Starting phenix.real_space_refine on Sun Nov 19 17:42:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mxe_24072/11_2023/7mxe_24072.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mxe_24072/11_2023/7mxe_24072.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mxe_24072/11_2023/7mxe_24072.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mxe_24072/11_2023/7mxe_24072.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mxe_24072/11_2023/7mxe_24072.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mxe_24072/11_2023/7mxe_24072.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5338 atoms to isotropic. 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 124 5.16 5 C 13833 2.51 5 N 3672 2.21 5 O 4520 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 10": "OE1" <-> "OE2" Residue "A PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 66": "NH1" <-> "NH2" Residue "A TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 100": "OD1" <-> "OD2" Residue "B ASP 17": "OD1" <-> "OD2" Residue "B TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 50": "NH1" <-> "NH2" Residue "B ASP 70": "OD1" <-> "OD2" Residue "B PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 584": "OE1" <-> "OE2" Residue "C ARG 588": "NH1" <-> "NH2" Residue "C ASP 589": "OD1" <-> "OD2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "C GLU 657": "OE1" <-> "OE2" Residue "D ARG 588": "NH1" <-> "NH2" Residue "D ASP 632": "OD1" <-> "OD2" Residue "F ARG 588": "NH1" <-> "NH2" Residue "F ASP 589": "OD1" <-> "OD2" Residue "F ASP 624": "OD1" <-> "OD2" Residue "F ASP 632": "OD1" <-> "OD2" Residue "F ASP 659": "OD1" <-> "OD2" Residue "G TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 78": "OD1" <-> "OD2" Residue "G PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 102": "OE1" <-> "OE2" Residue "G ASP 113": "OD1" <-> "OD2" Residue "G ASP 140": "OD1" <-> "OD2" Residue "G GLU 153": "OE1" <-> "OE2" Residue "G TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 325": "OD1" <-> "OD2" Residue "G ARG 327": "NH1" <-> "NH2" Residue "G PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 456": "NH1" <-> "NH2" Residue "G ARG 469": "NH1" <-> "NH2" Residue "H PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 66": "NH1" <-> "NH2" Residue "H ASP 85": "OD1" <-> "OD2" Residue "J TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 57": "OD1" <-> "OD2" Residue "J ASP 113": "OD1" <-> "OD2" Residue "J ASP 140": "OD1" <-> "OD2" Residue "J ASP 141": "OD1" <-> "OD2" Residue "J PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 164": "OE1" <-> "OE2" Residue "J TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 321": "OD1" <-> "OD2" Residue "J ARG 327": "NH1" <-> "NH2" Residue "J GLU 340": "OE1" <-> "OE2" Residue "J PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 412": "OD1" <-> "OD2" Residue "J ARG 456": "NH1" <-> "NH2" Residue "J ARG 469": "NH1" <-> "NH2" Residue "J ARG 504": "NH1" <-> "NH2" Residue "L ASP 1": "OD1" <-> "OD2" Residue "L ASP 17": "OD1" <-> "OD2" Residue "L TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 70": "OD1" <-> "OD2" Residue "L PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 10": "OE1" <-> "OE2" Residue "M PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 66": "NH1" <-> "NH2" Residue "M PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 164": "OE1" <-> "OE2" Residue "P TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 269": "OE1" <-> "OE2" Residue "P ASP 325": "OD1" <-> "OD2" Residue "P ARG 327": "NH1" <-> "NH2" Residue "P GLU 381": "OE1" <-> "OE2" Residue "P PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 456": "NH1" <-> "NH2" Residue "P ASP 457": "OD1" <-> "OD2" Residue "P ARG 469": "NH1" <-> "NH2" Residue "P ARG 503": "NH1" <-> "NH2" Residue "R TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 100": "NH1" <-> "NH2" Residue "R PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 85": "OD1" <-> "OD2" Residue "W TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 22149 Number of models: 1 Model: "" Number of chains: 51 Chain: "A" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1014 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "B" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 795 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 102} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 988 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "D" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 975 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "F" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 822 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 1, 'TRANS': 97} Chain: "G" Number of atoms: 3479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3479 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 22, 'TRANS': 419} Chain breaks: 3 Chain: "H" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1014 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "J" Number of atoms: 3479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3479 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 22, 'TRANS': 419} Chain breaks: 3 Chain: "L" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 823 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 102} Chain: "M" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1014 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "O" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 799 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 102} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "P" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3449 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 20, 'TRANS': 417} Chain breaks: 4 Chain: "R" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 989 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "W" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 840 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} 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 chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 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 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 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 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 chiralities: 2 Chain: "V" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "X" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "Y" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 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 chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 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 chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "i" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "j" 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 chiralities: 3 Chain: "k" 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 chiralities: 3 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 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 chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "r" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "s" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 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 chiralities: 2 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "J" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "P" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 11.86, per 1000 atoms: 0.54 Number of scatterers: 22149 At special positions: 0 Unit cell: (127.214, 156.637, 155.772, 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 124 16.00 O 4520 8.00 N 3672 7.00 C 13833 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS D 605 " - pdb=" SG CYS G 501 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 605 " - pdb=" SG CYS J 501 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.04 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.04 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 74 " distance=2.03 Simple disulfide: pdb=" SG CYS J 119 " - pdb=" SG CYS J 205 " distance=2.03 Simple disulfide: pdb=" SG CYS J 126 " - pdb=" SG CYS J 196 " distance=2.03 Simple disulfide: pdb=" SG CYS J 131 " - pdb=" SG CYS J 157 " distance=2.03 Simple disulfide: pdb=" SG CYS J 218 " - pdb=" SG CYS J 247 " distance=2.03 Simple disulfide: pdb=" SG CYS J 228 " - pdb=" SG CYS J 239 " distance=2.03 Simple disulfide: pdb=" SG CYS J 296 " - pdb=" SG CYS J 331 " distance=2.03 Simple disulfide: pdb=" SG CYS J 378 " - pdb=" SG CYS J 445 " distance=2.03 Simple disulfide: pdb=" SG CYS J 385 " - pdb=" SG CYS J 418 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.03 Simple disulfide: pdb=" SG CYS P 54 " - pdb=" SG CYS P 74 " distance=2.03 Simple disulfide: pdb=" SG CYS P 119 " - pdb=" SG CYS P 205 " distance=2.04 Simple disulfide: pdb=" SG CYS P 126 " - pdb=" SG CYS P 196 " distance=2.03 Simple disulfide: pdb=" SG CYS P 131 " - pdb=" SG CYS P 157 " distance=2.03 Simple disulfide: pdb=" SG CYS P 218 " - pdb=" SG CYS P 247 " distance=2.04 Simple disulfide: pdb=" SG CYS P 228 " - pdb=" SG CYS P 239 " distance=2.03 Simple disulfide: pdb=" SG CYS P 296 " - pdb=" SG CYS P 331 " distance=2.03 Simple disulfide: pdb=" SG CYS P 378 " - pdb=" SG CYS P 445 " distance=2.03 Simple disulfide: pdb=" SG CYS P 385 " - pdb=" SG CYS P 418 " distance=2.03 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 92 " distance=2.03 Simple disulfide: pdb=" SG CYS W 23 " - pdb=" SG CYS W 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=1, symmetry=0 Links applied ALPHA1-2 " MAN X 4 " - " MAN X 5 " " MAN Y 4 " - " MAN Y 5 " " MAN Y 5 " - " MAN Y 6 " " MAN Y 8 " - " MAN Y 9 " " MAN Y 10 " - " MAN Y 11 " " MAN i 4 " - " MAN i 5 " " MAN i 5 " - " MAN i 6 " " MAN i 8 " - " MAN i 9 " " MAN r 4 " - " MAN r 5 " " MAN r 5 " - " MAN r 6 " " MAN r 8 " - " MAN r 9 " ALPHA1-3 " BMA V 3 " - " MAN V 4 " " BMA X 3 " - " MAN X 4 " " BMA Y 3 " - " MAN Y 4 " " MAN Y 7 " - " MAN Y 8 " " BMA h 3 " - " MAN h 4 " " BMA i 3 " - " MAN i 4 " " MAN i 7 " - " MAN i 10 " " BMA r 3 " - " MAN r 4 " " MAN r 7 " - " MAN r 10 " " BMA s 3 " - " MAN s 4 " ALPHA1-6 " BMA X 3 " - " MAN X 6 " " BMA Y 3 " - " MAN Y 7 " " MAN Y 7 " - " MAN Y 10 " " BMA h 3 " - " MAN h 5 " " BMA i 3 " - " MAN i 7 " " MAN i 7 " - " MAN i 8 " " BMA r 3 " - " MAN r 7 " " MAN r 7 " - " MAN r 8 " " BMA s 3 " - " MAN s 5 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG I 1 " - " NAG I 2 " " NAG K 1 " - " NAG K 2 " " NAG N 1 " - " NAG N 2 " " NAG Q 1 " - " NAG Q 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 V 2 " - " BMA V 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " NAG-ASN " NAG C 701 " - " ASN C 611 " " NAG E 1 " - " ASN C 637 " " NAG F 701 " - " ASN F 611 " " NAG G 601 " - " ASN G 88 " " NAG G 602 " - " ASN G 295 " " NAG G 603 " - " ASN G 339 " " NAG G 604 " - " ASN G 355 " " NAG G 605 " - " ASN G 386 " " NAG G 606 " - " ASN G 392 " " NAG G 607 " - " ASN G 363 " " NAG G 608 " - " ASN G 448 " " NAG G 609 " - " ASN G 301 " " NAG I 1 " - " ASN D 637 " " NAG J 601 " - " ASN J 133 " " NAG J 602 " - " ASN J 301 " " NAG J 603 " - " ASN J 339 " " NAG J 604 " - " ASN J 355 " " NAG J 605 " - " ASN J 88 " " NAG K 1 " - " ASN F 637 " " NAG N 1 " - " ASN G 133 " " NAG P 601 " - " ASN P 88 " " NAG P 602 " - " ASN P 133 " " NAG P 603 " - " ASN P 197 " " NAG P 604 " - " ASN P 355 " " NAG P 605 " - " ASN P 392 " " NAG P 606 " - " ASN P 363 " " NAG P 607 " - " ASN P 301 " " NAG Q 1 " - " ASN G 156 " " NAG S 1 " - " ASN G 160 " " NAG T 1 " - " ASN G 197 " " NAG U 1 " - " ASN G 332 " " NAG V 1 " - " ASN G 262 " " NAG X 1 " - " ASN G 276 " " NAG Y 1 " - " ASN G 234 " " NAG Z 1 " - " ASN J 156 " " NAG a 1 " - " ASN J 160 " " NAG b 1 " - " ASN J 197 " " NAG c 1 " - " ASN J 295 " " NAG d 1 " - " ASN J 386 " " NAG e 1 " - " ASN J 392 " " NAG f 1 " - " ASN J 363 " " NAG g 1 " - " ASN J 332 " " NAG h 1 " - " ASN J 276 " " NAG i 1 " - " ASN J 234 " " NAG j 1 " - " ASN J 262 " " NAG k 1 " - " ASN J 448 " " NAG l 1 " - " ASN P 156 " " NAG m 1 " - " ASN P 160 " " NAG n 1 " - " ASN P 295 " " NAG o 1 " - " ASN P 448 " " NAG p 1 " - " ASN P 332 " " NAG q 1 " - " ASN P 262 " " NAG r 1 " - " ASN P 234 " " NAG s 1 " - " ASN P 276 " " NAG t 1 " - " ASN P 386 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.51 Conformation dependent library (CDL) restraints added in 3.8 seconds 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4842 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 44 sheets defined 13.6% alpha, 30.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.51 Creating SS restraints... Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.776A pdb=" N ASP B 82 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N PHE B 83 " --> pdb=" O ALA B 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 79 through 83' Processing helix chain 'C' and resid 536 through 541 removed outlier: 4.324A pdb=" N GLN C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 597 removed outlier: 3.749A pdb=" N ILE C 573 " --> pdb=" O THR C 569 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS C 574 " --> pdb=" O VAL C 570 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN C 575 " --> pdb=" O TRP C 571 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP C 589 " --> pdb=" O ARG C 585 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU C 592 " --> pdb=" O ARG C 588 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TRP C 596 " --> pdb=" O LEU C 592 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY C 597 " --> pdb=" O LEU C 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 635 removed outlier: 3.651A pdb=" N ASP C 632 " --> pdb=" O TRP C 628 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LYS C 633 " --> pdb=" O LEU C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 658 removed outlier: 3.622A pdb=" N ILE C 642 " --> pdb=" O TYR C 638 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU C 647 " --> pdb=" O TYR C 643 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU C 648 " --> pdb=" O GLY C 644 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER C 649 " --> pdb=" O LEU C 645 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLN C 650 " --> pdb=" O LEU C 646 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN C 658 " --> pdb=" O GLU C 654 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 removed outlier: 3.553A pdb=" N SER D 534 " --> pdb=" O MET D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 541 removed outlier: 4.161A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 595 removed outlier: 3.923A pdb=" N GLN D 575 " --> pdb=" O TRP D 571 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU D 576 " --> pdb=" O GLY D 572 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASP D 589 " --> pdb=" O ARG D 585 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU D 592 " --> pdb=" O ARG D 588 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU D 593 " --> pdb=" O ASP D 589 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY D 594 " --> pdb=" O GLN D 590 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE D 595 " --> pdb=" O GLN D 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 635 removed outlier: 3.670A pdb=" N ASP D 632 " --> pdb=" O TRP D 628 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LYS D 633 " --> pdb=" O LEU D 629 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU D 634 " --> pdb=" O GLN D 630 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE D 635 " --> pdb=" O TRP D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 650 removed outlier: 3.540A pdb=" N ILE D 642 " --> pdb=" O TYR D 638 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU D 647 " --> pdb=" O TYR D 643 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU D 648 " --> pdb=" O GLY D 644 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER D 649 " --> pdb=" O LEU D 645 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLN D 650 " --> pdb=" O LEU D 646 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 660 removed outlier: 3.563A pdb=" N ASP D 659 " --> pdb=" O ASN D 656 " (cutoff:3.500A) Processing helix chain 'F' and resid 574 through 595 removed outlier: 3.717A pdb=" N ALA F 578 " --> pdb=" O LYS F 574 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG F 579 " --> pdb=" O GLN F 575 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE F 595 " --> pdb=" O GLN F 591 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 626 removed outlier: 3.868A pdb=" N ILE F 622 " --> pdb=" O ASN F 618 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TRP F 623 " --> pdb=" O LEU F 619 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASP F 624 " --> pdb=" O SER F 620 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 removed outlier: 3.511A pdb=" N ILE F 635 " --> pdb=" O TRP F 631 " (cutoff:3.500A) Processing helix chain 'F' and resid 636 through 638 No H-bonds generated for 'chain 'F' and resid 636 through 638' Processing helix chain 'F' and resid 639 through 662 removed outlier: 3.552A pdb=" N TYR F 643 " --> pdb=" O THR F 639 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN F 651 " --> pdb=" O GLU F 647 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 113 removed outlier: 3.858A pdb=" N HIS G 105 " --> pdb=" O VAL G 101 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR G 106 " --> pdb=" O GLU G 102 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP G 113 " --> pdb=" O ILE G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 removed outlier: 3.928A pdb=" N LEU G 125 " --> pdb=" O LEU G 122 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N CYS G 126 " --> pdb=" O THR G 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 122 through 126' Processing helix chain 'G' and resid 335 through 350 removed outlier: 3.788A pdb=" N LYS G 344 " --> pdb=" O GLU G 340 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.910A pdb=" N THR G 372 " --> pdb=" O ASP G 368 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR G 373 " --> pdb=" O LEU G 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 368 through 373' Processing helix chain 'G' and resid 425 through 429 removed outlier: 4.153A pdb=" N GLN G 428 " --> pdb=" O ASN G 425 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 480 removed outlier: 3.686A pdb=" N TRP G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 98 No H-bonds generated for 'chain 'J' and resid 96 through 98' Processing helix chain 'J' and resid 99 through 113 removed outlier: 3.554A pdb=" N THR J 106 " --> pdb=" O GLU J 102 " (cutoff:3.500A) Processing helix chain 'J' and resid 177 through 179 No H-bonds generated for 'chain 'J' and resid 177 through 179' Processing helix chain 'J' and resid 335 through 350 removed outlier: 3.659A pdb=" N ASN J 339 " --> pdb=" O LYS J 335 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU J 340 " --> pdb=" O ALA J 336 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG J 350 " --> pdb=" O VAL J 346 " (cutoff:3.500A) Processing helix chain 'J' and resid 368 through 373 removed outlier: 3.546A pdb=" N THR J 372 " --> pdb=" O ASP J 368 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR J 373 " --> pdb=" O LEU J 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 368 through 373' Processing helix chain 'J' and resid 425 through 429 removed outlier: 3.997A pdb=" N GLN J 428 " --> pdb=" O ASN J 425 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG J 429 " --> pdb=" O MET J 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 425 through 429' Processing helix chain 'P' and resid 96 through 98 No H-bonds generated for 'chain 'P' and resid 96 through 98' Processing helix chain 'P' and resid 99 through 113 Processing helix chain 'P' and resid 122 through 126 removed outlier: 3.894A pdb=" N LEU P 125 " --> pdb=" O LEU P 122 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N