Starting phenix.real_space_refine on Sat Aug 10 14:25:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mxd_24071/08_2024/7mxd_24071.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mxd_24071/08_2024/7mxd_24071.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mxd_24071/08_2024/7mxd_24071.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mxd_24071/08_2024/7mxd_24071.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mxd_24071/08_2024/7mxd_24071.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mxd_24071/08_2024/7mxd_24071.cif" } resolution = 3.4 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 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 145 5.16 5 C 18502 2.51 5 N 4835 2.21 5 O 6011 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 106": "OE1" <-> "OE2" Residue "A ASP 152": "OD1" <-> "OD2" Residue "C TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 86": "OD1" <-> "OD2" Residue "C PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 107": "OD1" <-> "OD2" Residue "F TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 321": "OD1" <-> "OD2" Residue "F GLU 381": "OE1" <-> "OE2" Residue "G ASP 49": "OD1" <-> "OD2" Residue "G PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 91": "OE1" <-> "OE2" Residue "J ASP 81": "OD1" <-> "OD2" Residue "J PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 161": "OE1" <-> "OE2" Residue "K ASP 170": "OD1" <-> "OD2" Residue "S ASP 72": "OD1" <-> "OD2" Residue "S PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 1": "OD1" <-> "OD2" Residue "U PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 59": "OE1" <-> "OE2" Residue "X GLU 224": "OE1" <-> "OE2" Residue "Y ASP 17": "OD1" <-> "OD2" Residue "Y GLU 81": "OE1" <-> "OE2" Residue "Y GLU 143": "OE1" <-> "OE2" Residue "B GLU 588": "OE1" <-> "OE2" Residue "B GLU 632": "OE1" <-> "OE2" Residue "I PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 632": "OE1" <-> "OE2" Residue "H GLU 634": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 29496 Number of models: 1 Model: "" Number of chains: 58 Chain: "A" Number of atoms: 3731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3731 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 24, 'TRANS': 447} Chain: "C" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1676 Classifications: {'peptide': 216} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 201} Chain breaks: 1 Chain: "D" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1603 Classifications: {'peptide': 204} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 193} Chain: "F" Number of atoms: 3731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3731 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 24, 'TRANS': 447} Chain: "G" Number of atoms: 3731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3731 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 24, 'TRANS': 447} Chain: "J" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1676 Classifications: {'peptide': 216} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 201} Chain breaks: 1 Chain: "K" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1603 Classifications: {'peptide': 204} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 193} Chain: "S" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1676 Classifications: {'peptide': 216} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 201} Chain breaks: 1 Chain: "U" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1603 Classifications: {'peptide': 204} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 193} Chain: "X" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1653 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 206} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "Y" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1631 Classifications: {'peptide': 214} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 202} Chain: "B" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1090 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 2, 'TRANS': 133} Chain breaks: 1 Chain: "I" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1090 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 2, 'TRANS': 133} Chain breaks: 1 Chain: "H" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1090 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 2, 'TRANS': 133} Chain breaks: 1 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "O" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "e" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "p" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 117 Unusual residues: {'NAG': 8, 'PO4': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 122 Unusual residues: {'NAG': 8, 'PO4': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 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 dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "U" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 15.65, per 1000 atoms: 0.53 Number of scatterers: 29496 At special positions: 0 Unit cell: (174.08, 172.72, 171.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 145 16.00 P 3 15.00 O 6011 8.00 N 4835 7.00 C 18502 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=53, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.05 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 140 " - pdb=" SG CYS C 196 " distance=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 194 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.04 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 201 " - pdb=" SG CYS F 433 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.05 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 501 " - pdb=" SG CYS I 605 " distance=2.04 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 201 " - pdb=" SG CYS G 433 " 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 G 501 " - pdb=" SG CYS H 605 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 140 " - pdb=" SG CYS J 196 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Simple disulfide: pdb=" SG CYS K 134 " - pdb=" SG CYS K 194 " distance=2.04 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 92 " distance=2.03 Simple disulfide: pdb=" SG CYS S 140 " - pdb=" SG CYS S 196 " distance=2.03 Simple disulfide: pdb=" SG CYS U 23 " - pdb=" SG CYS U 88 " distance=2.04 Simple disulfide: pdb=" SG CYS U 134 " - pdb=" SG CYS U 194 " distance=2.03 Simple disulfide: pdb=" SG CYS X 22 " - pdb=" SG CYS X 96 " distance=2.03 Simple disulfide: pdb=" SG CYS X 139 " - pdb=" SG CYS Y 214 " distance=2.03 Simple disulfide: pdb=" SG CYS X 152 " - pdb=" SG CYS X 208 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 23 " - pdb=" SG CYS Y 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 134 " - pdb=" SG CYS Y 194 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS I 598 " - pdb=" SG CYS I 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 598 " - pdb=" SG CYS H 604 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN N 4 " - " MAN N 5 " " MAN N 5 " - " MAN N 6 " " MAN d 4 " - " MAN d 5 " " MAN o 4 " - " MAN o 5 " ALPHA1-3 " BMA N 3 " - " MAN N 4 " " MAN N 7 " - " MAN N 8 " " BMA O 3 " - " MAN O 7 " " MAN O 4 " - " MAN O 5 " " BMA d 3 " - " MAN d 4 " " BMA e 3 " - " MAN e 7 " " MAN e 4 " - " MAN e 5 " " BMA m 3 " - " MAN m 7 " " MAN m 4 " - " MAN m 5 " " BMA o 3 " - " MAN o 4 " " BMA p 3 " - " MAN p 7 " " MAN p 4 " - " MAN p 5 " ALPHA1-6 " BMA N 3 " - " MAN N 7 " " BMA O 3 " - " MAN O 4 " " MAN O 4 " - " MAN O 6 " " BMA d 3 " - " MAN d 6 " " BMA e 3 " - " MAN e 4 " " MAN e 4 " - " MAN e 6 " " BMA m 3 " - " MAN m 4 " " MAN m 4 " - " MAN m 6 " " BMA o 3 " - " MAN o 6 " " BMA p 3 " - " MAN p 4 " " MAN p 4 " - " MAN p 6 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG T 1 " - " NAG T 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " 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 d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " NAG-ASN " NAG A 601 " - " ASN A 133 " " NAG A 602 " - " ASN A 234 " " NAG A 603 " - " ASN A 301 " " NAG A 604 " - " ASN A 392 " " NAG A 605 " - " ASN A 149 " " NAG A 606 " - " ASN A 355 " " NAG A 607 " - " ASN A 405 " " NAG A 608 " - " ASN A 339 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG B 703 " - " ASN B 625 " " NAG B 704 " - " ASN