Starting phenix.real_space_refine on Sun Nov 19 01:16:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v8x_21111/11_2023/6v8x_21111_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v8x_21111/11_2023/6v8x_21111.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v8x_21111/11_2023/6v8x_21111.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v8x_21111/11_2023/6v8x_21111.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v8x_21111/11_2023/6v8x_21111_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v8x_21111/11_2023/6v8x_21111_neut.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.142 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 147 5.16 5 C 15531 2.51 5 N 4170 2.21 5 O 4977 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 298": "NH1" <-> "NH2" Residue "A PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 298": "NH1" <-> "NH2" Residue "E PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 298": "NH1" <-> "NH2" Residue "I PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 24825 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 3453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3453 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 22, 'TRANS': 416} Chain breaks: 4 Chain: "B" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1025 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Chain: "C" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1710 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 14, 'TRANS': 206} Chain: "D" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1615 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 195} Chain: "E" Number of atoms: 3453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3453 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 22, 'TRANS': 416} Chain breaks: 4 Chain: "F" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1025 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Chain: "G" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1710 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 14, 'TRANS': 206} Chain: "H" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1615 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 195} Chain: "I" Number of atoms: 3453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3453 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 22, 'TRANS': 416} Chain breaks: 4 Chain: "J" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1025 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Chain: "K" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1710 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 14, 'TRANS': 206} Chain: "L" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1615 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 195} Chain: "M" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "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: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "o" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "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: "A" 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: "B" 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: "E" 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: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "I" 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: "J" 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 Time building chain proxies: 13.07, per 1000 atoms: 0.53 Number of scatterers: 24825 At special positions: 0 Unit cell: (184.13, 202.543, 125.642, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 147 16.00 O 4977 8.00 N 4170 7.00 C 15531 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.07 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.01 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.07 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.12 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 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=2.11 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.09 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.24 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.31 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.00 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=1.91 Simple disulfide: pdb=" SG CYS C 32 " - pdb=" SG CYS C 98 " distance=1.98 Simple disulfide: pdb=" SG CYS C 140 " - pdb=" SG CYS C 196 " distance=2.04 Simple disulfide: pdb=" SG CYS C 216 " - pdb=" SG CYS D 216 " distance=2.00 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.19 Simple disulfide: pdb=" SG CYS D 136 " - pdb=" SG CYS D 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.07 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.01 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.07 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.12 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.04 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.10 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.09 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.24 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.31 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.00 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=1.91 Simple disulfide: pdb=" SG CYS G 32 " - pdb=" SG CYS G 98 " distance=1.98 Simple disulfide: pdb=" SG CYS G 140 " - pdb=" SG CYS G 196 " distance=2.04 Simple disulfide: pdb=" SG CYS G 216 " - pdb=" SG CYS H 216 " distance=2.00 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.19 Simple disulfide: pdb=" SG CYS H 136 " - pdb=" SG CYS H 196 " distance=2.04 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.07 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.01 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.06 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.12 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.04 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.11 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.09 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.24 Simple disulfide: pdb=" SG CYS I 501 " - pdb=" SG CYS J 605 " distance=2.31 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.00 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=1.91 Simple disulfide: pdb=" SG CYS K 32 " - pdb=" SG CYS K 98 " distance=1.98 Simple disulfide: pdb=" SG CYS K 140 " - pdb=" SG CYS K 196 " distance=2.04 Simple disulfide: pdb=" SG CYS K 216 " - pdb=" SG CYS L 216 " distance=2.00 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.19 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.04 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 ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA Y 3 " - " MAN Y 4 " " BMA k 3 " - " MAN k 4 " BETA1-4 " 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 Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " 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 k 2 " - " BMA k 3 " " 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 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 r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " 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-ASN " NAG A 613 " - " ASN A 448 " " NAG A 617 " - " ASN A 355 " " NAG A 627 " - " ASN A 133 " " NAG A 632 " - " ASN A 339 " " NAG B 701 " - " ASN B 611 " " NAG E 613 " - " ASN E 448 " " NAG E 617 " - " ASN E 355 " " NAG E 627 " - " ASN E 133 " " NAG E 632 " - " ASN E 339 " " NAG F 701 " - " ASN F 611 " " NAG I 613 " - " ASN I 448 " " NAG I 617 " - " ASN I 355 " " NAG I 627 " - " ASN I 133 " " NAG I 632 " - " ASN I 339 " " NAG J 701 " - " ASN J 611 " " NAG M 1 " - " ASN A 363 " " NAG N 1 " - " ASN A 392 " " NAG O 1 " - " ASN A 386 " " NAG P 1 " - " ASN A 262 " " NAG Q 1 " - " ASN A 276 " " NAG R 1 " - " ASN A 295 " " NAG S 1 " - " ASN A 160 " " NAG T 1 " - " ASN A 156 " " NAG U 1 " - " ASN A 197 " " NAG V 1 " - " ASN A 88 " " NAG W 1 " - " ASN A 332 " " NAG X 1 " - " ASN A 301 " " NAG Y 1 " - " ASN E 363 " " NAG Z 1 " - " ASN E 392 " " NAG a 1 " - " ASN E 386 " " NAG b 1 " - " ASN E 262 " " NAG c 1 " - " ASN E 276 " " NAG d 1 " - " ASN E 295 " " NAG e 1 " - " ASN E 160 " " NAG f 1 " - " ASN E 156 " " NAG g 1 " - " ASN E 197 " " NAG h 1 " - " ASN E 88 " " NAG i 1 " - " ASN E 332 " " NAG j 1 " - " ASN E 301 " " NAG k 1 " - " ASN I 363 " " NAG l 1 " - " ASN I 392 " " NAG m 1 " - " ASN I 386 " " NAG n 1 " - " ASN I 262 " " NAG o 1 " - " ASN I 276 " " NAG p 1 " - " ASN I 295 " " NAG q 1 " - " ASN I 160 " " NAG r 1 " - " ASN I 156 " " NAG s 1 " - " ASN I 197 " " NAG t 1 " - " ASN I 88 " " NAG u 1 " - " ASN I 332 " " NAG v 1 " - " ASN I 301 " Time building additional restraints: 11.10 Conformation dependent library (CDL) restraints added in 4.4 seconds 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5562 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 66 sheets defined 16.2% alpha, 24.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.99 Creating SS restraints... Processing helix chain 'A' and resid 99 through 115 removed outlier: 3.553A pdb=" N LEU A 111 " --> pdb=" O ASP A 107 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TRP A 112 " --> pdb=" O ILE A 108 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP A 113 " --> pdb=" O ILE A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 4.050A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 354 removed outlier: 3.534A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 474 through 478 removed outlier: 3.945A pdb=" N ASP A 477 " --> pdb=" O ASP A 474 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN A 478 " --> pdb=" O MET A 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 474 through 478' Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.872A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 596 removed outlier: 3.807A pdb=" N GLY B 572 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ALA B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU B 581 " --> pdb=" O GLN B 577 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU B 592 " --> pdb=" O ARG B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 615 removed outlier: 3.675A pdb=" N SER B 615 " --> pdb=" O SER B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 removed outlier: 4.036A pdb=" N TRP B 623 " --> pdb=" O LEU B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 removed outlier: 4.091A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE B 635 " --> pdb=" O TRP B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 646 removed outlier: 3.657A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 664 removed outlier: 5.107A pdb=" N GLN B 652 " --> pdb=" O GLU B 648 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N GLN B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP B 659 " --> pdb=" O LYS B 655 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU B 660 " --> pdb=" O ASN B 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 4.030A pdb=" N CYS C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 64 removed outlier: 3.722A pdb=" N GLN C 64 " --> pdb=" O ARG C 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 61 through 64' Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.651A pdb=" N THR C 87 " --> pdb=" O VAL C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 204 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'D' and resid 187 through 192 removed outlier: 4.140A pdb=" N LYS D 192 " --> pdb=" O GLU D 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 115 removed outlier: 3.554A pdb=" N LEU E 111 " --> pdb=" O ASP E 107 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TRP E 112 " --> pdb=" O ILE E 108 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP E 113 " --> pdb=" O ILE E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 removed outlier: 4.050A pdb=" N CYS E 126 " --> pdb=" O THR E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 354 removed outlier: 3.534A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 474 through 478 removed outlier: 3.945A pdb=" N ASP E 477 " --> pdb=" O ASP E 474 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN E 478 " --> pdb=" O MET E 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 474 through 478' Processing helix chain 'F' and resid 536 through 542 removed outlier: 3.872A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 566 through 596 removed outlier: 3.807A pdb=" N GLY F 572 " --> pdb=" O LEU F 568 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLN F 575 " --> pdb=" O TRP F 571 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ALA F 578 " --> pdb=" O LYS F 574 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU F 581 " --> pdb=" O GLN F 577 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL F 583 " --> pdb=" O ARG F 579 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU F 592 " --> pdb=" O ARG F 588 " (cutoff:3.500A) Processing helix chain 'F' and resid 611 through 615 removed outlier: 3.674A pdb=" N SER F 615 " --> pdb=" O SER F 612 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 624 removed outlier: 4.036A pdb=" N TRP F 623 " --> pdb=" O LEU F 619 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 removed outlier: 4.091A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE F 635 " --> pdb=" O TRP F 631 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 646 removed outlier: 3.657A pdb=" N ILE F 642 " --> pdb=" O TYR F 638 " (cutoff:3.500A) Processing helix chain 'F' and resid 646 through 664 removed outlier: 5.108A pdb=" N GLN F 652 " --> pdb=" O GLU F 648 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N GLN F 653 " --> pdb=" O SER F 649 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP F 659 " --> pdb=" O LYS F 655 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU F 660 " --> pdb=" O ASN F 656 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 4.030A pdb=" N CYS G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 64 removed outlier: 3.722A pdb=" N GLN G 64 " --> pdb=" O ARG G 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 61 through 64' Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.651A pdb=" N THR G 87 " --> pdb=" O VAL G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 201 through 204 Processing helix chain 'H' and resid 79 through 83 Processing helix chain 'H' and resid 187 through 192 removed outlier: 4.139A pdb=" N LYS H 192 " --> pdb=" O GLU H 189 " (cutoff:3.500A) Processing helix chain 'I' and resid 99 through 115 removed outlier: 3.553A pdb=" N LEU I 111 " --> pdb=" O ASP I 107 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TRP I 112 " --> pdb=" O ILE I 108 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP I 113 " --> pdb=" O ILE I 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 126 removed outlier: 4.050A pdb=" N CYS I 126 " --> pdb=" O THR I 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 341 through 354 removed outlier: 3.534A pdb=" N LYS I 351 " --> pdb=" O LYS I 347 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N HIS I 352 " --> pdb=" O GLN I 348 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 474 through 478 removed outlier: 3.945A pdb=" N ASP I 477 " --> pdb=" O ASP I 474 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN I 478 " --> pdb=" O MET I 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 474 through 478' Processing helix chain 'J' and resid 536 through 542 removed outlier: 3.872A pdb=" N GLN J 540 " --> pdb=" O THR J 536 " (cutoff:3.500A) Processing helix chain 'J' and resid 566 through 596 removed outlier: 3.807A pdb=" N GLY J 572 " --> pdb=" O LEU J 568 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLN J 575 " --> pdb=" O TRP J 571 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ALA J 578 " --> pdb=" O LYS J 574 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU J 581 " --> pdb=" O GLN J 577 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL J 583 " --> pdb=" O ARG J 579 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP J 589 " --> pdb=" O ARG J 585 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU J 592 " --> pdb=" O ARG J 588 " (cutoff:3.500A) Processing helix chain 'J' and resid 611 through 615 removed outlier: 3.674A pdb=" N SER J 615 " --> pdb=" O SER J 612 " (cutoff:3.500A) Processing helix chain 'J' and resid 619 through 624 removed outlier: 4.036A pdb=" N TRP J 623 " --> pdb=" O LEU J 619 " (cutoff:3.500A) Processing helix chain 'J' and resid 627 through 635 removed outlier: 4.091A pdb=" N LYS J 633 " --> pdb=" O LEU J 629 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE J 635 " --> pdb=" O TRP J 631 " (cutoff:3.500A) Processing helix chain 'J' and resid 638 through 646 removed outlier: 3.657A pdb=" N ILE J 642 " --> pdb=" O TYR J 638 " (cutoff:3.500A) Processing helix chain 'J' and resid 646 through 664 removed outlier: 5.108A pdb=" N GLN J 652 " --> pdb=" O GLU J 648 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N GLN J 653 " --> pdb=" O SER J 649 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP J 659 " --> pdb=" O LYS J 655 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU J 660 " --> pdb=" O ASN J 656 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 removed outlier: 4.030A pdb=" N CYS K 32 " --> pdb=" O PHE K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 64 removed outlier: 3.722A pdb=" N GLN K 64 " --> pdb=" O ARG K 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 61 through 64' Processing helix chain 'K' and resid 83 through 87 removed outlier: 3.652A pdb=" N THR K 87 " --> pdb=" O VAL K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 201 through 204 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'L' and resid 187 through 192 removed outlier: 4.140A pdb=" N LYS L 192 " --> pdb=" O GLU L 189 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.535A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.704A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS A 227 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 55 through 56 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 92 removed outlier: 3.817A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 172 Processing sheet with id=AA6, first strand: chain 'A' and resid 169 through 172 removed outlier: 4.671A pdb=" N LYS A 189 " --> pdb=" O CYS A 131 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.406A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.243A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.824A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 12.203A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 12.236A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.935A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.933A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 284 through 297 current: chain 'A' and resid 358 through 361 removed outlier: 3.541A pdb=" N SER A 393 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 271 through 273 removed outlier: 10.933A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.935A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.236A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 12.203A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.824A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 444 through 456 current: chain 'A' and resid 413 through 415 Processing sheet with id=AB1, first strand: chain 'A' and resid 304 through 308 Processing sheet with id=AB2, first strand: chain 'A' and resid 383 through 385 Processing sheet with id=AB3, first strand: chain 'C' and resid 11 through 12 Processing sheet with id=AB4, first strand: chain 'C' and resid 19 through 23 Processing sheet with id=AB5, first strand: chain 'C' and resid 57 through 59 removed outlier: 3.996A pdb=" N ASN C 58 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU C 46 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N