers final: 84 residues processed: 485 average time/residue: 0.3295 time to fit residues: 244.4686 Evaluate side-chains 452 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 362 time to evaluate : 2.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain C residue 16 CYS Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain H residue 82 ASN Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 31 SER Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 97 THR Chi-restraints excluded: chain N residue 104 LEU Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain F residue 629 MET Chi-restraints excluded: chain F residue 651 ILE Chi-restraints excluded: chain I residue 10 ASP Chi-restraints excluded: chain I residue 16 CYS Chi-restraints excluded: chain I residue 66 ASN Chi-restraints excluded: chain I residue 76 ILE Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 53 ILE Chi-restraints excluded: chain K residue 85 ASP Chi-restraints excluded: chain K residue 91 PHE Chi-restraints excluded: chain K residue 105 GLN Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 288 LEU Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 402 ASP Chi-restraints excluded: chain O residue 31 SER Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain O residue 93 ASN Chi-restraints excluded: chain O residue 104 LEU Chi-restraints excluded: chain G residue 523 LEU Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 603 ILE Chi-restraints excluded: chain G residue 629 MET Chi-restraints excluded: chain G residue 646 LEU Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 16 CYS Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 66 ASN Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 96 LEU Chi-restraints excluded: chain M residue 19 LYS Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 85 ASP Chi-restraints excluded: chain M residue 91 PHE Chi-restraints excluded: chain M residue 105 GLN Chi-restraints excluded: chain M residue 110 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 218 optimal weight: 2.9990 chunk 166 optimal weight: 0.7980 chunk 114 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 148 optimal weight: 0.7980 chunk 221 optimal weight: 0.9980 chunk 234 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 210 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 ASN B 620 ASN ** C 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 607 ASN ** I 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 GLN ** E 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 607 ASN G 620 ASN ** J 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.5072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21288 Z= 0.207 Angle : 0.687 8.586 28893 Z= 0.353 Chirality : 0.048 0.230 3447 Planarity : 0.004 0.043 3606 Dihedral : 7.071 53.592 4191 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.90 % Favored : 95.98 % Rotamer: Outliers : 4.64 % Allowed : 15.28 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 (0.16), residues: 2487 helix: 1.59 (0.25), residues: 417 sheet: 0.66 (0.21), residues: 684 loop : -1.43 (0.15), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 479 HIS 0.006 0.001 HIS I 27 PHE 0.018 0.002 PHE E 53 TYR 0.028 0.002 TYR K 100E ARG 0.006 0.000 ARG O 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 430 time to evaluate : 2.598 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.7411 (mtp) cc_final: 0.7191 (mtm) REVERT: A 209 SER cc_start: 0.7453 (t) cc_final: 0.7252 (p) REVERT: A 475 MET cc_start: 0.6933 (mmm) cc_final: 0.6401 (mmm) REVERT: L 83 PHE cc_start: 0.8539 (m-10) cc_final: 0.8209 (m-10) REVERT: B 540 GLN cc_start: 0.8657 (mm110) cc_final: 0.8036 (tt0) REVERT: B 629 MET cc_start: 0.7837 (mtp) cc_final: 0.7071 (mtm) REVERT: H 23 LYS cc_start: 0.9035 (tmmt) cc_final: 0.8301 (mmtm) REVERT: H 36 TRP cc_start: 0.7760 (m100) cc_final: 0.7230 (m100) REVERT: H 66 ARG cc_start: 0.7935 (mtm-85) cc_final: 0.7721 (mtm-85) REVERT: H 72 ASP cc_start: 0.7682 (t0) cc_final: 0.7321 (t0) REVERT: D 107 ASP cc_start: 0.8194 (OUTLIER) cc_final: 0.7881 (t70) REVERT: D 258 GLN cc_start: 0.8173 (mt0) cc_final: 0.7821 (mt0) REVERT: D 475 MET cc_start: 0.6954 (mmm) cc_final: 0.6490 (mmm) REVERT: D 479 TRP cc_start: 0.6300 (m-90) cc_final: 0.5937 (m-90) REVERT: F 543 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8848 (mm) REVERT: F 584 GLU cc_start: 0.8381 (pt0) cc_final: 0.7631 (tm-30) REVERT: F 585 ARG cc_start: 0.8629 (ttm-80) cc_final: 0.8369 (ttm170) REVERT: F 607 ASN cc_start: 0.8009 (OUTLIER) cc_final: 0.7746 (t0) REVERT: K 23 LYS cc_start: 0.9013 (tmmt) cc_final: 0.8306 (mmtm) REVERT: E 258 GLN cc_start: 0.7943 (mt0) cc_final: 0.7714 (mt0) REVERT: E 475 MET cc_start: 0.6812 (mmm) cc_final: 0.5282 (mmm) REVERT: E 479 TRP cc_start: 0.6237 (OUTLIER) cc_final: 0.5634 (m-90) REVERT: O 36 TYR cc_start: 0.6432 (m-80) cc_final: 0.6190 (m-10) REVERT: O 49 TYR cc_start: 0.7411 (t80) cc_final: 0.7189 (t80) REVERT: O 70 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8086 (mm-30) REVERT: G 540 GLN cc_start: 0.8713 (mm110) cc_final: 0.8285 (tt0) REVERT: M 23 LYS cc_start: 0.8993 (tmmt) cc_final: 0.8168 (mmtm) REVERT: M 30 ILE cc_start: 0.8523 (OUTLIER) cc_final: 0.8026 (tt) REVERT: M 100 PHE cc_start: 0.7445 (m-80) cc_final: 0.6885 (m-80) outliers start: 102 outliers final: 69 residues processed: 489 average time/residue: 0.3372 time to fit residues: 251.2916 Evaluate side-chains 453 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 379 time to evaluate : 2.