B 616 " " NAG D 301 " - " ASN D 72 " " NAG E 1 " - " ASN A 156 " " NAG F 603 " - " ASN F 133 " " NAG F 604 " - " ASN F 234 " " NAG F 605 " - " ASN F 301 " " NAG F 606 " - " ASN F 392 " " NAG F 607 " - " ASN F 149 " " NAG F 608 " - " ASN F 355 " " NAG F 609 " - " ASN F 405 " " NAG F 610 " - " ASN F 339 " " NAG G 601 " - " ASN G 133 " " NAG G 602 " - " ASN G 160 " " NAG G 603 " - " ASN G 197 " " NAG G 604 " - " ASN G 234 " " NAG G 605 " - " ASN G 301 " " NAG G 606 " - " ASN G 392 " " NAG G 607 " - " ASN G 149 " " NAG G 608 " - " ASN G 355 " " NAG G 609 " - " ASN G 339 " " NAG H 701 " - " ASN H 611 " " NAG H 702 " - " ASN H 637 " " NAG H 703 " - " ASN H 625 " " NAG I 701 " - " ASN I 611 " " NAG I 702 " - " ASN I 637 " " NAG I 703 " - " ASN I 616 " " NAG K 301 " - " ASN K 72 " " NAG L 1 " - " ASN A 160 " " NAG M 1 " - " ASN A 197 " " NAG N 1 " - " ASN A 262 " " NAG O 1 " - " ASN A 276 " " NAG P 1 " - " ASN A 295 " " NAG Q 1 " - " ASN A 386 " " NAG R 1 " - " ASN A 448 " " NAG T 1 " - " ASN A 88 " " NAG U 301 " - " ASN U 72 " " NAG V 1 " - " ASN A 334 " " NAG W 1 " - " ASN A 241 " " NAG Z 1 " - " ASN A 289 " " NAG a 1 " - " ASN I 625 " " NAG b 1 " - " ASN F 156 " " NAG c 1 " - " ASN F 197 " " NAG d 1 " - " ASN F 262 " " NAG e 1 " - " ASN F 276 " " NAG f 1 " - " ASN F 295 " " NAG g 1 " - " ASN F 386 " " NAG h 1 " - " ASN F 448 " " NAG i 1 " - " ASN F 88 " " NAG j 1 " - " ASN F 334 " " NAG k 1 " - " ASN F 241 " " NAG l 1 " - " ASN F 289 " " NAG m 1 " - " ASN F 160 " " NAG n 1 " - " ASN G 156 " " NAG o 1 " - " ASN G 262 " " NAG p 1 " - " ASN G 276 " " NAG q 1 " - " ASN G 295 " " NAG r 1 " - " ASN G 386 " " NAG s 1 " - " ASN G 448 " " NAG t 1 " - " ASN G 88 " " NAG u 1 " - " ASN G 334 " " NAG v 1 " - " ASN G 241 " " NAG w 1 " - " ASN G 289 " Time building additional restraints: 13.04 Conformation dependent library (CDL) restraints added in 5.0 seconds 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6576 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 78 sheets defined 14.9% alpha, 34.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.20 Creating SS restraints... Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.221A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET A 104 " --> pdb=" O MET A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.573A pdb=" N LEU A 125 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 353 removed outlier: 4.233A pdb=" N GLU A 351 " --> pdb=" O GLY A 347 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N HIS A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.560A pdb=" N ASP A 477 " --> pdb=" O ASN A 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.607A pdb=" N ASP C 31 " --> pdb=" O ASN C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.521A pdb=" N ASP C 86 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N THR C 87 " --> pdb=" O SER C 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 83 through 87' Processing helix chain 'C' and resid 185 through 189 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.716A pdb=" N ILE D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 126 removed outlier: 3.552A pdb=" N LEU D 125 " --> pdb=" O SER D 121 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS D 126 " --> pdb=" O ASP D 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 121 through 126' Processing helix chain 'D' and resid 182 through 187 Processing helix chain 'F' and resid 98 through 117 removed outlier: 4.390A pdb=" N GLU F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 126 Processing helix chain 'F' and resid 195 through 198 Processing helix chain 'F' and resid 335 through 353 removed outlier: 3.712A pdb=" N LYS F 343 " --> pdb=" O ASN F 339 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU F 351 " --> pdb=" O GLY F 347 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N HIS F 352 " --> pdb=" O LYS F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 474 through 479 removed outlier: 3.605A pdb=" N ASP F 477 " --> pdb=" O ASN F 474 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 117 removed outlier: 4.520A pdb=" N GLU G 102 " --> pdb=" O ASN G 98 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU G 116 " --> pdb=" O TRP G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 353 removed outlier: 3.986A pdb=" N GLU G 351 " --> pdb=" O GLY G 347 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N HIS G 352 " --> pdb=" O LYS G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.619A pdb=" N MET G 373 " --> pdb=" O LEU G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 476 through 481 removed outlier: 3.608A pdb=" N SER G 481 " --> pdb=" O ASP G 477 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.662A pdb=" N ASP J 31 " --> pdb=" O ASN J 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 87 removed outlier: 3.820A pdb=" N ASP J 86 " --> pdb=" O ARG J 83 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N THR J 87 " --> pdb=" O SER J 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 83 through 87' Processing helix chain 'J' and resid 185 through 189 Processing helix chain 'K' and resid 79 through 83 removed outlier: 4.011A pdb=" N ILE K 83 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 121 through 126 removed outlier: 3.766A pdb=" N LEU K 125 " --> pdb=" O SER K 121 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LYS K 126 " --> pdb=" O ASP K 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 121 through 126' Processing helix chain 'K' and resid 182 through 189 removed outlier: 3.588A pdb=" N HIS K 189 " --> pdb=" O ASP K 185 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.559A pdb=" N ASP S 31 " --> pdb=" O ASN S 28 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TYR S 32 " --> pdb=" O ILE S 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 28 through 32' Processing helix chain 'S' and resid 83 through 87 removed outlier: 3.921A pdb=" N THR S 87 " --> pdb=" O SER S 84 " (cutoff:3.500A) Processing helix chain 'U' and resid 79 through 83 removed outlier: 3.903A pdb=" N ILE U 83 " --> pdb=" O PRO U 80 " (cutoff:3.500A) Processing helix chain 'U' and resid 121 through 126 removed outlier: 3.749A pdb=" N LEU U 125 " --> pdb=" O SER U 121 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS U 126 " --> pdb=" O ASP U 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 121 through 126' Processing helix chain 'U' and resid 182 through 189 removed outlier: 3.635A pdb=" N TYR U 186 " --> pdb=" O SER U 182 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU U 187 " --> pdb=" O LYS U 183 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS U 188 " --> pdb=" O ALA U 184 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N HIS U 189 " --> pdb=" O ASP U 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 182 through 189' Processing helix chain 'X' and resid 61 through 65 Processing helix chain 'Y' and resid 121 through 125 Processing helix chain 'Y' and resid 182 through 187 removed outlier: 3.838A pdb=" N GLN Y 187 " --> pdb=" O ASN Y 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 535 removed outlier: 3.896A pdb=" N ASN B 535 " --> pdb=" O ALA B 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 532 through 535' Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.929A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 568 Processing helix chain 'B' and resid 569 through 574 removed outlier: 3.517A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 597 removed outlier: 4.098A pdb=" N VAL B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE B 592 " --> pdb=" O GLU B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 659 removed outlier: 3.952A pdb=" N ASP B 644 " --> pdb=" O SER B 640 " (cutoff:3.500A) Processing helix chain 'I' and resid 529 through 534 Processing helix chain 'I' and resid 536 through 542 removed outlier: 4.014A pdb=" N GLN I 540 " --> pdb=" O THR I 536 " (cutoff:3.500A) Processing helix chain 'I' and resid 547 through 551 removed outlier: 4.028A pdb=" N GLN I 550 " --> pdb=" O GLY I 547 " (cutoff:3.500A) Processing helix chain 'I' and resid 565 through 568 Processing helix chain 'I' and resid 569 through 597 removed outlier: 3.606A pdb=" N LYS I 574 " --> pdb=" O VAL I 570 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN I 575 " --> pdb=" O TRP I 571 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU I 576 " --> pdb=" O GLY I 572 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL I 589 " --> pdb=" O ARG I 585 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE I 592 " --> pdb=" O GLU I 588 " (cutoff:3.500A) Processing helix chain 'I' and resid 618 through 625 removed outlier: 3.943A pdb=" N ASN I 625 " --> pdb=" O GLN I 621 " (cutoff:3.500A) Processing helix chain 'I' and resid 627 through 635 Processing helix chain 'I' and resid 638 through 659 removed outlier: 4.069A pdb=" N ASP I 644 " --> pdb=" O SER I 640 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN I 650 " --> pdb=" O LEU I 646 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP I 659 " --> pdb=" O ILE I 655 " (cutoff:3.500A) Processing helix chain 'H' and resid 529 through 534 Processing helix chain 'H' and resid 547 through 551 removed outlier: 3.759A pdb=" N GLN H 550 " --> pdb=" O GLY H 547 " (cutoff:3.500A) Processing helix chain 'H' and resid 565 through 568 Processing helix chain 'H' and resid 569 through 597 removed outlier: 3.611A pdb=" N LYS H 574 " --> pdb=" O VAL H 570 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN H 575 " --> pdb=" O TRP H 571 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU H 576 " --> pdb=" O GLY H 572 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA H 582 " --> pdb=" O ALA H 578 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL H 589 " --> pdb=" O ARG H 585 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE H 592 " --> pdb=" O GLU H 588 " (cutoff:3.500A) Processing helix chain 'H' and resid 619 through 624 Processing helix chain 'H' and resid 627 through 635 Processing helix chain 'H' and resid 638 through 659 removed outlier: 4.071A pdb=" N ASP H 644 " --> pdb=" O SER H 640 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.148A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 93 Processing sheet with id=AA5, first strand: chain 'A' and resid 130 through 132 Processing sheet with id=AA6, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA7, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.859A pdb=" N LYS A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 284 through 312 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 271 through 274 current: chain 'A' and resid 441 through 456 Processing sheet with id=AA9, first strand: chain 'A' and resid 271 through 274 removed outlier: 6.614A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 414 through 421 removed outlier: 4.555A pdb=" N ASN A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N GLU A 293 " --> pdb=" O ASN A 334 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.956A pdb=" N LYS A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.747A pdb=" N ASN A 448 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 10.773A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 10.054A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.408A pdb=" N ILE A 294 " --> pdb=" O ASN A 444 " (cutoff:3.500A) removed outlier: 10.240A pdb=" N ASN A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.193A pdb=" N CYS A 296 " --> pdb=" O LYS A 442 " (cutoff:3.500A) removed outlier: 10.482A pdb=" N LYS A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 393 through 395 removed outlier: 3.737A pdb=" N SER A 393 " --> pdb=" O PHE A 361 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ILE A 359 " --> pdb=" O TRP A 395 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N THR A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N PHE A 468 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N SER A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 374 through 378 removed outlier: 4.218A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 358 through 361 removed outlier: 6.282A pdb=" N THR A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N PHE A 468 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N SER A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 5 through 6 Processing sheet with id=AB6, first strand: chain 'C' and resid 5 through 6 Processing sheet with id=AB7, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.612A pdb=" N ALA C 10 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N TRP C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.612A pdb=" N ALA C 10 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL C 102 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 120 through 124 removed outlier: 4.179A pdb=" N GLY C 139 " --> pdb=" O LEU C 124 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N TYR C 176 " --> pdb=" O ASP C 144 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 120 through 124 removed outlier: 4.179A pdb=" N GLY C 139 " --> pdb=" O LEU C 124 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N TYR C 176 " --> pdb=" O ASP C 144 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 151 through 154 Processing sheet with id=AC3, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.542A pdb=" N ASP D 105 " --> pdb=" O LEU D 11 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 19 through 24 Processing sheet with id=AC5, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.566A pdb=" N TYR D 49 " --> pdb=" O LYS D 53 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 116 through 118 removed outlier: 3.601A pdb=" N LEU D 135 " --> pdb=" O PHE D 116 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE D 118 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL D 133 " --> pdb=" O PHE D 118 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL D 133 " --> pdb=" O LEU D 179 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N LEU D 179 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU D 135 " --> pdb=" O SER D 177 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N SER D 177 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ASN D 137 " --> pdb=" O LEU D 175 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LEU D 175 " --> pdb=" O ASN D 137 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 145 through 146 removed outlier: 4.234A pdb=" N LYS D 145 " --> pdb=" O THR D 197 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR D 197 " --> pdb=" O LYS D 145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'F' and resid 494 through 499 removed outlier: 5.005A pdb=" N VAL I 608 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N VAL F 38 " --> pdb=" O THR I 606 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N THR I 606 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N TYR F 40 " --> pdb=" O CYS I 604 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N CYS I 604 " --> pdb=" O TYR F 40 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 45 through 47 Processing sheet with id=AD1, first strand: chain 'F' and resid 75 through 76 removed outlier: 3.623A pdb=" N VAL F 75 " --> pdb=" O CYS F 54 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 91 through 94 Processing sheet with id=AD3, first strand: chain 'F' and resid 120 through 121 removed outlier: 3.822A pdb=" N VAL F 120 " --> pdb=" O GLN F 203 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LYS F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 130 through 132 removed outlier: 3.539A pdb=" N GLY X 106 " --> pdb=" O ASP X 103 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 181 through 183 Processing sheet with id=AD6, first strand: chain 'F' and resid 259 through 261 removed outlier: 6.216A pdb=" N LEU F 260 " --> pdb=" O THR F 450 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N GLY F 441 " --> pdb=" O SER F 300 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N SER F 300 " --> pdb=" O GLY F 441 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE F 443 " --> pdb=" O ARG F 298 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N GLY F 451 " --> pdb=" O LYS F 290 " (cutoff:3.500A) removed outlier: 10.685A pdb=" N LYS F 290 " --> pdb=" O GLY F 451 " (cutoff:3.500A) removed outlier: 11.874A pdb=" N LEU F 453 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 11.780A pdb=" N LEU F 288 " --> pdb=" O LEU F 453 " (cutoff:3.500A) removed outlier: 10.810A pdb=" N THR F 455 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 