TRP C 50 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 121 through 123 Processing sheet with id=AB7, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AB8, first strand: chain 'C' and resid 153 through 154 removed outlier: 3.801A pdb=" N VAL C 198 " --> pdb=" O VAL C 207 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL C 207 " --> pdb=" O VAL C 198 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AC1, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.696A pdb=" N TRP D 35 " --> pdb=" O VAL D 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 19 through 24 removed outlier: 3.694A pdb=" N TYR D 71 " --> pdb=" O CYS D 23 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N SER D 65 " --> pdb=" O ASN D 72 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER D 63 " --> pdb=" O THR D 74 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 117 through 118 removed outlier: 5.389A pdb=" N ASN D 139 " --> pdb=" O LEU D 177 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU D 177 " --> pdb=" O ASN D 139 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 150 through 152 Processing sheet with id=AC5, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.535A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.705A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS E 227 " --> pdb=" O SER E 243 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 55 through 56 Processing sheet with id=AC8, first strand: chain 'E' and resid 91 through 92 removed outlier: 3.817A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 169 through 172 Processing sheet with id=AD1, first strand: chain 'E' and resid 169 through 172 removed outlier: 4.671A pdb=" N LYS E 189 " --> pdb=" O CYS E 131 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 200 through 203 removed outlier: 6.405A pdb=" N ALA E 200 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N TYR E 435 " --> pdb=" O ALA E 200 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.242A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.824A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 12.202A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 12.235A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.934A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.933A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 284 through 297 current: chain 'E' and resid 358 through 361 removed outlier: 3.541A pdb=" N SER E 393 " --> pdb=" O PHE E 361 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 271 through 273 removed outlier: 10.933A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.934A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 12.235A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 12.202A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 10.824A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 444 through 456 current: chain 'E' and resid 413 through 415 Processing sheet with id=AD5, first strand: chain 'E' and resid 304 through 308 Processing sheet with id=AD6, first strand: chain 'E' and resid 383 through 385 Processing sheet with id=AD7, first strand: chain 'G' and resid 11 through 12 Processing sheet with id=AD8, first strand: chain 'G' and resid 19 through 23 Processing sheet with id=AD9, first strand: chain 'G' and resid 57 through 59 removed outlier: 3.995A pdb=" N ASN G 58 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU G 46 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N TRP G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 121 through 123 Processing sheet with id=AE2, first strand: chain 'G' and resid 136 through 137 Processing sheet with id=AE3, first strand: chain 'G' and resid 153 through 154 removed outlier: 3.800A pdb=" N VAL G 198 " --> pdb=" O VAL G 207 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL G 207 " --> pdb=" O VAL G 198 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 169 through 170 Processing sheet with id=AE5, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.696A pdb=" N TRP H 35 " --> pdb=" O VAL H 47 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 19 through 24 removed outlier: 3.694A pdb=" N TYR H 71 " --> pdb=" O CYS H 23 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N SER H 65 " --> pdb=" O ASN H 72 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER H 63 " --> pdb=" O THR H 74 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 117 through 118 removed outlier: 5.390A pdb=" N ASN H 139 " --> pdb=" O LEU H 177 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU H 177 " --> pdb=" O ASN H 139 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 150 through 152 Processing sheet with id=AE9, first strand: chain 'I' and resid 494 through 499 removed outlier: 5.535A pdb=" N VAL I 36 " --> pdb=" O THR J 606 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.705A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS I 227 " --> pdb=" O SER I 243 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N VAL I 242 " --> pdb=" O LEU I 86 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 55 through 56 Processing sheet with id=AF3, first strand: chain 'I' and resid 91 through 92 removed outlier: 3.817A pdb=" N GLU I 91 " --> pdb=" O CYS I 239 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 169 through 172 Processing sheet with id=AF5, first strand: chain 'I' and resid 169 through 172 removed outlier: 4.671A pdb=" N LYS I 189 " --> pdb=" O CYS I 131 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 200 through 203 removed outlier: 6.405A pdb=" N ALA I 200 " --> pdb=" O ALA I 433 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N TYR I 435 " --> pdb=" O ALA I 200 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 259 through 261 removed outlier: 6.243A pdb=" N LEU I 260 " --> pdb=" O THR I 450 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLY I 451 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 10.824A pdb=" N THR I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 12.203A pdb=" N ILE I 453 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 12.236A pdb=" N PHE I 288 " --> pdb=" O ILE I 453 " (cutoff:3.500A) removed outlier: 10.934A pdb=" N THR I 455 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 10.933A pdb=" N VAL I 286 " --> pdb=" O THR I 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 284 through 297 current: chain 'I' and resid 358 through 361 removed outlier: 3.541A pdb=" N SER I 393 " --> pdb=" O PHE I 361 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 271 through 273 removed outlier: 10.933A pdb=" N VAL I 286 " --> pdb=" O