Starting phenix.real_space_refine on Sat Jul 4 12:15:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cyi_46045/07_2026/9cyi_46045.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cyi_46045/07_2026/9cyi_46045.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cyi_46045/07_2026/9cyi_46045.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cyi_46045/07_2026/9cyi_46045.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cyi_46045/07_2026/9cyi_46045.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cyi_46045/07_2026/9cyi_46045.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 108 5.16 5 C 12612 2.51 5 N 3436 2.21 5 O 4072 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20232 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 2999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 2999 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 13, 'TRANS': 374} Chain: "H" Number of atoms: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1019 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain: "L" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 833 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "B" Number of atoms: 2999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 2999 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 13, 'TRANS': 374} Chain: "E" Number of atoms: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1019 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain: "I" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 833 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "C" Number of atoms: 2999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 2999 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 13, 'TRANS': 374} Chain: "F" Number of atoms: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1019 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain: "J" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 833 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "D" Number of atoms: 2999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 2999 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 13, 'TRANS': 374} Chain: "G" Number of atoms: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1019 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain: "K" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 833 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "O" Number of atoms: 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: "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: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "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: 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: "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: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 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: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 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: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.65, per 1000 atoms: 0.23 Number of scatterers: 20232 At special positions: 0 Unit cell: (151.525, 151.525, 86.275, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 108 16.00 O 4072 8.00 N 3436 7.00 C 12612 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 417 " distance=2.04 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 129 " distance=2.04 Simple disulfide: pdb=" SG CYS A 175 " - pdb=" SG CYS A 193 " distance=2.03 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 289 " distance=2.03 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 337 " distance=2.03 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 447 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 417 " distance=2.04 Simple disulfide: pdb=" SG CYS B 124 " - pdb=" SG CYS B 129 " distance=2.04 Simple disulfide: pdb=" SG CYS B 175 " - pdb=" SG CYS B 193 " distance=2.03 Simple disulfide: pdb=" SG CYS B 183 " - pdb=" SG CYS B 230 " distance=2.03 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 289 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 337 " distance=2.03 Simple disulfide: pdb=" SG CYS B 421 " - pdb=" SG CYS B 447 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 417 " distance=2.04 Simple disulfide: pdb=" SG CYS C 124 " - pdb=" SG CYS C 129 " distance=2.04 Simple disulfide: pdb=" SG CYS C 175 " - pdb=" SG CYS C 193 " distance=2.03 Simple disulfide: pdb=" SG CYS C 183 " - pdb=" SG CYS C 230 " distance=2.03 Simple disulfide: pdb=" SG CYS C 232 " - pdb=" SG CYS C 237 " distance=2.03 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 291 " distance=2.03 Simple disulfide: pdb=" SG CYS C 280 " - pdb=" SG CYS C 289 " distance=2.03 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 337 " distance=2.03 Simple disulfide: pdb=" SG CYS C 421 " - pdb=" SG CYS C 447 