11.164A pdb=" N VAL F 286 " --> pdb=" O THR F 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 284 through 302 current: chain 'F' and resid 358 through 361 Processing sheet with id=AD7, first strand: chain 'F' and resid 271 through 273 removed outlier: 11.164A pdb=" N VAL F 286 " --> pdb=" O THR F 455 " (cutoff:3.500A) removed outlier: 10.810A pdb=" N THR F 455 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 11.780A pdb=" N LEU F 288 " --> pdb=" O LEU F 453 " (cutoff:3.500A) removed outlier: 11.874A pdb=" N LEU F 453 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 10.685A pdb=" N LYS F 290 " --> pdb=" O GLY F 451 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N GLY F 451 " --> pdb=" O LYS F 290 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE F 443 " --> pdb=" O ARG F 298 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N SER F 300 " --> pdb=" O GLY F 441 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N GLY F 441 " --> pdb=" O SER F 300 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 441 through 456 current: chain 'F' and resid 414 through 421 removed outlier: 4.220A pdb=" N PHE F 382 " --> pdb=" O LYS F 421 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 305 through 309 removed outlier: 3.729A pdb=" N GLN F 315 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 494 through 499 Processing sheet with id=AE1, first strand: chain 'G' and resid 45 through 47 Processing sheet with id=AE2, first strand: chain 'G' and resid 53 through 55 Processing sheet with id=AE3, first strand: chain 'G' and resid 91 through 93 Processing sheet with id=AE4, first strand: chain 'G' and resid 154 through 162 Processing sheet with id=AE5, first strand: chain 'G' and resid 181 through 183 Processing sheet with id=AE6, first strand: chain 'G' and resid 202 through 203 removed outlier: 6.711A pdb=" N LYS G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 259 through 261 removed outlier: 6.224A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 259 through 261 removed outlier: 6.224A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE G 359 " --> pdb=" O TRP G 395 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 315 through 322 removed outlier: 6.750A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N THR G 303 " --> pdb=" O GLY G 321 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ILE G 322 " --> pdb=" O ASN G 301 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ASN G 301 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N PHE G 382 " --> pdb=" O LYS G 421 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 315 through 322 removed outlier: 6.750A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N THR G 303 " --> pdb=" O GLY G 321 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ILE G 322 " --> pdb=" O ASN G 301 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ASN G 301 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE G 443 " --> pdb=" O ARG G 298 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N SER G 300 " --> pdb=" O GLY G 441 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N GLY G 441 " --> pdb=" O SER G 300 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 5 through 6 removed outlier: 3.734A pdb=" N VAL J 18 " --> pdb=" O LEU J 82 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.515A pdb=" N ALA J 10 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE J 34 " --> pdb=" O TRP J 50 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N TRP J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.515A pdb=" N ALA J 10 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL J 102 " --> pdb=" O ARG J 94 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 120 through 123 removed outlier: 6.208A pdb=" N TYR J 176 " --> pdb=" O ASP J 144 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL J 181 " --> pdb=" O HIS J 164 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 120 through 123 removed outlier: 6.208A pdb=" N TYR J 176 " --> pdb=" O ASP J 144 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 151 through 154 removed outlier: 3.558A pdb=" N THR J 151 " --> pdb=" O ASN J 199 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL J 207 " --> pdb=" O VAL J 198 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 18 through 24 Processing sheet with id=AF9, first strand: chain 'K' and resid 53 through 54 removed outlier: 6.403A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 114 through 118 removed outlier: 4.005A pdb=" N ASN K 137 " --> pdb=" O SER K 114 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL K 133 " --> pdb=" O PHE K 118 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N TYR K 173 " --> pdb=" O ASN K 138 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 149 through 150 Processing sheet with id=AG3, first strand: chain 'S' and resid 5 through 6 removed outlier: 3.974A pdb=" N VAL S 18 " --> pdb=" O LEU S 82 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'S' and resid 5 through 6 Processing sheet with id=AG5, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.304A pdb=" N ALA S 10 " --> pdb=" O THR S 110 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.304A pdb=" N ALA S 10 " --> pdb=" O THR S 110 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VAL S 102 " --> pdb=" O ARG S 94 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'S' and resid 120 through 123 removed outlier: 5.825A pdb=" N TYR S 176 " --> pdb=" O ASP S 144 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL S 181 " --> pdb=" O HIS S 164 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'S' and resid 120 through 123 removed outlier: 5.825A pdb=" N TYR S 176 " --> pdb=" O ASP S 144 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'S' and resid 151 through 154 removed outlier: 3.722A pdb=" N THR S 151 " --> pdb=" O ASN S 199 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N TYR S 194 " --> pdb=" O VAL S 211 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'U' and resid 11 through 12 removed outlier: 3.580A pdb=" N LEU U 11 " --> pdb=" O ARG U 103 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP U 105 " --> pdb=" O LEU U 11 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR U 86 " --> pdb=" O THR U 102 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N TRP U 35 " --> pdb=" O LEU U 47 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'U' and resid 19 through 24 Processing sheet with id=AH3, first strand: chain 'U' and resid 114 through 118 removed outlier: 3.551A pdb=" N PHE U 118 " --> pdb=" O VAL U 133 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL U 133 " --> pdb=" O PHE U 118 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER U 177 " --> pdb=" O CYS U 134 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N TYR U 173 " --> pdb=" O ASN U 138 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'U' and resid 145 through 146 removed outlier: 4.238A pdb=" N LYS U 145 " --> pdb=" O THR U 197 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N THR U 197 " --> pdb=" O LYS U 145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH4 Processing sheet with id=AH5, first strand: chain 'X' and resid 3 through 6 removed outlier: 3.514A pdb=" N ILE X 79 " --> pdb=" O CYS X 22 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'X' and resid 45 through 51 removed outlier: 4.077A pdb=" N TRP X 36 " --> pdb=" O ILE X 48 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ARG X 50 " --> pdb=" O CYS X 34 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N CYS X 34 " --> pdb=" O ARG X 50 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE X 37 " --> pdb=" O PHE X 95 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N GLY X 98 " --> pdb=" O LYS X 113 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS X 113 " --> pdb=" O GLY X 98 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'X' and resid 92 through 93 Processing sheet with id=AH8, first strand: chain 'X' and resid 132 through 136 removed outlier: 3.764A pdb=" N GLY X 151 " --> pdb=" O LEU X 136 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N TYR X 188 " --> pdb=" O ASP X 156 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'X' and resid 132 through 136 removed outlier: 