THR I 455 " (cutoff:3.500A) removed outlier: 10.934A pdb=" N THR I 455 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 12.236A pdb=" N PHE I 288 " --> pdb=" O ILE I 453 " (cutoff:3.500A) removed outlier: 12.203A pdb=" N ILE I 453 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 10.824A pdb=" N THR I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLY I 451 " --> pdb=" O THR I 290 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 444 through 456 current: chain 'I' and resid 413 through 415 Processing sheet with id=AF9, first strand: chain 'I' and resid 304 through 308 Processing sheet with id=AG1, first strand: chain 'I' and resid 383 through 385 Processing sheet with id=AG2, first strand: chain 'K' and resid 11 through 12 Processing sheet with id=AG3, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AG4, first strand: chain 'K' and resid 57 through 59 removed outlier: 3.997A pdb=" N ASN K 58 " --> pdb=" O TRP K 50 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU K 46 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N TRP K 36 " --> pdb=" O MET K 48 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N TRP K 50 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU K 34 " --> pdb=" O TRP K 50 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'K' and resid 121 through 123 Processing sheet with id=AG6, first strand: chain 'K' and resid 136 through 137 Processing sheet with id=AG7, first strand: chain 'K' and resid 153 through 154 removed outlier: 3.800A pdb=" N VAL K 198 " --> pdb=" O VAL K 207 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL K 207 " --> pdb=" O VAL K 198 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'K' and resid 169 through 170 Processing sheet with id=AG9, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.696A pdb=" N TRP L 35 " --> pdb=" O VAL L 47 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'L' and resid 19 through 24 removed outlier: 3.694A pdb=" N TYR L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N SER L 65 " --> pdb=" O ASN L 72 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER L 63 " --> pdb=" O THR L 74 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'L' and resid 117 through 118 removed outlier: 5.389A pdb=" N ASN L 139 " --> pdb=" O LEU L 177 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU L 177 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'L' and resid 150 through 152 594 hydrogen bonds defined for protein. 1530 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: 9.20 Time building geometry restraints manager: 11.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5411 1.32 - 1.46: 8151 1.46 - 1.59: 11581 1.59 - 1.72: 3 1.72 - 1.86: 192 Bond restraints: 25338 Sorted by residual: bond pdb=" N PRO I 299 " pdb=" CD PRO I 299 " ideal model delta sigma weight residual 1.473 1.577 -0.104 1.40e-02 5.10e+03 5.53e+01 bond pdb=" N PRO A 299 " pdb=" CD PRO A 299 " ideal model delta sigma weight residual 1.473 1.576 -0.103 1.40e-02 5.10e+03 5.44e+01 bond pdb=" N PRO E 299 " pdb=" CD PRO E 299 " ideal model delta sigma weight residual 1.473 1.576 -0.103 1.40e-02 5.10e+03 5.43e+01 bond pdb=" CB TRP G 50 " pdb=" CG TRP G 50 " ideal model delta sigma weight residual 1.498 1.300 0.198 3.10e-02 1.04e+03 4.09e+01 bond pdb=" CB TRP K 50 " pdb=" CG TRP K 50 " ideal model delta sigma weight residual 1.498 1.300 0.198 3.10e-02 1.04e+03 4.09e+01 ... (remaining 25333 not shown) Histogram of bond angle deviations from ideal: 94.27 - 102.27: 99 102.27 - 110.27: 7591 110.27 - 118.26: 12663 118.26 - 126.26: 13535 126.26 - 134.26: 528 Bond angle restraints: 34416 Sorted by residual: angle pdb=" C SER D 65 " pdb=" N ARG D 66 " pdb=" CA ARG D 66 " ideal model delta sigma weight residual 121.70 134.19 -12.49 1.80e+00 3.09e-01 4.81e+01 angle pdb=" C SER L 65 " pdb=" N ARG L 66 " pdb=" CA ARG L 66 " ideal model delta sigma weight residual 121.70 134.16 -12.46 1.80e+00 3.09e-01 4.79e+01 angle pdb=" C SER H 65 " pdb=" N ARG H 66 " pdb=" CA ARG H 66 " ideal model delta sigma weight residual 121.70 134.12 -12.42 1.80e+00 3.09e-01 4.76e+01 angle pdb=" C TRP C 50 " pdb=" CA TRP C 50 " pdb=" CB TRP C 50 " ideal model delta sigma weight residual 112.63 98.15 14.48 2.16e+00 2.14e-01 4.50e+01 angle pdb=" C TRP K 50 " pdb=" CA TRP K 50 " pdb=" CB TRP K 50 " ideal model delta sigma weight residual 112.63 98.16 14.47 2.16e+00 2.14e-01 4.49e+01 ... (remaining 34411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.59: 13696 16.59 - 33.17: 572 33.17 - 49.76: 150 49.76 - 66.35: 18 66.35 - 82.94: 12 Dihedral angle restraints: 14448 sinusoidal: 5817 harmonic: 8631 Sorted by residual: dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 92 " pdb=" CB CYS C 92 " ideal model delta sinusoidal sigma weight residual 93.00 175.94 -82.94 1 1.00e+01 1.00e-02 8.42e+01 dihedral pdb=" CB CYS G 22 " pdb=" SG CYS G 22 " pdb=" SG CYS G 92 " pdb=" CB CYS G 92 " ideal model delta sinusoidal sigma weight residual 93.00 175.92 -82.92 1 1.00e+01 1.00e-02 8.42e+01 dihedral pdb=" CB CYS K 22 " pdb=" SG CYS K 22 " pdb=" SG CYS K 92 " pdb=" CB CYS K 92 " ideal model delta sinusoidal sigma weight residual 93.00 175.92 -82.92 1 1.00e+01 1.00e-02 8.42e+01 ... (remaining 14445 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 3635 0.117 - 0.234: 466 0.234 - 0.351: 39 0.351 - 0.468: 12 0.468 - 0.585: 9 Chirality restraints: 4161 Sorted by residual: chirality pdb=" CB ILE E 309 " pdb=" CA ILE E 309 " pdb=" CG1 ILE E 309 " pdb=" CG2 ILE E 309 " both_signs ideal model delta sigma weight residual False 2.64 2.06 0.59 2.00e-01 2.50e+01 8.57e+00 chirality pdb=" CB ILE A 309 " pdb=" CA ILE A 309 " pdb=" CG1 ILE A 309 " pdb=" CG2 ILE A 309 " both_signs ideal model delta sigma weight residual False 2.64 2.07 0.58 2.00e-01 2.50e+01 8.39e+00 chirality pdb=" CB ILE I 309 " pdb=" CA ILE I 309 " pdb=" CG1 ILE I 309 " pdb=" CG2 ILE I 309 " both_signs ideal model delta sigma weight residual False 2.64 2.07 0.58 2.00e-01 2.50e+01 8.38e+00 ... (remaining 4158 not shown) Planarity restraints: 4311 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG X 1 " -0.152 2.00e-02 2.50e+03 1.29e-01 2.07e+02 pdb=" C7 NAG X 1 " 0.029 2.00e-02 2.50e+03 pdb=" C8 NAG X 1 " 0.036 2.00e-02 2.50e+03 pdb=" N2 NAG X 1 " 0.208 2.00e-02 2.50e+03 pdb=" O7 NAG X 1 " -0.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG j 1 " -0.152 2.00e-02 2.50e+03 1.29e-01 2.07e+02 pdb=" C7 NAG j 1 " 0.030 2.00e-02 2.50e+03 pdb=" C8 NAG j 1 " 0.036 2.00e-02 2.50e+03 pdb=" N2 NAG j 1 " 0.207 2.00e-02 2.50e+03 pdb=" O7 NAG j 1 " -0.