Starting phenix.real_space_refine (version: dev) on Thu Dec 22 21:54:50 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kdv_22830/12_2022/7kdv_22830.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kdv_22830/12_2022/7kdv_22830.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kdv_22830/12_2022/7kdv_22830.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kdv_22830/12_2022/7kdv_22830.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kdv_22830/12_2022/7kdv_22830.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kdv_22830/12_2022/7kdv_22830.pdb" } resolution = 4.59 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 51696 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 4823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4823 Classifications: {'peptide': 600} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 4, 'PTRANS': 41, 'TRANS': 552} Chain breaks: 1 Chain: "B" Number of atoms: 3628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3628 Classifications: {'peptide': 452} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 423} Chain: "C" Number of atoms: 4823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4823 Classifications: {'peptide': 600} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 4, 'PTRANS': 41, 'TRANS': 552} Chain breaks: 1 Chain: "D" Number of atoms: 3628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3628 Classifications: {'peptide': 452} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 423} Chain: "E" Number of atoms: 4823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4823 Classifications: {'peptide': 600} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 4, 'PTRANS': 41, 'TRANS': 552} Chain breaks: 1 Chain: "F" Number of atoms: 3628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3628 Classifications: {'peptide': 452} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 423} Chain: "G" Number of atoms: 4823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4823 Classifications: {'peptide': 600} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 4, 'PTRANS': 41, 'TRANS': 552} Chain breaks: 1 Chain: "H" Number of atoms: 3628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3628 Classifications: {'peptide': 452} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 423} Chain: "I" Number of atoms: 4823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4823 Classifications: {'peptide': 600} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 4, 'PTRANS': 41, 'TRANS': 552} Chain breaks: 1 Chain: "J" Number of atoms: 3628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3628 Classifications: {'peptide': 452} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 423} Chain: "K" Number of atoms: 4823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4823 Classifications: {'peptide': 600} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 4, 'PTRANS': 41, 'TRANS': 552} Chain breaks: 1 Chain: "L" Number of atoms: 3628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3628 Classifications: {'peptide': 452} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 423} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "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 dihedrals: 1 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "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: "C" 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: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "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: "G" 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: "H" 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 Chain: "K" 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: "L" 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: 26.51, per 1000 atoms: 0.51 Number of scatterers: 51696 At special positions: 0 Unit cell: (237.93, 221.45, 143.17, 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 246 16.00 O 9654 8.00 N 8484 7.00 C 33312 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS A 628 " - pdb=" SG CYS A 636 " distance=2.03 Simple disulfide: pdb=" SG CYS B 83 " - pdb=" SG CYS B 356 " distance=2.03 Simple disulfide: pdb=" SG CYS B 235 " - pdb=" SG CYS B 251 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 241 " distance=2.04 Simple disulfide: pdb=" SG CYS B 276 " - pdb=" SG CYS B 325 " distance=2.03 Simple disulfide: pdb=" SG CYS C 196 " - pdb=" SG CYS C 231 " distance=2.03 Simple disulfide: pdb=" SG CYS C 628 " - pdb=" SG CYS C 636 " distance=2.03 Simple disulfide: pdb=" SG CYS D 83 " - pdb=" SG CYS D 356 " distance=2.03 Simple disulfide: pdb=" SG CYS D 235 " - pdb=" SG CYS D 251 " distance=2.03 Simple disulfide: pdb=" SG CYS D 236 " - pdb=" SG CYS D 241 " distance=2.04 Simple disulfide: pdb=" SG CYS D 276 " - pdb=" SG CYS D 325 " distance=2.03 Simple disulfide: pdb=" SG CYS E 196 " - pdb=" SG CYS E 231 " distance=2.03 Simple disulfide: pdb=" SG CYS E 628 " - pdb=" SG CYS E 636 " distance=2.03 Simple disulfide: pdb=" SG CYS F 83 " - pdb=" SG CYS F 356 " distance=2.03 Simple disulfide: pdb=" SG CYS F 235 " - pdb=" SG CYS F 251 " distance=2.03 Simple disulfide: pdb=" SG CYS F 236 " - pdb=" SG CYS F 241 " distance=2.04 Simple disulfide: pdb=" SG CYS F 276 " - pdb=" SG CYS F 325 " distance=2.03 Simple disulfide: pdb=" SG CYS G 196 " - pdb=" SG CYS G 231 " distance=2.03 Simple disulfide: pdb=" SG CYS G 628 " - pdb=" SG CYS G 636 " distance=2.03 Simple disulfide: pdb=" SG CYS H 83 " - pdb=" SG CYS H 356 " distance=2.03 Simple disulfide: pdb=" SG CYS H 235 " - pdb=" SG CYS H 251 " distance=2.03 Simple disulfide: pdb=" SG CYS H 236 " - pdb=" SG CYS H 241 " distance=2.04 Simple disulfide: pdb=" SG CYS H 276 " - pdb=" SG CYS H 325 " distance=2.03 Simple disulfide: pdb=" SG CYS I 196 " - pdb=" SG CYS I 231 " distance=2.03 Simple disulfide: pdb=" SG CYS I 628 " - pdb=" SG CYS I 636 " distance=2.03 Simple disulfide: pdb=" SG CYS J 83 " - pdb=" SG CYS J 356 " distance=2.03 Simple disulfide: pdb=" SG CYS J 235 " - pdb=" SG CYS J 251 " distance=2.03 Simple disulfide: pdb=" SG CYS J 236 " - pdb=" SG CYS J 241 " distance=2.04 Simple disulfide: pdb=" SG CYS J 276 " - pdb=" SG CYS J 325 " distance=2.03 Simple disulfide: pdb=" SG CYS K 196 " - pdb=" SG CYS K 231 " distance=2.03 Simple disulfide: pdb=" SG CYS K 628 " - pdb=" SG CYS K 636 " distance=2.03 Simple disulfide: pdb=" SG CYS L 83 " - pdb=" SG CYS L 356 " distance=2.03 Simple disulfide: pdb=" SG CYS L 235 " - pdb=" SG CYS L 251 " distance=2.03 Simple disulfide: pdb=" SG CYS L 236 " - pdb=" SG CYS L 241 " distance=2.04 Simple disulfide: pdb=" SG CYS L 276 " - pdb=" SG CYS L 325 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " NAG-ASN " NAG A 701 " - " ASN A 248 " " NAG A 702 " - " ASN A 504 " " NAG A 703 " - " ASN A 510 " " NAG A 704 " - " ASN A 557 " " NAG B 501 " - " ASN B 140 " " NAG C 701 " - " ASN C 248 " " NAG C 702 " - " ASN C 504 " " NAG C 703 " - " ASN C 510 " " NAG C 704 " - " ASN C 557 " " NAG D 501 " - " ASN D 140 " " NAG E 701 " - " ASN E 248 " " NAG E 702 " - " ASN E 504 " " NAG E 703 " - " ASN E 510 " " NAG E 704 " - " ASN E 557 " " NAG F 501 " - " ASN F 140 " " NAG G 701 " - " ASN G 248 " " NAG G 702 " - " ASN G 504 " " NAG G 703 " - " ASN G 510 " " NAG G 704 " - " ASN G 557 " " NAG H 501 " - " ASN H 140 " " NAG I 701 " - " ASN I 248 " " NAG I 702 " - " ASN I 504 " " NAG I 703 " - " ASN I 510 " " NAG I 704 " - " ASN I 557 " " NAG J 501 " - " ASN J 140 " " NAG K 701 " - " ASN K 248 " " NAG K 702 " - " ASN K 504 " " NAG K 703 " - " ASN K 510 " " NAG K 704 " - " ASN K 557 " " NAG L 501 " - " ASN L 140 " " NAG M 1 " - " ASN A 500 " " NAG N 1 " - " ASN A 617 " " NAG O 1 " - " ASN B 327 " " NAG P 1 " - " ASN C 500 " " NAG Q 1 " - " ASN C 617 " " NAG R 1 " - " ASN D 327 " " NAG S 1 " - " ASN E 500 " " NAG T 1 " - " ASN E 617 " " NAG U 1 " - " ASN F 327 " " NAG V 1 " - " ASN G 500 " " NAG W 1 " - " ASN G 617 " " NAG X 1 " - " ASN H 327 " " NAG Y 1 " - " ASN I 500 " " NAG Z 1 " - " ASN I 617 " " NAG a 1 " - " ASN J 327 " " NAG b 1 " - " ASN K 500 " " NAG c 1 " - " ASN K 617 " " NAG d 1 " - " ASN L 327 " Time building additional restraints: 21.22 Conformation dependent library (CDL) restraints added in 7.2 seconds 12552 Ramachandran restraints generated. 6276 Oldfield, 0 Emsley, 6276 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11700 Finding SS restraints... Secondary structure from input PDB file: 204 helices and 78 sheets defined 32.2% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.26 Creating SS restraints... Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 65 through 77 Processing helix chain 'A' and resid 86 through 91 removed outlier: 3.666A pdb=" N HIS A 90 " --> pdb=" O PRO A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 103 Processing helix chain 'A' and resid 104 through 115 Processing helix chain 'A' and resid 131 through 136 Processing helix chain 'A' and resid 137 through 143 removed outlier: 3.556A pdb=" N LYS A 143 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 171 Proline residue: A 168 - end of helix Processing helix chain 'A' and resid 172 through 178 removed outlier: 6.067A pdb=" N TYR A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLN A 176 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 193 Processing helix chain 'A' and resid 197 through 213 removed outlier: 3.675A pdb=" N LEU A 201 " --> pdb=" O ASP A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 233 removed outlier: 3.534A pdb=" N LEU A 229 " --> pdb=" O SER A 225 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N CYS A 231 " --> pdb=" O LYS A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 260 removed outlier: 3.614A pdb=" N PHE A 259 " --> pdb=" O VAL A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 300 Processing helix chain 'A' and resid 345 through 356 Processing helix chain 'A' and resid 389 through 394 Processing helix chain 'A' and resid 517 through 525 Processing helix chain 'A' and resid 606 through 610 Processing helix chain 'B' and resid 67 through 71 Processing helix chain 'B' and resid 85 through 91 removed outlier: 3.927A pdb=" N LEU B 89 " --> pdb=" O SER B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 115 removed outlier: 3.504A pdb=" N ILE B 115 " --> pdb=" O TRP B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 159 Processing helix chain 'B' and resid 160 through 163 Processing helix chain 'B' and resid 174 through 188 removed outlier: 3.538A pdb=" N TYR B 178 " --> pdb=" O TYR B 174 " (cutoff:3.500A) Proline residue: B 180 - end of helix Processing helix chain 'B' and resid 205 through 220 Processing helix chain 'B' and