3.764A pdb=" N GLY X 151 " --> pdb=" O LEU X 136 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA X 148 " --> pdb=" O VAL X 196 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL X 196 " --> pdb=" O ALA X 148 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU X 150 " --> pdb=" O VAL X 194 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL X 194 " --> pdb=" O LEU X 150 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'X' and resid 162 through 166 removed outlier: 3.632A pdb=" N SER X 165 " --> pdb=" O ASN X 209 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'Y' and resid 4 through 7 removed outlier: 3.583A pdb=" N VAL Y 19 " --> pdb=" O ILE Y 75 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE Y 71 " --> pdb=" O CYS Y 23 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'Y' and resid 11 through 12 removed outlier: 7.162A pdb=" N VAL Y 11 " --> pdb=" O GLU Y 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI3 Processing sheet with id=AI4, first strand: chain 'Y' and resid 53 through 54 removed outlier: 3.657A pdb=" N LYS Y 45 " --> pdb=" O GLN Y 37 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N TRP Y 35 " --> pdb=" O LEU Y 47 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR Y 85 " --> pdb=" O ALA Y 38 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'Y' and resid 114 through 115 removed outlier: 4.050A pdb=" N VAL Y 132 " --> pdb=" O LEU Y 179 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'Y' and resid 146 through 148 915 hydrogen bonds defined for protein. 2307 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: 11.03 Time building geometry restraints manager: 14.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 9182 1.35 - 1.47: 7883 1.47 - 1.60: 12890 1.60 - 1.72: 0 1.72 - 1.85: 183 Bond restraints: 30138 Sorted by residual: bond pdb=" O3 PO4 F 602 " pdb=" P PO4 F 602 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 9.11e+00 bond pdb=" O3 PO4 F 601 " pdb=" P PO4 F 601 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 9.11e+00 bond pdb=" O3 PO4 A 609 " pdb=" P PO4 A 609 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 9.06e+00 bond pdb=" O4 PO4 F 601 " pdb=" P PO4 F 601 " ideal model delta sigma weight residual 1.568 1.508 0.060 2.00e-02 2.50e+03 8.91e+00 bond pdb=" O4 PO4 F 602 " pdb=" P PO4 F 602 " ideal model delta sigma weight residual 1.568 1.509 0.059 2.00e-02 2.50e+03 8.71e+00 ... (remaining 30133 not shown) Histogram of bond angle deviations from ideal: 97.92 - 105.15: 548 105.15 - 112.38: 16366 112.38 - 119.61: 9571 119.61 - 126.85: 14061 126.85 - 134.08: 477 Bond angle restraints: 41023 Sorted by residual: angle pdb=" N ASN F 156 " pdb=" CA ASN F 156 " pdb=" CB ASN F 156 " ideal model delta sigma weight residual 109.85 118.61 -8.76 1.49e+00 4.50e-01 3.45e+01 angle pdb=" N ASN I 625 " pdb=" CA ASN I 625 " pdb=" CB ASN I 625 " ideal model delta sigma weight residual 111.54 119.51 -7.97 1.45e+00 4.76e-01 3.02e+01 angle pdb=" C ASN I 625 " pdb=" CA ASN I 625 " pdb=" CB ASN I 625 " ideal model delta sigma weight residual 111.18 103.02 8.16 1.56e+00 4.11e-01 2.74e+01 angle pdb=" C ASN I 624 " pdb=" N ASN I 625 " pdb=" CA ASN I 625 " ideal model delta sigma weight residual 122.50 113.73 8.77 1.82e+00 3.02e-01 2.32e+01 angle pdb=" C LYS D 107 " pdb=" N ARG D 108 " pdb=" CA ARG D 108 " ideal model delta sigma weight residual 121.54 128.55 -7.01 1.91e+00 2.74e-01 1.35e+01 ... (remaining 41018 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.42: 18533 24.42 - 48.84: 979 48.84 - 73.26: 215 73.26 - 97.67: 103 97.67 - 122.09: 31 Dihedral angle restraints: 19861 sinusoidal: 9652 harmonic: 10209 Sorted by residual: dihedral pdb=" CB CYS U 134 " pdb=" SG CYS U 134 " pdb=" SG CYS U 194 " pdb=" CB CYS U 194 " ideal model delta sinusoidal sigma weight residual -86.00 3.48 -89.48 1 1.00e+01 1.00e-02 9.51e+01 dihedral pdb=" CB CYS F 501 " pdb=" SG CYS F 501 " pdb=" SG CYS I 605 " pdb=" CB CYS I 605 " ideal model delta sinusoidal sigma weight residual 93.00 4.13 88.87 1 1.00e+01 1.00e-02 9.41e+01 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 -86.00 -173.74 87.74 1 1.00e+01 1.00e-02 9.22e+01 ... (remaining 19858 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.253: 5007 0.253 - 0.506: 14 0.506 - 0.759: 1 0.759 - 1.012: 0 1.012 - 1.265: 2 Chirality restraints: 5024 Sorted by residual: chirality pdb=" C1 NAG b 1 " pdb=" ND2 ASN F 156 " pdb=" C2 NAG b 1 " pdb=" O5 NAG b 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.14 -1.26 2.00e-01 2.50e+01 4.00e+01 chirality pdb=" C1 NAG a 1 " pdb=" ND2 ASN I 625 " pdb=" C2 NAG a 1 " pdb=" O5 NAG a 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.14 -1.26 2.00e-01 2.50e+01 3.99e+01 chirality pdb=" C1 NAG I 701 " pdb=" ND2 ASN I 611 " pdb=" C2 NAG I 701 " pdb=" O5 NAG I 701 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 7.15e+00 ... (remaining 5021 not shown) Planarity restraints: 5115 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN F 156 " 0.069 2.00e-02 2.50e+03 6.67e-02 5.57e+01 pdb=" CG ASN F 156 " -0.081 2.00e-02 2.50e+03 pdb=" OD1 ASN F 156 " 0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN F 156 " -0.077 2.00e-02 2.50e+03 pdb=" C1 NAG b 1 " 0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN I 625 " 0.006 2.00e-02 2.50e+03 6.42e-02 5.16e+01 pdb=" CG ASN I 625 " -0.071 2.00e-02 2.50e+03 pdb=" OD1 ASN I 625 " 0.075 2.00e-02 2.50e+03 pdb=" ND2 ASN I 625 " -0.076 2.00e-02 2.50e+03 pdb=" C1 NAG a 1 " 0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 392 " 0.039 2.00e-02 2.50e+03 3.57e-02 1.59e+01 pdb=" CG ASN A 392 " -0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN A 392 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN A 392 " -0.038 2.00e-02 2.50e+03 pdb=" C1 NAG A 604 " 0.038 2.00e-02 2.50e+03 ... (remaining 5112 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 584 2.67 - 3.22: 27157 3.22 - 3.78: 41957 3.78 - 4.34: 59437 4.34 - 4.90: 97531 Nonbonded interactions: 226666 Sorted by model distance: nonbonded pdb=" OD1 ASN A 386 " pdb=" OG1 THR A 388 " model vdw 2.107 3.040 nonbonded pdb=" OG SER U 63 " pdb=" OG1 THR U 74 " model vdw 2.158 3.040 nonbonded pdb=" ND2 ASN F 67 " pdb=" O ASP F 211 " model vdw 2.175 3.120 nonbonded pdb=" O TYR Y 186 " pdb=" OH TYR Y 192 " model vdw 2.181 3.040 nonbonded pdb=" OG SER D 63 " pdb=" OG1 THR D 74 " model vdw 2.184 3.040 ... (remaining 226661 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 31 through 507 or resid 603 through 608)) selection = (chain 'F' and (resid 31 through 507 or resid 603 through 608)) selection = (chain 'G' and (resid 31 through 507 or resid 603 through 608)) } ncs_group { reference = (chain 'B' and (resid 519 through 661 or resid 701 through 703)) selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'C' selection = chain 'J' selection = chain 'S' } ncs_group { reference = chain 'D' selection = chain 'K' selection = chain 'U' } ncs_group { reference = chain 'E' selection = chain 'L' selection = chain 'M' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'n' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' } ncs_group { reference = (chain 'N' and (resid 2 or resid 5 through 8)) selection = (chain 'O' and (resid 1 or resid 4 through 7)) selection = (chain 'e' and (resid 1 or resid 4 through 7)) selection = (chain 'm' and (resid 1 or resid 4 through 7)) selection = (chain 'p' and (resid 1 or resid 4 through 7)) } ncs_group { reference = chain 'd' selection = chain 'o' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.190 Check model and map are aligned: 0.220 Set scattering table: 0.280 Process input model: 78.010 Find NCS groups from input model: 1.940 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 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 0.060 30138 Z= 0.307 Angle : 0.722 8.772 41023 Z= 0.346 Chirality : 0.057 1.265 5024 Planarity : 0.004 0.058 5042 Dihedral : 16.457 122.093 13126 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.57 % Twisted General : 0.18 % 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: -1.62 (0.14), residues: 3477 helix: -1.65 (0.23), residues: 422 sheet: -0.21 (0.16), residues: 1093 loop : -1.46 (0.14), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP I 610 HIS 0.004 0.001 HIS F 287 PHE 0.013 0.001 PHE G 53 TYR 0.015 0.001 TYR H 638 ARG 0.006 0.000 ARG F 504 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 355 time to evaluate : 3.