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG v 1 " 0.152 2.00e-02 2.50e+03 1.29e-01 2.07e+02 pdb=" C7 NAG v 1 " -0.029 2.00e-02 2.50e+03 pdb=" C8 NAG v 1 " -0.036 2.00e-02 2.50e+03 pdb=" N2 NAG v 1 " -0.208 2.00e-02 2.50e+03 pdb=" O7 NAG v 1 " 0.120 2.00e-02 2.50e+03 ... (remaining 4308 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 2726 2.72 - 3.27: 21824 3.27 - 3.81: 37757 3.81 - 4.36: 45871 4.36 - 4.90: 78416 Nonbonded interactions: 186594 Sorted by model distance: nonbonded pdb=" OE1 GLN G 6 " pdb=" OG1 THR G 107 " model vdw 2.180 2.440 nonbonded pdb=" OE1 GLN K 6 " pdb=" OG1 THR K 107 " model vdw 2.180 2.440 nonbonded pdb=" OE1 GLN C 6 " pdb=" OG1 THR C 107 " model vdw 2.180 2.440 nonbonded pdb=" OG1 THR A 303 " pdb=" N ASP A 322 " model vdw 2.257 2.520 nonbonded pdb=" OG1 THR E 303 " pdb=" N ASP E 322 " model vdw 2.257 2.520 ... (remaining 186589 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'Y' selection = chain 'k' } ncs_group { reference = chain 'N' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Z' selection = chain 'd' selection = chain 'e' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'l' selection = chain 'p' selection = chain 'q' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'T' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'f' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'r' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 12.540 Check model and map are aligned: 0.400 Set scattering table: 0.240 Process input model: 65.770 Find NCS groups from input model: 1.560 Set up NCS constraints: 0.520 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 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 : 0.017 0.198 25338 Z= 1.117 Angle : 1.481 14.483 34416 Z= 0.782 Chirality : 0.084 0.585 4161 Planarity : 0.009 0.129 4260 Dihedral : 9.758 58.097 8733 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.92 % Allowed : 8.49 % Favored : 90.59 % Rotamer: Outliers : 0.23 % Allowed : 1.83 % Favored : 97.95 % Cbeta Deviations : 0.32 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.90 (0.13), residues: 2943 helix: -4.12 (0.13), residues: 429 sheet: -2.05 (0.16), residues: 843 loop : -2.48 (0.14), residues: 1671 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 2628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 652 time to evaluate : 2.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 655 average time/residue: 1.5352 time to fit residues: 1139.3061 Evaluate side-chains 342 residues out of total 2628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 341 time to evaluate : 2.546 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.2481 time to fit residues: 4.0873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 245 optimal weight: 0.9990 chunk 220 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 75 optimal weight: 20.0000 chunk 148 optimal weight: 0.7980 chunk 117 optimal weight: 0.5980 chunk 228 optimal weight: 0.7980 chunk 88 optimal weight: 5.9990 chunk 138 optimal weight: 0.9990 chunk 169 optimal weight: 30.0000 chunk 264 optimal weight: 10.0000 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 130 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 GLN B 616 ASN B 651 ASN C 102 HIS ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN E 432 GLN ** F 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 630 GLN F 651 ASN G 197 ASN ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 130 GLN ** J 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 607 ASN J 651 ASN K 102 HIS K 197 ASN L 126 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25338 Z= 0.248 Angle : 0.825 9.504 34416 Z= 0.412 Chirality : 0.048 0.286 4161 Planarity : 0.006 0.046 4260 Dihedral : 6.112 51.854 3213 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.93 % Favored : 92.66 % Rotamer: Outliers : 3.84 % Allowed : 13.39 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.14), residues: 2943 helix: -2.57 (0.21), residues: 411 sheet: -1.72 (0.17), residues: 840 loop : -2.09 (0.14), residues: 1692 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 437 time to evaluate : 2.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 101 outliers final: 27 residues processed: 499 average time/residue: 1.4999 time to fit residues: 851.3650 Evaluate side-chains 371 residues out of total 2628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 344 time to evaluate : 2.998 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 22 residues processed: 7 average time/residue: 0.2686 time to fit residues: 7.1432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 146 optimal weight: 0.0040 chunk 82 optimal weight: 3.9990 chunk 219 optimal weight: 1.9990 chunk 179 optimal weight: 0.9980 chunk 72 optimal weight: 10.0000 chunk 264 optimal weight: 5.9990 chunk 285 optimal weight: 3.9990 chunk 235 optimal weight: 0.0050 chunk 262 optimal weight: 20.0000 chunk 90 optimal weight: 4.9990 chunk 212 optimal weight: 1.9990 overall best weight: 1.0010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS B 543 ASN B 630 GLN B 651 ASN ** F 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 616 ASN F 651 ASN H 126 GLN I 72 HIS J 543 ASN ** J 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 25338 Z= 0.267 Angle : 0.779 9.629 34416 Z= 0.388 Chirality : 0.048 0.349 4161 Planarity : 0.005 0.044 4260 Dihedral : 5.698 46.544 3213 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.58 % Favored : 92.08 % Rotamer: Outliers : 4.53 % Allowed : 15.98 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.15), residues: 2943 helix: -2.07 (0.23), residues: 405 sheet: -1.50 (0.18), residues: 825 loop : -1.85 (0.14), residues: 1713 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 2628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 384 time to evaluate : 3.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 119 outliers final: 52 residues processed: 475 average time/residue: 1.3631 time to fit residues: 745.7633 Evaluate side-chains 372 residues out of total 2628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 320 time to evaluate : 2.714 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 44 residues processed: 9 average time/residue: 0.6626 time to fit residues: 11.2318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 261 optimal weight: 8.9990 chunk 199 optimal weight: 0.2980 chunk 137 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 126 optimal weight: 0.2980 chunk 177 optimal weight: 3.9990 chunk 265 optimal weight: 40.0000 chunk 281 optimal weight: 9.9990 chunk 138 optimal weight: 0.9980 chunk 251 optimal weight: 0.9980 chunk 75 optimal weight: 20.0000 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN A 234 ASN ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 170 GLN E 283 ASN E 440 GLN F 543 ASN F 563 GLN F 564 HIS F 616 ASN F 651 ASN F 653 GLN G 102 HIS I 170 GLN J 563 GLN J 564 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 25338 Z= 0.271 Angle : 0.755 9.611 34416 Z= 0.375 Chirality : 0.048 0.356 4161 Planarity : 0.005 0.042 4260 Dihedral : 5.525 42.150 3213 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.48 % Favored : 92.22 % Rotamer: Outliers : 4.49 % Allowed : 17.47 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.15), residues: 2943 helix: -1.67 (0.25), residues: 393 sheet: -1.39 (0.17), residues: 861 loop : -1.70 (0.15), residues: 1689 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 357 time to evaluate : 2.