CYS P 126 " --> pdb=" O THR P 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 122 through 126' Processing helix chain 'P' and resid 335 through 350 removed outlier: 3.653A pdb=" N ASN P 339 " --> pdb=" O LYS P 335 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU P 340 " --> pdb=" O ALA P 336 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN P 348 " --> pdb=" O LYS P 344 " (cutoff:3.500A) Processing helix chain 'P' and resid 368 through 373 removed outlier: 3.583A pdb=" N THR P 373 " --> pdb=" O LEU P 369 " (cutoff:3.500A) Processing helix chain 'P' and resid 475 through 481 removed outlier: 3.766A pdb=" N TRP P 479 " --> pdb=" O MET P 475 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER P 481 " --> pdb=" O ASP P 477 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 64 removed outlier: 3.996A pdb=" N GLU R 64 " --> pdb=" O PRO R 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 61 through 64' Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.665A pdb=" N GLU A 10 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ARG A 38 " --> pdb=" O TYR A 47 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N TYR A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 100E through 100F Processing sheet with id=AA4, first strand: chain 'B' and resid 5 through 7 Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.541A pdb=" N GLU B 105 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 53 through 54 removed outlier: 6.676A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N TYR B 49 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N VAL B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 605 through 609 removed outlier: 7.580A pdb=" N THR C 606 " --> pdb=" O VAL P 38 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N VAL P 38 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N VAL C 608 " --> pdb=" O VAL P 36 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL P 36 " --> pdb=" O VAL C 608 " (cutoff:3.500A) removed outlier: 8.909A pdb=" N ILE P 491 " --> pdb=" O PRO P 43 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N TRP P 45 " --> pdb=" O VAL P 489 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N VAL P 489 " --> pdb=" O TRP P 45 " (cutoff:3.500A) removed outlier: 9.622A pdb=" N ASP P 47 " --> pdb=" O LYS P 487 " (cutoff:3.500A) removed outlier: 12.012A pdb=" N LYS P 487 " --> pdb=" O ASP P 47 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE P 225 " --> pdb=" O VAL P 245 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 604 through 609 removed outlier: 3.550A pdb=" N CYS D 604 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N VAL G 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 8.941A pdb=" N VAL G 38 " --> pdb=" O PRO G 498 " (cutoff:3.500A) removed outlier: 9.745A pdb=" N TYR G 40 " --> pdb=" O VAL G 496 " (cutoff:3.500A) removed outlier: 10.045A pdb=" N VAL G 496 " --> pdb=" O TYR G 40 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VAL G 42 " --> pdb=" O LEU G 494 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N LEU G 494 " --> pdb=" O VAL G 42 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL G 44 " --> pdb=" O GLU G 492 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 605 through 609 removed outlier: 7.723A pdb=" N THR F 606 " --> pdb=" O VAL J 38 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N VAL J 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N VAL F 608 " --> pdb=" O VAL J 36 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N ILE J 491 " --> pdb=" O PRO J 43 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N TRP J 45 " --> pdb=" O VAL J 489 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N VAL J 489 " --> pdb=" O TRP J 45 " (cutoff:3.500A) removed outlier: 8.781A pdb=" N ASP J 47 " --> pdb=" O LYS J 487 " (cutoff:3.500A) removed outlier: 11.861A pdb=" N LYS J 487 " --> pdb=" O ASP J 47 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL J 242 " --> pdb=" O LEU J 86 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 91 through 94 Processing sheet with id=AB2, first strand: chain 'G' and resid 169 through 177 removed outlier: 3.622A pdb=" N CYS G 131 " --> pdb=" O LYS G 189 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LYS G 189 " --> pdb=" O CYS G 131 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 259 through 261 removed outlier: 5.887A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE G 443 " --> pdb=" O ARG G 298 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL G 292 " --> pdb=" O ILE G 449 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ALA G 329 " --> pdb=" O CYS G 418 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N PHE G 382 " --> pdb=" O LYS G 421 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU G 381 " --> pdb=" O CYS G 378 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N CYS G 378 " --> pdb=" O GLU G 381 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE G 383 " --> pdb=" O PHE G 376 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE G 376 " --> pdb=" O PHE G 383 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 271 through 273 removed outlier: 6.980A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 304 through 312 removed outlier: 6.540A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB7, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.763A pdb=" N GLU H 10 " --> pdb=" O LEU H 108 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER H 110 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ARG H 38 " --> pdb=" O TYR H 47 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N TYR H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 100E through 100F Processing sheet with id=AB9, first strand: chain 'J' and resid 75 through 76 removed outlier: 7.342A pdb=" N CYS J 54 " --> pdb=" O VAL J 75 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 66 through 67 removed outlier: 7.765A pdb=" N HIS J 66 " --> pdb=" O SER J 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'J' and resid 91 through 94 Processing sheet with id=AC3, first strand: chain 'J' and resid 169 through 176 Processing sheet with id=AC4, first strand: chain 'J' and resid 271 through 274 removed outlier: 3.774A pdb=" N SER J 393 " --> pdb=" O PHE J 361 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 374 through 378 removed outlier: 3.608A pdb=" N CYS J 378 " --> pdb=" O GLU J 381 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU J 381 " --> pdb=" O CYS J 378 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE J 382 " --> pdb=" O LYS J 421 