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.7607 (m-30) cc_final: 0.7115 (m-30) REVERT: C 28 ASN cc_start: 0.6854 (t0) cc_final: 0.6585 (t0) REVERT: C 72 ASP cc_start: 0.8449 (p0) cc_final: 0.7691 (p0) REVERT: C 145 TYR cc_start: 0.6239 (p90) cc_final: 0.6005 (p90) REVERT: D 26 ASN cc_start: 0.8538 (p0) cc_final: 0.8294 (p0) REVERT: D 70 GLU cc_start: 0.7812 (pt0) cc_final: 0.7596 (pt0) REVERT: F 213 ILE cc_start: 0.8972 (mt) cc_final: 0.8654 (tt) REVERT: K 36 TYR cc_start: 0.8729 (m-80) cc_final: 0.8489 (m-80) REVERT: S 19 ARG cc_start: 0.7865 (ttm170) cc_final: 0.7557 (ttm170) REVERT: X 23 ASP cc_start: 0.7618 (m-30) cc_final: 0.7025 (m-30) REVERT: X 155 LYS cc_start: 0.7533 (mmmm) cc_final: 0.7296 (mmtt) REVERT: H 620 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7471 (tm-30) outliers start: 0 outliers final: 0 residues processed: 355 average time/residue: 0.4653 time to fit residues: 250.9313 Evaluate side-chains 281 residues out of total 3106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 281 time to evaluate : 3.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 292 optimal weight: 9.9990 chunk 262 optimal weight: 0.8980 chunk 145 optimal weight: 8.9990 chunk 89 optimal weight: 2.9990 chunk 176 optimal weight: 0.9980 chunk 140 optimal weight: 4.9990 chunk 271 optimal weight: 10.0000 chunk 104 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 chunk 201 optimal weight: 0.7980 chunk 314 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN F 229 ASN G 66 HIS ** G 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 204 ASN ** U 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.0888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 30138 Z= 0.243 Angle : 0.625 7.544 41023 Z= 0.316 Chirality : 0.048 0.567 5024 Planarity : 0.005 0.067 5042 Dihedral : 12.056 118.353 6696 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 0.68 % Allowed : 7.28 % Favored : 92.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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 (0.14), residues: 3477 helix: -0.50 (0.26), residues: 410 sheet: -0.07 (0.16), residues: 1115 loop : -1.39 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 37 HIS 0.004 0.001 HIS G 287 PHE 0.014 0.001 PHE G 53 TYR 0.018 0.001 TYR D 173 ARG 0.007 0.000 ARG Y 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 308 time to evaluate : 3.601 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.7578 (m-30) cc_final: 0.7108 (m-30) REVERT: C 145 TYR cc_start: 0.6217 (p90) cc_final: 0.5957 (p90) REVERT: D 26 ASN cc_start: 0.8634 (p0) cc_final: 0.8007 (p0) REVERT: D 70 GLU cc_start: 0.7697 (pt0) cc_final: 0.7492 (pt0) REVERT: F 213 ILE cc_start: 0.9056 (mt) cc_final: 0.8737 (tt) REVERT: G 86 MET cc_start: 0.7983 (mtp) cc_final: 0.7559 (mtp) REVERT: K 82 ASP cc_start: 0.6148 (m-30) cc_final: 0.5812 (m-30) REVERT: S 19 ARG cc_start: 0.7720 (ttm170) cc_final: 0.7314 (ttm170) REVERT: X 36 TRP cc_start: 0.7285 (m100) cc_final: 0.7059 (m100) REVERT: H 620 GLU cc_start: 0.7765 (tm-30) cc_final: 0.7524 (tm-30) outliers start: 21 outliers final: 14 residues processed: 318 average time/residue: 0.4704 time to fit residues: 227.4143 Evaluate side-chains 280 residues out of total 3106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 266 time to evaluate : 3.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 72 HIS Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain J residue 13 LYS Chi-restraints excluded: chain J residue 31 ASP Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain X residue 72 ILE Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain H residue 519 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 174 optimal weight: 0.0980 chunk 97 optimal weight: 2.9990 chunk 261 optimal weight: 0.0040 chunk 213 optimal weight: 20.0000 chunk 86 optimal weight: 5.9990 chunk 314 optimal weight: 0.7980 chunk 340 optimal weight: 1.9990 chunk 280 optimal weight: 10.0000 chunk 312 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 252 optimal weight: 5.9990 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN C 28 ASN J 164 HIS ** U 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 166 GLN ** H 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 30138 Z= 0.175 Angle : 0.577 8.255 41023 Z= 0.292 Chirality : 0.047 0.458 5024 Planarity : 0.004 0.056 5042 Dihedral : 10.860 117.903 6696 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.22 % Allowed : 9.70 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -1.10 (0.14), residues: 3477 helix: 0.01 (0.27), residues: 407 sheet: 0.02 (0.16), residues: 1114 loop : -1.37 (0.14), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 37 HIS 0.009 0.001 HIS G 66 PHE 0.012 0.001 PHE X 112 TYR 0.014 0.001 TYR C 90 ARG 0.007 0.000 ARG Y 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 295 time to evaluate : 3.558 Fit side-chains revert: symmetry clash REVERT: A 69 TRP cc_start: 0.7263 (m100) cc_final: 0.6944 (m100) REVERT: A 107 ASP cc_start: 0.7567 (m-30) cc_final: 0.7119 (m-30) REVERT: C 145 TYR cc_start: 0.6255 (p90) cc_final: 0.6023 (p90) REVERT: D 26 ASN cc_start: 0.8616 (p0) cc_final: 0.8084 (p0) REVERT: F 213 ILE cc_start: 0.9049 (mt) cc_final: 0.8711 (tt) REVERT: G 86 MET cc_start: 0.7804 (mtp) cc_final: 0.7528 (mtp) REVERT: J 76 TYR cc_start: 0.8937 (m-80) cc_final: 0.8580 (m-80) REVERT: K 82 ASP cc_start: 0.6137 (m-30) cc_final: 0.5804 (m-30) REVERT: S 19 ARG cc_start: 0.7691 (ttm170) cc_final: 0.7369 (ttm170) REVERT: S 74 ASP cc_start: 0.8466 (p0) cc_final: 0.8195 (p0) REVERT: H 620 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7531 (tm-30) outliers start: 38 outliers final: 22 residues processed: 312 average time/residue: 0.4480 time to fit residues: 214.1480 Evaluate side-chains 296 residues out of total 3106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 274 time to evaluate : 3.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 184 MET Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 72 ILE Chi-restraints excluded: chain X residue 79 ILE Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain H residue 519 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 310 optimal weight: 8.9990 chunk 236 optimal weight: 5.9990 chunk 163 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 150 optimal weight: 5.9990 chunk 211 optimal weight: 1.9990 chunk 315 optimal weight: 2.9990 chunk 334 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 299 optimal weight: 20.0000 chunk 90 optimal weight: 0.0970 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 GLN A 478 ASN C 28 ASN F 114 GLN G 66 HIS S 204 ASN U 138 ASN ** U 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 30138 Z= 0.401 Angle : 0.675 8.067 41023 Z= 0.338 Chirality : 0.049 0.308 5024 Planarity : 0.005 0.059 5042 Dihedral : 10.356 115.067 6696 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 1.55 % Allowed : 12.70 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.31 (0.14), residues: 3477 helix: -0.17 (0.27), residues: 413 sheet: -0.15 (0.16), residues: 1112 loop : -1.49 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP J 50 HIS 0.007 0.001 HIS G 375 PHE 0.020 0.002 PHE G 53 TYR 0.025 0.002 TYR D 173 ARG 0.007 0.000 ARG Y 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 283 time to evaluate : 3.313 Fit side-chains revert: symmetry clash REVERT: A 52 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9126 (mt) REVERT: A 107 ASP cc_start: 0.7657 (m-30) cc_final: 0.7246 (m-30) REVERT: C 145 TYR cc_start: 0.6350 (p90) cc_final: 0.6080 (p90) REVERT: D 26 ASN cc_start: 0.8741 (p0) cc_final: 0.8246 (p0) REVERT: F 175 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8312 (mt) REVERT: F 213 ILE cc_start: 0.9053 (mt) cc_final: 0.8702 (tt) REVERT: G 86 MET cc_start: 0.8256 (mtp) cc_final: 0.7926 (mtp) REVERT: G 205 CYS cc_start: 0.6844 (OUTLIER) cc_final: 0.6447 (m) REVERT: J 87 THR cc_start: 0.8412 (OUTLIER) cc_final: 0.8041 (t) REVERT: K 82 ASP cc_start: 0.6401 (m-30) cc_final: 0.6053 (m-30) REVERT: S 19 ARG cc_start: 0.7841 (ttm170) cc_final: 0.7517 (ttm170) REVERT: S 28 ASN cc_start: 0.7617 (t0) cc_final: 0.7402 (t0) REVERT: X 188 TYR cc_start: 0.5055 (m-80) cc_final: 0.4826 (m-80) REVERT: H 620 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7611 (tm-30) outliers start: 48 outliers final: 30 residues processed: 308 average time/residue: 0.4542 time to fit residues: 214.7146 Evaluate side-chains 300 residues out of total 3106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 266 time to evaluate : 3.