Starting phenix.real_space_refine on Wed Feb 21 22:11:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2f_23127/02_2024/7l2f_23127.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2f_23127/02_2024/7l2f_23127.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2f_23127/02_2024/7l2f_23127.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2f_23127/02_2024/7l2f_23127.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2f_23127/02_2024/7l2f_23127.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2f_23127/02_2024/7l2f_23127.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.017 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 132 5.16 5 C 20355 2.51 5 N 5263 2.21 5 O 6299 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 40": "OD1" <-> "OD2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 138": "OD1" <-> "OD2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A ARG 246": "NH1" <-> "NH2" Residue "A ASP 253": "OD1" <-> "OD2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A ARG 346": "NH1" <-> "NH2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "A GLU 484": "OE1" <-> "OE2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 619": "OE1" <-> "OE2" Residue "A ARG 646": "NH1" <-> "NH2" Residue "A GLU 725": "OE1" <-> "OE2" Residue "A GLU 748": "OE1" <-> "OE2" Residue "A GLU 773": "OE1" <-> "OE2" Residue "A PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 40": "OD1" <-> "OD2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 138": "OD1" <-> "OD2" Residue "B TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B ARG 246": "NH1" <-> "NH2" Residue "B ASP 253": "OD1" <-> "OD2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 466": "NH1" <-> "NH2" Residue "B GLU 516": "OE1" <-> "OE2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "B ARG 1039": "NH1" <-> "NH2" Residue "B GLU 1111": "OE1" <-> "OE2" Residue "B GLU 1144": "OE1" <-> "OE2" Residue "C ASP 40": "OD1" <-> "OD2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 138": "OD1" <-> "OD2" Residue "C TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C ARG 246": "NH1" <-> "NH2" Residue "C ASP 253": "OD1" <-> "OD2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 466": "NH1" <-> "NH2" Residue "C GLU 471": "OE1" <-> "OE2" Residue "C GLU 484": "OE1" <-> "OE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 619": "OE1" <-> "OE2" Residue "C GLU 661": "OE1" <-> "OE2" Residue "C GLU 748": "OE1" <-> "OE2" Residue "C GLU 773": "OE1" <-> "OE2" Residue "C PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "C ARG 1014": "NH1" <-> "NH2" Residue "C GLU 1017": "OE1" <-> "OE2" Residue "C GLU 1031": "OE1" <-> "OE2" Residue "H ASP 53": "OD1" <-> "OD2" Residue "H TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 85": "OE1" <-> "OE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 1": "OE1" <-> "OE2" Residue "L GLU 17": "OE1" <-> "OE2" Residue "L TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 53": "OD1" <-> "OD2" Residue "G TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 1": "OE1" <-> "OE2" Residue "J GLU 17": "OE1" <-> "OE2" Residue "J TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 53": "OD1" <-> "OD2" Residue "I TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 1": "OE1" <-> "OE2" Residue "K GLU 17": "OE1" <-> "OE2" Residue "K TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 32049 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 8512 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1088, 8509 Classifications: {'peptide': 1088} Link IDs: {'PTRANS': 55, 'TRANS': 1032} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 1088, 8509 Classifications: {'peptide': 1088} Link IDs: {'PTRANS': 55, 'TRANS': 1032} Chain breaks: 4 bond proxies already assigned to first conformer: 8706 Chain: "B" Number of atoms: 8512 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1088, 8509 Classifications: {'peptide': 1088} Link IDs: {'PTRANS': 55, 'TRANS': 1032} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 1088, 8509 Classifications: {'peptide': 1088} Link IDs: {'PTRANS': 55, 'TRANS': 1032} Chain breaks: 4 bond proxies already assigned to first conformer: 8706 Chain: "C" Number of atoms: 8517 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1089, 8514 Classifications: {'peptide': 1089} Link IDs: {'PTRANS': 55, 'TRANS': 1033} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 1089, 8514 Classifications: {'peptide': 1089} Link IDs: {'PTRANS': 55, 'TRANS': 1033} Chain breaks: 4 bond proxies already assigned to first conformer: 8711 Chain: "H" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1011 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "L" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 815 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 102} Chain: "G" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1011 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "J" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 815 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 102} Chain: "I" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1011 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "K" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 815 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 102} 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 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: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 31.62, per 1000 atoms: 0.99 Number of scatterers: 32049 At special positions: 0 Unit cell: (194.74, 190.46, 191.53, 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 132 16.00 O 6299 8.00 N 5263 7.00 C 20355 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.02 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=1.99 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " 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 a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " NAG-ASN " NAG A1301 " - " ASN A 709 " " NAG A1302 " - " ASN A1074 " " NAG A1303 " - " ASN A 657 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 61 " " NAG A1309 " - " ASN A 149 " " NAG A1310 " - " ASN A 165 " " NAG A1311 " - " ASN A 282 " " NAG A1312 " - " ASN A 17 " " NAG B1301 " - " ASN B1074 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 657 " " NAG B1304 " - " ASN B 603 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B 61 " " NAG B1307 " - " ASN B 149 " " NAG B1308 " - " ASN B 165 " " NAG B1309 " - " ASN B 331 " " NAG B1310 " - " ASN B 17 " " NAG B1311 " - " ASN B 282 " " NAG B1312 " - " ASN B 343 " " NAG C1301 " - " ASN C 709 " " NAG C1302 " - " ASN C1074 " " NAG C1303 " - " ASN C 343 " " NAG C1304 " - " ASN C 657 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 331 " " NAG C1308 " - " ASN C 61 " " NAG C1309 " - " ASN C 149 " " NAG C1310 " - " ASN C 165 " " NAG C1311 " - " ASN C 282 " " NAG C1312 " - " ASN C 17 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN A 122 " " NAG O 1 " - " ASN A 234 " " NAG P 1 " - " ASN B 717 " " NAG Q 1 " - " ASN B 801 " " NAG R 1 " - " ASN B1098 " " NAG S 1 " - " ASN B1134 " " NAG T 1 " - " ASN B 122 " " NAG U 1 " - " ASN B 234 " " NAG V 1 " - " ASN C 717 " " NAG W 1 " - " ASN C 801 " " NAG X 1 " - " ASN C1098 " " NAG Y 1 " - " ASN C1134 " " NAG Z 1 " - " ASN C 122 " " NAG a 1 " - " ASN C 234 " Time building additional restraints: 12.47 Conformation dependent library (CDL) restraints added in 9.8 seconds 7862 Ramachandran restraints generated. 