resid 224 through 236 removed outlier: 3.590A pdb=" N CYS B 236 " --> pdb=" O GLN B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 265 removed outlier: 3.571A pdb=" N SER B 265 " --> pdb=" O ILE B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 336 Processing helix chain 'B' and resid 337 through 344 Processing helix chain 'B' and resid 357 through 363 Processing helix chain 'B' and resid 371 through 382 removed outlier: 4.069A pdb=" N SER B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLN B 382 " --> pdb=" O LEU B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 409 removed outlier: 3.637A pdb=" N ASP B 402 " --> pdb=" O ASN B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 457 Processing helix chain 'B' and resid 457 through 470 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 65 through 77 Processing helix chain 'C' and resid 86 through 91 removed outlier: 3.667A pdb=" N HIS C 90 " --> pdb=" O PRO C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 103 Processing helix chain 'C' and resid 104 through 115 Processing helix chain 'C' and resid 131 through 136 Processing helix chain 'C' and resid 137 through 143 removed outlier: 3.556A pdb=" N LYS C 143 " --> pdb=" O LEU C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 171 Proline residue: C 168 - end of helix Processing helix chain 'C' and resid 172 through 178 removed outlier: 6.066A pdb=" N TYR C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLN C 176 " --> pdb=" O LEU C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 193 Processing helix chain 'C' and resid 197 through 213 removed outlier: 3.675A pdb=" N LEU C 201 " --> pdb=" O ASP C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 233 removed outlier: 3.534A pdb=" N LEU C 229 " --> pdb=" O SER C 225 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N CYS C 231 " --> pdb=" O LYS C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 260 removed outlier: 3.615A pdb=" N PHE C 259 " --> pdb=" O VAL C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 300 Processing helix chain 'C' and resid 345 through 356 Processing helix chain 'C' and resid 389 through 394 Processing helix chain 'C' and resid 517 through 525 Processing helix chain 'C' and resid 606 through 610 Processing helix chain 'D' and resid 67 through 71 Processing helix chain 'D' and resid 85 through 91 removed outlier: 3.927A pdb=" N LEU D 89 " --> pdb=" O SER D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 115 removed outlier: 3.503A pdb=" N ILE D 115 " --> pdb=" O TRP D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 159 Processing helix chain 'D' and resid 160 through 163 Processing helix chain 'D' and resid 174 through 188 removed outlier: 3.539A pdb=" N TYR D 178 " --> pdb=" O TYR D 174 " (cutoff:3.500A) Proline residue: D 180 - end of helix Processing helix chain 'D' and resid 205 through 220 Processing helix chain 'D' and resid 224 through 236 removed outlier: 3.590A pdb=" N CYS D 236 " --> pdb=" O GLN D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 265 removed outlier: 3.570A pdb=" N SER D 265 " --> pdb=" O ILE D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 336 Processing helix chain 'D' and resid 337 through 344 Processing helix chain 'D' and resid 357 through 363 Processing helix chain 'D' and resid 371 through 382 removed outlier: 4.070A pdb=" N SER D 381 " --> pdb=" O LYS D 377 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLN D 382 " --> pdb=" O LEU D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 409 removed outlier: 3.637A pdb=" N ASP D 402 " --> pdb=" O ASN D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 457 Processing helix chain 'D' and resid 457 through 470 Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 65 through 77 Processing helix chain 'E' and resid 86 through 91 removed outlier: 3.666A pdb=" N HIS E 90 " --> pdb=" O PRO E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 103 Processing helix chain 'E' and resid 104 through 115 Processing helix chain 'E' and resid 131 through 136 Processing helix chain 'E' and resid 137 through 143 removed outlier: 3.556A pdb=" N LYS E 143 " --> pdb=" O LEU E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 171 Proline residue: E 168 - end of helix Processing helix chain 'E' and resid 172 through 178 removed outlier: 6.067A pdb=" N TYR E 175 " --> pdb=" O PRO E 172 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLN E 176 " --> pdb=" O LEU E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 193 Processing helix chain 'E' and resid 197 through 213 removed outlier: 3.675A pdb=" N LEU E 201 " --> pdb=" O ASP E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 233 removed outlier: 3.535A pdb=" N LEU E 229 " --> pdb=" O SER E 225 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N CYS E 231 " --> pdb=" O LYS E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 260 removed outlier: 3.615A pdb=" N PHE E 259 " --> pdb=" O VAL E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 300 Processing helix chain 'E' and resid 345 through 356 Processing helix chain 'E' and resid 389 through 394 Processing helix chain 'E' and resid 517 through 525 Processing helix chain 'E' and resid 606 through 610 Processing helix chain 'F' and resid 67 through 71 Processing helix chain 'F' and resid 85 through 91 removed outlier: 3.926A pdb=" N LEU F 89 " --> pdb=" O SER F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 115 removed outlier: 3.504A pdb=" N ILE F 115 " --> pdb=" O TRP F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 159 Processing helix chain 'F' and resid 160 through 163 Processing helix chain 'F' and resid 174 through 188 removed outlier: 3.538A pdb=" N TYR F 178 " --> pdb=" O TYR F 174 " (cutoff:3.500A) Proline residue: F 180 - end of helix Processing helix chain 'F' and resid 205 through 220 Processing helix chain 'F' and resid 224 through 236 removed outlier: 3.590A pdb=" N CYS F 236 " --> pdb=" O GLN F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 265 removed outlier: 3.570A pdb=" N SER F 265 " --> pdb=" O ILE F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 336 Processing helix chain 'F' and resid 337 through 344 Processing helix chain 'F' and resid 357 through 363 Processing helix chain 'F' and resid 371 through 382 removed outlier: 4.069A pdb=" N SER F 381 " --> pdb=" O LYS F 377 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLN F 382 " --> pdb=" O LEU F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 409 removed outlier: 3.637A pdb=" N ASP F 402 " --> pdb=" O ASN F 398 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 457 Processing helix chain 'F' and resid 457 through 470 Processing helix chain 'G' and resid 62 through 64 No H-bonds generated for 'chain 'G' and resid 62 through 64' Processing helix chain 'G' and resid 65 through 77 Processing helix chain 'G' and resid 86 through 91 removed outlier: 3.666A pdb=" N HIS G 90 " --> pdb=" O PRO G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 103 Processing helix chain 'G' and resid 104 through 115 Processing helix chain 'G' and resid 131 through 136 Processing helix chain 'G' and resid 137 through 143 removed outlier: 3.555A pdb=" N LYS G 143 " --> pdb=" O LEU G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 171 Proline residue: G 168 - end of helix Processing helix chain 'G' and resid 172 through 178 removed outlier: 6.067A pdb=" N TYR G 175 " --> pdb=" O PRO G 172 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLN G 176 " --> pdb=" O LEU G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 189 through 193 Processing helix chain 'G' and resid 197 through 213 removed outlier: 3.676A pdb=" N LEU G 201 " --> pdb=" O ASP G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 233 removed outlier: 3.535A pdb=" N LEU G 229 " --> pdb=" O SER G 225 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N CYS G 231 " --> pdb=" O LYS G 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 260 removed outlier: 3.615A pdb=" N PHE G 259 " --> pdb=" O VAL G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 300 Processing helix chain 'G' and resid 345 through 356 Processing helix chain 'G' and resid 389 through 394 Processing helix chain 'G' and resid 517 through 525 Processing helix chain 'G' and resid 606 through 610 Processing helix chain 'H' and resid 67 through 71 Processing helix chain 'H' and resid 85 through 91 removed outlier: 3.927A pdb=" N LEU H 89 " --> pdb=" O SER H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 115 removed outlier: 3.503A pdb=" N ILE H 115 " --> pdb=" O TRP H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 159 Processing helix chain 'H' and resid 160 through 163 Processing helix chain 'H' and resid 174 through 188 removed outlier: 3.537A pdb=" N TYR H 178 " --> pdb=" O TYR H 174 " (cutoff:3.500A) Proline residue: H 180 - end of helix Processing helix chain 'H' and resid 205 through 220 Processing helix chain 'H' and resid 224 through 236 removed outlier: 3.590A pdb=" N CYS H 236 " --> pdb=" O GLN H 232 " (cutoff:3.500A) Processing helix chain 'H' and resid 248 through 265 removed outlier: 3.571A pdb=" N SER H 265 " --> pdb=" O ILE H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 328 through 336 Processing helix chain 'H' and resid 337 through 344 Processing helix chain 'H' and resid 357 through 363 Processing helix chain 'H' and resid 371 through 382 removed outlier: 4.069A pdb=" N SER H 381 " --> pdb=" O LYS H 377 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLN H 382 " --> pdb=" O LEU H 378 " (cutoff:3.500A) Processing helix chain 'H' and resid 398 through 409 removed outlier: 3.638A pdb=" N ASP H 402 " --> pdb=" O ASN H 398 " (cutoff:3.500A) Processing helix chain 'H' and resid 452 through 457 Processing helix chain 'H' and resid 457 through 470 Processing helix chain 'I' and resid 62 through 64 No H-bonds generated for 'chain 'I' and resid 62 through 64' Processing helix chain 'I' and resid 65 through 77 Processing helix chain 'I' and resid 86 through 91 removed outlier: 3.666A pdb=" N HIS I 90 " --> pdb=" O PRO I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 103 Processing helix chain 'I' and resid 104 through 115 Processing helix chain 'I' and resid 131 through 136 Processing helix chain 'I' and resid 137 through 143 removed outlier: 3.556A pdb=" N LYS I 143 " --> pdb=" O LEU I 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 152 through 171 Proline residue: I 168 - end of helix Processing helix chain 'I' and resid 172 through 178 removed outlier: 6.067A pdb=" N TYR I 175 " --> pdb=" O PRO I 172 