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain F residue 67 ASN Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 184 MET Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain J residue 53 LYS Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain S residue 80 MET Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 72 ILE Chi-restraints excluded: chain X residue 79 ILE Chi-restraints excluded: chain X residue 113 LYS Chi-restraints excluded: chain Y residue 105 GLU Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain H residue 519 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 278 optimal weight: 20.0000 chunk 189 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 249 optimal weight: 6.9990 chunk 137 optimal weight: 0.8980 chunk 285 optimal weight: 4.9990 chunk 231 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 170 optimal weight: 0.9990 chunk 300 optimal weight: 4.9990 chunk 84 optimal weight: 20.0000 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN C 28 ASN ** U 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 624 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 30138 Z= 0.263 Angle : 0.608 7.970 41023 Z= 0.306 Chirality : 0.047 0.308 5024 Planarity : 0.004 0.073 5042 Dihedral : 9.868 114.637 6696 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 1.71 % Allowed : 13.54 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.25 (0.14), residues: 3477 helix: -0.03 (0.27), residues: 413 sheet: -0.11 (0.16), residues: 1086 loop : -1.45 (0.14), residues: 1978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 50 HIS 0.004 0.001 HIS G 72 PHE 0.015 0.001 PHE G 53 TYR 0.020 0.001 TYR D 173 ARG 0.006 0.000 ARG Y 61 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 275 time to evaluate : 3.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.9082 (mt) REVERT: A 107 ASP cc_start: 0.7623 (m-30) cc_final: 0.7203 (m-30) REVERT: C 87 THR cc_start: 0.8062 (OUTLIER) cc_final: 0.7763 (t) REVERT: C 95 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.8737 (pt0) REVERT: C 145 TYR cc_start: 0.6322 (p90) cc_final: 0.6043 (p90) REVERT: C 178 LEU cc_start: 0.7194 (OUTLIER) cc_final: 0.6778 (pp) REVERT: D 26 ASN cc_start: 0.8667 (p0) cc_final: 0.8139 (p0) REVERT: F 175 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8193 (mp) REVERT: F 213 ILE cc_start: 0.9039 (mt) cc_final: 0.8686 (tt) REVERT: G 86 MET cc_start: 0.8090 (mtp) cc_final: 0.7563 (mtp) REVERT: K 82 ASP cc_start: 0.6390 (m-30) cc_final: 0.6049 (m-30) REVERT: S 19 ARG cc_start: 0.7802 (ttm170) cc_final: 0.7470 (ttm170) REVERT: X 188 TYR cc_start: 0.4987 (m-80) cc_final: 0.4570 (m-80) REVERT: H 620 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7650 (tm-30) outliers start: 53 outliers final: 34 residues processed: 306 average time/residue: 0.4534 time to fit residues: 212.9536 Evaluate side-chains 303 residues out of total 3106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 264 time to evaluate : 3.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 95 GLN Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 184 MET Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 373 MET Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain J residue 53 LYS Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain S residue 80 MET Chi-restraints excluded: chain S residue 211 VAL Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 72 ILE Chi-restraints excluded: chain X residue 79 ILE Chi-restraints excluded: chain X residue 113 LYS Chi-restraints excluded: chain X residue 223 VAL Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain I residue 604 CYS Chi-restraints excluded: chain H residue 519 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 112 optimal weight: 3.9990 chunk 301 optimal weight: 8.9990 chunk 66 optimal weight: 20.0000 chunk 196 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 chunk 334 optimal weight: 3.9990 chunk 277 optimal weight: 10.0000 chunk 154 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 175 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 478 ASN G 67 ASN S 204 ASN U 147 GLN X 176 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 30138 Z= 0.541 Angle : 0.748 8.992 41023 Z= 0.373 Chirality : 0.051 0.303 5024 Planarity : 0.005 0.067 5042 Dihedral : 10.150 111.019 6696 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 2.38 % Allowed : 14.37 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.14), residues: 3477 helix: -0.49 (0.26), residues: 431 sheet: -0.34 (0.16), residues: 1089 loop : -1.65 (0.13), residues: 1957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP J 50 HIS 0.010 0.001 HIS G 375 PHE 0.022 0.002 PHE A 53 TYR 0.024 0.002 TYR D 49 ARG 0.007 0.001 ARG Y 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 265 time to evaluate : 3.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9091 (mt) REVERT: A 107 ASP cc_start: 0.7580 (m-30) cc_final: 0.7163 (m-30) REVERT: C 87 THR cc_start: 0.8187 (OUTLIER) cc_final: 0.7846 (t) REVERT: C 95 GLN cc_start: 0.9088 (OUTLIER) cc_final: 0.8682 (pt0) REVERT: C 145 TYR cc_start: 0.6451 (p90) cc_final: 0.6211 (p90) REVERT: C 178 LEU cc_start: 0.7350 (OUTLIER) cc_final: 0.6938 (pp) REVERT: F 175 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8301 (mt) REVERT: F 213 ILE cc_start: 0.9118 (mt) cc_final: 0.8747 (tt) REVERT: F 426 MET cc_start: 0.7358 (tpp) cc_final: 0.6788 (tpt) REVERT: G 86 MET cc_start: 0.8483 (mtp) cc_final: 0.8109 (mtp) REVERT: K 82 ASP cc_start: 0.6432 (m-30) cc_final: 0.6094 (m-30) REVERT: S 19 ARG cc_start: 0.7650 (ttm170) cc_final: 0.7323 (ttm170) REVERT: S 28 ASN cc_start: 0.7772 (t0) cc_final: 0.7329 (t0) REVERT: S 31 ASP cc_start: 0.7328 (m-30) cc_final: 0.6872 (m-30) REVERT: X 157 TYR cc_start: 0.4979 (p90) cc_final: 0.4696 (p90) REVERT: I 654 ASP cc_start: 0.8329 (m-30) cc_final: 0.7982 (m-30) REVERT: H 620 GLU cc_start: 0.7946 (tm-30) cc_final: 0.7717 (tm-30) outliers start: 74 outliers final: 53 residues processed: 313 average time/residue: 0.4718 time to fit residues: 230.4499 Evaluate side-chains 311 residues out of total 3106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 253 time to evaluate : 3.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 95 GLN Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain F residue 67 ASN Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 184 MET Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 413 THR Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain J residue 53 LYS Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 143 LYS Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 80 MET Chi-restraints excluded: chain S residue 211 VAL Chi-restraints excluded: chain X residue 6 GLU Chi-restraints excluded: chain X residue 72 ILE Chi-restraints excluded: chain X residue 79 ILE Chi-restraints excluded: chain X residue 113 LYS Chi-restraints excluded: chain X residue 150 LEU Chi-restraints excluded: chain X residue 223 VAL Chi-restraints excluded: chain Y residue 105 GLU Chi-restraints excluded: chain Y residue 197 THR Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain I residue 604 CYS Chi-restraints excluded: chain I residue 611 ASN Chi-restraints excluded: chain I residue 629 ILE Chi-restraints excluded: chain I residue 658 VAL Chi-restraints excluded: chain H residue 519 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 322 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 190 optimal weight: 0.9990 chunk 244 optimal weight: 0.9990 chunk 189 optimal weight: 0.9980 chunk 281 optimal weight: 0.8980 chunk 186 optimal weight: 0.5980 chunk 333 optimal weight: 0.5980 chunk 208 optimal weight: 9.9990 chunk 203 optimal weight: 0.7980 chunk 153 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN A 478 ASN S 35 HIS U 147 GLN X 176 HIS Y 137 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30138 Z= 0.178 Angle : 0.586 8.986 41023 Z= 0.295 Chirality : 0.046 0.308 5024 Planarity : 0.004 0.070 5042 Dihedral : 9.361 112.008 6696 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.61 % Allowed : 15.57 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.14), residues: 3477 helix: 0.07 (0.27), residues: 419 sheet: -0.09 (0.16), residues: 1081 loop : -1.47 (0.14), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 479 HIS 0.004 0.001 HIS G 72 PHE 0.012 0.001 PHE X 112 TYR 0.014 0.001 TYR D 173 ARG 0.011 0.000 ARG K 211 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 284 time to evaluate : 3.