Starting phenix.real_space_refine (version: dev) on Fri Dec 16 08:07:50 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mxd_24071/12_2022/7mxd_24071.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mxd_24071/12_2022/7mxd_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_24071/12_2022/7mxd_24071.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mxd_24071/12_2022/7mxd_24071.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mxd_24071/12_2022/7mxd_24071.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mxd_24071/12_2022/7mxd_24071.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-4807/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 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 chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 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: 6 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: 5 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 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: 1 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 chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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 chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 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: 4 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: 5 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 chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 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: 5 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 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: 4 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: 5 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 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 chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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 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 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 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 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 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 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 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 chiralities: 3 Time building chain proxies: 17.38, per 1000 atoms: 0.59 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: 13.62 Conformation dependent library (CDL) restraints added in 4.0 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: 2.06 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: 10.82 Time building geometry restraints manager: 14.52 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 - 21.83: 16705 21.83 - 43.65: 1029 43.65 - 65.48: 129 65.48 - 87.31: 54 87.31 - 109.13: 9 Dihedral angle restraints: 17926 sinusoidal: 7717 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 17923 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.253: 5015 0.253 - 0.506: 6 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 2.440 nonbonded pdb=" OG SER U 63 " pdb=" OG1 THR U 74 " model vdw 2.158 2.440 nonbonded pdb=" ND2 ASN F 67 " pdb=" O ASP F 211 " model vdw 2.175 2.520 nonbonded pdb=" O TYR Y 186 " pdb=" OH TYR Y 192 " model vdw 2.181 2.440 nonbonded pdb=" OG SER D 63 " pdb=" OG1 THR D 74 " model vdw 2.184 2.440 ... (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 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 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. 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: 0.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 6.350 Check model and map are aligned: 0.480 Convert atoms to be neutral: 0.250 Process input model: 77.580 Find NCS groups from input model: 2.240 Set up NCS constraints: 0.520 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 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 : 0.004 0.060 30138 Z= 0.259 Angle : 0.584 8.772 41023 Z= 0.322 Chirality : 0.053 1.265 5024 Planarity : 0.004 0.058 5042 Dihedral : 14.064 109.133 11191 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer Outliers : 0.00 % 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 *********************** 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 : 3.504 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 355 average time/residue: 0.4567 time to fit residues: 247.7185 Evaluate side-chains 279 residues out of total 3106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 279 time to evaluate : 3.736 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.9448 ------------------------------------------------------------------------------- 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: 10.0000 chunk 262 optimal weight: 0.0020 chunk 145 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 176 optimal weight: 0.4980 chunk 140 optimal weight: 3.9990 chunk 271 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 314 optimal weight: 0.8980 overall best weight: 0.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN C 28 ASN G 66 HIS S 204 ASN ** U 147 GLN ** 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: 0.7998 moved from start: 0.0766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 30138 Z= 0.198 Angle : 0.549 7.305 41023 Z= 0.296 Chirality : 0.047 0.753 5024 Planarity : 0.004 0.065 5042 Dihedral : 6.848 111.295 4761 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer Outliers : 0.74 % 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: -1.20 (0.14), residues: 3477 helix: -0.39 (0.26), residues: 410 sheet: -0.01 (0.16), residues: 1087 loop : -1.36 (0.14), residues: 1980 *********************** 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 316 residues out of total 3106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 293 time to evaluate : 3.255 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 15 residues processed: 304 average time/residue: 0.4824 time to fit residues: 224.7537 Evaluate side-chains 276 residues out of total 3106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 261 time to evaluate : 3.381 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2810 time to fit residues: 12.1751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 174 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 261 optimal weight: 6.9990 chunk 213 optimal weight: 0.0980 chunk 86 optimal weight: 5.9990 chunk 314 optimal weight: 0.0570 chunk 340 optimal weight: 1.9990 chunk 280 optimal weight: 30.0000 chunk 312 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 252 optimal weight: 0.6980 overall best weight: 0.7500 ------------------------------------------------------------------------------- 