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLN I 176 " --> pdb=" O LEU I 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 189 through 193 Processing helix chain 'I' and resid 197 through 213 removed outlier: 3.675A pdb=" N LEU I 201 " --> pdb=" O ASP I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 225 through 233 removed outlier: 3.536A pdb=" N LEU I 229 " --> pdb=" O SER I 225 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N CYS I 231 " --> pdb=" O LYS I 227 " (cutoff:3.500A) Processing helix chain 'I' and resid 248 through 260 removed outlier: 3.614A pdb=" N PHE I 259 " --> pdb=" O VAL I 255 " (cutoff:3.500A) Processing helix chain 'I' and resid 286 through 300 Processing helix chain 'I' and resid 345 through 356 Processing helix chain 'I' and resid 389 through 394 Processing helix chain 'I' and resid 517 through 525 Processing helix chain 'I' and resid 606 through 610 Processing helix chain 'J' and resid 67 through 71 Processing helix chain 'J' and resid 85 through 91 removed outlier: 3.927A pdb=" N LEU J 89 " --> pdb=" O SER J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 115 removed outlier: 3.504A pdb=" N ILE J 115 " --> pdb=" O TRP J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 141 through 159 Processing helix chain 'J' and resid 160 through 163 Processing helix chain 'J' and resid 174 through 188 removed outlier: 3.539A pdb=" N TYR J 178 " --> pdb=" O TYR J 174 " (cutoff:3.500A) Proline residue: J 180 - end of helix Processing helix chain 'J' and resid 205 through 220 Processing helix chain 'J' and resid 224 through 236 removed outlier: 3.591A pdb=" N CYS J 236 " --> pdb=" O GLN J 232 " (cutoff:3.500A) Processing helix chain 'J' and resid 248 through 265 removed outlier: 3.571A pdb=" N SER J 265 " --> pdb=" O ILE J 261 " (cutoff:3.500A) Processing helix chain 'J' and resid 328 through 336 Processing helix chain 'J' and resid 337 through 344 Processing helix chain 'J' and resid 357 through 363 Processing helix chain 'J' and resid 371 through 382 removed outlier: 4.069A pdb=" N SER J 381 " --> pdb=" O LYS J 377 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLN J 382 " --> pdb=" O LEU J 378 " (cutoff:3.500A) Processing helix chain 'J' and resid 398 through 409 removed outlier: 3.638A pdb=" N ASP J 402 " --> pdb=" O ASN J 398 " (cutoff:3.500A) Processing helix chain 'J' and resid 452 through 457 Processing helix chain 'J' and resid 457 through 470 Processing helix chain 'K' and resid 62 through 64 No H-bonds generated for 'chain 'K' and resid 62 through 64' Processing helix chain 'K' and resid 65 through 77 Processing helix chain 'K' and resid 86 through 91 removed outlier: 3.666A pdb=" N HIS K 90 " --> pdb=" O PRO K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 100 through 103 Processing helix chain 'K' and resid 104 through 115 Processing helix chain 'K' and resid 131 through 136 Processing helix chain 'K' and resid 137 through 143 removed outlier: 3.556A pdb=" N LYS K 143 " --> pdb=" O LEU K 140 " (cutoff:3.500A) Processing helix chain 'K' and resid 152 through 171 Proline residue: K 168 - end of helix Processing helix chain 'K' and resid 172 through 178 removed outlier: 6.067A pdb=" N TYR K 175 " --> pdb=" O PRO K 172 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLN K 176 " --> pdb=" O LEU K 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 189 through 193 Processing helix chain 'K' and resid 197 through 213 removed outlier: 3.675A pdb=" N LEU K 201 " --> pdb=" O ASP K 197 " (cutoff:3.500A) Processing helix chain 'K' and resid 225 through 233 removed outlier: 3.535A pdb=" N LEU K 229 " --> pdb=" O SER K 225 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N CYS K 231 " --> pdb=" O LYS K 227 " (cutoff:3.500A) Processing helix chain 'K' and resid 248 through 260 removed outlier: 3.614A pdb=" N PHE K 259 " --> pdb=" O VAL K 255 " (cutoff:3.500A) Processing helix chain 'K' and resid 286 through 300 Processing helix chain 'K' and resid 345 through 356 Processing helix chain 'K' and resid 389 through 394 Processing helix chain 'K' and resid 517 through 525 Processing helix chain 'K' and resid 606 through 610 Processing helix chain 'L' and resid 67 through 71 Processing helix chain 'L' and resid 85 through 91 removed outlier: 3.926A pdb=" N LEU L 89 " --> pdb=" O SER L 85 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 115 removed outlier: 3.504A pdb=" N ILE L 115 " --> pdb=" O TRP L 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 141 through 159 Processing helix chain 'L' and resid 160 through 163 Processing helix chain 'L' and resid 174 through 188 removed outlier: 3.538A pdb=" N TYR L 178 " --> pdb=" O TYR L 174 " (cutoff:3.500A) Proline residue: L 180 - end of helix Processing helix chain 'L' and resid 205 through 220 Processing helix chain 'L' and resid 224 through 236 removed outlier: 3.590A pdb=" N CYS L 236 " --> pdb=" O GLN L 232 " (cutoff:3.500A) Processing helix chain 'L' and resid 248 through 265 removed outlier: 3.571A pdb=" N SER L 265 " --> pdb=" O ILE L 261 " (cutoff:3.500A) Processing helix chain 'L' and resid 328 through 336 Processing helix chain 'L' and resid 337 through 344 Processing helix chain 'L' and resid 357 through 363 Processing helix chain 'L' and resid 371 through 382 removed outlier: 4.069A pdb=" N SER L 381 " --> pdb=" O LYS L 377 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLN L 382 " --> pdb=" O LEU L 378 " (cutoff:3.500A) Processing helix chain 'L' and resid 398 through 409 removed outlier: 3.637A pdb=" N ASP L 402 " --> pdb=" O ASN L 398 " (cutoff:3.500A) Processing helix chain 'L' and resid 452 through 457 Processing helix chain 'L' and resid 457 through 470 Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 36 Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 55 removed outlier: 6.196A pdb=" N ILE A 52 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N GLN A 82 " --> pdb=" O ILE A 52 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLY A 54 " --> pdb=" O GLN A 82 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N TYR A 84 " --> pdb=" O GLY A 54 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ILE A 81 " --> pdb=" O ILE A 120 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ARG A 122 " --> pdb=" O ILE A 81 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N MET A 83 " --> pdb=" O ARG A 122 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N VAL A 119 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL A 184 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU A 121 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N PHE A 219 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N VAL A 184 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N THR A 221 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU A 218 " --> pdb=" O TYR A 238 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N THR A 240 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N THR A 220 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ASP A 242 " --> pdb=" O THR A 220 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ASP A 222 " --> pdb=" O ASP A 242 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N ALA A 239 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N SER A 268 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N VAL A 241 " --> pdb=" O SER A 268 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N PHE A 270 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLU A 269 " --> pdb=" O ASN A 305 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N TYR A 307 " --> pdb=" O GLU A 269 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N TYR A 271 " --> pdb=" O TYR A 307 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 321 through 322 removed outlier: 3.769A pdb=" N ASN A 322 " --> pdb=" O GLU A 326 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU A 326 " --> pdb=" O ASN A 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 376 through 379 Processing sheet with id=AA5, first strand: chain 'A' and resid 382 through 385 removed outlier: 6.438A pdb=" N PHE A 553 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY A 591 " --> pdb=" O VAL A 583 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE A 585 " --> pdb=" O ASN A 589 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ASN A 589 " --> pdb=" O ILE A 585 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 399 through 401 removed outlier: 3.774A pdb=" N ARG A 444 " --> pdb=" O GLU A 480 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ALA A 445 " --> pdb=" O ILE A 456 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE A 456 " --> pdb=" O ALA A 445 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL A 447 " --> pdb=" O GLN A 454 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 427 through 433 removed outlier: 6.277A pdb=" N ASN A 429 " --> pdb=" O GLY A 469 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N GLY A 469 " --> pdb=" O ASN A 429 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 441 through 442 Processing sheet with id=AA9, first strand: chain 'B' and resid 44 through 50 removed outlier: 3.541A pdb=" N TYR B 131 " --> pdb=" O HIS B 56 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 44 through 50 removed outlier: 3.895A pdb=" N HIS B 58 " --> pdb=" O GLU B 122 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N LEU B 167 " --> pdb=" O GLN B 195 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N LEU B 197 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU B 169 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N VAL B 199 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLY B 171 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE B 434 " --> pdb=" O THR B 445 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N VAL B 431 " --> pdb=" O VAL B 422 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N VAL B 422 " --> pdb=" O VAL B 431 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY B 433 " --> pdb=" O TRP B 420 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N GLU B 437 " --> pdb=" O GLN B 416 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N GLN B 416 " --> pdb=" O GLU B 437 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AB3, first strand: chain 'B' and resid 139 through 140 removed outlier: 6.978A pdb=" N THR B 139 " --> pdb=" O ARG B 365 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 289 through 292 removed outlier: 5.906A pdb=" N LEU B 290 " --> pdb=" O ARG B 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 33 through 36 Processing sheet with id=AB6, first strand: chain 'C' and