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.9049 (mt) REVERT: A 107 ASP cc_start: 0.7609 (m-30) cc_final: 0.7131 (m-30) REVERT: A 166 ARG cc_start: 0.7673 (mtm-85) cc_final: 0.6937 (mtm180) REVERT: C 87 THR cc_start: 0.8069 (OUTLIER) cc_final: 0.7805 (t) REVERT: C 95 GLN cc_start: 0.9021 (OUTLIER) cc_final: 0.8682 (pt0) REVERT: F 175 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8165 (mp) REVERT: F 186 ASN cc_start: 0.7745 (t0) cc_final: 0.7535 (t0) REVERT: F 213 ILE cc_start: 0.9047 (mt) cc_final: 0.8687 (tt) REVERT: F 426 MET cc_start: 0.7195 (tpp) cc_final: 0.6774 (tpt) REVERT: G 86 MET cc_start: 0.8013 (mtp) cc_final: 0.7463 (mtp) REVERT: G 95 MET cc_start: 0.7708 (OUTLIER) cc_final: 0.7472 (mtp) REVERT: K 82 ASP cc_start: 0.6356 (m-30) cc_final: 0.6023 (m-30) REVERT: S 19 ARG cc_start: 0.7713 (ttm170) cc_final: 0.7370 (ttm170) REVERT: S 28 ASN cc_start: 0.7590 (t0) cc_final: 0.7264 (t0) REVERT: S 31 ASP cc_start: 0.7286 (m-30) cc_final: 0.6924 (m-30) REVERT: X 36 TRP cc_start: 0.7565 (m100) cc_final: 0.7331 (m100) REVERT: H 620 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7640 (tm-30) outliers start: 50 outliers final: 34 residues processed: 313 average time/residue: 0.4707 time to fit residues: 226.3405 Evaluate side-chains 310 residues out of total 3106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 271 time to evaluate : 3.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 95 GLN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 184 MET Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain S residue 80 MET Chi-restraints excluded: chain S residue 211 VAL Chi-restraints excluded: chain X residue 6 GLU Chi-restraints excluded: chain X residue 72 ILE Chi-restraints excluded: chain X residue 79 ILE Chi-restraints excluded: chain Y residue 137 ASN Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain I residue 604 CYS Chi-restraints excluded: chain I residue 611 ASN Chi-restraints excluded: chain I residue 634 GLU Chi-restraints excluded: chain I residue 658 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 206 optimal weight: 0.9980 chunk 133 optimal weight: 1.9990 chunk 199 optimal weight: 0.0870 chunk 100 optimal weight: 0.6980 chunk 65 optimal weight: 6.9990 chunk 64 optimal weight: 9.9990 chunk 212 optimal weight: 7.9990 chunk 227 optimal weight: 5.9990 chunk 164 optimal weight: 0.4980 chunk 31 optimal weight: 3.9990 chunk 262 optimal weight: 0.8980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN U 147 GLN ** X 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30138 Z= 0.166 Angle : 0.572 9.662 41023 Z= 0.287 Chirality : 0.046 0.310 5024 Planarity : 0.004 0.062 5042 Dihedral : 8.935 111.597 6696 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.84 % Allowed : 16.27 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -1.06 (0.14), residues: 3477 helix: 0.54 (0.28), residues: 393 sheet: 0.02 (0.16), residues: 1097 loop : -1.43 (0.14), residues: 1987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 427 HIS 0.007 0.001 HIS C 200 PHE 0.012 0.001 PHE X 112 TYR 0.028 0.001 TYR C 145 ARG 0.008 0.000 ARG K 211 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 275 time to evaluate : 3.100 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.9030 (mt) REVERT: A 107 ASP cc_start: 0.7580 (m-30) cc_final: 0.7088 (m-30) REVERT: A 166 ARG cc_start: 0.7697 (mtm-85) cc_final: 0.6937 (mtm180) REVERT: A 440 ARG cc_start: 0.8342 (ttp-170) cc_final: 0.8111 (ptm160) REVERT: C 87 THR cc_start: 0.8008 (OUTLIER) cc_final: 0.7715 (t) REVERT: C 95 GLN cc_start: 0.9041 (OUTLIER) cc_final: 0.8709 (pt0) REVERT: C 178 LEU cc_start: 0.6887 (OUTLIER) cc_final: 0.6545 (pp) REVERT: F 175 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8189 (mp) REVERT: F 213 ILE cc_start: 0.9081 (mt) cc_final: 0.8758 (tt) REVERT: F 426 MET cc_start: 0.7191 (tpp) cc_final: 0.6785 (tpt) REVERT: G 95 MET cc_start: 0.7673 (OUTLIER) cc_final: 0.7441 (mtp) REVERT: G 205 CYS cc_start: 0.6436 (OUTLIER) cc_final: 0.6030 (m) REVERT: J 87 THR cc_start: 0.8404 (OUTLIER) cc_final: 0.8084 (t) REVERT: K 82 ASP cc_start: 0.6368 (m-30) cc_final: 0.6068 (m-30) REVERT: S 19 ARG cc_start: 0.7761 (ttm170) cc_final: 0.7461 (ttm170) REVERT: H 620 GLU cc_start: 0.7885 (tm-30) cc_final: 0.7627 (tm-30) outliers start: 57 outliers final: 37 residues processed: 312 average time/residue: 0.4534 time to fit residues: 217.3701 Evaluate side-chains 309 residues out of total 3106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 264 time to evaluate : 3.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 95 GLN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 501 CYS Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 184 MET Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 373 MET Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 80 MET Chi-restraints excluded: chain S residue 211 VAL Chi-restraints excluded: chain U residue 147 GLN Chi-restraints excluded: chain X residue 72 ILE Chi-restraints excluded: chain X residue 79 ILE Chi-restraints excluded: chain X residue 81 LEU Chi-restraints excluded: chain X residue 223 VAL Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain I residue 569 THR Chi-restraints excluded: chain I residue 604 CYS Chi-restraints excluded: chain I residue 611 ASN Chi-restraints excluded: chain I residue 634 GLU Chi-restraints excluded: chain I residue 658 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.1403 > 50: distance: 35 - 187: 7.193 distance: 44 - 175: 5.471 distance: 47 - 172: 3.973 distance: 58 - 158: 33.806 distance: 110 - 183: 6.365 distance: 113 - 180: 3.624 distance: 141 - 146: 3.242 distance: 147 - 148: 9.320 distance: 147 - 150: 4.956 distance: 148 - 149: 11.175 distance: 148 - 155: 16.491 distance: 150 - 151: 3.911 distance: 151 - 152: 3.301 distance: 155 - 156: 6.472 distance: 156 - 157: 9.988 distance: 156 - 159: 10.212 distance: 157 - 158: 27.270 distance: 157 - 166: 18.198 distance: 160 - 161: 8.718 distance: 160 - 162: 4.733 distance: 161 - 163: 6.445 distance: 162 - 164: 7.322 distance: 163 - 165: 6.323 distance: 164 - 165: 8.719 distance: 166 - 167: 3.618 distance: 167 - 168: 5.458 distance: 167 - 170: 9.811 distance: 168 - 169: 4.284 distance: 168 - 172: 5.725 distance: 170 - 171: 3.361 distance: 172 - 173: 3.365 distance: 173 - 174: 3.831 distance: 174 - 175: 3.159 distance: 176 - 177: 5.314 distance: 177 - 178: 3.202 distance: 177 - 179: 6.624 distance: 180 - 181: 10.257 distance: 181 - 182: 11.643 distance: 181 - 184: 15.914 distance: 182 - 183: 4.946 distance: 182 - 187: 4.766 distance: 184 - 185: 10.191 distance: 184 - 186: 3.542 distance: 187 - 188: 12.148 distance: 188 - 189: 13.783 distance: 188 - 191: 15.551 distance: 189 - 190: 22.679 distance: 189 - 195: 21.296 distance: 191 - 192: 7.759 distance: 191 - 193: 6.305 distance: 192 - 194: 9.691 distance: 195 - 196: 3.785 distance: 196 - 197: 10.716 distance: 196 - 199: 13.906 distance: 197 - 198: 18.844 distance: 197 - 202: 6.969 distance: 199 - 200: 8.792 distance: 199 - 201: 29.249 distance: 202 - 203: 26.965 distance: 203 - 204: 34.278 distance: 204 - 205: 24.871 distance: 204 - 206: 14.843 distance: 206 - 207: 3.250 distance: 207 - 208: 15.185 distance: 207 - 210: 3.867 distance: 208 - 209: 25.592 distance: 208 - 214: 9.369 distance: 210 - 211: 10.893 distance: 211 - 212: 6.426 distance: 211 - 213: 7.481 distance: 214 - 215: 9.162 distance: 215 - 216: 21.697 distance: 215 - 218: 9.829 distance: 216 - 217: 8.365 distance: 216 - 223: 15.741 distance: 218 - 219: 11.942 distance: 219 - 220: 12.473 distance: 220 - 221: 7.764 distance: 220 - 222: 23.330