3931 Oldfield, 0 Emsley, 3931 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7376 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 66 sheets defined 21.6% alpha, 27.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.21 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 365 through 372 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.498A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 618 No H-bonds generated for 'chain 'A' and resid 616 through 618' Processing helix chain 'A' and resid 619 through 625 Processing helix chain 'A' and resid 630 through 638 Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.555A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 752 Processing helix chain 'A' and resid 752 through 783 removed outlier: 5.763A pdb=" N SER A 758 " --> pdb=" O LEU A 754 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N PHE A 759 " --> pdb=" O GLN A 755 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N CYS A 760 " --> pdb=" O TYR A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.558A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.916A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.663A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.700A pdb=" N SER A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 968 removed outlier: 3.602A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER A 968 " --> pdb=" O LYS A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.614A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 5.587A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.567A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 364 through 372 removed outlier: 3.759A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.656A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 616 through 618 No H-bonds generated for 'chain 'B' and resid 616 through 618' Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 630 through 638 removed outlier: 3.506A pdb=" N TYR B 636 " --> pdb=" O THR B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 748 through 783 removed outlier: 5.065A pdb=" N SER B 758 " --> pdb=" O LEU B 754 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N PHE B 759 " --> pdb=" O GLN B 755 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N CYS B 760 " --> pdb=" O TYR B 756 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA B 783 " --> pdb=" O GLN B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 853 through 857 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.585A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.709A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 942 Processing helix chain 'B' and resid 945 through 966 Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 5.593A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.545A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 365 through 372 Processing helix chain 'C' and resid 383 through 388 removed outlier: 4.365A pdb=" N ASN C 388 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.388A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.699A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 618 No H-bonds generated for 'chain 'C' and resid 616 through 618' Processing helix chain 'C' and resid 619 through 625 Processing helix chain 'C' and resid 630 through 638 removed outlier: 3.725A pdb=" N TYR C 636 " --> pdb=" O THR C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 748 through 756 removed outlier: 3.586A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 783 removed outlier: 3.531A pdb=" N THR C 761 " --> pdb=" O GLY C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 796 through 800 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 853 through 857 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.714A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.753A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.661A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 942 removed outlier: 3.505A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA C 942 " --> pdb=" O LEU C 938 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 968 removed outlier: 3.718A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER C 968 " --> pdb=" O LYS C 964 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.047A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.452A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 100D removed outlier: 3.536A pdb=" N PHE H 100B" --> pdb=" O ASP H 98 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.721A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 100D removed outlier: 3.536A pdb=" N PHE G 100B" --> pdb=" O ASP G 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.721A pdb=" N PHE J 83 " --> pdb=" O PRO J 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 100D removed outlier: 3.535A pdb=" N PHE I 100B" --> pdb=" O ASP I 98 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.721A pdb=" N PHE K 83 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 6.705A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.764A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 9.587A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.624A pdb=" N THR A 51 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 12.637A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 12.278A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 9.247A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 10.694A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N TRP A 152 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.279A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 3.890A pdb=" N ILE A 584 " --> pdb=" O SER A 555 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU A 585 " --> pdb=" O VAL A 576 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.717A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER A 514 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.908A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.596A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 660 removed outlier: 5.966A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.739A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.315A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.766A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 30 Processing sheet with id=AC2, first strand: chain 'B' and resid 36 through 37 removed outlier: 6.706A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.764A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 9.588A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.681A pdb=" N PHE B 55 " --> pdb=" O GLN B 271 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 12.638A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 12.277A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 9.247A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 