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ALA J 329 " --> pdb=" O CYS J 418 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N SER J 334 " --> pdb=" O GLN J 293 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N GLN J 293 " --> pdb=" O SER J 334 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL J 292 " --> pdb=" O ILE J 449 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE J 443 " --> pdb=" O ARG J 298 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ASN J 300 " --> pdb=" O GLY J 441 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N GLY J 441 " --> pdb=" O ASN J 300 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 304 through 307 Processing sheet with id=AC7, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AC8, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AC9, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.817A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N TYR L 49 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=AD2, first strand: chain 'M' and resid 10 through 12 removed outlier: 3.688A pdb=" N GLU M 10 " --> pdb=" O LEU M 108 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N SER M 110 " --> pdb=" O GLU M 10 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LYS M 12 " --> pdb=" O SER M 110 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ARG M 38 " --> pdb=" O TYR M 47 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N TYR M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 10 through 12 removed outlier: 3.688A pdb=" N GLU M 10 " --> pdb=" O LEU M 108 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N SER M 110 " --> pdb=" O GLU M 10 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LYS M 12 " --> pdb=" O SER M 110 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 100E through 100F removed outlier: 3.590A pdb=" N VAL M 100I" --> pdb=" O HIS M 100F" (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'O' and resid 5 through 7 Processing sheet with id=AD6, first strand: chain 'O' and resid 10 through 13 removed outlier: 7.373A pdb=" N LEU O 11 " --> pdb=" O GLU O 105 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N VAL O 33 " --> pdb=" O TYR O 49 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N TYR O 49 " --> pdb=" O VAL O 33 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N TRP O 35 " --> pdb=" O LEU O 47 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'P' and resid 91 through 94 removed outlier: 3.522A pdb=" N GLU P 91 " --> pdb=" O CYS P 239 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'P' and resid 169 through 177 Processing sheet with id=AD9, first strand: chain 'P' and resid 271 through 274 Processing sheet with id=AE1, first strand: chain 'P' and resid 374 through 378 removed outlier: 4.290A pdb=" N ALA P 329 " --> pdb=" O CYS P 418 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE P 443 " --> pdb=" O ARG P 298 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'P' and resid 304 through 312 removed outlier: 6.660A pdb=" N GLN P 315 " --> pdb=" O ILE P 309 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'R' and resid 3 through 7 removed outlier: 3.629A pdb=" N SER R 7 " --> pdb=" O THR R 21 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N THR R 21 " --> pdb=" O SER R 7 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N CYS R 22 " --> pdb=" O PHE R 78 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N PHE R 78 " --> pdb=" O CYS R 22 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'R' and resid 57 through 59 removed outlier: 6.684A pdb=" N TRP R 36 " --> pdb=" O VAL R 48 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ARG R 50 " --> pdb=" O TRP R 35 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TRP R 35 " --> pdb=" O ARG R 50 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'R' and resid 57 through 59 removed outlier: 6.684A pdb=" N TRP R 36 " --> pdb=" O VAL R 48 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ARG R 50 " --> pdb=" O TRP R 35 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TRP R 35 " --> pdb=" O ARG R 50 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'W' and resid 19 through 24 Processing sheet with id=AE7, first strand: chain 'W' and resid 45 through 50 removed outlier: 5.850A pdb=" N PHE W 46 " --> pdb=" O GLN W 37 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLN W 37 " --> pdb=" O PHE W 46 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N MET W 48 " --> pdb=" O TRP W 35 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'W' and resid 89 through 92 663 hydrogen bonds defined for protein. 1740 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: 8.41 Time building geometry restraints manager: 11.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6833 1.34 - 1.47: 5867 1.47 - 1.59: 9723 1.59 - 1.72: 0 1.72 - 1.84: 166 Bond restraints: 22589 Sorted by residual: bond pdb=" C THR P 123 " pdb=" N PRO P 124 " ideal model delta sigma weight residual 1.331 1.395 -0.063 7.90e-03 1.60e+04 6.42e+01 bond pdb=" C PRO A 75 " pdb=" N PRO A 76 " ideal model delta sigma weight residual 1.332 1.389 -0.058 1.30e-02 5.92e+03 1.97e+01 bond pdb=" N PRO A 76 " pdb=" CD PRO A 76 " ideal model delta sigma weight residual 1.473 1.531 -0.058 1.40e-02 5.10e+03 1.73e+01 bond pdb=" N PRO J 313 " pdb=" CD PRO J 313 " ideal model delta sigma weight residual 1.473 1.528 -0.055 1.40e-02 5.10e+03 1.55e+01 bond pdb=" N ASN D 656 " pdb=" CA ASN D 656 " ideal model delta sigma weight residual 1.460 1.485 -0.024 8.20e-03 1.49e+04 8.78e+00 ... (remaining 22584 not shown) Histogram of bond angle deviations from ideal: 100.67 - 108.23: 1202 108.23 - 115.80: 14594 115.80 - 123.37: 13876 123.37 - 130.93: 883 130.93 - 138.50: 127 Bond angle restraints: 30682 Sorted by residual: angle pdb=" C PRO A 75 " pdb=" N PRO A 76 " pdb=" CA PRO A 76 " ideal model delta sigma weight residual 119.76 113.91 5.85 1.03e+00 9.43e-01 3.23e+01 angle pdb=" C ASP P 140 " pdb=" N ASP P 141 " pdb=" CA ASP P 141 " ideal model delta sigma weight residual 122.61 130.89 -8.28 1.56e+00 4.11e-01 2.82e+01 angle pdb=" C SER P 460 " pdb=" N THR P 461 " pdb=" CA THR P 461 " ideal model delta sigma weight residual 121.54 130.34 -8.80 1.91e+00 2.74e-01 2.12e+01 angle pdb=" CA PRO J 313 " pdb=" N PRO J 313 " pdb=" CD PRO J 313 " ideal model delta sigma weight residual 112.00 106.12 5.88 1.40e+00 5.10e-01 1.76e+01 angle pdb=" C ASN D 656 " pdb=" CA ASN D 656 " pdb=" CB ASN D 656 " ideal model delta sigma weight residual 116.53 110.50 6.03 1.47e+00 4.63e-01 1.68e+01 ... (remaining 30677 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 