Starting phenix.real_space_refine on Sun Feb 25 13:52:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kdv_22830/02_2024/7kdv_22830.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kdv_22830/02_2024/7kdv_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_22830/02_2024/7kdv_22830.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kdv_22830/02_2024/7kdv_22830.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kdv_22830/02_2024/7kdv_22830.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kdv_22830/02_2024/7kdv_22830.pdb" } resolution = 4.59 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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 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. 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: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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 dihedrals: 6 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 dihedrals: 6 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: 9 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 dihedrals: 6 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 dihedrals: 6 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: 9 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 9 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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 dihedrals: 12 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 dihedrals: 3 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 dihedrals: 12 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 dihedrals: 3 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 dihedrals: 12 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 dihedrals: 3 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 dihedrals: 12 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 dihedrals: 3 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 dihedrals: 12 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 dihedrals: 3 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 dihedrals: 12 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 26.16, 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: 20.86 Conformation dependent library (CDL) restraints added in 9.3 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: 6.79 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: 25.18 Time building geometry restraints manager: 22.61 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=" C1 NAG F 501 " pdb=" O5 NAG F 501 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.19e+00 bond pdb=" C1 NAG B 501 " pdb=" O5 NAG B 501 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.15e+00 bond pdb=" C1 NAG J 501 " pdb=" O5 NAG J 501 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.14e+00 bond pdb=" C1 NAG D 501 " pdb=" O5 NAG D 501 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.12e+00 bond pdb=" C1 NAG L 501 " pdb=" O5 NAG L 501 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.11e+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 - 21.30: 30631 21.30 - 42.61: 1349 42.61 - 63.91: 252 63.91 - 85.22: 90 85.22 - 106.52: 36 Dihedral angle restraints: 32358 sinusoidal: 13998 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 32355 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 6046 0.054 - 0.108: 1566 0.108 - 0.162: 259 0.162 - 0.215: 19 0.215 - 0.269: 12 Chirality restraints: 7902 Sorted by residual: chirality pdb=" C5 BMA R 3 " pdb=" C4 BMA R 3 " pdb=" C6 BMA R 3 " pdb=" O5 BMA R 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" C5 BMA O 3 " pdb=" C4 BMA O 3 " pdb=" C6 BMA O 3 " pdb=" O5 BMA O 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" C5 BMA X 3 " pdb=" C4 BMA X 3 " pdb=" C6 BMA X 3 " pdb=" O5 BMA X 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.80e+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. 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: 1.330 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: 0.050 Extract box with map and model: 9.660 Check model and map are aligned: 0.750 Set scattering table: 0.470 Process input model: 137.990 Find NCS groups from input model: 3.930 Set up NCS constraints: 1.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 158.