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain C residue 16 CYS Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain H residue 82 ASN Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 31 SER Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain F residue 607 ASN Chi-restraints excluded: chain I residue 16 CYS Chi-restraints excluded: chain I residue 76 ILE Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain K residue 85 ASP Chi-restraints excluded: chain K residue 91 PHE Chi-restraints excluded: chain K residue 105 GLN Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 479 TRP Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 31 SER Chi-restraints excluded: chain O residue 93 ASN Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 592 LEU Chi-restraints excluded: chain G residue 603 ILE Chi-restraints excluded: chain G residue 646 LEU Chi-restraints excluded: chain J residue 16 CYS Chi-restraints excluded: chain J residue 60 SER Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 96 LEU Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 82 ASN Chi-restraints excluded: chain M residue 85 ASP Chi-restraints excluded: chain M residue 91 PHE Chi-restraints excluded: chain M residue 105 GLN Chi-restraints excluded: chain M residue 110 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 195 optimal weight: 7.9990 chunk 133 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 174 optimal weight: 7.9990 chunk 96 optimal weight: 9.9990 chunk 200 optimal weight: 7.9990 chunk 162 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 119 optimal weight: 20.0000 chunk 210 optimal weight: 0.1980 chunk 59 optimal weight: 0.8980 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 ASN ** C 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 ASN H 64 GLN ** D 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 607 ASN G 620 ASN ** J 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 64 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.5408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 21288 Z= 0.334 Angle : 0.723 10.854 28893 Z= 0.371 Chirality : 0.048 0.250 3447 Planarity : 0.005 0.088 3606 Dihedral : 6.909 59.762 4191 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.35 % Favored : 93.53 % Rotamer: Outliers : 5.96 % Allowed : 15.78 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.67 (0.16), residues: 2487 helix: 1.31 (0.25), residues: 423 sheet: 0.42 (0.20), residues: 702 loop : -1.56 (0.15), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP M 36 HIS 0.007 0.001 HIS A 374 PHE 0.018 0.003 PHE O 98 TYR 0.027 0.002 TYR K 100E ARG 0.008 0.001 ARG K 66 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 380 time to evaluate : 2.616 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: 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 217 TYR cc_start: 0.6590 (OUTLIER) cc_final: 0.5665 (m-80) REVERT: A 475 MET cc_start: 0.7263 (mmm) cc_final: 0.6077 (mmm) REVERT: A 479 TRP cc_start: 0.6540 (m-90) cc_final: 0.6184 (m-90) REVERT: L 83 PHE cc_start: 0.8621 (m-10) cc_final: 0.8335 (m-10) REVERT: B 540 GLN cc_start: 0.8698 (mm110) cc_final: 0.8112 (tt0) REVERT: B 629 MET cc_start: 0.7952 (mtp) cc_final: 0.7514 (mtm) REVERT: H 23 LYS cc_start: 0.9039 (tmmt) cc_final: 0.8293 (mmtm) REVERT: H 66 ARG cc_start: 0.8028 (mtm-85) cc_final: 0.7818 (mtm-85) REVERT: H 72 ASP cc_start: 0.7614 (t0) cc_final: 0.7234 (t0) REVERT: D 107 ASP cc_start: 0.8400 (OUTLIER) cc_final: 0.7972 (t70) REVERT: N 36 TYR cc_start: 0.6315 (m-80) cc_final: 0.5967 (m-80) REVERT: F 543 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8917 (mm) REVERT: F 629 MET cc_start: 0.7407 (OUTLIER) cc_final: 0.7160 (mtt) REVERT: K 23 LYS cc_start: 0.8978 (tmmt) cc_final: 0.8335 (mmtm) REVERT: K 30 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8170 (tt) REVERT: E 217 TYR cc_start: 0.6991 (OUTLIER) cc_final: 0.5734 (m-80) REVERT: E 475 MET cc_start: 0.7183 (mmm) cc_final: 0.6233 (mmm) REVERT: E 479 TRP cc_start: 0.6440 (m-90) cc_final: 0.6092 (m-90) REVERT: O 70 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8122 (mm-30) REVERT: O 83 PHE cc_start: 0.8716 (m-10) cc_final: 0.8397 (m-80) REVERT: G 540 GLN cc_start: 0.8720 (mm110) cc_final: 0.8311 (tt0) REVERT: G 657 GLU cc_start: 0.8724 (tp30) cc_final: 0.8453 (tp30) REVERT: M 12 LYS cc_start: 0.8173 (mttt) cc_final: 0.7892 (mttt) REVERT: M 23 LYS cc_start: 0.9022 (tmmt) cc_final: 0.8212 (mmtm) REVERT: M 30 ILE cc_start: 0.8580 (OUTLIER) cc_final: 0.7983 (tt) outliers start: 131 outliers final: 99 residues processed: 464 average time/residue: 0.3551 time to fit residues: 251.4497 Evaluate side-chains 459 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 353 time to evaluate : 2.