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.04 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 92 " - pdb=" SG CYS D 417 " distance=2.04 Simple disulfide: pdb=" SG CYS D 124 " - pdb=" SG CYS D 129 " distance=2.04 Simple disulfide: pdb=" SG CYS D 175 " - pdb=" SG CYS D 193 " distance=2.03 Simple disulfide: pdb=" SG CYS D 183 " - pdb=" SG CYS D 230 " distance=2.03 Simple disulfide: pdb=" SG CYS D 232 " - pdb=" SG CYS D 237 " distance=2.03 Simple disulfide: pdb=" SG CYS D 278 " - pdb=" SG CYS D 291 " distance=2.03 Simple disulfide: pdb=" SG CYS D 280 " - pdb=" SG CYS D 289 " distance=2.03 Simple disulfide: pdb=" SG CYS D 318 " - pdb=" SG CYS D 337 " distance=2.03 Simple disulfide: pdb=" SG CYS D 421 " - pdb=" SG CYS D 447 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN N 4 " - " MAN N 5 " " MAN R 4 " - " MAN R 5 " " MAN V 4 " - " MAN V 5 " " MAN Z 4 " - " MAN Z 5 " ALPHA1-3 " BMA N 3 " - " MAN N 4 " " MAN N 6 " - " MAN N 7 " " BMA R 3 " - " MAN R 4 " " MAN R 6 " - " MAN R 7 " " BMA V 3 " - " MAN V 4 " " MAN V 6 " - " MAN V 7 " " BMA Z 3 " - " MAN Z 4 " " MAN Z 6 " - " MAN Z 7 " ALPHA1-6 " BMA N 3 " - " MAN N 6 " " MAN N 6 " - " MAN N 8 " " BMA R 3 " - " MAN R 6 " " MAN R 6 " - " MAN R 8 " " BMA V 3 " - " MAN V 6 " " MAN V 6 " - " MAN V 8 " " BMA Z 3 " - " MAN Z 6 " " MAN Z 6 " - " MAN Z 8 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " NAG-ASN " NAG A 502 " - " ASN A 234 " " NAG A 503 " - " ASN A 86 " " NAG B 502 " - " ASN B 234 " " NAG B 503 " - " ASN B 86 " " NAG C 502 " - " ASN C 234 " " NAG C 503 " - " ASN C 86 " " NAG D 502 " - " ASN D 234 " " NAG D 503 " - " ASN D 86 " " NAG M 1 " - " ASN A 146 " " NAG N 1 " - " ASN A 200 " " NAG O 1 " - " ASN A 367 " " NAG P 1 " - " ASN A 245 " " NAG Q 1 " - " ASN B 146 " " NAG R 1 " - " ASN B 200 " " NAG S 1 " - " ASN B 367 " " NAG T 1 " - " ASN B 245 " " NAG U 1 " - " ASN C 146 " " NAG V 1 " - " ASN C 200 " " NAG W 1 " - " ASN C 367 " " NAG X 1 " - " ASN C 245 " " NAG Y 1 " - " ASN D 146 " " NAG Z 1 " - " ASN D 200 " " NAG a 1 " - " ASN D 367 " " NAG b 1 " - " ASN D 245 " Time building additional restraints: 2.00 Conformation dependent library (CDL) restraints added in 827.9 milliseconds 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4512 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 44 sheets defined 1.9% alpha, 37.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 104 through 110 removed outlier: 3.689A pdb=" N ALA A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 44 removed outlier: 3.536A pdb=" N GLY H 44 " --> pdb=" O PRO H 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 110 removed outlier: 3.689A pdb=" N ALA B 110 " --> pdb=" O ILE B 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 44 removed outlier: 3.534A pdb=" N GLY E 44 " --> pdb=" O PRO E 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 110 removed outlier: 3.690A pdb=" N ALA C 110 " --> pdb=" O ILE C 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 44 removed outlier: 3.535A pdb=" N GLY F 44 " --> pdb=" O PRO F 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 110 removed outlier: 3.691A pdb=" N ALA D 110 " --> pdb=" O ILE D 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 44 removed outlier: 3.535A pdb=" N GLY G 44 " --> pdb=" O PRO G 41 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 102 removed outlier: 6.772A pdb=" N VAL A 445 " --> pdb=" O PHE A 100 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N LYS A 102 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ILE A 443 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY A 448 " --> pdb=" O ARG A 420 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ARG A 420 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 124 removed outlier: 4.640A pdb=" N TRP A 115 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N THR A 138 " --> pdb=" O TRP A 115 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N THR A 117 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N GLN A 136 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N GLU A 119 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU A 134 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR A 157 " --> pdb=" O GLY A 135 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LEU A 158 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS A 172 " --> pdb=" O MET A 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 179 through 184 removed outlier: 3.676A pdb=" N SER A 179 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP A 213 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N TYR A 207 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N LEU A 211 " --> pdb=" O TYR A 207 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 231 through 233 removed outlier: 3.717A pdb=" N VAL A 231 