resid 52 through 55 removed outlier: 6.197A pdb=" N ILE C 52 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N GLN C 82 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLY C 54 " --> pdb=" O GLN C 82 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N TYR C 84 " --> pdb=" O GLY C 54 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ILE C 81 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ARG C 122 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N MET C 83 " --> pdb=" O ARG C 122 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N VAL C 119 " --> pdb=" O ILE C 182 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL C 184 " --> pdb=" O VAL C 119 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU C 121 " --> pdb=" O VAL C 184 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N PHE C 219 " --> pdb=" O ILE C 182 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N VAL C 184 " --> pdb=" O PHE C 219 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N THR C 221 " --> pdb=" O VAL C 184 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU C 218 " --> pdb=" O TYR C 238 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N THR C 240 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N THR C 220 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ASP C 242 " --> pdb=" O THR C 220 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ASP C 222 " --> pdb=" O ASP C 242 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N ALA C 239 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N SER C 268 " --> pdb=" O ALA C 239 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N VAL C 241 " --> pdb=" O SER C 268 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N PHE C 270 " --> pdb=" O VAL C 241 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLU C 269 " --> pdb=" O ASN C 305 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N TYR C 307 " --> pdb=" O GLU C 269 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N TYR C 271 " --> pdb=" O TYR C 307 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 321 through 322 removed outlier: 3.770A pdb=" N ASN C 322 " --> pdb=" O GLU C 326 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU C 326 " --> pdb=" O ASN C 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 376 through 379 Processing sheet with id=AB9, first strand: chain 'C' and resid 382 through 385 removed outlier: 6.438A pdb=" N PHE C 553 " --> pdb=" O PHE C 383 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY C 591 " --> pdb=" O VAL C 583 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE C 585 " --> pdb=" O ASN C 589 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ASN C 589 " --> pdb=" O ILE C 585 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 399 through 401 removed outlier: 3.773A pdb=" N ARG C 444 " --> pdb=" O GLU C 480 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA C 445 " --> pdb=" O ILE C 456 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE C 456 " --> pdb=" O ALA C 445 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL C 447 " --> pdb=" O GLN C 454 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 427 through 433 removed outlier: 6.277A pdb=" N ASN C 429 " --> pdb=" O GLY C 469 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N GLY C 469 " --> pdb=" O ASN C 429 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 441 through 442 Processing sheet with id=AC4, first strand: chain 'D' and resid 44 through 50 removed outlier: 3.542A pdb=" N TYR D 131 " --> pdb=" O HIS D 56 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 44 through 50 removed outlier: 3.895A pdb=" N HIS D 58 " --> pdb=" O GLU D 122 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N LEU D 167 " --> pdb=" O GLN D 195 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N LEU D 197 " --> pdb=" O LEU D 167 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU D 169 " --> pdb=" O LEU D 197 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N VAL D 199 " --> pdb=" O LEU D 169 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLY D 171 " --> pdb=" O VAL D 199 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE D 434 " --> pdb=" O THR D 445 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N VAL D 431 " --> pdb=" O VAL D 422 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N VAL D 422 " --> pdb=" O VAL D 431 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY D 433 " --> pdb=" O TRP D 420 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N GLU D 437 " --> pdb=" O GLN D 416 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N GLN D 416 " --> pdb=" O GLU D 437 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 96 through 98 Processing sheet with id=AC7, first strand: chain 'D' and resid 139 through 140 removed outlier: 6.977A pdb=" N THR D 139 " --> pdb=" O ARG D 365 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'D' and resid 289 through 292 removed outlier: 5.905A pdb=" N LEU D 290 " --> pdb=" O ARG D 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'E' and resid 33 through 36 Processing sheet with id=AD1, first strand: chain 'E' and resid 52 through 55 removed outlier: 6.196A pdb=" N ILE E 52 " --> pdb=" O ALA E 80 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N GLN E 82 " --> pdb=" O ILE E 52 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLY E 54 " --> pdb=" O GLN E 82 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N TYR E 84 " --> pdb=" O GLY E 54 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ILE E 81 " --> pdb=" O ILE E 120 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ARG E 122 " --> pdb=" O ILE E 81 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N MET E 83 " --> pdb=" O ARG E 122 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N VAL E 119 " --> pdb=" O ILE E 182 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL E 184 " --> pdb=" O VAL E 119 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU E 121 " --> pdb=" O VAL E 184 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N PHE E 219 " --> pdb=" O ILE E 182 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N VAL E 184 " --> pdb=" O PHE E 219 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N THR E 221 " --> pdb=" O VAL E 184 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU E 218 " --> pdb=" O TYR E 238 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N THR E 240 " --> pdb=" O LEU E 218 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N THR E 220 " --> pdb=" O THR E 240 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ASP E 242 " --> pdb=" O THR E 220 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ASP E 222 " --> pdb=" O ASP E 242 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N ALA E 239 " --> pdb=" O ILE E 266 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N SER E 268 " --> pdb=" O ALA E 239 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N VAL E 241 " --> pdb=" O SER E 268 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N PHE E 270 " --> pdb=" O VAL E 241 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU E 269 " --> pdb=" O ASN E 305 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N TYR E 307 " --> pdb=" O GLU E 269 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N TYR E 271 " --> pdb=" O TYR E 307 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 321 through 322 removed outlier: 3.769A pdb=" N ASN E 322 " --> pdb=" O GLU E 326 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU E 326 " --> pdb=" O ASN E 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'E' and resid 376 through 379 Processing sheet with id=AD4, first strand: chain 'E' and resid 382 through 385 removed outlier: 6.437A pdb=" N PHE E 553 " --> pdb=" O PHE E 383 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY E 591 " --> pdb=" O VAL E 583 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE E 585 " --> pdb=" O ASN E 589 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ASN E 589 " --> pdb=" O ILE E 585 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 399 through 401 removed outlier: 3.773A pdb=" N ARG E 444 " --> pdb=" O GLU E 480 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA E 445 " --> pdb=" O ILE E 456 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE E 456 " --> pdb=" O ALA E 445 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL E 447 " --> pdb=" O GLN E 454 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 427 through 433 removed outlier: 6.277A pdb=" N ASN E 429 " --> pdb=" O GLY E 469 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N GLY E 469 " --> pdb=" O ASN E 429 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 441 through 442 Processing sheet with id=AD8, first strand: chain 'F' and resid 44 through 50 removed outlier: 3.541A pdb=" N TYR F 131 " --> pdb=" O HIS F 56 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 44 through 50 removed outlier: 3.895A pdb=" N HIS F 58 " --> pdb=" O GLU F 122 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N LEU F 167 " --> pdb=" O GLN F 195 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LEU F 197 " --> pdb=" O LEU F 167 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU F 169 " --> pdb=" O LEU F 197 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N VAL F 199 " --> pdb=" O LEU F 169 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLY F 171 " --> pdb=" O VAL F 199 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE F 434 " --> pdb=" O THR F 445 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N VAL F 431 " --> pdb=" O VAL F 422 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N VAL F 422 " --> pdb=" O VAL F 431 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY F 433 " --> pdb=" O TRP F 420 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N GLU F 437 " --> pdb=" O GLN F 416 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N GLN F 416 " --> pdb=" O GLU F 437 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 96 through 98 Processing sheet with id=AE2, first strand: chain 'F' and resid 139 through 140 removed outlier: 6.978A pdb=" N THR F 139 " --> pdb=" O ARG F 365 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'F' and resid 289 through 292 removed outlier: 5.905A pdb=" N LEU F 290 " --> pdb=" O ARG F 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'G' and resid 33 through 36 Processing sheet with id=AE5, first strand: chain 'G' and resid 52 through 55 removed outlier: 6.196A pdb=" N ILE G 52 " --> pdb=" O ALA G 80 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N GLN G 82 " --> pdb=" O ILE