11546 17.96 - 35.93: 790 35.93 - 53.89: 110 53.89 - 71.86: 18 71.86 - 89.82: 8 Dihedral angle restraints: 12472 sinusoidal: 4940 harmonic: 7532 Sorted by residual: dihedral pdb=" CB CYS G 126 " pdb=" SG CYS G 126 " pdb=" SG CYS G 196 " pdb=" CB CYS G 196 " ideal model delta sinusoidal sigma weight residual 93.00 169.55 -76.55 1 1.00e+01 1.00e-02 7.37e+01 dihedral pdb=" CB CYS P 119 " pdb=" SG CYS P 119 " pdb=" SG CYS P 205 " pdb=" CB CYS P 205 " ideal model delta sinusoidal sigma weight residual -86.00 -159.61 73.61 1 1.00e+01 1.00e-02 6.89e+01 dihedral pdb=" CB CYS J 119 " pdb=" SG CYS J 119 " pdb=" SG CYS J 205 " pdb=" CB CYS J 205 " ideal model delta sinusoidal sigma weight residual -86.00 -146.09 60.09 1 1.00e+01 1.00e-02 4.81e+01 ... (remaining 12469 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 3288 0.075 - 0.150: 507 0.150 - 0.225: 23 0.225 - 0.300: 15 0.300 - 0.375: 2 Chirality restraints: 3835 Sorted by residual: chirality pdb=" C2 NAG I 2 " pdb=" C1 NAG I 2 " pdb=" C3 NAG I 2 " pdb=" N2 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.12 -0.38 2.00e-01 2.50e+01 3.52e+00 chirality pdb=" C5 BMA h 3 " pdb=" C4 BMA h 3 " pdb=" C6 BMA h 3 " pdb=" O5 BMA h 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.58 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" C5 BMA Y 3 " pdb=" C4 BMA Y 3 " pdb=" C6 BMA Y 3 " pdb=" O5 BMA Y 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 3832 not shown) Planarity restraints: 3769 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 701 " 0.075 2.00e-02 2.50e+03 6.15e-02 4.73e+01 pdb=" C7 NAG F 701 " -0.020 2.00e-02 2.50e+03 pdb=" C8 NAG F 701 " 0.057 2.00e-02 2.50e+03 pdb=" N2 NAG F 701 " -0.097 2.00e-02 2.50e+03 pdb=" O7 NAG F 701 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 611 " -0.033 2.00e-02 2.50e+03 3.65e-02 1.67e+01 pdb=" CG ASN F 611 " 0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN F 611 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN F 611 " 0.058 2.00e-02 2.50e+03 pdb=" C1 NAG F 701 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 701 " -0.044 2.00e-02 2.50e+03 3.63e-02 1.64e+01 pdb=" C7 NAG C 701 " 0.012 2.00e-02 2.50e+03 pdb=" C8 NAG C 701 " -0.033 2.00e-02 2.50e+03 pdb=" N2 NAG C 701 " 0.058 2.00e-02 2.50e+03 pdb=" O7 NAG C 701 " 0.008 2.00e-02 2.50e+03 ... (remaining 3766 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.34: 14 2.34 - 2.98: 10497 2.98 - 3.62: 26666 3.62 - 4.26: 45623 4.26 - 4.90: 77335 Nonbonded interactions: 160135 Sorted by model distance: nonbonded pdb=" CE LYS D 655 " pdb=" NE2 GLN D 658 " model vdw 1.698 3.520 nonbonded pdb=" O GLU D 657 " pdb=" N ASP D 659 " model vdw 2.116 2.520 nonbonded pdb=" CA GLY D 597 " pdb=" OE1 GLN D 650 " model vdw 2.211 3.440 nonbonded pdb=" O LEU W 4 " pdb=" OG1 THR W 24 " model vdw 2.266 2.440 nonbonded pdb=" CD LYS D 655 " pdb=" NE2 GLN D 658 " model vdw 2.281 3.520 ... (remaining 160130 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'B' selection = (chain 'L' and (resid 1 through 19 or (resid 20 and (name N or name CA or name C \ or name O or name CB )) or resid 21 through 41 or (resid 42 through 43 and (nam \ e N or name CA or name C or name O or name CB )) or resid 44 through 62 or (resi \ d 63 and (name N or name CA or name C or name O or name CB )) or resid 64 throug \ h 99 or (resid 100 and (name N or name CA or name C or name O or name CB )) or r \ esid 101 through 102 or (resid 103 and (name N or name CA or name C or name O or \ name CB )) or resid 104 through 106 or (resid 107 and (name N or name CA or nam \ e C or name O or name CB )))) selection = (chain 'O' and (resid 1 through 106 or (resid 107 and (name N or name CA or name \ C or name O or name CB )))) } ncs_group { reference = (chain 'C' and resid 520 through 660) selection = (chain 'D' and (resid 520 through 546 or resid 567 through 660)) } ncs_group { reference = chain 'E' selection = chain 'I' selection = chain 'K' selection = chain 'N' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 't' } ncs_group { reference = (chain 'G' and (resid 33 through 77 or resid 82 through 504 or resid 601 through \ 605)) selection = (chain 'J' and (resid 33 through 77 or resid 82 through 504 or resid 601 through \ 605)) selection = (chain 'P' and (resid 33 through 504 or resid 601 through 605)) } ncs_group { reference = (chain 'Y' and (resid 2 or resid 5 through 11)) selection = (chain 'i' and (resid 1 or resid 4 through 10)) selection = (chain 'r' and (resid 1 or resid 4 through 10)) } ncs_group { reference = chain 'h' selection = chain 's' } ncs_group { reference = chain 'j' selection = chain 'k' selection = chain 'p' selection = chain 'q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.180 Construct map_model_manager: 0.020 Extract box with map and model: 9.450 Check model and map are aligned: 0.350 Set scattering table: 0.220 Process input model: 60.750 Find NCS groups from input model: 1.690 Set up NCS constraints: 0.370 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 22589 Z= 0.318 Angle : 0.773 13.501 30682 Z= 0.370 Chirality : 0.053 0.375 3835 Planarity : 0.004 0.062 3714 Dihedral : 11.422 89.824 7510 Min Nonbonded Distance : 1.698 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.37 % Favored : 96.59 % Rotamer: Outliers : 0.35 % Allowed : 4.37 % Favored : 95.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.14), residues: 2580 helix: -3.38 (0.18), residues: 307 sheet: -1.02 (0.17), residues: 868 loop : -2.87 (0.13), residues: 1405 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 463 time to evaluate : 2.616 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 470 average time/residue: 0.3601 time to fit residues: 254.6185 Evaluate side-chains 295 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 294 time to evaluate : 2.430 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1871 time to fit residues: 3.5968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 9.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 149 optimal weight: 7.9990 chunk 232 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 575 GLN C 577 GLN C 607 ASN C 650 GLN D 590 GLN D 658 GLN F 575 GLN F 591 GLN F 607 ASN G 82 GLN G 302 ASN G 411 ASN J 103 GLN J 183 GLN J 203 GLN L 6 GLN ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 43 GLN O 3 GLN O 38 GLN P 33 ASN P 103 GLN P 315 GLN P 356 ASN P 428 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 22589 Z= 0.409 Angle : 0.703 13.709 30682 Z= 0.348 Chirality : 0.047 0.272 3835 Planarity : 0.005 0.050 3714 Dihedral : 4.114 25.525 2809 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.13 % Allowed : 12.70 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: -2.58 (0.15), residues: 2580 helix: -1.83 (0.26), residues: 345 sheet: -0.63 (0.17), residues: 894 loop : -2.51 (0.14), residues: 1341 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 291 time to evaluate : 2.