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N HIS A 264 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N GLU A 258 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ILE A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 280 through 281 Processing sheet with id=AA6, first strand: chain 'A' and resid 353 through 355 removed outlier: 3.547A pdb=" N VAL A 360 " --> pdb=" O VAL A 379 " (cutoff:3.500A) removed outlier: 8.766A pdb=" N LEU A 372 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N VAL A 398 " --> pdb=" O LEU A 372 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N TYR A 374 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N VAL A 396 " --> pdb=" O TYR A 374 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N THR A 376 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ARG A 394 " --> pdb=" O THR A 376 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 11 through 12 removed outlier: 7.276A pdb=" N MET H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N GLY H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.382A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP H 101 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 17 through 19 removed outlier: 3.629A pdb=" N SER H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP H 72 " --> pdb=" O SER H 77 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.584A pdb=" N ILE L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE L 75 " --> pdb=" O ILE L 19 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.580A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR L 102 " --> pdb=" O TYR L 86 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 96 through 102 removed outlier: 6.772A pdb=" N VAL B 445 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N LYS B 102 " --> pdb=" O ILE B 443 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ILE B 443 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY B 448 " --> pdb=" O ARG B 420 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ARG B 420 " --> pdb=" O GLY B 448 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 115 through 124 removed outlier: 4.640A pdb=" N TRP B 115 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N THR B 138 " --> pdb=" O TRP B 115 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N THR B 117 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N GLN B 136 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N GLU B 119 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU B 134 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR B 157 " --> pdb=" O GLY B 135 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LEU B 158 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS B 172 " --> pdb=" O MET B 160 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 179 through 184 removed outlier: 3.665A pdb=" N SER B 179 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP B 213 " --> pdb=" O PHE B 205 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N TYR B 207 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N LEU B 211 " --> pdb=" O TYR B 207 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 231 through 233 removed outlier: 3.718A pdb=" N VAL B 231 " --> pdb=" O THR B 238 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS B 264 " --> pdb=" O PHE B 256 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N GLU B 258 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ILE B 262 " --> pdb=" O GLU B 258 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 280 through 281 Processing sheet with id=AB8, first strand: chain 'B' and resid 353 through 355 removed outlier: 3.547A pdb=" N VAL B 360 " --> pdb=" O VAL B 379 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N LEU B 372 " --> pdb=" O VAL B 398 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N VAL B 398 " --> pdb=" O LEU B 372 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N TYR B 374 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N VAL B 396 " --> pdb=" O TYR B 374 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N THR B 376 " --> pdb=" O ARG B 394 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ARG B 394 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 11 through 12 removed outlier: 7.280A pdb=" N MET E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N GLY E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.382A pdb=" N CYS E 92 " --> pdb=" O TRP E 103 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N TRP E 103 " --> pdb=" O CYS E 92 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ARG E 94 " --> pdb=" O ASP E 101 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP E 101 " --> pdb=" O ARG E 94 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 17 through 19 removed outlier: 3.630A pdb=" N SER E 77 " --> pdb=" O ASP