G 52 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLY G 54 " --> pdb=" O GLN G 82 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N TYR G 84 " --> pdb=" O GLY G 54 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ILE G 81 " --> pdb=" O ILE G 120 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ARG G 122 " --> pdb=" O ILE G 81 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N MET G 83 " --> pdb=" O ARG G 122 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N VAL G 119 " --> pdb=" O ILE G 182 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL G 184 " --> pdb=" O VAL G 119 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU G 121 " --> pdb=" O VAL G 184 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N PHE G 219 " --> pdb=" O ILE G 182 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N VAL G 184 " --> pdb=" O PHE G 219 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N THR G 221 " --> pdb=" O VAL G 184 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU G 218 " --> pdb=" O TYR G 238 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N THR G 240 " --> pdb=" O LEU G 218 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N THR G 220 " --> pdb=" O THR G 240 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ASP G 242 " --> pdb=" O THR G 220 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ASP G 222 " --> pdb=" O ASP G 242 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N ALA G 239 " --> pdb=" O ILE G 266 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N SER G 268 " --> pdb=" O ALA G 239 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N VAL G 241 " --> pdb=" O SER G 268 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N PHE G 270 " --> pdb=" O VAL G 241 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU G 269 " --> pdb=" O ASN G 305 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N TYR G 307 " --> pdb=" O GLU G 269 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N TYR G 271 " --> pdb=" O TYR G 307 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 321 through 322 removed outlier: 3.769A pdb=" N ASN G 322 " --> pdb=" O GLU G 326 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU G 326 " --> pdb=" O ASN G 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'G' and resid 376 through 379 Processing sheet with id=AE8, first strand: chain 'G' and resid 382 through 385 removed outlier: 6.437A pdb=" N PHE G 553 " --> pdb=" O PHE G 383 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY G 591 " --> pdb=" O VAL G 583 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE G 585 " --> pdb=" O ASN G 589 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ASN G 589 " --> pdb=" O ILE G 585 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 399 through 401 removed outlier: 3.774A pdb=" N ARG G 444 " --> pdb=" O GLU G 480 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA G 445 " --> pdb=" O ILE G 456 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE G 456 " --> pdb=" O ALA G 445 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL G 447 " --> pdb=" O GLN G 454 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 427 through 433 removed outlier: 6.277A pdb=" N ASN G 429 " --> pdb=" O GLY G 469 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N GLY G 469 " --> pdb=" O ASN G 429 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 441 through 442 Processing sheet with id=AF3, first strand: chain 'H' and resid 44 through 50 removed outlier: 3.541A pdb=" N TYR H 131 " --> pdb=" O HIS H 56 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 44 through 50 removed outlier: 3.895A pdb=" N HIS H 58 " --> pdb=" O GLU H 122 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N LEU H 167 " --> pdb=" O GLN H 195 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LEU H 197 " --> pdb=" O LEU H 167 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU H 169 " --> pdb=" O LEU H 197 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N VAL H 199 " --> pdb=" O LEU H 169 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLY H 171 " --> pdb=" O VAL H 199 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE H 434 " --> pdb=" O THR H 445 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N VAL H 431 " --> pdb=" O VAL H 422 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N VAL H 422 " --> pdb=" O VAL H 431 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY H 433 " --> pdb=" O TRP H 420 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N GLU H 437 " --> pdb=" O GLN H 416 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N GLN H 416 " --> pdb=" O GLU H 437 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 96 through 98 Processing sheet with id=AF6, first strand: chain 'H' and resid 139 through 140 removed outlier: 6.978A pdb=" N THR H 139 " --> pdb=" O ARG H 365 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'H' and resid 289 through 292 removed outlier: 5.906A pdb=" N LEU H 290 " --> pdb=" O ARG H 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'I' and resid 33 through 36 Processing sheet with id=AF9, first strand: chain 'I' and resid 52 through 55 removed outlier: 6.197A pdb=" N ILE I 52 " --> pdb=" O ALA I 80 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N GLN I 82 " --> pdb=" O ILE I 52 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N GLY I 54 " --> pdb=" O GLN I 82 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N TYR I 84 " --> pdb=" O GLY I 54 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ILE I 81 " --> pdb=" O ILE I 120 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ARG I 122 " --> pdb=" O ILE I 81 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N MET I 83 " --> pdb=" O ARG I 122 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N VAL I 119 " --> pdb=" O ILE I 182 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL I 184 " --> pdb=" O VAL I 119 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU I 121 " --> pdb=" O VAL I 184 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N PHE I 219 " --> pdb=" O ILE I 182 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N VAL I 184 " --> pdb=" O PHE I 219 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N THR I 221 " --> pdb=" O VAL I 184 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU I 218 " --> pdb=" O TYR I 238 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N THR I 240 " --> pdb=" O LEU I 218 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N THR I 220 " --> pdb=" O THR I 240 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ASP I 242 " --> pdb=" O THR I 220 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ASP I 222 " --> pdb=" O ASP I 242 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N ALA I 239 " --> pdb=" O ILE I 266 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N SER I 268 " --> pdb=" O ALA I 239 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N VAL I 241 " --> pdb=" O SER I 268 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N PHE I 270 " --> pdb=" O VAL I 241 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLU I 269 " --> pdb=" O ASN I 305 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N TYR I 307 " --> pdb=" O GLU I 269 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N TYR I 271 " --> pdb=" O TYR I 307 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'I' and resid 321 through 322 removed outlier: 3.769A pdb=" N ASN I 322 " --> pdb=" O GLU I 326 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU I 326 " --> pdb=" O ASN I 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'I' and resid 376 through 379 Processing sheet with id=AG3, first strand: chain 'I' and resid 382 through 385 removed outlier: 6.438A pdb=" N PHE I 553 " --> pdb=" O PHE I 383 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLY I 591 " --> pdb=" O VAL I 583 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE I 585 " --> pdb=" O ASN I 589 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ASN I 589 " --> pdb=" O ILE I 585 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'I' and resid 399 through 401 removed outlier: 3.773A pdb=" N ARG I 444 " --> pdb=" O GLU I 480 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA I 445 " --> pdb=" O ILE I 456 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE I 456 " --> pdb=" O ALA I 445 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL I 447 " --> pdb=" O GLN I 454 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'I' and resid 427 through 433 removed outlier: 6.278A pdb=" N ASN I 429 " --> pdb=" O GLY I 469 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N GLY I 469 " --> pdb=" O ASN I 429 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'I' and resid 441 through 442 Processing sheet with id=AG7, first strand: chain 'J' and resid 44 through 50 removed outlier: 3.541A pdb=" N TYR J 131 " --> pdb=" O HIS J 56 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'J' and resid 44 through 50 removed outlier: 3.895A pdb=" N HIS J 58 " --> pdb=" O GLU J 122 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N LEU J 167 " --> pdb=" O GLN J 195 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N LEU J 197 " --> pdb=" O LEU J 167 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU J 169 " --> pdb=" O LEU J 197 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N VAL J 199 " --> pdb=" O LEU J 169 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLY J 171 " --> pdb=" O VAL J 199 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE J 434 " --> pdb=" O THR J 445 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N VAL J 431 " --> pdb=" O VAL J 422 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N VAL J 422 " --> pdb=" O VAL J 431 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY J 433 " --> pdb=" O TRP J 420 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N GLU J 437 " --> pdb=" O GLN J 416 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N GLN J 416 " --> pdb=" O GLU J 437 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'J' and resid 96 through 98 Processing sheet with id=AH1, first strand: chain 'J' and resid 139 through 140 removed outlier: 6.978A pdb=" N THR J 139 " --> pdb=" O ARG J 365 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH1 Processing sheet with id=AH2, first strand: chain 'J' and resid 289 through 292 removed outlier: 5.906A pdb=" N LEU J 290 " --> pdb=" O ARG J 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH2 Processing sheet with id=AH3, first strand: chain 'K' and resid 33 through 36 Processing sheet with