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 118 outliers final: 53 residues processed: 444 average time/residue: 1.3996 time to fit residues: 714.3011 Evaluate side-chains 370 residues out of total 2628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 317 time to evaluate : 2.625 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 44 residues processed: 9 average time/residue: 0.4556 time to fit residues: 9.3573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 234 optimal weight: 3.9990 chunk 159 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 209 optimal weight: 1.9990 chunk 116 optimal weight: 0.2980 chunk 240 optimal weight: 0.5980 chunk 194 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 143 optimal weight: 0.3980 chunk 252 optimal weight: 0.9980 chunk 70 optimal weight: 10.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 616 ASN F 651 ASN F 653 GLN ** I 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 563 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.4682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 25338 Z= 0.233 Angle : 0.730 9.641 34416 Z= 0.361 Chirality : 0.047 0.391 4161 Planarity : 0.005 0.042 4260 Dihedral : 5.276 39.799 3213 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.09 % Favored : 91.61 % Rotamer: Outliers : 4.22 % Allowed : 18.49 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.15), residues: 2943 helix: -1.42 (0.26), residues: 393 sheet: -1.33 (0.17), residues: 867 loop : -1.61 (0.15), residues: 1683 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 347 time to evaluate : 2.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 111 outliers final: 64 residues processed: 427 average time/residue: 1.4097 time to fit residues: 695.0823 Evaluate side-chains 374 residues out of total 2628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 310 time to evaluate : 2.883 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 52 residues processed: 13 average time/residue: 0.4478 time to fit residues: 12.3060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 94 optimal weight: 9.9990 chunk 253 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 165 optimal weight: 40.0000 chunk 69 optimal weight: 0.9990 chunk 281 optimal weight: 9.9990 chunk 233 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 93 optimal weight: 9.9990 chunk 147 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 GLN ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN B 653 GLN D 72 ASN ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN E 170 GLN E 188 ASN ** F 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 616 ASN F 651 ASN H 72 ASN ** I 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 170 GLN I 234 ASN ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 440 GLN J 563 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.4985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 25338 Z= 0.410 Angle : 0.826 9.664 34416 Z= 0.409 Chirality : 0.050 0.433 4161 Planarity : 0.005 0.046 4260 Dihedral : 5.659 38.206 3213 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.83 % Favored : 90.86 % Rotamer: Outliers : 5.37 % Allowed : 18.23 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.15), residues: 2943 helix: -1.49 (0.26), residues: 393 sheet: -1.48 (0.17), residues: 846 loop : -1.63 (0.15), residues: 1704 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 2628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 329 time to evaluate : 2.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 141 outliers final: 75 residues processed: 437 average time/residue: 1.3117 time to fit residues: 666.1243 Evaluate side-chains 379 residues out of total 2628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 304 time to evaluate : 2.767 Switching outliers to nearest non-outliers outliers start: 75 outliers final: 63 residues processed: 15 average time/residue: 0.5262 time to fit residues: 14.8378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 271 optimal weight: 0.0670 chunk 31 optimal weight: 0.6980 chunk 160 optimal weight: 0.6980 chunk 205 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 237 optimal weight: 3.9990 chunk 157 optimal weight: 0.7980 chunk 280 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 170 optimal weight: 8.9990 chunk 129 optimal weight: 0.6980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 616 ASN F 651 ASN F 653 GLN H 72 ASN ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.5185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 25338 Z= 0.210 Angle : 0.738 9.989 34416 Z= 0.365 Chirality : 0.047 0.441 4161 Planarity : 0.005 0.043 4260 Dihedral : 5.239 37.451 3213 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.75 % Favored : 91.95 % Rotamer: Outliers : 4.00 % Allowed : 19.90 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.15), residues: 2943 helix: -1.11 (0.27), residues: 393 sheet: -1.35 (0.18), residues: 834 loop : -1.57 (0.15), residues: 1716 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 338 time to evaluate : 2.