E 72 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP E 72 " --> pdb=" O SER E 77 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.583A pdb=" N ILE I 19 " --> pdb=" O ILE I 75 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE I 75 " --> pdb=" O ILE I 19 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 53 through 54 removed outlier: 6.581A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR I 102 " --> pdb=" O TYR I 86 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 96 through 102 removed outlier: 6.771A pdb=" N VAL C 445 " --> pdb=" O PHE C 100 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N LYS C 102 " --> pdb=" O ILE C 443 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ILE C 443 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY C 448 " --> pdb=" O ARG C 420 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ARG C 420 " --> pdb=" O GLY C 448 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 115 through 124 removed outlier: 4.640A pdb=" N TRP C 115 " --> pdb=" O THR C 138 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N THR C 138 " --> pdb=" O TRP C 115 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N THR C 117 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N GLN C 136 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N GLU C 119 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU C 134 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR C 157 " --> pdb=" O GLY C 135 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LEU C 158 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS C 172 " --> pdb=" O MET C 160 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 179 through 184 removed outlier: 3.681A pdb=" N SER C 179 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP C 213 " --> pdb=" O PHE C 205 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N TYR C 207 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N LEU C 211 " --> pdb=" O TYR C 207 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 231 through 233 removed outlier: 3.718A pdb=" N VAL C 231 " --> pdb=" O THR C 238 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS C 264 " --> pdb=" O PHE C 256 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N GLU C 258 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ILE C 262 " --> pdb=" O GLU C 258 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 280 through 281 Processing sheet with id=AD1, first strand: chain 'C' and resid 353 through 355 removed outlier: 3.546A pdb=" N VAL C 360 " --> pdb=" O VAL C 379 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N LEU C 372 " --> pdb=" O VAL C 398 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N VAL C 398 " --> pdb=" O LEU C 372 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N TYR C 374 " --> pdb=" O VAL C 396 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N VAL C 396 " --> pdb=" O TYR C 374 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N THR C 376 " --> pdb=" O ARG C 394 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ARG C 394 " --> pdb=" O THR C 376 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 11 through 12 removed outlier: 7.277A pdb=" N MET F 34 " --> pdb=" O GLY F 50 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N GLY F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 11 through 12 removed outlier: 6.382A pdb=" N CYS F 92 " --> pdb=" O TRP F 103 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N TRP F 103 " --> pdb=" O CYS F 92 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ARG F 94 " --> pdb=" O ASP F 101 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP F 101 " --> pdb=" O ARG F 94 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 17 through 19 removed outlier: 3.631A pdb=" N SER F 77 " --> pdb=" O ASP F 72 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP F 72 " --> pdb=" O SER F 77 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 4 through 7 removed outlier: 3.583A pdb=" N ILE J 19 " --> pdb=" O ILE J 75 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE J 75 " --> pdb=" O ILE J 19 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 53 through 54 removed outlier: 6.581A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR J 102 " --> pdb=" O TYR J 86 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 96 through 102 removed outlier: 6.770A pdb=" N VAL D 445 " --> pdb=" O PHE D 100 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N LYS D 102 " --> pdb=" O ILE D 443 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ILE D 443 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY D 448 " --> pdb=" O ARG D 420 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ARG D 420 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 115 through 124 removed outlier: 4.640A