id=AH4, first strand: chain 'K' and resid 52 through 55 removed outlier: 6.196A pdb=" N ILE K 52 " --> pdb=" O ALA K 80 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N GLN K 82 " --> pdb=" O ILE K 52 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLY K 54 " --> pdb=" O GLN K 82 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N TYR K 84 " --> pdb=" O GLY K 54 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ILE K 81 " --> pdb=" O ILE K 120 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ARG K 122 " --> pdb=" O ILE K 81 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N MET K 83 " --> pdb=" O ARG K 122 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N VAL K 119 " --> pdb=" O ILE K 182 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL K 184 " --> pdb=" O VAL K 119 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU K 121 " --> pdb=" O VAL K 184 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N PHE K 219 " --> pdb=" O ILE K 182 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N VAL K 184 " --> pdb=" O PHE K 219 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N THR K 221 " --> pdb=" O VAL K 184 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU K 218 " --> pdb=" O TYR K 238 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N THR K 240 " --> pdb=" O LEU K 218 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N THR K 220 " --> pdb=" O THR K 240 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ASP K 242 " --> pdb=" O THR K 220 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ASP K 222 " --> pdb=" O ASP K 242 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N ALA K 239 " --> pdb=" O ILE K 266 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N SER K 268 " --> pdb=" O ALA K 239 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N VAL K 241 " --> pdb=" O SER K 268 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N PHE K 270 " --> pdb=" O VAL K 241 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU K 269 " --> pdb=" O ASN K 305 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N TYR K 307 " --> pdb=" O GLU K 269 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N TYR K 271 " --> pdb=" O TYR K 307 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'K' and resid 321 through 322 removed outlier: 3.769A pdb=" N ASN K 322 " --> pdb=" O GLU K 326 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU K 326 " --> pdb=" O ASN K 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH5 Processing sheet with id=AH6, first strand: chain 'K' and resid 376 through 379 Processing sheet with id=AH7, first strand: chain 'K' and resid 382 through 385 removed outlier: 6.438A pdb=" N PHE K 553 " --> pdb=" O PHE K 383 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY K 591 " --> pdb=" O VAL K 583 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE K 585 " --> pdb=" O ASN K 589 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ASN K 589 " --> pdb=" O ILE K 585 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'K' and resid 399 through 401 removed outlier: 3.773A pdb=" N ARG K 444 " --> pdb=" O GLU K 480 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ALA K 445 " --> pdb=" O ILE K 456 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE K 456 " --> pdb=" O ALA K 445 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL K 447 " --> pdb=" O GLN K 454 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'K' and resid 427 through 433 removed outlier: 6.277A pdb=" N ASN K 429 " --> pdb=" O GLY K 469 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N GLY K 469 " --> pdb=" O ASN K 429 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'K' and resid 441 through 442 Processing sheet with id=AI2, first strand: chain 'L' and resid 44 through 50 removed outlier: 3.542A pdb=" N TYR L 131 " --> pdb=" O HIS L 56 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'L' and resid 44 through 50 removed outlier: 3.895A pdb=" N HIS L 58 " --> pdb=" O GLU L 122 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N LEU L 167 " --> pdb=" O GLN L 195 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N LEU L 197 " --> pdb=" O LEU L 167 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU L 169 " --> pdb=" O LEU L 197 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N VAL L 199 " --> pdb=" O LEU L 169 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLY L 171 " --> pdb=" O VAL L 199 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE L 434 " --> pdb=" O THR L 445 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N VAL L 431 " --> pdb=" O VAL L 422 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N VAL L 422 " --> pdb=" O VAL L 431 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY L 433 " --> pdb=" O TRP L 420 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N GLU L 437 " --> pdb=" O GLN L 416 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N GLN L 416 " --> pdb=" O GLU L 437 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'L' and resid 96 through 98 Processing sheet with id=AI5, first strand: chain 'L' and resid 139 through 140 removed outlier: 6.978A pdb=" N THR L 139 " --> pdb=" O ARG L 365 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI5 Processing sheet with id=AI6, first strand: chain 'L' and resid 289 through 292 removed outlier: 5.906A pdb=" N LEU L 290 " --> pdb=" O ARG L 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI6 1842 hydrogen bonds defined for protein. 4950 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: 24.40 Time building geometry restraints manager: 23.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 16349 1.35 - 1.47: 13837 1.47 - 1.59: 22608 1.59 - 1.71: 0 1.71 - 1.83: 390 Bond restraints: 53184 Sorted by residual: bond pdb=" CG PRO I 371 " pdb=" CD PRO I 371 " ideal model delta sigma weight residual 1.503 1.466 0.037 3.40e-02 8.65e+02 1.22e+00 bond pdb=" CG PRO A 371 " pdb=" CD PRO A 371 " ideal model delta sigma weight residual 1.503 1.466 0.037 3.40e-02 8.65e+02 1.18e+00 bond pdb=" CG PRO C 371 " pdb=" CD PRO C 371 " ideal model delta sigma weight residual 1.503 1.466 0.037 3.40e-02 8.65e+02 1.17e+00 bond pdb=" CG PRO E 371 " pdb=" CD PRO E 371 " ideal model delta sigma weight residual 1.503 1.466 0.037 3.40e-02 8.65e+02 1.17e+00 bond pdb=" CG PRO K 371 " pdb=" CD PRO K 371 " ideal model delta sigma weight residual 1.503 1.467 0.036 3.40e-02 8.65e+02 1.15e+00 ... (remaining 53179 not shown) Histogram of bond angle deviations from ideal: 99.07 - 106.08: 1804 106.08 - 113.09: 27869 113.09 - 120.09: 19201 120.09 - 127.10: 22794 127.10 - 134.11: 752 Bond angle restraints: 72420 Sorted by residual: angle pdb=" C ALA I 316 " pdb=" N TYR I 317 " pdb=" CA TYR I 317 " ideal model delta sigma weight residual 122.49 115.02 7.47 1.57e+00 4.06e-01 2.27e+01 angle pdb=" C ALA A 316 " pdb=" N TYR A 317 " pdb=" CA TYR A 317 " ideal model delta sigma weight residual 122.49 115.05 7.44 1.57e+00 4.06e-01 2.25e+01 angle pdb=" C ALA E 316 " pdb=" N TYR E 317 " pdb=" CA TYR E 317 " ideal model delta sigma weight residual 122.49 115.06 7.43 1.57e+00 4.06e-01 2.24e+01 angle pdb=" C ALA K 316 " pdb=" N TYR K 317 " pdb=" CA TYR K 317 " ideal model delta sigma weight residual 122.49 115.06 7.43 1.57e+00 4.06e-01 2.24e+01 angle pdb=" C ALA C 316 " pdb=" N TYR C 317 " pdb=" CA TYR C 317 " ideal model delta sigma weight residual 122.49 115.06 7.43 1.57e+00 4.06e-01 2.24e+01 ... (remaining 72415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.19: 28988 17.19 - 34.38: 1859 34.38 - 51.57: 335 51.57 - 68.76: 90 68.76 - 85.95: 42 Dihedral angle restraints: 31314 sinusoidal: 12954 harmonic: 18360 Sorted by residual: dihedral pdb=" CA PRO G 432 " pdb=" C PRO G 432 " pdb=" N ILE G 433 " pdb=" CA ILE G 433 " ideal model delta harmonic sigma weight residual 180.00 156.42 23.58 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA PRO E 432 " pdb=" C PRO E 432 " pdb=" N ILE E 433 " pdb=" CA ILE E 433 " ideal model delta harmonic sigma weight residual 180.00 156.44 23.56 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA PRO K 432 " pdb=" C PRO K 432 " pdb=" N ILE K 433 " pdb=" CA ILE K 433 " ideal model delta harmonic sigma weight residual 180.00 156.44 23.56 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 31311 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 5943 0.051 - 0.102: 1562 0.102 - 0.153: 351 0.153 - 0.204: 38 0.204 - 0.255: 8 Chirality restraints: 7902 Sorted by residual: chirality pdb=" CA LYS I 495 " pdb=" N LYS I 495 " pdb=" C LYS I 495 " pdb=" CB LYS I 495 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA LYS A 495 " pdb=" N LYS A 495 " pdb=" C LYS A 495 " pdb=" CB LYS A 495 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA LYS E 495 " pdb=" N LYS E 495 " pdb=" C LYS E 495 " pdb=" CB LYS E 495 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 7899 not shown) Planarity restraints: 9360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL F 184 " -0.019 2.00e-02 2.50e+03 3.73e-02 1.39e+01 pdb=" C VAL F 184 " 0.065 2.00e-02 2.50e+03 pdb=" O VAL F 184 " -0.024 2.00e-02 2.50e+03 pdb=" N LEU F 185 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL L 184 " -0.019 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C VAL L 184 " 0.064 2.00e-02 2.50e+03 pdb=" O VAL L 184 " -0.024 2.00e-02 2.50e+03 pdb=" N LEU L 185 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL H 184 " 0.019 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C VAL H 184 " -0.064 2.00e-02 2.50e+03 pdb=" O VAL H 184 " 0.024 2.00e-02 2.50e+03 pdb=" N LEU H 185 " 0.021 2.00e-02 2.50e+03 ... (remaining 9357 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 1283 2.67 - 3.23: 51622 3.23 - 3.78: 85706 3.78 - 4.34: 117673 4.34 - 4.90: 185560 Nonbonded interactions: 441844 Sorted by model distance: nonbonded pdb=" O ILE L 261 " pdb=" OG SER L 265 " model vdw 2.109 2.440 nonbonded pdb=" O ILE D 261 " pdb=" OG SER D 265 " model vdw 2.109 2.440 nonbonded pdb=" O ILE H 261 " pdb=" OG SER H 265 " model vdw 2.110 2.440 nonbonded pdb=" O ILE F 261 " pdb=" OG SER F 265 " model vdw 2.110 2.440 nonbonded pdb=" O ILE B 261 " pdb=" OG SER B 265 " model vdw 2.110 2.440 ... (remaining 441839 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 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'c' } ncs_group { reference = chain 'O' selection = chain 'R' selection = chain 'U' selection = chain 'X' selection = chain 'a' selection = chain 'd' } Set up NCS constraints Number of NCS constrained groups: 4 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' } pdb_interpretation.ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'c' } pdb_interpretation.ncs_group { reference = chain 'O' selection = chain 'R' selection = chain 'U' selection = chain 'X' selection = chain 'a' selection = chain 'd' } Set refine NCS operators NCS operators will be refined. Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 246 5.16 5 C 33312 2.51 5 N 8484 2.21 5 O 9654 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.560 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: 0.000 Extract box with map and model: 11.450 Check model and map are aligned: 0.710 Convert atoms to be neutral: 0.380 Process input model: 131.350 Find NCS groups from input model: 4.050 Set up NCS constraints: 0.700 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.030 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 156.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 53184 Z= 0.279 Angle : 0.821 8.933 72420 Z= 0.461 Chirality : 0.048 0.255 7902 Planarity : 0.007 0.062 9312 Dihedral : 12.346 85.949 19506 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.45 % Favored : 94.17 % Rotamer Outliers : 0.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.22 % Cis-general : 0.20 % 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: -1.39 (0.10), residues: 6276 helix: -0.42 (0.13), residues: 1536 sheet: -0.43 (0.14), residues: 1146 loop : -1.32 (0.10), residues: 3594 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12552 Ramachandran restraints generated. 6276 Oldfield, 0 Emsley, 6276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12552 Ramachandran restraints generated. 6276 Oldfield, 0 Emsley, 6276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 52 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 58 average time/residue: 0.2414 time to fit residues: 17.2395 Evaluate side-chains 30 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 29 time to evaluate : 0.610 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0496 time to fit residues: 0.8979 Evaluate side-chains 68 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 65 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 67 average time/residue: 0.2298 time to fit residues: 18.0927 Evaluate side-chains 37 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.418 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5488 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0022 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0010 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0026 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 630 random chunks: chunk 531 optimal weight: 8.9990 chunk 477 optimal weight: 0.5980 chunk 264 optimal weight: 0.0040 chunk 163 optimal weight: 5.9990 chunk 322 optimal weight: 20.0000 chunk 255 optimal weight: 0.0010 chunk 493 optimal weight: 0.0030 chunk 191 optimal weight: 0.7980 chunk 300 optimal weight: 10.0000 chunk 367 optimal weight: 0.9980 chunk 572 optimal weight: 30.0000 overall best weight: 0.2808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 82 GLN E 188 ASN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 147 ASN L 369 GLN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 53184 Z= 0.204 Angle : 0.661 9.775 72420 Z= 0.336 Chirality : 0.043 0.185 7902 Planarity : 0.005 0.080 9312 Dihedral : 4.960 22.198 7404 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.22 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.10), residues: 6276 helix: 1.32 (0.14), residues: 1608 sheet: -0.26 (0.14), residues: 1110 loop : -0.94 (0.10), residues: 3558 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11360 Ramachandran restraints generated. 5680 Oldfield, 0 Emsley, 5680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11360 Ramachandran restraints generated. 5680 Oldfield, 0 Emsley, 5680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.2150 time to fit residues: 10.8387 Evaluate side-chains 25 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.623 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7514 Evaluate side-chains 48 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.387 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 outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.2434 time to fit residues: 13.7840 Evaluate side-chains 30 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.464 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6144 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0024 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0010 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0031 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 630 random chunks: chunk 317 optimal weight: 10.0000 chunk 177 optimal weight: 8.9990 chunk 476 optimal weight: 0.0980 chunk 389 optimal weight: 0.8980 chunk 157 optimal weight: 7.9990 chunk 573 optimal weight: 30.0000 chunk 619 optimal weight: 3.9990 chunk 510 optimal weight: 9.9990 chunk 568 optimal weight: 20.0000 chunk 195 optimal weight: 0.2980 chunk 459 optimal weight: 0.0670 overall best weight: 1.0720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 188 ASN E 356 GLN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 113 ASN L 147 ASN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 53184 Z= 0.199 Angle : 0.671 10.155 72420 Z= 0.338 Chirality : 0.044 0.244 7902 Planarity : 0.006 0.088 9312 Dihedral : 4.967 22.701 7404 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.22 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.10), residues: 6276 helix: 1.23 (0.13), residues: 1608 sheet: -0.34 (0.13), residues: 1098 loop : -0.96 (0.10), residues: 3570 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11360 Ramachandran restraints generated. 5680 Oldfield, 0 Emsley, 5680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11360 Ramachandran restraints generated. 5680 Oldfield, 0 Emsley, 5680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1930 time to fit residues: 9.1330 Evaluate side-chains 23 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.581 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8072 Evaluate side-chains 37 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.2287 time to fit residues: 10.3916 Evaluate side-chains 27 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.451 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6127 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0025 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0012 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0031 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 630 random chunks: chunk 566 optimal weight: 0.4980 chunk 430 optimal weight: 1.9990 chunk 297 optimal weight: 20.0000 chunk 63 optimal weight: 20.0000 chunk 273 optimal weight: 20.0000 chunk 384 optimal weight: 10.0000 chunk 575 optimal weight: 10.0000 chunk 608 optimal weight: 30.0000 chunk 300 optimal weight: 9.9990 chunk 545 optimal weight: 9.9990 chunk 164 optimal weight: 0.2980 overall best weight: 4.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 188 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 147 ASN L 410 ASN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 53184 Z= 0.214 Angle : 0.662 11.192 72420 Z= 0.330 Chirality : 0.043 0.221 7902 Planarity : 0.006 0.070 9312 Dihedral : 4.913 22.778 7404 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.22 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.10), residues: 6276 helix: 1.35 (0.13), residues: 1620 sheet: -0.35 (0.14), residues: 1104 loop : -0.96 (0.10), residues: 3552 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.1727 time to fit residues: 6.9610 Evaluate side-chains 19 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.589 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8131 Evaluate side-chains 35 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1918 time to fit residues: 8.4307 Evaluate side-chains 27 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.398 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5486 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0022 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0010 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0028 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 630 random chunks: chunk 507 optimal weight: 20.0000 chunk 345 optimal weight: 0.0020 chunk 8 optimal weight: 0.0980 chunk 453 optimal weight: 30.0000 chunk 251 optimal weight: 0.8980 chunk 519 optimal weight: 0.9990 chunk 420 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 310 optimal weight: 0.0870 chunk 546 optimal weight: 30.0000 chunk 153 optimal weight: 20.0000 overall best weight: 0.4168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 188 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 53184 Z= 0.195 Angle : 0.674 15.851 72420 Z= 0.329 Chirality : 0.043 0.232 7902 Planarity : 0.006 0.055 9312 Dihedral : 4.903 23.880 7404 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.22 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.10), residues: 6276 helix: 1.28 (0.13), residues: 1620 sheet: -0.41 (0.14), residues: 1092 loop : -0.96 (0.10), residues: 3564 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.1731 time to fit residues: 6.2003 Evaluate side-chains 19 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.616 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7363 Evaluate side-chains 35 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 34 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 35 average time/residue: 0.1898 time to fit residues: 8.4106 Evaluate side-chains 26 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.430 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5916 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0023 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0012 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0033 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 630 random chunks: chunk 204 optimal weight: 0.8980 chunk 548 optimal weight: 9.9990 chunk 120 optimal weight: 0.0000 chunk 357 optimal weight: 4.9990 chunk 150 optimal weight: 9.9990 chunk 609 optimal weight: 0.7980 chunk 506 optimal weight: 0.0870 chunk 282 optimal weight: 8.9990 chunk 50 optimal weight: 0.6980 chunk 201 optimal weight: 3.9990 chunk 320 optimal weight: 9.9990 overall best weight: 0.4962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 188 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 53184 Z= 0.195 Angle : 0.674 15.851 72420 Z= 0.329 Chirality : 0.043 0.232 7902 Planarity : 0.006 0.055 9312 Dihedral : 4.903 23.880 7404 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 22.