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 71 outliers final: 43 residues processed: 344 average time/residue: 0.3327 time to fit residues: 178.4167 Evaluate side-chains 295 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 252 time to evaluate : 2.527 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 43 outliers final: 1 residues processed: 43 average time/residue: 0.1923 time to fit residues: 18.9359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 129 optimal weight: 0.4980 chunk 72 optimal weight: 8.9990 chunk 193 optimal weight: 4.9990 chunk 158 optimal weight: 0.9980 chunk 64 optimal weight: 6.9990 chunk 232 optimal weight: 0.9990 chunk 251 optimal weight: 5.9990 chunk 207 optimal weight: 0.8980 chunk 230 optimal weight: 7.9990 chunk 79 optimal weight: 0.7980 chunk 186 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN D 653 GLN G 103 GLN G 411 ASN L 6 GLN P 33 ASN P 183 GLN W 1 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 22589 Z= 0.142 Angle : 0.513 11.554 30682 Z= 0.253 Chirality : 0.042 0.271 3835 Planarity : 0.003 0.036 3714 Dihedral : 3.691 25.795 2809 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.50 % Allowed : 15.22 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: -2.08 (0.16), residues: 2580 helix: -1.08 (0.29), residues: 344 sheet: -0.37 (0.18), residues: 826 loop : -2.15 (0.14), residues: 1410 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 269 time to evaluate : 2.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 16 residues processed: 293 average time/residue: 0.3346 time to fit residues: 154.4069 Evaluate side-chains 272 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 256 time to evaluate : 2.590 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 2 residues processed: 16 average time/residue: 0.1922 time to fit residues: 9.2206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 230 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 25 optimal weight: 0.4980 chunk 111 optimal weight: 10.0000 chunk 156 optimal weight: 8.9990 chunk 233 optimal weight: 10.0000 chunk 247 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 221 optimal weight: 7.9990 chunk 66 optimal weight: 9.9990 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 590 GLN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 653 GLN F 607 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 22589 Z= 0.388 Angle : 0.695 13.631 30682 Z= 0.338 Chirality : 0.047 0.280 3835 Planarity : 0.004 0.058 3714 Dihedral : 4.331 26.358 2809 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.32 % Favored : 93.64 % Rotamer: Outliers : 2.78 % Allowed : 16.94 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: -2.03 (0.16), residues: 2580 helix: -1.12 (0.28), residues: 351 sheet: -0.41 (0.17), residues: 919 loop : -2.14 (0.15), residues: 1310 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 255 time to evaluate : 2.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 41 residues processed: 301 average time/residue: 0.3455 time to fit residues: 161.2603 Evaluate side-chains 276 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 235 time to evaluate : 2.712 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 2 residues processed: 41 average time/residue: 0.2176 time to fit residues: 20.1294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 206 optimal weight: 0.0980 chunk 140 optimal weight: 6.9990 chunk 3 optimal weight: 0.7980 chunk 184 optimal weight: 0.9990 chunk 102 optimal weight: 7.9990 chunk 211 optimal weight: 10.0000 chunk 171 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 126 optimal weight: 7.9990 chunk 222 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 652 GLN D 653 GLN F 591 GLN F 607 ASN G 170 GLN ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 22589 Z= 0.167 Angle : 0.542 14.479 30682 Z= 0.265 Chirality : 0.043 0.263 3835 Planarity : 0.003 0.037 3714 Dihedral : 3.978 25.495 2809 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.32 % Allowed : 18.13 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.16), residues: 2580 helix: -0.65 (0.30), residues: 345 sheet: -0.19 (0.18), residues: 848 loop : -1.86 (0.15), residues: 1387 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 257 time to evaluate : 2.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 12 residues processed: 280 average time/residue: 0.3327 time to fit residues: 146.6354 Evaluate side-chains 259 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 247 time to evaluate : 2.372 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 2 residues processed: 12 average time/residue: 0.2036 time to fit residues: 8.1244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 83 optimal weight: 9.9990 chunk 222 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 145 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 chunk 247 optimal weight: 10.0000 chunk 205 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 chunk 81 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 653 GLN ** F 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 22589 Z= 0.323 Angle : 0.628 15.899 30682 Z= 0.306 Chirality : 0.045 0.272 3835 Planarity : 0.004 0.046 3714 Dihedral : 4.204 26.019 2809 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 1.90 % Allowed : 18.39 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.16), residues: 2580 helix: -0.63 (0.29), residues: 346 sheet: -0.21 (0.18), residues: 862 loop : -1.86 (0.15), residues: 1372 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 244 time to evaluate : 2.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 29 residues processed: 272 average time/residue: 0.3558 time to fit residues: 152.4604 Evaluate side-chains 264 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 235 time to evaluate : 2.561 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 2 residues processed: 29 average time/residue: 0.2086 time to fit residues: 14.8829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 238 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 180 optimal weight: 9.9990 chunk 140 optimal weight: 10.0000 chunk 208 optimal weight: 9.9990 chunk 138 optimal weight: 1.9990 chunk 246 optimal weight: 20.0000 chunk 154 optimal weight: 4.9990 chunk 150 optimal weight: 8.9990 chunk 113 optimal weight: 0.6980 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 653 GLN F 616 ASN P 195 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 22589 Z= 0.315 Angle : 0.630 16.712 30682 Z= 0.308 Chirality : 0.046 0.276 3835 Planarity : 0.004 0.044 3714 Dihedral : 4.326 26.109 2809 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.97 % Allowed : 19.41 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.16), residues: 2580 helix: -0.58 (0.29), residues: 346 sheet: -0.11 (0.18), residues: 874 loop : -1.88 (0.15), residues: 1360 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 239 time to evaluate : 2.