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 16 CYS Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 82 ASN Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 333 ILE Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 31 SER Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 97 THR Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain F residue 629 MET Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 647 GLU Chi-restraints excluded: chain I residue 10 ASP Chi-restraints excluded: chain I residue 16 CYS Chi-restraints excluded: chain I residue 66 ASN Chi-restraints excluded: chain I residue 76 ILE Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain K residue 85 ASP Chi-restraints excluded: chain K residue 91 PHE Chi-restraints excluded: chain K residue 105 GLN Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 402 ASP Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 31 SER Chi-restraints excluded: chain O residue 93 ASN Chi-restraints excluded: chain G residue 543 LEU Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 592 LEU Chi-restraints excluded: chain G residue 603 ILE Chi-restraints excluded: chain G residue 607 ASN Chi-restraints excluded: chain G residue 646 LEU Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 16 CYS Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 96 LEU Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 82 ASN Chi-restraints excluded: chain M residue 84 SER Chi-restraints excluded: chain M residue 85 ASP Chi-restraints excluded: chain M residue 91 PHE Chi-restraints excluded: chain M residue 105 GLN Chi-restraints excluded: chain M residue 110 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 79 optimal weight: 4.9990 chunk 211 optimal weight: 8.9990 chunk 46 optimal weight: 7.9990 chunk 137 optimal weight: 9.9990 chunk 57 optimal weight: 0.8980 chunk 235 optimal weight: 5.9990 chunk 195 optimal weight: 0.9980 chunk 108 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 123 optimal weight: 6.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN B 607 ASN B 620 ASN ** C 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 ASN H 64 GLN ** D 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 607 ASN ** I 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 607 ASN G 620 ASN G 656 ASN ** J 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 64 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.5652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 21288 Z= 0.359 Angle : 0.732 10.621 28893 Z= 0.377 Chirality : 0.048 0.254 3447 Planarity : 0.005 0.054 3606 Dihedral : 6.870 58.152 4191 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.88 % Favored : 92.92 % Rotamer: Outliers : 6.32 % Allowed : 16.83 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.93 (0.16), residues: 2487 helix: 1.00 (0.24), residues: 441 sheet: 0.24 (0.20), residues: 711 loop : -1.73 (0.15), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP M 36 HIS 0.007 0.001 HIS E 374 PHE 0.035 0.003 PHE N 83 TYR 0.027 0.002 TYR K 100E ARG 0.010 0.001 ARG N 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 363 time to evaluate : 2.476 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: 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 217 TYR cc_start: 0.6623 (OUTLIER) cc_final: 0.5596 (m-80) REVERT: A 258 GLN cc_start: 0.8546 (mt0) cc_final: 0.8293 (mt0) REVERT: A 475 MET cc_start: 0.7291 (mmm) cc_final: 0.6658 (mmm) REVERT: L 83 PHE cc_start: 0.8682 (m-10) cc_final: 0.8341 (m-80) REVERT: B 530 MET cc_start: 0.8409 (mmm) cc_final: 0.8054 (mmt) REVERT: B 540 GLN cc_start: 0.8687 (mm110) cc_final: 0.8134 (tt0) REVERT: B 629 MET cc_start: 0.8088 (mtp) cc_final: 0.7814 (mtm) REVERT: C 94 GLN cc_start: 0.7192 (tp40) cc_final: 0.6922 (tp40) REVERT: H 23 LYS cc_start: 0.8972 (tmmt) cc_final: 0.8217 (mmtm) REVERT: H 72 ASP cc_start: 0.7580 (t0) cc_final: 0.7209 (t0) REVERT: D 107 ASP cc_start: 0.8378 (OUTLIER) cc_final: 0.8043 (t70) REVERT: D 258 GLN cc_start: 0.8546 (mt0) cc_final: 0.8238 (mt0) REVERT: D 453 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8819 (mt) REVERT: D 475 MET cc_start: 0.7523 (mmm) cc_final: 0.6431 (mmm) REVERT: N 36 TYR cc_start: 0.6424 (m-80) cc_final: 0.6154 (m-80) REVERT: N 49 TYR cc_start: 0.7265 (OUTLIER) cc_final: 0.7005 (t80) REVERT: N 83 PHE cc_start: 0.8778 (m-80) cc_final: 0.8537 (m-80) REVERT: F 543 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8869 (mm) REVERT: F 629 MET cc_start: 0.7560 (OUTLIER) cc_final: 0.7271 (mtt) REVERT: I 85 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7759 (tm-30) REVERT: K 23 LYS cc_start: 0.8987 (tmmt) cc_final: 0.8333 (mmtm) REVERT: E 217 TYR cc_start: 0.6923 (OUTLIER) cc_final: 0.5636 (m-80) REVERT: E 258 GLN cc_start: 0.8314 (mt0) cc_final: 0.7936 (mt0) REVERT: E 475 MET cc_start: 0.7364 (mmm) cc_final: 0.6377 (mmm) REVERT: E 479 TRP cc_start: 0.6451 (m-90) cc_final: 0.6177 (m-90) REVERT: O 83 PHE cc_start: 0.8714 (m-10) cc_final: 0.8443 (m-80) REVERT: G 540 GLN cc_start: 0.8708 (mm110) cc_final: 0.8349 (tt0) REVERT: G 657 GLU cc_start: 0.8757 (tp30) cc_final: 0.8487 (tp30) REVERT: M 23 LYS cc_start: 0.9039 (tmmt) cc_final: 0.8205 (mmtm) REVERT: M 84 SER cc_start: 0.9141 (OUTLIER) cc_final: 0.8896 (p) REVERT: M 100 PHE cc_start: 0.7473 (m-80) cc_final: 0.7233 (m-80) outliers start: 139 outliers final: 111 residues processed: 449 average time/residue: 0.3322 time to fit residues: 227.0118 Evaluate side-chains 466 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 347 time to evaluate : 2.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 607 ASN Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 16 CYS Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 82 ASN Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 333 ILE Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 31 SER Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain F residue 629 MET Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 647 GLU Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain I residue 10 ASP Chi-restraints excluded: chain I residue 16 CYS Chi-restraints excluded: chain I residue 66 ASN Chi-restraints excluded: chain I residue 76 ILE Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain K residue 84 SER Chi-restraints excluded: chain K residue 85 ASP Chi-restraints excluded: chain K residue 91 PHE Chi-restraints excluded: chain K residue 105 GLN Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 402 ASP Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain O residue 31 SER Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 93 ASN Chi-restraints excluded: chain G residue 543 LEU Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 592 LEU Chi-restraints excluded: chain G residue 603 ILE Chi-restraints excluded: chain G residue 626 MET Chi-restraints excluded: chain G residue 646 LEU Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 10 ASP Chi-restraints excluded: chain J residue 16 CYS Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 96 LEU Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 82 ASN Chi-restraints excluded: chain M residue 84 SER Chi-restraints excluded: chain M residue 85 ASP Chi-restraints excluded: chain M residue 91 PHE Chi-restraints excluded: chain M residue 105 GLN Chi-restraints excluded: chain M residue 110 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 226 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 171 optimal weight: 6.9990 chunk 197 optimal weight: 0.9980 chunk 131 optimal weight: 0.8980 chunk 234 optimal weight: 10.0000 chunk 146 optimal weight: 7.9990 chunk 142 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 144 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 620 ASN ** C 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 79 GLN ** O 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 620 ASN ** J 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.5776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 21288 Z= 0.204 Angle : 0.680 11.225 28893 Z= 0.344 Chirality : 0.046 0.229 3447 Planarity : 0.005 0.050 3606 Dihedral : 6.360 56.393 4191 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.23 % Favored : 94.65 % Rotamer: Outliers : 4.82 % Allowed : 18.64 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.43 (0.16), residues: 2487 helix: 1.70 (0.25), residues: 420 sheet: 0.79 (0.21), residues: 618 loop : -1.48 (0.15), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP D 479 HIS 0.003 0.001 HIS E 374 PHE 0.031 0.002 PHE N 83 TYR 0.028 0.002 TYR K 100E ARG 0.011 0.001 ARG N 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 385 time to evaluate : 2.416 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.7431 (mtp) cc_final: 0.7204 (mtm) REVERT: A 258 GLN cc_start: 0.8240 (mt0) cc_final: 0.7924 (mt0) REVERT: A 479 TRP cc_start: 0.6561 (m-90) cc_final: 0.6160 (m-90) REVERT: L 46 LEU cc_start: 0.7788 (tp) cc_final: 0.7412 (tp) REVERT: L 83 PHE cc_start: 0.8697 (m-10) cc_final: 0.8328 (m-80) REVERT: B 540 GLN cc_start: 0.8638 (mm110) cc_final: 0.8149 (tt0) REVERT: B 584 GLU cc_start: 0.8430 (pt0) cc_final: 0.7657 (tm-30) REVERT: B 629 MET cc_start: 0.7931 (mtp) cc_final: 0.7462 (mtm) REVERT: C 94 GLN cc_start: 0.7044 (tp40) cc_final: 0.6832 (tp40) REVERT: H 23 LYS cc_start: 0.8959 (tmmt) cc_final: 0.8242 (mmtm) REVERT: H 72 ASP cc_start: 0.7604 (t0) cc_final: 0.7243 (t0) REVERT: D 107 ASP cc_start: 0.8356 (OUTLIER) cc_final: 0.7994 (t70) REVERT: D 258 GLN cc_start: 0.8300 (mt0) cc_final: 0.7824 (mt0) REVERT: N 83 PHE cc_start: 0.8696 (m-80) cc_final: 0.8464 (m-80) REVERT: F 584 GLU cc_start: 0.8421 (pt0) cc_final: 0.7637 (tm-30) REVERT: F 629 MET cc_start: 0.7120 (OUTLIER) cc_final: 0.6598 (mtt) REVERT: I 76 ILE cc_start: 0.9362 (OUTLIER) cc_final: 0.9110 (pt) REVERT: I 80 ASP cc_start: 0.8161 (t0) cc_final: 0.7882 (t0) REVERT: I 85 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7701 (tm-30) REVERT: I 94 GLN cc_start: 0.7030 (tp40) cc_final: 0.6293 (tp40) REVERT: K 23 LYS cc_start: 0.8959 (tmmt) cc_final: 0.8365 (mmtm) REVERT: K 30 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.8210 (tt) REVERT: E 258 GLN cc_start: 0.8022 (mt0) cc_final: 0.7805 (mt0) REVERT: E 475 MET cc_start: 0.7147 (mmm) cc_final: 0.5776 (mmm) REVERT: E 479 TRP cc_start: 0.6333 (m-90) cc_final: 0.5770 (m-90) REVERT: O 36 TYR cc_start: 0.6007 (m-80) cc_final: 0.5762 (m-10) REVERT: O 46 LEU cc_start: 0.8162 (tp) cc_final: 0.7931 (tp) REVERT: O 83 PHE cc_start: 0.8707 (m-10) cc_final: 0.8444 (m-80) REVERT: G 540 GLN cc_start: 0.8645 (mm110) cc_final: 0.8303 (tt0) REVERT: G 657 GLU cc_start: 0.8749 (tp30) cc_final: 0.8479 (tp30) REVERT: M 23 LYS cc_start: 0.8987 (tmmt) cc_final: 0.8238 (mmtm) REVERT: M 85 ASP cc_start: 0.8402 (OUTLIER) cc_final: 0.7622 (t0) outliers start: 106 outliers final: 90 residues processed: 443 average time/residue: 0.3441 time to fit residues: 231.1138 Evaluate side-chains 445 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 350 time to evaluate : 2.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 16 CYS Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 31 SER Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain F residue 629 MET Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 647 GLU Chi-restraints excluded: chain I residue 10 ASP Chi-restraints excluded: chain I residue 16 CYS Chi-restraints excluded: chain I residue 76 ILE Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 84 SER Chi-restraints excluded: chain K residue 85 ASP Chi-restraints excluded: chain K residue 91 PHE Chi-restraints excluded: chain K residue 105 GLN Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 402 ASP Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 31 SER Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 93 ASN Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 592 LEU Chi-restraints excluded: chain G residue 603 ILE Chi-restraints excluded: chain G residue 626 MET Chi-restraints excluded: chain G residue 646 LEU Chi-restraints excluded: chain G residue 661 LEU Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 10 ASP Chi-restraints excluded: chain J residue 16 CYS Chi-restraints excluded: chain J residue 60 SER Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 96 LEU Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 84 SER Chi-restraints excluded: chain M residue 85 ASP Chi-restraints excluded: chain M residue 91 PHE Chi-restraints excluded: chain M residue 105 GLN Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 110 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 93 optimal weight: 0.9990 chunk 139 optimal weight: 0.6980 chunk 70 optimal weight: 20.0000 chunk 46 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 148 optimal weight: 6.9990 chunk 159 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 184 optimal weight: 1.9990 chunk 213 optimal weight: 0.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 ASN B 620 ASN ** C 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 ASN ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 79 GLN G 620 ASN ** J 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 64 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.5922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 21288 Z= 0.233 Angle : 0.684 11.735 28893 Z= 0.346 Chirality : 0.046 0.236 3447 Planarity : 0.005 0.052 3606 Dihedral : 6.251 57.229 4191 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.35 % Favored : 93.53 % Rotamer: Outliers : 5.28 % Allowed : 18.96 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.61 (0.16), residues: 2487 helix: 1.47 (0.25), residues: 438 sheet: 0.48 (0.20), residues: 678 loop : -1.58 (0.15), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 479 HIS 0.004 0.001 HIS E 374 PHE 0.028 0.002 PHE N 83 TYR 0.027 0.002 TYR M 100E ARG 0.010 0.000 ARG N 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 365 time to evaluate : 2.380 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: 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 100 MET cc_start: 0.7532 (mtp) cc_final: 0.7294 (mtm) REVERT: A 217 TYR cc_start: 0.6615 (OUTLIER) cc_final: 0.5519 (m-80) REVERT: A 258 GLN cc_start: 0.8353 (mt0) cc_final: 0.8021 (mt0) REVERT: L 46 LEU cc_start: 0.7696 (tp) cc_final: 0.7293 (tp) REVERT: L 83 PHE cc_start: 0.8680 (m-10) cc_final: 0.8256 (m-80) REVERT: B 540 GLN cc_start: 0.8641 (mm110) cc_final: 0.8170 (tt0) REVERT: B 629 MET cc_start: 0.7953 (mtp) cc_final: 0.7699 (mtm) REVERT: H 23 LYS cc_start: 0.8960 (tmmt) cc_final: 0.8236 (mmtm) REVERT: H 72 ASP cc_start: 0.7596 (t0) cc_final: 0.7239 (t0) REVERT: D 107 ASP cc_start: 0.8377 (OUTLIER) cc_final: 0.8023 (t70) REVERT: D 258 GLN cc_start: 0.8387 (mt0) cc_final: 0.8081 (mt0) REVERT: D 453 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8721 (mt) REVERT: N 46 LEU cc_start: 0.7996 (tp) cc_final: 0.7788 (tp) REVERT: F 629 MET cc_start: 0.7190 (OUTLIER) cc_final: 0.6672 (mtt) REVERT: F 647 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7926 (tt0) REVERT: I 76 ILE cc_start: 0.9343 (OUTLIER) cc_final: 0.9111 (pt) REVERT: I 85 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7763 (tm-30) REVERT: K 23 LYS cc_start: 0.8941 (tmmt) cc_final: 0.8304 (mmtm) REVERT: K 30 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.8110 (tt) REVERT: E 258 GLN cc_start: 0.8131 (mt0) cc_final: 0.7842 (mt0) REVERT: E 475 MET cc_start: 0.7236 (mmm) cc_final: 0.6328 (mmm) REVERT: E 479 TRP cc_start: 0.6394 (m-90) cc_final: 0.6086 (m-90) REVERT: O 83 PHE cc_start: 0.8784 (m-10) cc_final: 0.8477 (m-80) REVERT: G 530 MET cc_start: 0.7884 (mmm) cc_final: 0.7598 (mmt) REVERT: G 540 GLN cc_start: 0.8657 (mm110) cc_final: 0.8323 (tt0) REVERT: G 657 GLU cc_start: 0.8765 (tp30) cc_final: 0.8526 (tp30) REVERT: J 94 GLN cc_start: 0.7153 (tp40) cc_final: 0.6797 (tp40) REVERT: M 23 LYS cc_start: 0.8976 (tmmt) cc_final: 0.8232 (mmtm) REVERT: M 85 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.7574 (t0) outliers start: 116 outliers final: 101 residues processed: 433 average time/residue: 0.3411 time to fit residues: 224.2719 Evaluate side-chains 455 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 346 time to evaluate : 2.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 16 CYS Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 333 ILE Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 408 THR Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 31 SER Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain F residue 626 MET Chi-restraints excluded: chain F residue 629 MET Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 647 GLU Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain I residue 10 ASP Chi-restraints excluded: chain I residue 16 CYS Chi-restraints excluded: chain I residue 76 ILE Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 16 SER Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 85 ASP Chi-restraints excluded: chain K residue 91 PHE Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 402 ASP Chi-restraints excluded: chain E residue 408 THR Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 49 TYR Chi-restraints excluded: chain O residue 75 ILE Chi-restraints excluded: chain O residue 93 ASN Chi-restraints excluded: chain G residue 543 LEU Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 592 LEU Chi-restraints excluded: chain G residue 603 ILE Chi-restraints excluded: chain G residue 626 MET Chi-restraints excluded: chain G residue 646 LEU Chi-restraints excluded: chain G residue 661 LEU Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 10 ASP Chi-restraints excluded: chain J residue 16 CYS Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 96 LEU Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 84 SER Chi-restraints excluded: chain M residue 85 ASP Chi-restraints excluded: chain M residue 91 PHE Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 110 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 224 optimal weight: 6.9990 chunk 204 optimal weight: 8.9990 chunk 218 optimal weight: 10.0000 chunk 131 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 171 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 197 optimal weight: 4.9990 chunk 206 optimal weight: 20.0000 chunk 217 optimal weight: 10.0000 chunk 143 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 620 ASN ** C 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 620 ASN ** I 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 620 ASN ** J 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.6159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 21288 Z= 0.463 Angle : 0.829 12.456 28893 Z= 0.426 Chirality : 0.051 0.273 3447 Planarity : 0.006 0.058 3606 Dihedral : 6.938 56.499 4191 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 21.45 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.12 % Favored : 91.64 % Rotamer: Outliers : 5.46 % Allowed : 19.42 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.23 (0.16), residues: 2487 helix: 0.57 (0.24), residues: 459 sheet: 0.20 (0.20), residues: 660 loop : -1.91 (0.15), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP E 45 HIS 0.009 0.002 HIS E 374 PHE 0.023 0.004 PHE N 98 TYR 0.030 0.003 TYR K 100E ARG 0.016 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 338 time to evaluate : 2.430 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.7912 (mtp) cc_final: 0.7634 (mtm) REVERT: A 217 TYR cc_start: 0.6722 (OUTLIER) cc_final: 0.5470 (m-80) REVERT: A 258 GLN cc_start: 0.8772 (mt0) cc_final: 0.8549 (mt0) REVERT: A 475 MET cc_start: 0.7552 (mmm) cc_final: 0.7330 (mmm) REVERT: A 478 ASN cc_start: 0.8373 (m110) cc_final: 0.8031 (m110) REVERT: L 46 LEU cc_start: 