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 53184 Z= 0.304 Angle : 0.849 8.933 72420 Z= 0.467 Chirality : 0.050 0.269 7902 Planarity : 0.007 0.062 9312 Dihedral : 13.451 106.520 20550 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.45 % Favored : 94.17 % Rotamer: Outliers : 0.98 % Allowed : 4.02 % Favored : 95.00 % 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: -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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP L 420 HIS 0.004 0.001 HIS B 451 PHE 0.021 0.002 PHE D 42 TYR 0.025 0.004 TYR F 273 ARG 0.009 0.001 ARG A 484 *********************** 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 : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 LEU cc_start: 0.8985 (mt) cc_final: 0.8771 (mt) outliers start: 6 outliers final: 1 residues processed: 58 average time/residue: 0.2658 time to fit residues: 18.7966 Evaluate side-chains 31 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 30 time to evaluate : 0.639 Evaluate side-chains 68 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 65 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 LEU cc_start: 0.8660 (mt) cc_final: 0.8121 (mp) REVERT: B 371 MET cc_start: 0.8793 (mmp) cc_final: 0.7477 (mmm) REVERT: B 387 LEU cc_start: 0.8585 (tp) cc_final: 0.8296 (tp) outliers start: 3 outliers final: 0 residues processed: 67 average time/residue: 0.2322 time to fit residues: 18.1727 Evaluate side-chains 38 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.384 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 : 0.002 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 ------------------------------------------------------------------------------- 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: 0.0980 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: 0.3002 ------------------------------------------------------------------------------- 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: 0.7423 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 53184 Z= 0.195 Angle : 0.660 8.790 72420 Z= 0.336 Chirality : 0.043 0.171 7902 Planarity : 0.006 0.088 9312 Dihedral : 7.959 70.395 8448 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % 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: -0.32 (0.10), residues: 6276 helix: 1.33 (0.14), residues: 1608 sheet: -0.25 (0.14), residues: 1110 loop : -0.93 (0.10), residues: 3558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G 139 HIS 0.005 0.001 HIS C 277 PHE 0.022 0.002 PHE D 405 TYR 0.027 0.002 TYR I 307 ARG 0.008 0.001 ARG L 226 *********************** 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 : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 70 LEU cc_start: 0.8888 (mt) cc_final: 0.8638 (mt) REVERT: E 308 MET cc_start: 0.7809 (mmp) cc_final: 0.7348 (mmm) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.2283 time to fit residues: 11.3484 Evaluate side-chains 28 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.566 Evaluate side-chains 48 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 87 ASP cc_start: 0.8439 (t0) cc_final: 0.8128 (t0) REVERT: L 371 MET cc_start: 0.8772 (mmp) cc_final: 0.8421 (mmm) REVERT: L 413 MET cc_start: 0.5987 (mmp) cc_final: 0.5319 (tpp) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.2521 time to fit residues: 14.1821 Evaluate side-chains 30 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.413 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: 0.0022 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 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 : 0.003 ------------------------------------------------------------------------------- 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: 0.8980 chunk 177 optimal weight: 6.9990 chunk 476 optimal weight: 0.7980 chunk 389 optimal weight: 0.5980 chunk 157 optimal weight: 7.9990 chunk 573 optimal weight: 20.0000 chunk 619 optimal weight: 6.9990 chunk 510 optimal weight: 20.0000 chunk 568 optimal weight: 9.9990 chunk 195 optimal weight: 6.9990 chunk 459 optimal weight: 4.9990 overall best weight: 2.8584 ------------------------------------------------------------------------------- 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 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: 0.7456 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.119 53184 Z= 0.314 Angle : 0.740 15.864 72420 Z= 0.371 Chirality : 0.045 0.276 7902 Planarity : 0.009 0.235 9312 Dihedral : 7.896 68.474 8448 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % 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: -0.35 (0.10), residues: 6276 helix: 1.26 (0.13), residues: 1602 sheet: -0.25 (0.13), residues: 1110 loop : -0.93 (0.10), residues: 3564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP G 66 HIS 0.018 0.002 HIS K 211 PHE 0.030 0.003 PHE D 308 TYR 0.034 0.003 TYR E 200 ARG 0.017 0.001 ARG C 207 *********************** REFINEMENT MACRO_CYCLE 3 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 34 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 70 LEU cc_start: 0.8987 (mt) cc_final: 0.8626 (mt) REVERT: I 306 LEU cc_start: 0.7935 (mt) cc_final: 0.7727 (mt) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.2170 time to fit residues: 9.6752 Evaluate side-chains 26 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.545 Evaluate side-chains 36 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.431 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: L 67 ASP cc_start: 0.8365 (m-30) cc_final: 0.8155 (m-30) REVERT: L 87 ASP cc_start: 0.8427 (t0) cc_final: 0.8199 (t70) REVERT: L 371 MET cc_start: 0.8817 (mmp) cc_final: 0.8500 (mmm) REVERT: L 