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 105 outliers final: 71 residues processed: 421 average time/residue: 1.4277 time to fit residues: 697.0616 Evaluate side-chains 376 residues out of total 2628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 305 time to evaluate : 3.003 Switching outliers to nearest non-outliers outliers start: 71 outliers final: 63 residues processed: 9 average time/residue: 0.6265 time to fit residues: 11.5304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 173 optimal weight: 6.9990 chunk 112 optimal weight: 0.9980 chunk 167 optimal weight: 9.9990 chunk 84 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 178 optimal weight: 0.3980 chunk 191 optimal weight: 10.0000 chunk 138 optimal weight: 0.0370 chunk 26 optimal weight: 4.9990 chunk 220 optimal weight: 0.0370 overall best weight: 0.8938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 616 ASN F 640 GLN F 651 ASN H 72 ASN ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 563 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.5323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 25338 Z= 0.241 Angle : 0.749 10.652 34416 Z= 0.370 Chirality : 0.047 0.463 4161 Planarity : 0.005 0.048 4260 Dihedral : 5.160 36.881 3213 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.82 % Favored : 91.88 % Rotamer: Outliers : 3.96 % Allowed : 20.70 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.15), residues: 2943 helix: -1.19 (0.27), residues: 396 sheet: -1.39 (0.17), residues: 870 loop : -1.59 (0.15), residues: 1677 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 335 time to evaluate : 2.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 104 outliers final: 71 residues processed: 416 average time/residue: 1.3860 time to fit residues: 670.1355 Evaluate side-chains 381 residues out of total 2628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 310 time to evaluate : 2.623 Switching outliers to nearest non-outliers outliers start: 71 outliers final: 64 residues processed: 9 average time/residue: 0.6290 time to fit residues: 11.2792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 255 optimal weight: 1.9990 chunk 268 optimal weight: 10.0000 chunk 245 optimal weight: 0.0870 chunk 261 optimal weight: 9.9990 chunk 157 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 chunk 205 optimal weight: 0.0470 chunk 80 optimal weight: 3.9990 chunk 236 optimal weight: 1.9990 chunk 247 optimal weight: 1.9990 chunk 260 optimal weight: 0.0980 overall best weight: 0.6058 ------------------------------------------------------------------------------- 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 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN ** F 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 616 ASN F 653 GLN ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 563 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.5466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 25338 Z= 0.211 Angle : 0.747 12.028 34416 Z= 0.367 Chirality : 0.047 0.493 4161 Planarity : 0.005 0.052 4260 Dihedral : 5.042 36.019 3213 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.78 % Favored : 91.91 % Rotamer: Outliers : 3.35 % Allowed : 21.84 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.15), residues: 2943 helix: -1.03 (0.28), residues: 390 sheet: -1.19 (0.18), residues: 831 loop : -1.56 (0.15), residues: 1722 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 334 time to evaluate : 2.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 88 outliers final: 70 residues processed: 406 average time/residue: 1.3245 time to fit residues: 625.4456 Evaluate side-chains 373 residues out of total 2628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 303 time to evaluate : 2.882 Switching outliers to nearest non-outliers outliers start: 70 outliers final: 66 residues processed: 7 average time/residue: 1.0504 time to fit residues: 12.5409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 171 optimal weight: 0.8980 chunk 276 optimal weight: 0.7980 chunk 168 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 192 optimal weight: 20.0000 chunk 289 optimal weight: 9.9990 chunk 266 optimal weight: 40.0000 chunk 230 optimal weight: 0.0870 chunk 23 optimal weight: 1.9990 chunk 178 optimal weight: 0.0970 chunk 141 optimal weight: 0.9980 overall best weight: 0.5756 ------------------------------------------------------------------------------- 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 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 616 ASN F 618 ASN ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 139 ASN I 130 GLN I 188 ASN ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.5575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 25338 Z= 0.211 Angle : 0.762 12.479 34416 Z= 0.374 Chirality : 0.047 0.505 4161 Planarity : 0.005 0.055 4260 Dihedral : 5.007 35.539 3213 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.92 % Favored : 91.78 % Rotamer: Outliers : 3.23 % Allowed : 22.37 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.21 % 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: -1.99 (0.15), residues: 2943 helix: -0.98 (0.28), residues: 390 sheet: -1.20 (0.18), residues: 774 loop : -1.46 (0.15), residues: 1779 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 329 time to evaluate : 2.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 85 outliers final: 63 residues processed: 399 average time/residue: 1.3514 time to fit residues: 625.9483 Evaluate side-chains 364 residues out of total 2628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 301 time to evaluate : 2.862 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 60 residues processed: 4 average time/residue: 0.5840 time to fit residues: 7.0219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 183 optimal weight: 2.9990 chunk 245 optimal weight: 0.0010 chunk 70 optimal weight: 6.9990 chunk 212 optimal weight: 0.0030 chunk 34 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 231 optimal weight: 0.9990 chunk 96 optimal weight: 9.9990 chunk 237 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- 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 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 616 ASN ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 651 ASN F 653 GLN H 139 ASN ** I 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.142976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.108428 restraints weight = 55104.323| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 4.63 r_work: 0.3440 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.5681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 25338 Z= 0.212 Angle : 0.771 16.239 34416 Z= 0.375 Chirality : 0.047 0.513 4161 Planarity : 0.005 0.055 4260 Dihedral : 4.956 35.191 3213 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.68 % Favored : 92.01 % Rotamer: Outliers : 3.35 % Allowed : 22.53 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.21 % 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: -1.95 (0.15), residues: 2943 helix: -1.00 (0.28), residues: 390 sheet: -1.13 (0.19), residues: 768 loop : -1.45 (0.14), residues: 1785 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10824.92 seconds wall clock time: 192 minutes 59.54 seconds (11579.54 seconds total)