10.693A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N TRP B 152 " --> pdb=" O HIS B 146 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.279A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AC7, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.978A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.524A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.083A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.223A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.257A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.286A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD9, first strand: chain 'C' and resid 28 through 30 Processing sheet with id=AE1, first strand: chain 'C' and resid 36 through 37 removed outlier: 6.706A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.764A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 9.587A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.680A pdb=" N PHE C 55 " --> pdb=" O GLN C 271 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 12.638A pdb=" N PHE C 238 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 12.277A pdb=" N ASN C 137 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 9.247A pdb=" N THR C 240 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LEU C 242 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 10.694A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N TRP C 152 " --> pdb=" O HIS C 146 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.280A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.686A pdb=" N PHE C 643 " --> pdb=" O LEU C 650 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.714A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.926A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE C 402 " --> pdb=" O TYR C 508 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.263A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.891A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.081A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 712 through 715 removed outlier: 3.613A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.657A pdb=" N LEU C 727 " --> pdb=" O VAL C1060 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL C1060 " --> pdb=" O LEU C 727 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.199A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1123 removed outlier: 3.779A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 6 through 7 removed outlier: 3.973A pdb=" N SER H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 10 through 11 removed outlier: 4.390A pdb=" N THR H 110 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TRP H 36 " --> pdb=" O GLY H 49 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR H 58 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 10 through 11 removed outlier: 4.390A pdb=" N THR H 110 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.514A pdb=" N SER L 7 " --> pdb=" O SER L 22 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.522A pdb=" N ALA L 34 " --> pdb=" O GLN L 89 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 6 through 7 removed outlier: 3.972A pdb=" N SER G 21 " --> pdb=" O SER G 7 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU G 18 " --> pdb=" O MET G 82 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET G 82 " --> pdb=" O LEU G 18 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR G 77 " --> pdb=" O ASP G 72 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 10 through 11 removed outlier: 4.389A pdb=" N THR G 110 " --> pdb=" O GLY G 10 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TRP G 36 " --> pdb=" O GLY G 49 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR G 58 " --> pdb=" O VAL G 50 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'G' and resid 10 through 11 removed outlier: 4.389A pdb=" N THR G 110 " --> pdb=" O GLY G 10 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL G 102 " --> pdb=" O ARG G 94 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'J' and resid 5 through 7 removed outlier: 3.514A pdb=" N SER J 7 " --> pdb=" O SER J 22 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER J 22 " --> pdb=" O SER J 7 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE J 71 " --> pdb=" O CYS J 23 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.521A pdb=" N ALA J 34 " --> pdb=" O GLN J 89 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N GLN J 37 " --> pdb=" O LEU J 46 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU J 46 " --> pdb=" O GLN J 37 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'I' and resid 6 through 7 removed outlier: 3.973A pdb=" N SER I 21 " --> pdb=" O SER I 7 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR I 77 " --> pdb=" O ASP I 72 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'I' and resid 10 through 11 removed outlier: 4.389A pdb=" N THR I 110 " --> pdb=" O GLY I 10 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TRP I 36 " --> pdb=" O GLY I 49 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR I 58 " --> pdb=" O VAL I 50 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'I' and resid 10 through 11 removed outlier: 4.389A pdb=" N THR I 110 " --> pdb=" O GLY I 10 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'K' and resid 5 through 7 removed outlier: 3.514A pdb=" N SER K 7 " --> pdb=" O SER K 22 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER K 22 " --> pdb=" O SER K 7 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE K 71 " --> pdb=" O CYS K 23 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.521A pdb=" N ALA K 34 " --> pdb=" O GLN K 89 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N GLN K 37 " --> pdb=" O LEU K 46 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LEU K 46 " --> pdb=" O GLN K 37 " (cutoff:3.500A) 1149 hydrogen bonds defined for protein. 3156 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: 15.36 Time building geometry restraints manager: 13.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6803 1.33 - 1.46: 9210 1.46 - 1.58: 16612 1.58 - 1.71: 0 1.71 - 1.84: 168 Bond restraints: 32793 Sorted by residual: bond pdb=" N GLN A 498 " pdb=" CA GLN A 498 " ideal model delta sigma weight residual 1.453 1.488 -0.035 8.30e-03 1.45e+04 1.74e+01 bond pdb=" C GLY C 526 " pdb=" N PRO C 527 " ideal model delta sigma weight residual 1.331 1.361 -0.030 7.90e-03 1.60e+04 1.40e+01 bond pdb=" N LEU I 18 " pdb=" CA LEU I 18 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.13e-02 7.83e+03 1.06e+01 bond pdb=" N ASP B 294 " pdb=" CA ASP B 294 " ideal model delta sigma weight residual 1.455 1.486 -0.031 9.60e-03 1.09e+04 1.04e+01 bond pdb=" N VAL C 289 " pdb=" CA VAL C 289 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.19e-02 7.06e+03 1.04e+01 ... (remaining 32788 not shown) Histogram of bond angle deviations from ideal: 93.19 - 101.43: 43 101.43 - 109.68: 4717 109.68 - 117.92: 20360 117.92 - 126.16: 19105 126.16 - 134.41: 404 Bond angle restraints: 44629 Sorted by residual: angle pdb=" N ASN A1098 " pdb=" CA ASN A1098 " pdb=" C ASN A1098 " ideal model delta sigma weight