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 F 397 ASN K 155 GLN ** U 147 GLN ** 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: 0.7986 moved from start: 0.1037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 30138 Z= 0.175 Angle : 0.510 6.761 41023 Z= 0.274 Chirality : 0.045 0.662 5024 Planarity : 0.004 0.055 5042 Dihedral : 6.689 111.305 4761 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer Outliers : 0.71 % 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: -1.04 (0.14), residues: 3477 helix: 0.01 (0.26), residues: 411 sheet: 0.10 (0.16), residues: 1077 loop : -1.32 (0.14), residues: 1989 *********************** 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 308 residues out of total 3106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 286 time to evaluate : 3.412 Fit side-chains outliers start: 22 outliers final: 13 residues processed: 300 average time/residue: 0.4642 time to fit residues: 213.1505 Evaluate side-chains 275 residues out of total 3106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 262 time to evaluate : 3.361 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2886 time to fit residues: 11.3301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 310 optimal weight: 9.9990 chunk 236 optimal weight: 2.9990 chunk 163 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 150 optimal weight: 0.0010 chunk 211 optimal weight: 4.9990 chunk 315 optimal weight: 0.6980 chunk 334 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 299 optimal weight: 6.9990 chunk 90 optimal weight: 0.0570 overall best weight: 1.1508 ------------------------------------------------------------------------------- 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 C 28 ASN C 204 ASN F 114 GLN F 397 ASN G 66 HIS J 46 GLN J 62 GLN ** K 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 46 GLN S 62 GLN S 204 ASN U 138 ASN ** U 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 30138 Z= 0.214 Angle : 0.516 6.975 41023 Z= 0.276 Chirality : 0.044 0.269 5024 Planarity : 0.004 0.055 5042 Dihedral : 6.685 111.211 4761 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer Outliers : 1.00 % 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: -1.02 (0.14), residues: 3477 helix: 0.13 (0.27), residues: 413 sheet: 0.14 (0.16), residues: 1070 loop : -1.34 (0.14), residues: 1994 *********************** 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 303 residues out of total 3106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 272 time to evaluate : 3.440 Fit side-chains revert: symmetry clash outliers start: 31 outliers final: 16 residues processed: 292 average time/residue: 0.4710 time to fit residues: 212.4593 Evaluate side-chains 268 residues out of total 3106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 252 time to evaluate : 3.622 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 16 outliers final: 1 residues processed: 16 average time/residue: 0.2963 time to fit residues: 13.5488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 4 optimal weight: 3.9990 chunk 249 optimal weight: 6.9990 chunk 137 optimal weight: 0.0770 chunk 285 optimal weight: 7.9990 chunk 231 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 170 optimal weight: 0.4980 chunk 300 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 overall best weight: 2.7144 ------------------------------------------------------------------------------- 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 F 397 ASN G 67 ASN ** U 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 624 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1305 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= 0.410 Angle : 0.611 8.251 41023 Z= 0.326 Chirality : 0.047 0.290 5024 Planarity : 0.005 0.058 5042 Dihedral : 6.954 110.535 4761 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer Outliers : 1.26 % 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: -1.29 (0.14), residues: 3477 helix: -0.17 (0.26), residues: 419 sheet: -0.09 (0.16), residues: 1089 loop : -1.49 (0.14), residues: 1969 *********************** 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 305 residues out of total 3106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 266 time to evaluate : 3.475 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 23 residues processed: 290 average time/residue: 0.4816 time to fit residues: 214.7504 Evaluate side-chains 273 residues out of total 3106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 250 time to evaluate : 3.399 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 23 outliers final: 1 residues processed: 23 average time/residue: 0.2961 time to fit residues: 16.7746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 112 optimal weight: 0.9990 chunk 301 optimal weight: 20.0000 chunk 66 optimal weight: 40.0000 chunk 196 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 chunk 334 optimal weight: 0.9990 chunk 277 optimal weight: 10.0000 chunk 154 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 110 optimal weight: 0.1980 chunk 175 optimal weight: 0.5980 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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 46 GLN C 62 GLN F 397 ASN K 155 GLN S 35 HIS ** U 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 30138 Z= 0.175 Angle : 0.509 8.100 41023 Z= 0.273 Chirality : 0.044 0.262 5024 Planarity : 0.004 0.053 5042 Dihedral : 6.748 110.931 4761 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer Outliers : 0.93 % 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: -1.04 (0.14), residues: 3477 helix: 0.24 (0.27), residues: 407 sheet: 0.12 (0.16), residues: 1079 loop : -1.39 (0.14), residues: 1991 *********************** 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 298 residues out of total 3106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 269 time to evaluate : 3.751 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 18 residues processed: 289 average time/residue: 0.4693 time to fit residues: 209.6239 Evaluate side-chains 266 residues out of total 3106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 248 time to evaluate : 3.479 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 18 outliers final: 1 residues processed: 18 average time/residue: 0.3219 time to fit residues: 15.1157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 322 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 190 optimal weight: 2.9990 chunk 244 optimal weight: 0.9990 chunk 189 optimal weight: 0.9980 chunk 281 optimal weight: 5.9990 chunk 186 optimal weight: 2.9990 chunk 333 optimal weight: 2.9990 chunk 