413 MET cc_start: 0.6032 (mmp) cc_final: 0.5725 (tpp) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.2238 time to fit residues: 9.7705 Evaluate side-chains 27 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.408 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 : 0.002 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 ------------------------------------------------------------------------------- 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: 8.9990 chunk 430 optimal weight: 1.9990 chunk 297 optimal weight: 30.0000 chunk 63 optimal weight: 8.9990 chunk 273 optimal weight: 20.0000 chunk 384 optimal weight: 10.0000 chunk 575 optimal weight: 3.9990 chunk 608 optimal weight: 30.0000 chunk 300 optimal weight: 0.8980 chunk 545 optimal weight: 10.0000 chunk 164 optimal weight: 0.9980 overall best weight: 3.3786 ------------------------------------------------------------------------------- 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 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 147 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 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.164 53184 Z= 0.334 Angle : 0.741 15.856 72420 Z= 0.372 Chirality : 0.045 0.276 7902 Planarity : 0.009 0.235 9312 Dihedral : 7.896 68.473 8448 Min Nonbonded Distance : 1.017 Molprobity Statistics. All-atom Clashscore : 23.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % 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: -0.35 (0.10), residues: 6276 helix: 1.26 (0.13), residues: 1602 sheet: -0.25 (0.13), residues: 1110 loop : -0.93 (0.10), residues: 3564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 66 HIS 0.018 0.002 HIS K 211 PHE 0.030 0.003 PHE D 308 TYR 0.034 0.003 TYR E 200 ARG 0.017 0.001 ARG A 207 *********************** 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 30 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 70 LEU cc_start: 0.9013 (mt) cc_final: 0.8641 (mt) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.1795 time to fit residues: 7.4147 Evaluate side-chains 26 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.518 Evaluate side-chains 36 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.420 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: L 67 ASP cc_start: 0.8367 (m-30) cc_final: 0.8158 (m-30) REVERT: L 371 MET cc_start: 0.8818 (mmp) cc_final: 0.8500 (mmm) REVERT: L 413 MET cc_start: 0.6376 (mmp) cc_final: 0.5727 (tpp) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.1974 time to fit residues: 8.7767 Evaluate side-chains 27 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.424 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 : 0.002 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 ------------------------------------------------------------------------------- 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: 30.0000 chunk 345 optimal weight: 0.0050 chunk 8 optimal weight: 0.0980 chunk 453 optimal weight: 8.9990 chunk 251 optimal weight: 20.0000 chunk 519 optimal weight: 8.9990 chunk 420 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 310 optimal weight: 10.0000 chunk 546 optimal weight: 20.0000 chunk 153 optimal weight: 20.0000 overall best weight: 5.6202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 188 ASN I 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 ** both conformations clash, **PLEASE CHECK MANUALLY** L 147 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 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 53184 Z= 0.268 Angle : 0.715 10.041 72420 Z= 0.356 Chirality : 0.045 0.249 7902 Planarity : 0.008 0.178 9312 Dihedral : 7.438 61.149 8448 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % 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: -0.58 (0.10), residues: 6276 helix: 1.05 (0.13), residues: 1650 sheet: -0.45 (0.13), residues: 1110 loop : -1.07 (0.10), residues: 3516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP C 318 HIS 0.024 0.002 HIS C 211 PHE 0.033 0.002 PHE K 49 TYR 0.039 0.003 TYR C 175 ARG 0.014 0.001 ARG E 207 *********************** 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 29 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 70 LEU cc_start: 0.9047 (mt) cc_final: 0.8768 (mt) REVERT: I 308 MET cc_start: 0.7567 (mmm) cc_final: 0.6474 (mmm) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.1798 time to fit residues: 7.3242 Evaluate side-chains 23 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.510 Evaluate side-chains 36 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 67 ASP cc_start: 0.8401 (m-30) cc_final: 0.8193 (m-30) REVERT: L 87 ASP cc_start: 0.8119 (t0) cc_final: 0.7683 (t0) REVERT: L 371 MET cc_start: 0.8840 (mmp) cc_final: 0.8419 (mmm) REVERT: L 413 MET cc_start: 0.6600 (mmp) cc_final: 0.6093 (tpp) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.2016 time to fit residues: 8.9564 Evaluate side-chains 26 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.466 