residual 113.20 105.13 8.07 1.21e+00 6.83e-01 4.45e+01 angle pdb=" N GLY C 594 " pdb=" CA GLY C 594 " pdb=" C GLY C 594 " ideal model delta sigma weight residual 114.67 107.93 6.74 1.10e+00 8.26e-01 3.75e+01 angle pdb=" N GLY A 339 " pdb=" CA GLY A 339 " pdb=" C GLY A 339 " ideal model delta sigma weight residual 115.08 105.84 9.24 1.54e+00 4.22e-01 3.60e+01 angle pdb=" N PRO A 792 " pdb=" CA PRO A 792 " pdb=" C PRO A 792 " ideal model delta sigma weight residual 110.70 117.63 -6.93 1.22e+00 6.72e-01 3.23e+01 angle pdb=" N PHE C 592 " pdb=" CA PHE C 592 " pdb=" C PHE C 592 " ideal model delta sigma weight residual 111.28 105.74 5.54 1.09e+00 8.42e-01 2.58e+01 ... (remaining 44624 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.26: 19228 21.26 - 42.51: 1017 42.51 - 63.77: 113 63.77 - 85.03: 35 85.03 - 106.28: 9 Dihedral angle restraints: 20402 sinusoidal: 8870 harmonic: 11532 Sorted by residual: dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual 93.00 160.82 -67.82 1 1.00e+01 1.00e-02 5.98e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -150.32 64.32 1 1.00e+01 1.00e-02 5.44e+01 dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual -86.00 -135.66 49.66 1 1.00e+01 1.00e-02 3.39e+01 ... (remaining 20399 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.231: 5126 0.231 - 0.461: 72 0.461 - 0.692: 2 0.692 - 0.923: 2 0.923 - 1.154: 2 Chirality restraints: 5204 Sorted by residual: chirality pdb=" C1 NAG a 2 " pdb=" O4 NAG a 1 " pdb=" C2 NAG a 2 " pdb=" O5 NAG a 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-02 2.50e+03 4.80e+02 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-02 2.50e+03 1.23e+02 chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-02 2.50e+03 1.22e+02 ... (remaining 5201 not shown) Planarity restraints: 5725 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG a 2 " -0.354 2.00e-02 2.50e+03 3.05e-01 1.16e+03 pdb=" C7 NAG a 2 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG a 2 " -0.126 2.00e-02 2.50e+03 pdb=" N2 NAG a 2 " 0.542 2.00e-02 2.50e+03 pdb=" O7 NAG a 2 " -0.148 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG T 2 " 0.342 2.00e-02 2.50e+03 2.96e-01 1.09e+03 pdb=" C7 NAG T 2 " -0.079 2.00e-02 2.50e+03 pdb=" C8 NAG T 2 " 0.065 2.00e-02 2.50e+03 pdb=" N2 NAG T 2 " -0.522 2.00e-02 2.50e+03 pdb=" O7 NAG T 2 " 0.194 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1307 " 0.335 2.00e-02 2.50e+03 2.90e-01 1.05e+03 pdb=" C7 NAG A1307 " -0.077 2.00e-02 2.50e+03 pdb=" C8 NAG A1307 " 0.051 2.00e-02 2.50e+03 pdb=" N2 NAG A1307 " -0.509 2.00e-02 2.50e+03 pdb=" O7 NAG A1307 " 0.200 2.00e-02 2.50e+03 ... (remaining 5722 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 7102 2.79 - 3.32: 28400 3.32 - 3.85: 52485 3.85 - 4.37: 60591 4.37 - 4.90: 102662 Nonbonded interactions: 251240 Sorted by model distance: nonbonded pdb=" O ASP A 994 " pdb=" OG1 THR A 998 " model vdw 2.265 2.440 nonbonded pdb=" O GLY A 232 " pdb=" N ARG C 466 " model vdw 2.266 2.520 nonbonded pdb=" O ASP B 994 " pdb=" OG1 THR B 998 " model vdw 2.281 2.440 nonbonded pdb=" O GLU C 661 " pdb=" OH TYR C 695 " model vdw 2.293 2.440 nonbonded pdb=" OG1 THR C 912 " pdb=" OD1 ASN C 914 " model vdw 2.315 2.440 ... (remaining 251235 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 476 or resid 478 through 1147 or resid 1301 thr \ ough 1312)) selection = (chain 'B' and (resid 14 through 476 or resid 478 through 1147 or resid 1301 thr \ ough 1312)) selection = (chain 'C' and (resid 14 through 476 or resid 478 through 829 or resid 853 throu \ gh 1147 or resid 1301 through 1312)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' 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 'Z' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'O' selection = chain 'a' } 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=0.33 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: 3.870 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: 0.030 Extract box with map and model: 19.170 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 105.840 Find NCS groups from input model: 2.630 Set up NCS constraints: 0.520 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 134.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 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 : 0.008 0.066 32793 Z= 0.504 Angle : 1.149 12.910 44629 Z= 0.782 Chirality : 0.085 1.154 5204 Planarity : 0.016 0.305 5671 Dihedral : 12.540 106.284 12882 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.47 % Allowed : 3.44 % Favored : 96.10 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.56 % 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: -0.15 (0.13), residues: 3931 helix: 0.91 (0.19), residues: 716 sheet: 0.47 (0.17), residues: 976 loop : -0.69 (0.12), residues: 2239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 886 HIS 0.024 0.002 HIS A1048 PHE 0.036 0.002 PHE C 888 TYR 0.023 0.002 TYR C 741 ARG 0.018 0.001 ARG C 466 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7862 Ramachandran restraints generated. 3931 Oldfield, 0 Emsley, 3931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7862 Ramachandran restraints generated. 3931 Oldfield, 0 Emsley, 3931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 442 time to evaluate : 3.589 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: A 406 GLU cc_start: 0.9122 (mt-10) cc_final: 0.8095 (mt-10) REVERT: A 740 MET cc_start: 0.8631 (ppp) cc_final: 0.8418 (ppp) REVERT: A 776 LYS cc_start: 0.9618 (mmmt) cc_final: 0.9367 (ptpp) REVERT: A 1023 ASN cc_start: 0.9299 (m110) cc_final: 0.9014 (m110) REVERT: B 338 PHE cc_start: 0.8596 (m-80) cc_final: 0.8372 (m-10) REVERT: B 378 LYS cc_start: 0.8739 (tttt) cc_final: 0.8413 (ttmm) REVERT: B 759 PHE cc_start: 0.9015 (t80) cc_final: 0.8769 (t80) REVERT: B 763 LEU cc_start: 0.9709 (mp) cc_final: 0.9505 (mt) REVERT: C 741 TYR cc_start: 0.8791 (t80) cc_final: 0.8421 (t80) REVERT: K 46 LEU cc_start: 0.7913 (tp) cc_final: 0.7483 (tt) outliers start: 16 outliers final: 3 residues processed: 457 average time/residue: 0.4608 time to fit residues: 328.4305 Evaluate side-chains 214 residues out of total 3429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 211 time to evaluate : 3.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain C residue 56 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 329 optimal weight: 4.9990 chunk 295 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 199 optimal weight: 2.9990 chunk 157 optimal weight: 10.0000 chunk 305 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 chunk 185 optimal weight: 0.9980 chunk 227 optimal weight: 0.8980 chunk 354 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN A 965 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN A1023 ASN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN B 173 GLN B 764 ASN B 787 GLN B 853 GLN B 856 ASN B 914 ASN B1011 GLN C 23 GLN C 52 GLN ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 563 GLN C 607 GLN ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN C 957 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 ASN L 37 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 32793 Z= 0.193 Angle : 0.629 8.952 44629 Z= 0.323 Chirality : 0.045 0.333 5204 Planarity : 0.004 0.058 5671 Dihedral : 6.722 65.550 5863 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.31 % Allowed : 10.74 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 0.04 (0.13), residues: 3931 helix: 1.35 (0.19), residues: 712 sheet: 0.59 (0.17), residues: 980 loop : -0.66 (0.12), residues: 2239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 886 HIS 0.006 0.001 HIS A1048 PHE 0.054 0.002 PHE B 318 TYR 0.036 0.001 TYR A 365 ARG 0.007 0.001 ARG C 995 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7862 Ramachandran restraints generated. 