pdb=" N TRP D 115 " --> pdb=" O THR D 138 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N THR D 138 " --> pdb=" O TRP D 115 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N THR D 117 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N GLN D 136 " --> pdb=" O THR D 117 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N GLU D 119 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU D 134 " --> pdb=" O GLU D 119 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR D 157 " --> pdb=" O GLY D 135 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU D 158 " --> pdb=" O VAL D 174 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS D 172 " --> pdb=" O MET D 160 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 179 through 184 removed outlier: 3.680A pdb=" N SER D 179 " --> pdb=" O ILE D 194 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP D 213 " --> pdb=" O PHE D 205 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N TYR D 207 " --> pdb=" O LEU D 211 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N LEU D 211 " --> pdb=" O TYR D 207 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 231 through 233 removed outlier: 3.717A pdb=" N VAL D 231 " --> pdb=" O THR D 238 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N HIS D 264 " --> pdb=" O PHE D 256 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLU D 258 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ILE D 262 " --> pdb=" O GLU D 258 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 280 through 281 Processing sheet with id=AE3, first strand: chain 'D' and resid 353 through 355 removed outlier: 3.546A pdb=" N VAL D 360 " --> pdb=" O VAL D 379 " (cutoff:3.500A) removed outlier: 8.766A pdb=" N LEU D 372 " --> pdb=" O VAL D 398 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N VAL D 398 " --> pdb=" O LEU D 372 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N TYR D 374 " --> pdb=" O VAL D 396 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N VAL D 396 " --> pdb=" O TYR D 374 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N THR D 376 " --> pdb=" O ARG D 394 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ARG D 394 " --> pdb=" O THR D 376 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 11 through 12 removed outlier: 7.278A pdb=" N MET G 34 " --> pdb=" O GLY G 50 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N GLY G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.382A pdb=" N CYS G 92 " --> pdb=" O TRP G 103 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N TRP G 103 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARG G 94 " --> pdb=" O ASP G 101 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP G 101 " --> pdb=" O ARG G 94 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 17 through 19 removed outlier: 3.626A pdb=" N SER G 77 " --> pdb=" O ASP G 72 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP G 72 " --> pdb=" O SER G 77 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.584A pdb=" N ILE K 19 " --> pdb=" O ILE K 75 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE K 75 " --> pdb=" O ILE K 19 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 53 through 54 removed outlier: 6.581A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR K 102 " --> pdb=" O TYR K 86 " (cutoff:3.500A) 516 hydrogen bonds defined for protein. 1380 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: 4.33 Time building geometry restraints manager: 2.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6407 1.34 - 1.46: 5349 1.46 - 1.58: 8808 1.58 - 1.70: 4 1.70 - 1.82: 128 Bond restraints: 20696 Sorted by residual: bond pdb=" C1 MAN N 8 " pdb=" O5 MAN N 8 " ideal model delta sigma weight residual 1.399 1.501 -0.102 2.00e-02 2.50e+03 2.62e+01 bond pdb=" C1 MAN R 8 " pdb=" O5 MAN R 8 " ideal model delta sigma weight residual 1.399 1.501 -0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" C1 MAN V 8 " pdb=" O5 MAN V 8 " ideal model delta sigma weight residual 1.399 1.501 -0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" C1 MAN Z 8 " pdb=" O5 MAN Z 8 " ideal model delta sigma weight residual 1.399 1.501 -0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" C1 MAN N 8 " pdb=" C2 MAN N 8 " ideal model delta sigma weight residual 1.526 1.615 -0.089 2.00e-02 2.50e+03 1.98e+01 ... (remaining 20691 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 25961 1.67 - 3.35: 1737 3.35 - 5.02: 302 5.02 - 6.69: 64 6.69 - 8.37: 24 Bond angle restraints: 28088 Sorted by residual: angle pdb=" N VAL E 40 " pdb=" CA VAL E 40 " pdb=" C VAL E 40 " ideal model delta sigma weight residual 112.61 117.41 -4.80 1.45e+00 4.76e-01 1.10e+01 angle pdb=" N VAL H 40 " pdb=" CA VAL H 40 " pdb=" C VAL H 40 " ideal model delta sigma weight residual 112.61 117.40 -4.79 1.45e+00 4.76e-01 