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: 0.0026 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 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 ------------------------------------------------------------------------------- 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: 10.0000 chunk 548 optimal weight: 0.5980 chunk 120 optimal weight: 0.6980 chunk 357 optimal weight: 8.9990 chunk 150 optimal weight: 0.3980 chunk 609 optimal weight: 9.9990 chunk 506 optimal weight: 6.9990 chunk 282 optimal weight: 7.9990 chunk 50 optimal weight: 0.0170 chunk 201 optimal weight: 10.0000 chunk 320 optimal weight: 2.9990 overall best weight: 0.9420 ------------------------------------------------------------------------------- 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 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.7496 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 53184 Z= 0.179 Angle : 0.655 9.250 72420 Z= 0.326 Chirality : 0.044 0.254 7902 Planarity : 0.006 0.055 9312 Dihedral : 6.606 49.078 8448 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.11 % Allowed : 1.20 % Favored : 98.70 % 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: -0.62 (0.10), residues: 6276 helix: 0.95 (0.13), residues: 1620 sheet: -0.38 (0.14), residues: 1122 loop : -1.07 (0.10), residues: 3534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP G 87 HIS 0.023 0.002 HIS I 211 PHE 0.052 0.002 PHE E 49 TYR 0.040 0.003 TYR A 175 ARG 0.014 0.001 ARG C 207 *********************** 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 30 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 73 MET cc_start: 0.8657 (mtm) cc_final: 0.8262 (mtp) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.1669 time to fit residues: 7.0919 Evaluate side-chains 22 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.568 Evaluate side-chains 38 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 67 ASP cc_start: 0.8371 (m-30) cc_final: 0.8148 (m-30) REVERT: L 87 ASP cc_start: 0.7948 (t0) cc_final: 0.7424 (t0) REVERT: L 371 MET cc_start: 0.8821 (mmp) cc_final: 0.8395 (mmm) REVERT: L 413 MET cc_start: 0.6643 (mmp) cc_final: 0.5398 (tpp) outliers start: 1 outliers final: 0 residues processed: 38 average time/residue: 0.1841 time to fit residues: 8.7761 Evaluate side-chains 29 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.425 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 : 0.002 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 ------------------------------------------------------------------------------- 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: 8.9990 chunk 68 optimal weight: 20.0000 chunk 347 optimal weight: 8.9990 chunk 445 optimal weight: 2.9990 chunk 344 optimal weight: 20.0000 chunk 513 optimal weight: 3.9990 chunk 340 optimal weight: 0.7980 chunk 607 optimal weight: 1.9990 chunk 380 optimal weight: 6.9990 chunk 370 optimal weight: 0.0010 chunk 280 optimal weight: 8.9990 overall best weight: 1.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 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 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 239 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 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.3102 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= 0.191 Angle : 0.651 11.067 72420 Z= 0.320 Chirality : 0.044 0.239 7902 Planarity : 0.006 0.056 9312 Dihedral : 6.033 38.822 8448 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % 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: -0.69 (0.10), residues: 6276 helix: 0.84 (0.13), residues: 1650 sheet: -0.41 (0.14), residues: 1074 loop : -1.12 (0.10), residues: 3552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP G 87 HIS 0.023 0.002 HIS C 211 PHE 0.026 0.002 PHE K 49 TYR 0.038 0.003 TYR K 175 ARG 0.014 0.001 ARG G 207 *********************** 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 27 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 73 MET cc_start: 0.8602 (mtm) cc_final: 0.8255 (ptp) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.1830 time to fit residues: 7.0481 Evaluate side-chains 23 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.597 Evaluate side-chains 35 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 67 ASP cc_start: 0.8396 (m-30) cc_final: 0.8176 (m-30) REVERT: L 87 ASP cc_start: 0.7945 (t0) cc_final: 0.7381 (t0) REVERT: L 371 MET cc_start: 0.8822 (mmp) cc_final: 0.8400 (mmm) REVERT: L 413 MET cc_start: 0.6594 (mmp) cc_final: 0.6297 (tpp) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.2110 time to fit residues: 9.2589 Evaluate side-chains 27 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.464 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 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 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 ------------------------------------------------------------------------------- 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: 0.0670 chunk 242 optimal weight: 10.0000 chunk 362 optimal weight: 30.0000 chunk 182 optimal weight: 40.0000 chunk 119 optimal weight: 0.4980 chunk 117 optimal weight: 7.9990 chunk 386 optimal weight: 0.0170 chunk 413 optimal weight: 20.0000 chunk 300 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 477 optimal weight: 9.9990 overall best weight: 1.