3931 Oldfield, 0 Emsley, 3931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7862 Ramachandran restraints generated. 3931 Oldfield, 0 Emsley, 3931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 238 time to evaluate : 4.010 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 378 LYS cc_start: 0.8353 (mmtm) cc_final: 0.8096 (mptt) REVERT: A 406 GLU cc_start: 0.9011 (mt-10) cc_final: 0.8364 (mt-10) REVERT: A 740 MET cc_start: 0.8687 (ppp) cc_final: 0.8463 (ppp) REVERT: A 776 LYS cc_start: 0.9585 (mmmt) cc_final: 0.9353 (ptpp) REVERT: A 1023 ASN cc_start: 0.9309 (m-40) cc_final: 0.9031 (m-40) REVERT: B 378 LYS cc_start: 0.8766 (tttt) cc_final: 0.8490 (ttmm) REVERT: B 914 ASN cc_start: 0.8698 (OUTLIER) cc_final: 0.8240 (p0) REVERT: B 1004 LEU cc_start: 0.9766 (mt) cc_final: 0.9417 (mt) REVERT: C 378 LYS cc_start: 0.8404 (mtmm) cc_final: 0.8198 (mtpp) REVERT: C 988 GLU cc_start: 0.8172 (pm20) cc_final: 0.7932 (pm20) REVERT: C 1012 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8858 (mt) REVERT: H 4 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.7285 (mt) REVERT: K 46 LEU cc_start: 0.7877 (tp) cc_final: 0.7535 (tt) outliers start: 45 outliers final: 21 residues processed: 271 average time/residue: 0.4329 time to fit residues: 191.4601 Evaluate side-chains 220 residues out of total 3429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 196 time to evaluate : 3.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1013 ILE Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain K residue 70 ASP Chi-restraints excluded: chain K residue 106 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 196 optimal weight: 2.9990 chunk 109 optimal weight: 6.9990 chunk 294 optimal weight: 5.9990 chunk 241 optimal weight: 8.9990 chunk 97 optimal weight: 0.5980 chunk 354 optimal weight: 20.0000 chunk 383 optimal weight: 10.0000 chunk 315 optimal weight: 4.9990 chunk 351 optimal weight: 10.0000 chunk 120 optimal weight: 4.9990 chunk 284 optimal weight: 7.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 804 GLN A1054 GLN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1054 GLN C 23 GLN C 115 GLN C 188 ASN ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1058 HIS ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN I 39 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.124 32793 Z= 0.460 Angle : 0.762 15.295 44629 Z= 0.396 Chirality : 0.046 0.299 5204 Planarity : 0.005 0.068 5671 Dihedral : 6.230 57.713 5861 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.01 % Allowed : 11.27 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -0.35 (0.13), residues: 3931 helix: 0.86 (0.19), residues: 726 sheet: -0.03 (0.16), residues: 1067 loop : -0.67 (0.13), residues: 2138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP I 52 HIS 0.008 0.002 HIS A 207 PHE 0.037 0.003 PHE B1089 TYR 0.029 0.002 TYR B 421 ARG 0.008 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7862 Ramachandran restraints generated. 3931 Oldfield, 0 Emsley, 3931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7862 Ramachandran restraints generated. 3931 Oldfield, 0 Emsley, 3931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 200 time to evaluate : 3.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 TYR cc_start: 0.8009 (t80) cc_final: 0.7576 (t80) REVERT: A 740 MET cc_start: 0.8740 (ppp) cc_final: 0.8348 (ppp) REVERT: A 1023 ASN cc_start: 0.9365 (m-40) cc_final: 0.9083 (m-40) REVERT: A 1050 MET cc_start: 0.8405 (ptm) cc_final: 0.7699 (ptt) REVERT: B 378 LYS cc_start: 0.8649 (tttt) cc_final: 0.8260 (ttmm) REVERT: B 1004 LEU cc_start: 0.9785 (mt) cc_final: 0.9543 (mt) REVERT: C 378 LYS cc_start: 0.8517 (mtmm) cc_final: 0.8284 (mtpp) REVERT: H 4 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7997 (mt) REVERT: H 43 LYS cc_start: 0.4542 (mtmm) cc_final: 0.3566 (tmtt) REVERT: I 73 ASN cc_start: 0.7708 (m-40) cc_final: 0.7473 (m-40) REVERT: K 46 LEU cc_start: 0.7984 (tp) cc_final: 0.7759 (tt) outliers start: 69 outliers final: 37 residues processed: 251 average time/residue: 0.4287 time to fit residues: 176.5476 Evaluate side-chains 205 residues out of total 3429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 167 time to evaluate : 3.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1013 ILE Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 24 ARG Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain K residue 106 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 350 optimal weight: 0.9990 chunk 266 optimal weight: 5.9990 chunk 184 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 169 optimal weight: 9.9990 chunk 238 optimal weight: 5.9990 chunk 356 optimal weight: 2.9990 chunk 376 optimal weight: 10.0000 chunk 186 optimal weight: 3.9990 chunk 337 optimal weight: 20.0000 chunk 101 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 913 GLN A 949 GLN A 953 ASN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN ** B 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN C1002 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 HIS ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32793 Z= 0.201 Angle : 0.593 10.560 44629 Z= 0.305 Chirality : 0.043 0.258 5204 Planarity : 0.004 0.044 5671 Dihedral : 5.576 57.386 5861 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.14 % Allowed : 13.04 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -0.16 (0.13), residues: 3931 helix: 1.24 (0.20), residues: 719 sheet: 0.01 (0.16), residues: 1047 loop : -0.59 (0.12), residues: 2165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP I 52 HIS 0.005 0.001 HIS A1048 PHE 0.032 0.001 PHE B 318 TYR 0.018 0.001 TYR A 369 ARG 0.006 0.000 ARG H 66 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7862 Ramachandran restraints generated. 3931 Oldfield, 0 Emsley, 3931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7862 Ramachandran restraints generated. 3931 Oldfield, 0 Emsley, 3931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 196 time to evaluate : 3.