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.22 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.10), residues: 6276 helix: 1.28 (0.13), residues: 1620 sheet: -0.41 (0.14), residues: 1092 loop : -0.96 (0.10), residues: 3564 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.1849 time to fit residues: 6.6017 Evaluate side-chains 19 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.615 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8195 Evaluate side-chains 34 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.1909 time to fit residues: 8.1542 Evaluate side-chains 25 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.440 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4970 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0017 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0009 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0025 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 630 random chunks: chunk 587 optimal weight: 20.0000 chunk 68 optimal weight: 3.9990 chunk 347 optimal weight: 9.9990 chunk 445 optimal weight: 0.0770 chunk 344 optimal weight: 20.0000 chunk 513 optimal weight: 7.9990 chunk 340 optimal weight: 0.0060 chunk 607 optimal weight: 0.9990 chunk 380 optimal weight: 20.0000 chunk 370 optimal weight: 0.8980 chunk 280 optimal weight: 8.9990 overall best weight: 1.1958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 188 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 53184 Z= 0.195 Angle : 0.674 15.851 72420 Z= 0.329 Chirality : 0.043 0.232 7902 Planarity : 0.006 0.055 9312 Dihedral : 4.903 23.880 7404 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 21.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.22 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.10), residues: 6276 helix: 1.28 (0.13), residues: 1620 sheet: -0.41 (0.14), residues: 1092 loop : -0.96 (0.10), residues: 3564 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.1741 time to fit residues: 6.2272 Evaluate side-chains 19 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.555 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7636 Evaluate side-chains 34 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.1881 time to fit residues: 8.0492 Evaluate side-chains 26 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.396 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5320 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0021 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0009 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0026 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 630 random chunks: chunk 375 optimal weight: 0.9980 chunk 242 optimal weight: 10.0000 chunk 362 optimal weight: 30.0000 chunk 182 optimal weight: 0.1980 chunk 119 optimal weight: 5.9990 chunk 117 optimal weight: 0.0270 chunk 386 optimal weight: 5.9990 chunk 413 optimal weight: 20.0000 chunk 300 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 477 optimal weight: 0.5980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 188 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 53184 Z= 0.195 Angle : 0.674 15.851 72420 Z= 0.329 Chirality : 0.043 0.232 7902 Planarity : 0.006 0.055 9312 Dihedral : 4.903 23.880 7404 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 22.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.22 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.10), residues: 6276 helix: 1.28 (0.13), residues: 1620 sheet: -0.41 (0.14), residues: 1092 loop : -0.96 (0.10), residues: 3564 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.1679 time to fit residues: 6.0639 Evaluate side-chains 19 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.550 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7426 Evaluate side-chains 34 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.1875 time to fit residues: 8.0161 Evaluate side-chains 25 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.388 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6165 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0023 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0010 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0030 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 630 random chunks: chunk 552 optimal weight: 0.0970 chunk 581 optimal weight: 0.8980 chunk 530 optimal weight: 3.9990 chunk 565 optimal weight: 6.9990 chunk 340 optimal weight: 4.9990 chunk 246 optimal weight: 40.0000 chunk 444 optimal weight: 5.9990 chunk 173 optimal weight: 0.5980 chunk 511 optimal weight: 0.8980 chunk 535 optimal weight: 7.9990 chunk 563 optimal weight: 0.0470 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 188 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 53184 Z= 0.195 Angle : 0.674 15.851 72420 Z= 0.329 Chirality : 0.043 0.232 7902 Planarity : 0.006 0.055 9312 Dihedral : 4.903 23.880 7404 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 21.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.22 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.10), residues: 6276 helix: 1.28 (0.13), residues: 1620 sheet: -0.41 (0.14), residues: 1092 loop : -0.96 (0.10), residues: 3564 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.1726 time to fit residues: 6.2215 Evaluate side-chains 19 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.543 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7562 Evaluate side-chains 34 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.1891 time to fit residues: 8.0816 Evaluate side-chains 26 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.411 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5428 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0022 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0011 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0029 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 630 random chunks: chunk 371 optimal weight: 0.9990 chunk 598 optimal weight: 8.9990 chunk 365 optimal weight: 0.0060 chunk 283 optimal weight: 0.5980 chunk 415 optimal weight: 0.0980 chunk 627 optimal weight: 3.9990 chunk 577 optimal weight: 0.0010 chunk 499 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 386 optimal weight: 0.8980 chunk 306 optimal weight: 0.0970 overall best weight: 0.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 188 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 53184 Z= 0.195 Angle : 0.674 15.850 72420 Z= 0.329 Chirality : 0.043 0.232 7902 Planarity : 0.006 0.055 9312 Dihedral : 4.903 23.880 7404 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 22.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.22 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.10), residues: 6276 helix: 1.28 (0.13), residues: 1620 sheet: -0.41 (0.14), residues: 1092 loop : -0.96 (0.10), residues: 3564 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.1739 time to fit residues: 6.3142 Evaluate side-chains 19 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.588 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6525 Evaluate side-chains 34 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.1901 time to fit residues: 8.0676 Evaluate side-chains 25 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.484 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5953 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0022 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0011 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0027 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 630 random chunks: chunk 396 optimal weight: 20.0000 chunk 532 optimal weight: 0.2980 chunk 153 optimal weight: 10.0000 chunk 460 optimal weight: 40.0000 chunk 73 optimal weight: 0.9980 chunk 138 optimal weight: 0.0770 chunk 500 optimal weight: 8.9990 chunk 209 optimal weight: 9.9990 chunk 514 optimal weight: 0.0060 chunk 63 optimal weight: 20.0000 chunk 92 optimal weight: 0.0870 overall best weight: 0.2932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 188 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.023822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2340 r_free = 0.2340 target = 0.018199 restraints weight = 71532.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2368 r_free = 0.2368 target = 0.018920 restraints weight = 46698.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2390 r_free = 0.2390 target = 0.019445 restraints weight = 34353.831| |-----------------------------------------------------------------------------| r_work (final): 0.2427 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.031746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.023457 restraints weight = 49796.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.024185 restraints weight = 35713.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.024748 restraints weight = 27984.824| |-----------------------------------------------------------------------------| r_work (final): 0.2597 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2554 r_free = 0.2554 target = 0.048119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2570 r_free = 0.2570 target = 0.046269 restraints weight = 312.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.046626 restraints weight = 100.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.046898 restraints weight = 54.113| |-----------------------------------------------------------------------------| r_work (final): 0.2544 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2519 r_free = 0.2519 target = 0.038817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2542 r_free = 0.2542 target = 0.038424 restraints weight = 814.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2536 r_free = 0.2536 target = 0.038536 restraints weight = 190.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.038597 restraints weight = 98.450| |-----------------------------------------------------------------------------| r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 53184 Z= 0.195 Angle : 0.674 15.850 72420 Z= 0.329 Chirality : 0.043 0.232 7902 Planarity : 0.006 0.055 9312 Dihedral : 4.903 23.880 7404 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 21.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.22 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.10), residues: 6276 helix: 1.28 (0.13), residues: 1620 sheet: -0.41 (0.14), residues: 1092 loop : -0.96 (0.10), residues: 3564 =============================================================================== Job complete usr+sys time: 5723.59 seconds wall clock time: 108 minutes 27.21 seconds (6507.21 seconds total)