0.7745 (tp) cc_final: 0.7491 (tp) REVERT: L 83 PHE cc_start: 0.8721 (m-10) cc_final: 0.8303 (m-80) REVERT: B 540 GLN cc_start: 0.8714 (mm110) cc_final: 0.8219 (tt0) REVERT: H 23 LYS cc_start: 0.8923 (tmmt) cc_final: 0.8160 (mmtm) REVERT: H 72 ASP cc_start: 0.7656 (t0) cc_final: 0.7308 (t0) REVERT: D 107 ASP cc_start: 0.8460 (OUTLIER) cc_final: 0.8057 (t70) REVERT: D 258 GLN cc_start: 0.8697 (mt0) cc_final: 0.8433 (mt0) REVERT: D 453 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8916 (mt) REVERT: F 629 MET cc_start: 0.7751 (OUTLIER) cc_final: 0.7306 (mtp) REVERT: I 76 ILE cc_start: 0.9369 (OUTLIER) cc_final: 0.9136 (pt) REVERT: I 80 ASP cc_start: 0.8303 (t0) cc_final: 0.7971 (t0) REVERT: I 85 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7846 (tm-30) REVERT: I 94 GLN cc_start: 0.7204 (tp40) cc_final: 0.6764 (tp40) REVERT: K 23 LYS cc_start: 0.8981 (tmmt) cc_final: 0.8271 (mmtm) REVERT: E 217 TYR cc_start: 0.7001 (OUTLIER) cc_final: 0.5491 (m-80) REVERT: E 258 GLN cc_start: 0.8629 (mt0) cc_final: 0.8424 (mt0) REVERT: E 475 MET cc_start: 0.7567 (mmm) cc_final: 0.7320 (mmm) REVERT: O 83 PHE cc_start: 0.8818 (m-10) cc_final: 0.8490 (m-80) REVERT: G 540 GLN cc_start: 0.8711 (mm110) cc_final: 0.8389 (tt0) REVERT: G 657 GLU cc_start: 0.8830 (tp30) cc_final: 0.8569 (tp30) REVERT: M 23 LYS cc_start: 0.8964 (tmmt) cc_final: 0.8162 (mmtm) REVERT: M 36 TRP cc_start: 0.7598 (m100) cc_final: 0.7145 (m100) REVERT: M 85 ASP cc_start: 0.8360 (OUTLIER) cc_final: 0.7566 (t0) outliers start: 120 outliers final: 104 residues processed: 411 average time/residue: 0.3394 time to fit residues: 213.9618 Evaluate side-chains 444 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 333 time to evaluate : 2.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 16 CYS Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 82 ASN Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 333 ILE Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 408 THR Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 31 SER Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain F residue 629 MET Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 10 ASP Chi-restraints excluded: chain I residue 16 CYS Chi-restraints excluded: chain I residue 66 ASN Chi-restraints excluded: chain I residue 76 ILE Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 16 SER Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 85 ASP Chi-restraints excluded: chain K residue 91 PHE Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 402 ASP Chi-restraints excluded: chain E residue 408 THR Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 75 ILE Chi-restraints excluded: chain O residue 93 ASN Chi-restraints excluded: chain G residue 543 LEU Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 592 LEU Chi-restraints excluded: chain G residue 603 ILE Chi-restraints excluded: chain G residue 626 MET Chi-restraints excluded: chain G residue 646 LEU Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 10 ASP Chi-restraints excluded: chain J residue 16 CYS Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 96 LEU Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 30 ILE Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 84 SER Chi-restraints excluded: chain M residue 85 ASP Chi-restraints excluded: chain M residue 91 PHE Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 110 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 230 optimal weight: 20.0000 chunk 140 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 160 optimal weight: 2.9990 chunk 242 optimal weight: 0.0030 chunk 222 optimal weight: 20.0000 chunk 192 optimal weight: 0.9980 chunk 20 optimal weight: 8.9990 chunk 148 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 153 optimal weight: 0.9990 overall best weight: 0.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 620 ASN ** C 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 GLN ** D 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 620 ASN ** I 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 620 ASN ** J 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 64 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.6234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 21288 Z= 0.208 Angle : 0.727 12.385 28893 Z= 0.367 Chirality : 0.047 0.230 3447 Planarity : 0.005 0.056 3606 Dihedral : 6.287 54.070 4191 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.63 % Favored : 94.25 % Rotamer: Outliers : 4.23 % Allowed : 21.10 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.70 (0.16), residues: 2487 helix: 1.63 (0.25), residues: 411 sheet: 0.56 (0.21), residues: 624 loop : -1.65 (0.15), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP K 36 HIS 0.003 0.001 HIS D 216 PHE 0.027 0.002 PHE N 62 TYR 0.031 0.002 TYR K 100E ARG 0.014 0.001 ARG L 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 355 time to evaluate : 2.477 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.7399 (mtp) cc_final: 