208 optimal weight: 6.9990 chunk 203 optimal weight: 0.8980 chunk 153 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 46 GLN C 62 GLN G 67 ASN S 35 HIS ** U 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 30138 Z= 0.295 Angle : 0.553 7.937 41023 Z= 0.294 Chirality : 0.045 0.275 5024 Planarity : 0.004 0.056 5042 Dihedral : 6.798 110.736 4761 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer Outliers : 0.74 % 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: -1.12 (0.14), residues: 3477 helix: 0.04 (0.27), residues: 419 sheet: 0.03 (0.16), residues: 1091 loop : -1.41 (0.14), residues: 1967 *********************** 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 281 residues out of total 3106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 258 time to evaluate : 3.500 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 10 residues processed: 275 average time/residue: 0.4889 time to fit residues: 206.5402 Evaluate side-chains 258 residues out of total 3106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 248 time to evaluate : 3.499 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 10 outliers final: 1 residues processed: 10 average time/residue: 0.2682 time to fit residues: 9.8302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 206 optimal weight: 3.9990 chunk 133 optimal weight: 0.9980 chunk 199 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 212 optimal weight: 4.9990 chunk 227 optimal weight: 5.9990 chunk 164 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 262 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 46 GLN C 62 GLN ** U 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 30138 Z= 0.350 Angle : 0.585 8.027 41023 Z= 0.312 Chirality : 0.046 0.280 5024 Planarity : 0.005 0.073 5042 Dihedral : 6.912 110.357 4761 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer Outliers : 0.77 % 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: -1.26 (0.14), residues: 3477 helix: -0.21 (0.26), residues: 437 sheet: -0.08 (0.16), residues: 1097 loop : -1.47 (0.14), residues: 1943 *********************** 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 282 residues out of total 3106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 258 time to evaluate : 4.495 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 15 residues processed: 273 average time/residue: 0.4886 time to fit residues: 204.5721 Evaluate side-chains 269 residues out of total 3106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 254 time to evaluate : 3.564 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 15 outliers final: 1 residues processed: 15 average time/residue: 0.3090 time to fit residues: 12.9559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 303 optimal weight: 7.9990 chunk 319 optimal weight: 0.7980 chunk 291 optimal weight: 2.9990 chunk 310 optimal weight: 8.9990 chunk 187 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 244 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 280 optimal weight: 20.0000 chunk 293 optimal weight: 7.9990 chunk 309 optimal weight: 0.5980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 30138 Z= 0.285 Angle : 0.558 7.582 41023 Z= 0.298 Chirality : 0.045 0.280 5024 Planarity : 0.004 0.069 5042 Dihedral : 6.894 110.470 4761 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer Outliers : 0.39 % 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: -0.17 (0.26), residues: 437 sheet: -0.04 (0.16), residues: 1093 loop : -1.46 (0.14), residues: 1947 *********************** REFINEMENT MACRO_CYCLE 9 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 263 residues out of total 3106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 251 time to evaluate : 3.444 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 258 average time/residue: 0.4848 time to fit residues: 190.6837 Evaluate side-chains 255 residues out of total 3106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 248 time to evaluate : 3.284 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.2793 time to fit residues: 7.8102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 204 optimal weight: 7.9990 chunk 328 optimal weight: 0.9990 chunk 200 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 228 optimal weight: 0.5980 chunk 344 optimal weight: 0.7980 chunk 317 optimal weight: 0.6980 chunk 274 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 212 optimal weight: 1.9990 chunk 168 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 30138 Z= 0.179 Angle : 0.514 9.439 41023 Z= 0.274 Chirality : 0.044 0.249 5024 Planarity : 0.004 0.064 5042 Dihedral : 6.702 111.021 4761 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer Outliers : 0.10 % 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: -1.03 (0.14), residues: 3477 helix: 0.23 (0.27), residues: 420 sheet: 0.12 (0.16), residues: 1078 loop : -1.38 (0.14), residues: 1979 ********************** REFINEMENT MACRO_CYCLE 10 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 277 residues out of total 3106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 274 time to evaluate : 3.884 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 277 average time/residue: 0.4852 time to fit residues: 205.5197 Evaluate side-chains 263 residues out of total 3106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 262 time to evaluate : 3.539 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.2587 time to fit residues: 5.3618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 218 optimal weight: 0.9980 chunk 292 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 chunk 253 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 274 optimal weight: 1.9990 chunk 115 optimal weight: 7.9990 chunk 282 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 67 ASN ** K 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.155851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.122426 restraints weight = 44982.695| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 3.98 r_work: 0.3031 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 30138 Z= 0.240 Angle : 0.537 8.772 41023 Z= 0.285 Chirality : 0.045 0.320 5024 Planarity : 0.004 0.063 5042 Dihedral : 6.731 110.887 4761 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer Outliers : 0.35 % 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: -1.05 (0.14), residues: 3477 helix: 0.25 (0.27), residues: 417 sheet: 0.11 (0.16), residues: 1078 loop : -1.41 (0.14), residues: 1982 =============================================================================== Job complete usr+sys time: 5393.79 seconds wall clock time: 99 minutes 56.55 seconds (5996.55 seconds total)