1.09e+01 angle pdb=" N VAL F 40 " pdb=" CA VAL F 40 " pdb=" C VAL F 40 " ideal model delta sigma weight residual 112.61 117.40 -4.79 1.45e+00 4.76e-01 1.09e+01 angle pdb=" N VAL G 40 " pdb=" CA VAL G 40 " pdb=" C VAL G 40 " ideal model delta sigma weight residual 112.61 117.40 -4.79 1.45e+00 4.76e-01 1.09e+01 angle pdb=" N GLN F 39 " pdb=" CA GLN F 39 " pdb=" C GLN F 39 " ideal model delta sigma weight residual 110.80 117.76 -6.96 2.13e+00 2.20e-01 1.07e+01 ... (remaining 28083 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.88: 11974 24.88 - 49.75: 873 49.75 - 74.63: 141 74.63 - 99.51: 48 99.51 - 124.39: 16 Dihedral angle restraints: 13052 sinusoidal: 5948 harmonic: 7104 Sorted by residual: dihedral pdb=" CD ARG L 24 " pdb=" NE ARG L 24 " pdb=" CZ ARG L 24 " pdb=" NH1 ARG L 24 " ideal model delta sinusoidal sigma weight residual 0.00 -86.59 86.59 1 1.00e+01 1.00e-02 9.03e+01 dihedral pdb=" CD ARG I 24 " pdb=" NE ARG I 24 " pdb=" CZ ARG I 24 " pdb=" NH1 ARG I 24 " ideal model delta sinusoidal sigma weight residual 0.00 -86.59 86.59 1 1.00e+01 1.00e-02 9.03e+01 dihedral pdb=" CD ARG K 24 " pdb=" NE ARG K 24 " pdb=" CZ ARG K 24 " pdb=" NH1 ARG K 24 " ideal model delta sinusoidal sigma weight residual 0.00 -86.54 86.54 1 1.00e+01 1.00e-02 9.02e+01 ... (remaining 13049 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 2745 0.081 - 0.161: 441 0.161 - 0.242: 34 0.242 - 0.322: 4 0.322 - 0.403: 4 Chirality restraints: 3228 Sorted by residual: chirality pdb=" CB VAL G 48 " pdb=" CA VAL G 48 " pdb=" CG1 VAL G 48 " pdb=" CG2 VAL G 48 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 4.05e+00 chirality pdb=" CB VAL H 48 " pdb=" CA VAL H 48 " pdb=" CG1 VAL H 48 " pdb=" CG2 VAL H 48 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 4.04e+00 chirality pdb=" CB VAL E 48 " pdb=" CA VAL E 48 " pdb=" CG1 VAL E 48 " pdb=" CG2 VAL E 48 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 4.01e+00 ... (remaining 3225 not shown) Planarity restraints: 3548 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG J 24 " 0.992 9.50e-02 1.11e+02 4.45e-01 1.24e+02 pdb=" NE ARG J 24 " -0.073 2.00e-02 2.50e+03 pdb=" CZ ARG J 24 " 0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG J 24 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG J 24 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG K 24 " 0.992 9.50e-02 1.11e+02 4.45e-01 1.24e+02 pdb=" NE ARG K 24 " -0.073 2.00e-02 2.50e+03 pdb=" CZ ARG K 24 " 0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG K 24 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG K 24 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG L 24 " -0.992 9.50e-02 1.11e+02 4.45e-01 1.24e+02 pdb=" NE ARG L 24 " 0.073 2.00e-02 2.50e+03 pdb=" CZ ARG L 24 " -0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG L 24 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG L 24 " -0.005 2.00e-02 2.50e+03 ... (remaining 3545 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 6559 2.84 - 3.35: 17807 3.35 - 3.87: 34901 3.87 - 4.38: 41828 4.38 - 4.90: 72620 Nonbonded interactions: 173715 Sorted by model distance: nonbonded pdb=" O HIS D 347 " pdb="CA CA D 501 " model vdw 2.321 3.250 nonbonded pdb=" O HIS C 347 " pdb="CA CA C 501 " model vdw 2.321 3.250 nonbonded pdb=" O HIS B 347 " pdb="CA CA B 501 " model vdw 2.321 3.250 nonbonded pdb=" O HIS A 347 " pdb="CA CA A 501 " model vdw 2.321 3.250 nonbonded pdb=" O5 MAN Z 6 " pdb=" O6 MAN Z 6 " model vdw 2.352 2.432 ... (remaining 173710 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'a' selection = chain 'b' } ncs_group { reference = chain 'N' selection = chain 'R' selection = chain 'V' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.960 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: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 20.140 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 20804 Z= 0.280 Angle : 1.011 18.318 28368 Z= 0.488 Chirality : 0.058 0.403 3228 Planarity : 0.024 0.445 3524 Dihedral : 17.534 124.386 8408 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.56 % Allowed : 20.29 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.79 (0.15), residues: 2480 helix: -2.28 (0.74), residues: 24 sheet: -1.88 (0.16), residues: 840 loop : -1.88 (0.14), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.053 0.003 ARG F 38 TYR 0.042 0.002 TYR E 90 PHE 0.046 0.003 PHE G 29 TRP 0.016 0.001 TRP H 52A HIS 0.005 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00628 / 0.28 (20696) covalent geometry : angle 0.94562 / 0.47 (28088) SS BOND : bond 0.00311 / 0.18 ( 44) SS BOND : angle 1.18475 / 0.82 ( 88) hydrogen bonds : bond 0.24742 / 16.90 ( 496) hydrogen bonds : angle 11.27358 / 8.09 ( 1380) link_ALPHA1-2 : bond 0.01387 / 0.70 ( 4) link_ALPHA1-2 : angle 4.12158 / 2.11 ( 12) link_ALPHA1-3 : bond 0.00322 / 0.21 ( 8) link_ALPHA1-3 : angle 2.44842 / 1.46 ( 24) link_ALPHA1-6 : bond 0.03024 / 1.80 ( 8) link_ALPHA1-6 : angle 6.79728 / 4.19 ( 24) link_BETA1-4 : bond 0.00824 / 0.54 ( 20) link_BETA1-4 : angle 5.33533 / 3.13 ( 60) link_NAG-ASN : bond 0.00162 / 0.10 ( 24) link_NAG-ASN : angle 2.81168 / 1.79 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 302 time to evaluate : 0.750 Fit side-chains REVERT: A 119 GLU cc_start: 0.8466 (mp0) cc_final: 0.8249 (mp0) REVERT: B 119 GLU cc_start: 0.8468 (mp0) cc_final: 0.8248 (mp0) REVERT: C 119 GLU cc_start: 0.8465 (mp0) cc_final: 0.8246 (mp0) REVERT: D 119 GLU cc_start: 0.8461 (mp0) cc_final: 0.8245 (mp0) outliers start: 12 outliers final: 12 residues processed: 314 average time/residue: 0.1526 time to fit residues: 74.7213 Evaluate side-chains 276 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 264 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 GLN Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain B residue 273 GLN Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain C residue 273 GLN Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain D residue 273 GLN Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 279 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 0.7980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 235 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 ASN A 273 GLN A 274 HIS A 336 HIS H 73 ASN L 45 ASN B 147 ASN B 273 GLN B 274 HIS B 336 HIS I 45 ASN C 147 ASN C 273 GLN C 274 HIS C 336 HIS F 73 ASN J 45 ASN D 147 ASN D 273 GLN D 274 HIS D 336 HIS G 73 ASN K 45 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.148969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.105835 restraints weight = 25509.261| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.57 r_work: 0.3100 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20804 Z= 0.186 Angle : 0.759 10.660 28368 Z= 0.369 Chirality : 0.050 0.197 3228 Planarity : 0.005 0.055 3524 Dihedral : 11.627 93.401 4044 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.71 % Allowed : 20.06 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.15), residues: 2480 helix: -1.24 (0.92), residues: 24 sheet: -1.41 (0.17), residues: 904 loop : -1.69 (0.14), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 24 TYR 0.014 0.002 TYR K 87 PHE 0.013 0.002 PHE H 29 TRP 0.014 0.001 TRP C 178 HIS 0.003 0.001 HIS D 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 (20696) covalent geometry : angle 0.71560 / 0.36 (28088) SS BOND : bond 0.00733 / 0.30 ( 44) SS BOND : angle 1.63186 / 1.11 ( 88) hydrogen bonds : bond 0.04675 / 3.16 ( 496) hydrogen bonds : angle 7.83175 / 5.61 ( 1380) link_ALPHA1-2 : bond 0.01301 / 0.65 ( 4) link_ALPHA1-2 : angle 4.16898 / 2.20 ( 12) link_ALPHA1-3 : bond 0.00962 / 0.61 ( 8) link_ALPHA1-3 : angle 1.89682 / 1.15 ( 24) link_ALPHA1-6 : bond 0.01383 / 0.79 ( 8) link_ALPHA1-6 : angle 3.39056 / 2.06 ( 24) link_BETA1-4 : bond 0.00792 / 0.51 ( 20) link_BETA1-4 : angle 3.43451 / 2.08 ( 60) link_NAG-ASN : bond 0.00209 / 0.12 ( 24) link_NAG-ASN : angle 2.53612 / 1.64 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 303 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8577 (mt0) REVERT: H 19 ARG cc_start: 0.6533 (OUTLIER) cc_final: 0.6231 (tpt-90) REVERT: L 87 TYR cc_start: 0.7735 (m-80) cc_final: 0.7483 (m-80) REVERT: B 273 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8570 (mt0) REVERT: E 19 ARG cc_start: 0.6530 (OUTLIER) cc_final: 0.6226 (tpt-90) REVERT: E 102 LEU cc_start: 0.7348 (OUTLIER) cc_final: 0.6983 (mp) REVERT: I 87 TYR cc_start: 0.7739 (m-80) cc_final: 0.7492 (m-80) REVERT: C 273 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8572 (mt0) REVERT: F 19 ARG cc_start: 0.6519 (OUTLIER) cc_final: 0.6230 (tpt-90) REVERT: J 87 TYR cc_start: 0.7740 (m-80) cc_final: 0.7490 (m-80) REVERT: D 273 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8566 (mt0) REVERT: G 19 ARG cc_start: 0.6517 (OUTLIER) cc_final: 0.6226 (tpt-90) REVERT: G 102 LEU cc_start: 0.7340 (OUTLIER) cc_final: 0.6974 (mp) REVERT: K 87 TYR cc_start: 0.7722 (m-80) cc_final: 0.7475 (m-80) outliers start: 58 outliers final: 24 residues processed: 351 average time/residue: 0.1348 time to fit residues: 74.4245 Evaluate side-chains 310 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 276 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 273 GLN Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 273 GLN Chi-restraints excluded: chain E residue 19 ARG Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 273 GLN Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 273 GLN Chi-restraints excluded: chain G residue 19 ARG Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 22 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 84 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 227 optimal weight: 0.0980 chunk 176 optimal weight: 2.9990 chunk 137 optimal weight: 0.7980 chunk 194 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 217 optimal weight: 2.9990 chunk 39 optimal weight: 0.3980 chunk 199 optimal weight: 7.