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 697 MET cc_start: 0.8535 (mmp) cc_final: 0.8045 (mmm) REVERT: A 740 MET cc_start: 0.8652 (ppp) cc_final: 0.8323 (ppp) REVERT: A 1023 ASN cc_start: 0.9322 (m-40) cc_final: 0.9026 (m110) REVERT: A 1050 MET cc_start: 0.7990 (ptm) cc_final: 0.7592 (ppp) REVERT: B 378 LYS cc_start: 0.8687 (tttt) cc_final: 0.8307 (ttmm) REVERT: B 697 MET cc_start: 0.8854 (tmm) cc_final: 0.8025 (tmm) REVERT: B 741 TYR cc_start: 0.8677 (t80) cc_final: 0.8473 (t80) REVERT: B 1004 LEU cc_start: 0.9757 (mt) cc_final: 0.9505 (mt) REVERT: B 1092 GLU cc_start: 0.7725 (pm20) cc_final: 0.7307 (pm20) REVERT: C 378 LYS cc_start: 0.8477 (mtmm) cc_final: 0.8257 (mtpp) REVERT: C 1004 LEU cc_start: 0.9548 (mt) cc_final: 0.9236 (mt) REVERT: H 43 LYS cc_start: 0.4607 (mtmm) cc_final: 0.3924 (tmtt) REVERT: H 82 MET cc_start: 0.6331 (mpp) cc_final: 0.4969 (mmt) REVERT: I 73 ASN cc_start: 0.7570 (m-40) cc_final: 0.7317 (m-40) outliers start: 39 outliers final: 26 residues processed: 229 average time/residue: 0.4088 time to fit residues: 156.6174 Evaluate side-chains 196 residues out of total 3429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 170 time to evaluate : 3.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain K residue 106 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 313 optimal weight: 3.9990 chunk 213 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 280 optimal weight: 9.9990 chunk 155 optimal weight: 4.9990 chunk 321 optimal weight: 0.0980 chunk 260 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 192 optimal weight: 0.9980 chunk 338 optimal weight: 0.6980 chunk 95 optimal weight: 4.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN A 953 ASN B 49 HIS B 188 ASN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN ** B 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN C 804 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 32793 Z= 0.199 Angle : 0.575 15.886 44629 Z= 0.294 Chirality : 0.043 0.242 5204 Planarity : 0.004 0.058 5671 Dihedral : 5.209 55.704 5861 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.40 % Allowed : 13.22 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -0.09 (0.13), residues: 3931 helix: 1.31 (0.20), residues: 728 sheet: -0.03 (0.16), residues: 1068 loop : -0.50 (0.13), residues: 2135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 64 HIS 0.005 0.001 HIS B 519 PHE 0.026 0.001 PHE B 318 TYR 0.016 0.001 TYR A1138 ARG 0.007 0.000 ARG I 83 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7862 Ramachandran restraints generated. 3931 Oldfield, 0 Emsley, 3931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7862 Ramachandran restraints generated. 3931 Oldfield, 0 Emsley, 3931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 3429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 185 time to evaluate : 3.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 697 MET cc_start: 0.8557 (mmp) cc_final: 0.7998 (mmm) REVERT: A 740 MET cc_start: 0.8635 (ppp) cc_final: 0.8288 (ppp) REVERT: A 1023 ASN cc_start: 0.9329 (m-40) cc_final: 0.9038 (m-40) REVERT: A 1029 MET cc_start: 0.9022 (mmm) cc_final: 0.8589 (tpp) REVERT: A 1050 MET cc_start: 0.8066 (ptm) cc_final: 0.7738 (ppp) REVERT: A 1107 ARG cc_start: 0.8050 (ttt180) cc_final: 0.7637 (tpt-90) REVERT: B 378 LYS cc_start: 0.8697 (tttt) cc_final: 0.8253 (ttmm) REVERT: B 697 MET cc_start: 0.8861 (tmm) cc_final: 0.8112 (tmm) REVERT: B 731 MET cc_start: 0.9380 (ptm) cc_final: 0.9174 (ptm) REVERT: B 1004 LEU cc_start: 0.9758 (mt) cc_final: 0.9520 (mt) REVERT: B 1031 GLU cc_start: 0.8174 (tp30) cc_final: 0.7899 (tm-30) REVERT: B 1092 GLU cc_start: 0.7702 (pm20) cc_final: 0.7333 (pm20) REVERT: C 378 LYS cc_start: 0.8448 (mtmm) cc_final: 0.8235 (mtpp) REVERT: C 508 TYR cc_start: 0.8436 (m-10) cc_final: 0.8196 (m-10) REVERT: C 1012 LEU cc_start: 0.9101 (mt) cc_final: 0.8799 (mt) REVERT: C 1023 ASN cc_start: 0.8974 (m110) cc_final: 0.8549 (m110) REVERT: H 43 LYS cc_start: 0.4512 (mtmm) cc_final: 0.3920 (tmtt) REVERT: J 46 LEU cc_start: 0.8055 (mt) cc_final: 0.7828 (mt) REVERT: I 43 LYS cc_start: 0.5016 (tptt) cc_final: 0.4801 (tmtt) REVERT: I 73 ASN cc_start: 0.7562 (m-40) cc_final: 0.7279 (m-40) REVERT: I 100 ASP cc_start: 0.6509 (t0) cc_final: 0.6300 (t0) REVERT: K 46 LEU cc_start: 0.7708 (tt) cc_final: 0.7455 (tp) outliers start: 48 outliers final: 32 residues processed: 225 average time/residue: 0.4335 time to fit residues: 164.9671 Evaluate side-chains 199 residues out of total 3429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 167 time to evaluate : 3.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 75 LYS Chi-restraints excluded: chain K residue 103 LYS Chi-restraints excluded: chain K residue 106 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 126 optimal weight: 0.2980 chunk 339 optimal weight: 8.9990 chunk 74 optimal weight: 6.9990 chunk 221 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 377 optimal weight: 2.9990 chunk 313 optimal weight: 7.9990 chunk 174 optimal weight: 0.3980 chunk 31 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 198 optimal weight: 4.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN A 953 ASN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 32793 Z= 0.178 Angle : 0.557 14.460 44629 Z= 0.284 Chirality : 0.043 0.232 5204 Planarity : 0.003 0.045 5671 Dihedral : 5.012 55.376 5861 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.08 % Allowed : 13.94 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -0.05 (0.13), residues: 3931 helix: 1.38 (0.20), residues: 728 sheet: -0.04 (0.16), residues: 1067 loop : -0.47 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 64 HIS 0.005 0.001 HIS B 519 PHE 0.026 0.001 PHE B 318 TYR 0.019 0.001 TYR C1138 ARG 0.004 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7862 Ramachandran restraints generated. 3931 Oldfield, 0 Emsley, 3931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7862 Ramachandran restraints generated. 3931 Oldfield, 0 Emsley, 3931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 176 time to evaluate : 3.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 TYR cc_start: 0.8372 (OUTLIER) cc_final: 0.7321 (p90) REVERT: A 697 MET cc_start: 0.8554 (mmp) cc_final: 0.8245 (mmm) REVERT: A 740 MET cc_start: 0.8647 (ppp) cc_final: 0.8283 (ppp) REVERT: A 1023 ASN cc_start: 0.9319 (m-40) cc_final: 0.9028 (m-40) REVERT: A 1029 MET cc_start: 0.8958 (mmm) cc_final: 0.8503 (tpp) REVERT: A 1050 MET cc_start: 0.8037 (ptm) cc_final: 0.7747 (ppp) REVERT: A 1107 ARG cc_start: 0.8058 (ttt180) cc_final: 0.7650 (tpt-90) REVERT: B 378 LYS cc_start: 0.8692 (tttt) cc_final: 0.8251 (ttmm) REVERT: B 697 MET cc_start: 0.8833 (tmm) cc_final: 0.8107 (tmm) REVERT: B 731 MET cc_start: 0.9377 (ptm) cc_final: 0.9159 (ptm) REVERT: B 741 TYR cc_start: 0.8769 (t80) cc_final: 0.8451 (t80) REVERT: B 1004 LEU cc_start: 0.9747 (mt) cc_final: 0.9488 (mt) REVERT: B 1031 GLU cc_start: 0.8210 (tp30) cc_final: 0.7989 (tp30) REVERT: B 1092 GLU cc_start: 0.7633 (pm20) cc_final: 0.7285 (pm20) REVERT: C 378 LYS cc_start: 0.8457 (mtmm) cc_final: 0.8230 (mtpp) REVERT: C 508 TYR cc_start: 0.8441 (m-10) cc_final: 0.8192 (m-10) REVERT: H 43 LYS cc_start: 0.4775 (mtmm) cc_final: 0.4206 (tmtt) REVERT: G 98 ASP cc_start: 0.7234 (p0) cc_final: 0.6950 (p0) REVERT: J 46 LEU cc_start: 0.8064 (mt) cc_final: 0.7822 (mt) REVERT: I 73 ASN cc_start: 0.7643 (m-40) cc_final: 0.7401 (m-40) REVERT: I 100 ASP cc_start: 0.6507 (t0) cc_final: 0.6290 (t0) REVERT: K 54 ARG cc_start: 0.6407 (mtt-85) cc_final: 0.6129 (mtt-85) outliers start: 37 outliers final: 27 residues processed: 208 average time/residue: 0.4257 time to fit residues: 149.1012 Evaluate side-chains 192 residues out of total 3429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 164 time to evaluate : 3.