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 188 ASN I 214 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** 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: 0.7516 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 53184 Z= 0.173 Angle : 0.627 9.464 72420 Z= 0.310 Chirality : 0.043 0.228 7902 Planarity : 0.005 0.052 9312 Dihedral : 5.832 34.972 8448 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % 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: -0.70 (0.10), residues: 6276 helix: 0.85 (0.13), residues: 1650 sheet: -0.42 (0.14), residues: 1110 loop : -1.13 (0.10), residues: 3516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP G 87 HIS 0.022 0.002 HIS G 211 PHE 0.027 0.002 PHE E 49 TYR 0.037 0.002 TYR K 175 ARG 0.015 0.001 ARG C 207 *********************** 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 28 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 73 MET cc_start: 0.8582 (mtm) cc_final: 0.8306 (mtt) REVERT: I 308 MET cc_start: 0.7837 (tpt) cc_final: 0.7522 (tpp) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.1807 time to fit residues: 7.2090 Evaluate side-chains 22 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.595 Evaluate side-chains 34 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 87 ASP cc_start: 0.7912 (t0) cc_final: 0.7396 (t0) REVERT: L 371 MET cc_start: 0.8822 (mmp) cc_final: 0.8412 (mmm) REVERT: L 413 MET cc_start: 0.6640 (mmp) cc_final: 0.6297 (tpp) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.2021 time to fit residues: 8.5225 Evaluate side-chains 27 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.389 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: 0.0020 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 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 ------------------------------------------------------------------------------- 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: 2.9990 chunk 581 optimal weight: 1.9990 chunk 530 optimal weight: 8.9990 chunk 565 optimal weight: 7.9990 chunk 340 optimal weight: 0.9990 chunk 246 optimal weight: 9.9990 chunk 444 optimal weight: 4.9990 chunk 173 optimal weight: 0.0670 chunk 511 optimal weight: 6.9990 chunk 535 optimal weight: 5.9990 chunk 563 optimal weight: 0.9980 overall best weight: 1.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 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 113 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: 0.7515 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 53184 Z= 0.183 Angle : 0.627 9.464 72420 Z= 0.310 Chirality : 0.043 0.228 7902 Planarity : 0.006 0.094 9312 Dihedral : 5.832 34.972 8448 Min Nonbonded Distance : 1.619 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % 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: -0.70 (0.10), residues: 6276 helix: 0.85 (0.13), residues: 1650 sheet: -0.42 (0.14), residues: 1110 loop : -1.13 (0.10), residues: 3516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 87 HIS 0.022 0.002 HIS K 211 PHE 0.027 0.002 PHE K 49 TYR 0.037 0.002 TYR E 175 ARG 0.015 0.001 ARG A 207 *********************** 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 27 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 308 MET cc_start: 0.7835 (tpt) cc_final: 0.7589 (tpp) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.1892 time to fit residues: 7.2136 Evaluate side-chains 21 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.568 Evaluate side-chains 32 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.469 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: L 87 ASP cc_start: 0.7936 (t0) cc_final: 0.7397 (t0) REVERT: L 371 MET cc_start: 0.8813 (mmp) cc_final: 0.8406 (mmm) REVERT: L 413 MET cc_start: 0.6640 (mmp) cc_final: 0.6291 (tpp) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.2306 time to fit residues: 9.1052 Evaluate side-chains 27 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.460 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 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 ------------------------------------------------------------------------------- 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: 0.0040 chunk 598 optimal weight: 6.9990 chunk 365 optimal weight: 5.9990 chunk 283 optimal weight: 2.9990 chunk 415 optimal weight: 0.1980 chunk 627 optimal weight: 50.0000 chunk 577 optimal weight: 2.9990 chunk 499 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 386 optimal weight: 3.9990 chunk 306 optimal weight: 4.9990 overall best weight: 1.