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 13 residues processed: 256 average time/residue: 0.3595 time to fit residues: 143.2162 Evaluate side-chains 243 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 230 time to evaluate : 2.422 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 2 residues processed: 13 average time/residue: 0.1883 time to fit residues: 7.7295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 152 optimal weight: 0.8980 chunk 98 optimal weight: 0.6980 chunk 147 optimal weight: 8.9990 chunk 74 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 chunk 168 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 22 optimal weight: 0.0470 chunk 193 optimal weight: 0.8980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 658 GLN ** F 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 76 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 22589 Z= 0.130 Angle : 0.532 14.657 30682 Z= 0.260 Chirality : 0.042 0.260 3835 Planarity : 0.003 0.034 3714 Dihedral : 3.900 22.787 2809 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.71 % Allowed : 19.59 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.16), residues: 2580 helix: -0.18 (0.30), residues: 339 sheet: 0.10 (0.18), residues: 863 loop : -1.66 (0.16), residues: 1378 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 255 time to evaluate : 2.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 11 residues processed: 266 average time/residue: 0.3407 time to fit residues: 143.1027 Evaluate side-chains 256 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 245 time to evaluate : 2.439 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 2 residues processed: 11 average time/residue: 0.1986 time to fit residues: 7.2649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 224 optimal weight: 10.0000 chunk 236 optimal weight: 8.9990 chunk 215 optimal weight: 7.9990 chunk 229 optimal weight: 9.9990 chunk 138 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 180 optimal weight: 10.0000 chunk 70 optimal weight: 7.9990 chunk 207 optimal weight: 8.9990 chunk 217 optimal weight: 0.9990 chunk 150 optimal weight: 4.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 GLN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN D 653 GLN O 38 GLN P 195 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.087 22589 Z= 0.597 Angle : 0.808 17.860 30682 Z= 0.395 Chirality : 0.052 0.293 3835 Planarity : 0.005 0.060 3714 Dihedral : 4.848 29.124 2809 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.95 % Favored : 92.02 % Rotamer: Outliers : 1.10 % Allowed : 20.07 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.16), residues: 2580 helix: -0.77 (0.29), residues: 346 sheet: -0.13 (0.18), residues: 804 loop : -1.90 (0.15), residues: 1430 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 236 time to evaluate : 2.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 14 residues processed: 252 average time/residue: 0.3677 time to fit residues: 143.0509 Evaluate side-chains 240 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 226 time to evaluate : 2.668 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 2 residues processed: 14 average time/residue: 0.2018 time to fit residues: 8.9552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 243 optimal weight: 0.9990 chunk 148 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 255 optimal weight: 3.9990 chunk 234 optimal weight: 0.9990 chunk 203 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 chunk 156 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 161 optimal weight: 0.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 6 GLN W 92 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 22589 Z= 0.170 Angle : 0.591 16.435 30682 Z= 0.289 Chirality : 0.044 0.267 3835 Planarity : 0.003 0.039 3714 Dihedral : 4.301 25.224 2809 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.26 % Allowed : 20.95 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.16), residues: 2580 helix: -0.36 (0.30), residues: 345 sheet: 0.08 (0.18), residues: 842 loop : -1.75 (0.16), residues: 1393 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 243 time to evaluate : 2.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 247 average time/residue: 0.3533 time to fit residues: 136.2623 Evaluate side-chains 247 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 243 time to evaluate : 2.520 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 4 average time/residue: 0.2025 time to fit residues: 5.0559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 187 optimal weight: 9.9990 chunk 29 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 203 optimal weight: 0.2980 chunk 85 optimal weight: 6.9990 chunk 208 optimal weight: 8.9990 chunk 25 optimal weight: 0.0040 chunk 37 optimal weight: 9.9990 chunk 178 optimal weight: 4.9990 overall best weight: 2.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 653 GLN ** F 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.098048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.078007 restraints weight = 38573.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.079911 restraints weight = 29459.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.080329 restraints weight = 23459.536| |-----------------------------------------------------------------------------| r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 22589 Z= 0.260 Angle : 0.612 16.136 30682 Z= 0.298 Chirality : 0.045 0.272 3835 Planarity : 0.003 0.039 3714 Dihedral : 4.277 25.467 2809 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 0.44 % Allowed : 20.95 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.16), residues: 2580 helix: -0.32 (0.30), residues: 345 sheet: 0.10 (0.18), residues: 848 loop : -1.73 (0.16), residues: 1387 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4114.56 seconds wall clock time: 76 minutes 35.83 seconds (4595.83 seconds total)