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain K residue 106 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 363 optimal weight: 9.9990 chunk 42 optimal weight: 8.9990 chunk 214 optimal weight: 0.8980 chunk 275 optimal weight: 0.4980 chunk 213 optimal weight: 5.9990 chunk 317 optimal weight: 0.5980 chunk 210 optimal weight: 0.9980 chunk 375 optimal weight: 0.8980 chunk 235 optimal weight: 1.9990 chunk 229 optimal weight: 1.9990 chunk 173 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN A 953 ASN B 49 HIS B 317 ASN ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 82AASN ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 32793 Z= 0.153 Angle : 0.547 15.225 44629 Z= 0.278 Chirality : 0.042 0.221 5204 Planarity : 0.003 0.046 5671 Dihedral : 4.843 54.997 5861 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.14 % Allowed : 14.26 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 0.01 (0.13), residues: 3931 helix: 1.41 (0.20), residues: 728 sheet: 0.08 (0.16), residues: 1049 loop : -0.47 (0.13), residues: 2154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 64 HIS 0.005 0.001 HIS B 519 PHE 0.024 0.001 PHE A 275 TYR 0.016 0.001 TYR B 741 ARG 0.004 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7862 Ramachandran restraints generated. 3931 Oldfield, 0 Emsley, 3931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7862 Ramachandran restraints generated. 3931 Oldfield, 0 Emsley, 3931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 3429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 177 time to evaluate : 3.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 TYR cc_start: 0.8321 (OUTLIER) cc_final: 0.7271 (p90) REVERT: A 406 GLU cc_start: 0.9211 (mt-10) cc_final: 0.8644 (mt-10) REVERT: A 697 MET cc_start: 0.8630 (mmp) cc_final: 0.8033 (mmm) REVERT: A 740 MET cc_start: 0.8625 (ppp) cc_final: 0.8288 (ppp) REVERT: A 1005 GLN cc_start: 0.9359 (OUTLIER) cc_final: 0.8955 (pm20) REVERT: A 1023 ASN cc_start: 0.9307 (m-40) cc_final: 0.9013 (m-40) REVERT: A 1107 ARG cc_start: 0.8050 (ttt180) cc_final: 0.7647 (tpt-90) REVERT: B 378 LYS cc_start: 0.8668 (tttt) cc_final: 0.8222 (ttmm) REVERT: B 697 MET cc_start: 0.8882 (tmm) cc_final: 0.8223 (tmm) REVERT: B 731 MET cc_start: 0.9393 (ptm) cc_final: 0.9162 (ptm) REVERT: B 741 TYR cc_start: 0.8744 (t80) cc_final: 0.8472 (t80) REVERT: B 1004 LEU cc_start: 0.9750 (mt) cc_final: 0.9508 (mt) REVERT: B 1031 GLU cc_start: 0.8264 (tp30) cc_final: 0.8044 (tp30) REVERT: C 378 LYS cc_start: 0.8432 (mtmm) cc_final: 0.8203 (mtpp) REVERT: C 508 TYR cc_start: 0.8429 (m-10) cc_final: 0.8173 (m-10) REVERT: C 1012 LEU cc_start: 0.9077 (mt) cc_final: 0.8792 (mt) REVERT: H 43 LYS cc_start: 0.4672 (mtmm) cc_final: 0.4211 (tmtt) REVERT: H 82 MET cc_start: 0.4026 (mmt) cc_final: 0.3801 (mmm) REVERT: L 90 GLN cc_start: 0.6538 (OUTLIER) cc_final: 0.6140 (pm20) REVERT: I 73 ASN cc_start: 0.7696 (m-40) cc_final: 0.7470 (m-40) REVERT: I 100 ASP cc_start: 0.6491 (t0) cc_final: 0.6262 (t0) outliers start: 39 outliers final: 25 residues processed: 207 average time/residue: 0.4182 time to fit residues: 145.6595 Evaluate side-chains 193 residues out of total 3429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 165 time to evaluate : 3.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 82 ASN Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 75 LYS Chi-restraints excluded: chain K residue 106 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 232 optimal weight: 4.9990 chunk 150 optimal weight: 0.5980 chunk 224 optimal weight: 0.6980 chunk 113 optimal weight: 5.9990 chunk 73 optimal weight: 8.9990 chunk 72 optimal weight: 0.9990 chunk 238 optimal weight: 2.9990 chunk 256 optimal weight: 0.7980 chunk 185 optimal weight: 0.0970 chunk 35 optimal weight: 5.9990 chunk 295 optimal weight: 7.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN A 953 ASN B 317 ASN ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 32793 Z= 0.145 Angle : 0.548 14.983 44629 Z= 0.276 Chirality : 0.042 0.212 5204 Planarity : 0.003 0.047 5671 Dihedral : 4.744 54.746 5860 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.93 % Allowed : 14.91 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 0.05 (0.13), residues: 3931 helix: 1.53 (0.20), residues: 714 sheet: 0.12 (0.16), residues: 1051 loop : -0.48 (0.13), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 64 HIS 0.005 0.001 HIS B 519 PHE 0.024 0.001 PHE A 275 TYR 0.017 0.001 TYR C1138 ARG 0.005 0.000 ARG C1000 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7862 Ramachandran restraints generated. 3931 Oldfield, 0 Emsley, 3931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7862 Ramachandran restraints generated. 3931 Oldfield, 0 Emsley, 3931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 3429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 177 time to evaluate : 3.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 TYR cc_start: 0.8336 (OUTLIER) cc_final: 0.7320 (p90) REVERT: A 406 GLU cc_start: 0.9204 (mt-10) cc_final: 0.8632 (mt-10) REVERT: A 697 MET cc_start: 0.8505 (mmp) cc_final: 0.7895 (mmm) REVERT: A 740 MET cc_start: 0.8617 (ppp) cc_final: 0.8280 (ppp) REVERT: A 869 MET cc_start: 0.9187 (mtp) cc_final: 0.8898 (ptp) REVERT: A 1023 ASN cc_start: 0.9293 (m-40) cc_final: 0.9006 (m-40) REVERT: A 1029 MET cc_start: 0.8952 (mmm) cc_final: 0.8621 (tpp) REVERT: A 1107 ARG cc_start: 0.8017 (ttt180) cc_final: 0.7628 (tpt-90) REVERT: B 378 LYS cc_start: 0.8658 (tttt) cc_final: 0.8205 (ttmm) REVERT: B 697 MET cc_start: 0.8908 (tmm) cc_final: 0.8211 (tmm) REVERT: B 731 MET cc_start: 0.9363 (ptm) cc_final: 0.9115 (ptm) REVERT: B 741 TYR cc_start: 0.8748 (t80) cc_final: 0.8442 (t80) REVERT: B 1004 LEU cc_start: 0.9739 (mt) cc_final: 0.9482 (mt) REVERT: B 1031 GLU cc_start: 0.8283 (tp30) cc_final: 0.8071 (tp30) REVERT: B 1092 GLU cc_start: 0.7739 (pm20) cc_final: 0.7243 (pm20) REVERT: C 378 LYS cc_start: 0.8419 (mtmm) cc_final: 0.8184 (mtpp) REVERT: C 508 TYR cc_start: 0.8413 (m-10) cc_final: 0.8163 (m-10) REVERT: C 1012 LEU cc_start: 0.9039 (mt) cc_final: 0.8757 (mt) REVERT: H 43 LYS cc_start: 0.4599 (mtmm) cc_final: 0.4203 (tmtt) REVERT: H 82 MET cc_start: 0.3809 (mmt) cc_final: 0.3599 (mmm) REVERT: J 46 LEU cc_start: 0.8021 (mt) cc_final: 0.7775 (mt) REVERT: I 73 ASN cc_start: 0.7653 (m-40) cc_final: 0.7440 (m-40) REVERT: I 100 ASP cc_start: 0.6499 (t0) cc_final: 0.6260 (t0) outliers start: 32 outliers final: 24 residues processed: 203 average time/residue: 0.3965 time to fit residues: 136.2301 Evaluate side-chains 187 residues out of total 3429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 162 time to evaluate : 3.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain K residue 106 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 341 optimal weight: 9.9990 chunk 360 optimal weight: 9.9990 chunk 328 optimal weight: 5.9990 chunk 350 optimal weight: 0.6980 chunk 210 optimal weight: 0.0270 chunk 152 optimal weight: 0.9980 chunk 275 optimal weight: 0.0470 chunk 107 optimal weight: 5.9990 chunk 316 optimal weight: 7.9990 chunk 331 optimal weight: 10.0000 chunk 349 optimal weight: 8.9990 overall best weight: 1.