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 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 113 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: 0.7520 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 53184 Z= 0.189 Angle : 0.675 18.842 72420 Z= 0.325 Chirality : 0.047 0.648 7902 Planarity : 0.006 0.056 9312 Dihedral : 5.659 32.169 8448 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % 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: -0.72 (0.10), residues: 6276 helix: 0.81 (0.13), residues: 1650 sheet: -0.50 (0.14), residues: 1122 loop : -1.11 (0.10), residues: 3504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP L 60 HIS 0.022 0.002 HIS A 211 PHE 0.028 0.002 PHE G 49 TYR 0.037 0.003 TYR E 175 ARG 0.014 0.001 ARG C 207 ********************** 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 27 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.1700 time to fit residues: 6.4945 Evaluate side-chains 22 residues out of total 524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.577 Evaluate side-chains 32 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 87 ASP cc_start: 0.7838 (t0) cc_final: 0.7338 (t0) REVERT: L 371 MET cc_start: 0.8811 (mmp) cc_final: 0.8395 (mmm) REVERT: L 413 MET cc_start: 0.6766 (mmp) cc_final: 0.6313 (tpp) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.2005 time to fit residues: 7.9969 Evaluate side-chains 26 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.389 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: 0.0021 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 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 ------------------------------------------------------------------------------- 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: 0.2980 chunk 532 optimal weight: 8.9990 chunk 153 optimal weight: 8.9990 chunk 460 optimal weight: 9.9990 chunk 73 optimal weight: 4.9990 chunk 138 optimal weight: 6.9990 chunk 500 optimal weight: 8.9990 chunk 209 optimal weight: 10.0000 chunk 514 optimal weight: 0.2980 chunk 63 optimal weight: 20.0000 chunk 92 optimal weight: 0.0670 overall best weight: 2.5322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 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 113 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 = 0.2607 r_free = 0.2607 target = 0.023916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2354 r_free = 0.2354 target = 0.018073 restraints weight = 71082.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2381 r_free = 0.2381 target = 0.018794 restraints weight = 46245.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2404 r_free = 0.2404 target = 0.019336 restraints weight = 34134.867| |-----------------------------------------------------------------------------| r_work (final): 0.2433 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.032311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.023924 restraints weight = 49201.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.024654 restraints weight = 35683.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.025206 restraints weight = 28181.456| |-----------------------------------------------------------------------------| r_work (final): 0.2609 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2197 r_free = 0.2197 target = 0.039321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2205 r_free = 0.2205 target = 0.036596 restraints weight = 196.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2210 r_free = 0.2210 target = 0.037705 restraints weight = 76.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2219 r_free = 0.2219 target = 0.038222 restraints weight = 34.170| |-----------------------------------------------------------------------------| r_work (final): 0.2188 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.044330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.042581 restraints weight = 482.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.043120 restraints weight = 184.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.043443 restraints weight = 112.587| |-----------------------------------------------------------------------------| r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 53184 Z= 0.189 Angle : 0.675 18.842 72420 Z= 0.325 Chirality : 0.047 0.648 7902 Planarity : 0.006 0.056 9312 Dihedral : 5.659 32.169 8448 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 18.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % 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: -0.72 (0.10), residues: 6276 helix: 0.81 (0.13), residues: 1650 sheet: -0.50 (0.14), residues: 1122 loop : -1.11 (0.10), residues: 3504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP F 60 HIS 0.022 0.002 HIS K 211 PHE 0.028 0.002 PHE A 49 TYR 0.037 0.003 TYR K 175 ARG 0.014 0.001 ARG C 207 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6661.42 seconds wall clock time: 126 minutes 7.72 seconds (7567.72 seconds total)