0.7128 (mtm) REVERT: A 202 THR cc_start: 0.9098 (m) cc_final: 0.8709 (p) REVERT: A 258 GLN cc_start: 0.8264 (mt0) cc_final: 0.7912 (mt0) REVERT: A 475 MET cc_start: 0.7098 (mmm) cc_final: 0.6787 (mmm) REVERT: L 46 LEU cc_start: 0.7688 (tp) cc_final: 0.7447 (tp) REVERT: L 83 PHE cc_start: 0.8608 (m-10) cc_final: 0.8254 (m-80) REVERT: B 540 GLN cc_start: 0.8629 (mm110) cc_final: 0.8318 (tt0) REVERT: B 584 GLU cc_start: 0.8239 (pt0) cc_final: 0.7500 (tm-30) REVERT: B 629 MET cc_start: 0.7238 (mtm) cc_final: 0.6907 (mtm) REVERT: C 76 ILE cc_start: 0.9369 (OUTLIER) cc_final: 0.9168 (pt) REVERT: H 23 LYS cc_start: 0.8997 (tmmt) cc_final: 0.8238 (mmtm) REVERT: H 72 ASP cc_start: 0.7530 (t0) cc_final: 0.7202 (t0) REVERT: D 107 ASP cc_start: 0.8343 (OUTLIER) cc_final: 0.8046 (t70) REVERT: D 202 THR cc_start: 0.9193 (m) cc_final: 0.8840 (p) REVERT: D 479 TRP cc_start: 0.6502 (m-90) cc_final: 0.5542 (m-90) REVERT: F 629 MET cc_start: 0.7265 (OUTLIER) cc_final: 0.6839 (mtt) REVERT: I 76 ILE cc_start: 0.9344 (OUTLIER) cc_final: 0.9138 (pt) REVERT: I 80 ASP cc_start: 0.8215 (t0) cc_final: 0.7873 (t0) REVERT: I 85 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7752 (tm-30) REVERT: I 94 GLN cc_start: 0.7094 (tp40) cc_final: 0.6618 (tp40) REVERT: E 258 GLN cc_start: 0.8140 (mt0) cc_final: 0.7932 (mt0) REVERT: E 475 MET cc_start: 0.7176 (mmm) cc_final: 0.6082 (mmm) REVERT: E 479 TRP cc_start: 0.6153 (m-90) cc_final: 0.5914 (m-90) REVERT: O 21 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8409 (mt) REVERT: O 83 PHE cc_start: 0.8775 (m-10) cc_final: 0.8449 (m-80) REVERT: G 540 GLN cc_start: 0.8647 (mm110) cc_final: 0.8391 (tt0) REVERT: G 657 GLU cc_start: 0.8756 (tp30) cc_final: 0.8480 (tp30) REVERT: M 23 LYS cc_start: 0.8966 (tmmt) cc_final: 0.8214 (mmtm) REVERT: M 85 ASP cc_start: 0.8220 (OUTLIER) cc_final: 0.7534 (t0) outliers start: 93 outliers final: 78 residues processed: 410 average time/residue: 0.3367 time to fit residues: 210.8051 Evaluate side-chains 425 residues out of total 2199 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 341 time to evaluate : 2.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 16 CYS Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 91 PHE Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 408 THR Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain F residue 629 MET Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 10 ASP Chi-restraints excluded: chain I residue 16 CYS Chi-restraints excluded: chain I residue 76 ILE Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 85 ASP Chi-restraints excluded: chain K residue 91 PHE Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 408 THR Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 93 ASN Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 592 LEU Chi-restraints excluded: chain G residue 603 ILE Chi-restraints excluded: chain G residue 626 MET Chi-restraints excluded: chain G residue 646 LEU Chi-restraints excluded: chain G residue 661 LEU Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 10 ASP Chi-restraints excluded: chain J residue 16 CYS Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain M residue 84 SER Chi-restraints excluded: chain M residue 85 ASP Chi-restraints excluded: chain M residue 91 PHE Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 110 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 177 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 193 optimal weight: 0.8980 chunk 80 optimal weight: 0.5980 chunk 198 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 169 optimal weight: 0.8980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 620 ASN ** I 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 620 ASN ** J 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.126795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.099338 restraints weight = 53746.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.102904 restraints weight = 29539.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.105415 restraints weight = 19637.642| |-----------------------------------------------------------------------------| r_work (final): 0.4113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.6323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 21288 Z= 0.248 Angle : 0.728 12.640 28893 Z= 0.369 Chirality : 0.047 0.244 3447 Planarity : 0.005 0.053 3606 Dihedral : 6.229 54.786 4191 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.16 % Favored : 92.68 % Rotamer: Outliers : 4.46 % Allowed : 20.87 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.67 (0.17), residues: 2487 helix: 1.75 (0.26), residues: 408 sheet: 0.37 (0.21), residues: 675 loop : -1.62 (0.15), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP D 479 HIS 0.004 0.001 HIS E 374 PHE 0.021 0.002 PHE N 62 TYR 0.029 0.002 TYR K 100E ARG 0.013 0.001 ARG L 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4942.95 seconds wall clock time: 91 minutes 3.23 seconds (5463.23 seconds total)