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN G 82AASN ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32793 Z= 0.207 Angle : 0.572 13.536 44629 Z= 0.291 Chirality : 0.042 0.225 5204 Planarity : 0.003 0.048 5671 Dihedral : 4.836 54.854 5860 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.05 % Allowed : 14.99 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 0.00 (0.13), residues: 3931 helix: 1.35 (0.20), residues: 721 sheet: 0.08 (0.15), residues: 1085 loop : -0.46 (0.13), residues: 2125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 64 HIS 0.004 0.001 HIS B 519 PHE 0.021 0.001 PHE A 275 TYR 0.016 0.001 TYR B 741 ARG 0.005 0.000 ARG C1000 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7862 Ramachandran restraints generated. 3931 Oldfield, 0 Emsley, 3931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7862 Ramachandran restraints generated. 3931 Oldfield, 0 Emsley, 3931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 3429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 165 time to evaluate : 4.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 TYR cc_start: 0.8390 (OUTLIER) cc_final: 0.7365 (p90) REVERT: A 697 MET cc_start: 0.8594 (mmp) cc_final: 0.7988 (mmm) REVERT: A 740 MET cc_start: 0.8698 (ppp) cc_final: 0.8317 (ppp) REVERT: A 1023 ASN cc_start: 0.9304 (m-40) cc_final: 0.9014 (m-40) REVERT: A 1107 ARG cc_start: 0.8034 (ttt180) cc_final: 0.7632 (tpt-90) REVERT: B 378 LYS cc_start: 0.8649 (tttt) cc_final: 0.8193 (ttmm) REVERT: B 697 MET cc_start: 0.8880 (tmm) cc_final: 0.8171 (tmm) REVERT: B 1004 LEU cc_start: 0.9753 (mt) cc_final: 0.9493 (mt) REVERT: B 1031 GLU cc_start: 0.8354 (tp30) cc_final: 0.8056 (tp30) REVERT: B 1092 GLU cc_start: 0.7798 (pm20) cc_final: 0.7350 (pm20) REVERT: C 378 LYS cc_start: 0.8440 (mtmm) cc_final: 0.8210 (mtpp) REVERT: C 508 TYR cc_start: 0.8484 (m-10) cc_final: 0.8233 (m-10) REVERT: C 1029 MET cc_start: 0.9304 (tpt) cc_final: 0.9032 (tpt) REVERT: H 43 LYS cc_start: 0.4816 (mtmm) cc_final: 0.4320 (tmtt) REVERT: I 100 ASP cc_start: 0.6564 (t0) cc_final: 0.6316 (t0) outliers start: 36 outliers final: 29 residues processed: 195 average time/residue: 0.4050 time to fit residues: 134.0968 Evaluate side-chains 182 residues out of total 3429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 152 time to evaluate : 3.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 82 ASN Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain K residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 230 optimal weight: 3.9990 chunk 370 optimal weight: 30.0000 chunk 226 optimal weight: 0.8980 chunk 175 optimal weight: 0.0970 chunk 257 optimal weight: 4.9990 chunk 388 optimal weight: 4.9990 chunk 357 optimal weight: 2.9990 chunk 309 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 238 optimal weight: 6.9990 chunk 189 optimal weight: 0.7980 overall best weight: 1.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.146 32793 Z= 0.255 Angle : 0.701 59.200 44629 Z= 0.392 Chirality : 0.043 0.225 5204 Planarity : 0.004 0.170 5671 Dihedral : 4.841 54.855 5860 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.11 % Allowed : 14.99 % Favored : 83.90 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.56 % 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: -0.01 (0.13), residues: 3931 helix: 1.34 (0.20), residues: 721 sheet: 0.07 (0.15), residues: 1085 loop : -0.47 (0.13), residues: 2125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 64 HIS 0.022 0.001 HIS A1064 PHE 0.021 0.001 PHE A 275 TYR 0.027 0.001 TYR J 87 ARG 0.007 0.000 ARG K 54 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7862 Ramachandran restraints generated. 3931 Oldfield, 0 Emsley, 3931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7862 Ramachandran restraints generated. 3931 Oldfield, 0 Emsley, 3931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 3429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 153 time to evaluate : 3.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 TYR cc_start: 0.8387 (OUTLIER) cc_final: 0.7367 (p90) REVERT: A 697 MET cc_start: 0.8602 (mmp) cc_final: 0.7988 (mmm) REVERT: A 740 MET cc_start: 0.8700 (ppp) cc_final: 0.8315 (ppp) REVERT: A 1023 ASN cc_start: 0.9306 (m-40) cc_final: 0.9015 (m-40) REVERT: A 1107 ARG cc_start: 0.8039 (ttt180) cc_final: 0.7634 (tpt-90) REVERT: B 378 LYS cc_start: 0.8645 (tttt) cc_final: 0.8203 (ttmm) REVERT: B 697 MET cc_start: 0.8882 (tmm) cc_final: 0.8158 (tmm) REVERT: B 1004 LEU cc_start: 0.9754 (mt) cc_final: 0.9494 (mt) REVERT: B 1031 GLU cc_start: 0.8350 (tp30) cc_final: 0.8057 (tp30) REVERT: B 1092 GLU cc_start: 0.7798 (pm20) cc_final: 0.7351 (pm20) REVERT: C 378 LYS cc_start: 0.8439 (mtmm) cc_final: 0.8213 (mtpp) REVERT: C 508 TYR cc_start: 0.8483 (m-10) cc_final: 0.8236 (m-10) REVERT: C 1029 MET cc_start: 0.9289 (tpt) cc_final: 0.9031 (tpt) REVERT: H 43 LYS cc_start: 0.4816 (mtmm) cc_final: 0.4322 (tmtt) REVERT: I 100 ASP cc_start: 0.6564 (t0) cc_final: 0.6317 (t0) outliers start: 38 outliers final: 35 residues processed: 184 average time/residue: 0.4177 time to fit residues: 131.4128 Evaluate side-chains 188 residues out of total 3429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 152 time to evaluate : 3.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 777 ASN Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 245 optimal weight: 0.0980 chunk 329 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 285 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 309 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 318 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 105 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 = 0.3425 r_free = 0.3425 target = 0.053787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.037167 restraints weight = 237713.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.038776 restraints weight = 111555.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.039824 restraints weight = 70286.536| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2960 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2960 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.146 32793 Z= 0.255 Angle : 0.701 59.200 44629 Z= 0.392 Chirality : 0.043 0.225 5204 Planarity : 0.004 0.170 5671 Dihedral : 4.841 54.855 5860 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.08 % Allowed : 15.11 % Favored : 83.81 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.56 % 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: -0.01 (0.13), residues: 3931 helix: 1.34 (0.20), residues: 721 sheet: 0.07 (0.15), residues: 1085 loop : -0.47 (0.13), residues: 2125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 64 HIS 0.022 0.001 HIS A1064 PHE 0.021 0.001 PHE A 275 TYR 0.027 0.001 TYR J 87 ARG 0.007 0.000 ARG K 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6258.71 seconds wall clock time: 115 minutes 40.57 seconds (6940.57 seconds total)