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 ASN A 391 GLN A 395 GLN A 465 ASN ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 45 ASN B 147 ASN B 391 GLN B 395 GLN B 465 ASN ** E 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 ASN I 45 ASN C 147 ASN C 391 GLN C 395 GLN C 465 ASN ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 45 ASN D 147 ASN D 391 GLN D 395 GLN D 465 ASN ** G 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 45 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.150510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.109855 restraints weight = 25011.033| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.04 r_work: 0.3182 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20804 Z= 0.159 Angle : 0.709 9.540 28368 Z= 0.345 Chirality : 0.047 0.186 3228 Planarity : 0.005 0.050 3524 Dihedral : 10.469 85.619 4036 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.99 % Allowed : 21.50 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.16), residues: 2480 helix: -0.66 (1.03), residues: 24 sheet: -1.23 (0.17), residues: 868 loop : -1.45 (0.14), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 18 TYR 0.015 0.002 TYR E 91 PHE 0.011 0.002 PHE C 354 TRP 0.013 0.001 TRP C 178 HIS 0.004 0.001 HIS D 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (20696) covalent geometry : angle 0.67197 / 0.34 (28088) SS BOND : bond 0.00568 / 0.24 ( 44) SS BOND : angle 1.55233 / 1.02 ( 88) hydrogen bonds : bond 0.03944 / 2.68 ( 496) hydrogen bonds : angle 7.09165 / 5.07 ( 1380) link_ALPHA1-2 : bond 0.01215 / 0.61 ( 4) link_ALPHA1-2 : angle 3.95436 / 2.13 ( 12) link_ALPHA1-3 : bond 0.01042 / 0.66 ( 8) link_ALPHA1-3 : angle 1.65725 / 1.00 ( 24) link_ALPHA1-6 : bond 0.00758 / 0.45 ( 8) link_ALPHA1-6 : angle 2.44212 / 1.49 ( 24) link_BETA1-4 : bond 0.00965 / 0.64 ( 20) link_BETA1-4 : angle 3.04846 / 1.87 ( 60) link_NAG-ASN : bond 0.00176 / 0.11 ( 24) link_NAG-ASN : angle 2.42896 / 1.55 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 288 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 TYR cc_start: 0.9343 (p90) cc_final: 0.8920 (p90) REVERT: A 273 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8554 (mt0) REVERT: H 95 THR cc_start: 0.7344 (m) cc_final: 0.6867 (p) REVERT: B 121 TYR cc_start: 0.9341 (p90) cc_final: 0.8927 (p90) REVERT: B 273 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8575 (mt0) REVERT: E 95 THR cc_start: 0.7313 (m) cc_final: 0.6827 (p) REVERT: E 102 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.7036 (mp) REVERT: C 121 TYR cc_start: 0.9341 (p90) cc_final: 0.8918 (p90) REVERT: C 273 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.8540 (mt0) REVERT: F 95 THR cc_start: 0.7324 (m) cc_final: 0.6845 (p) REVERT: D 121 TYR cc_start: 0.9339 (p90) cc_final: 0.8915 (p90) REVERT: D 273 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8570 (mt0) REVERT: G 95 THR cc_start: 0.7312 (m) cc_final: 0.6831 (p) REVERT: G 102 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.7043 (mp) outliers start: 64 outliers final: 38 residues processed: 328 average time/residue: 0.1380 time to fit residues: 71.9095 Evaluate side-chains 311 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 267 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 273 GLN Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 273 GLN Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain E residue 32 TYR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 273 GLN Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain F residue 32 TYR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 273 GLN Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 22 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 237 optimal weight: 2.9990 chunk 226 optimal weight: 8.9990 chunk 173 optimal weight: 9.9990 chunk 164 optimal weight: 0.6980 chunk 197 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 128 optimal weight: 5.9990 chunk 137 optimal weight: 0.7980 chunk 57 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 ASN A 168 HIS A 465 ASN L 45 ASN B 147 ASN B 168 HIS B 465 ASN I 45 ASN C 147 ASN C 168 HIS C 465 ASN J 45 ASN D 147 ASN D 168 HIS D 465 ASN K 45 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.147020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.105439 restraints weight = 25033.554| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.16 r_work: 0.3119 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 20804 Z= 0.257 Angle : 0.757 9.520 28368 Z= 0.370 Chirality : 0.050 0.197 3228 Planarity : 0.005 0.046 3524 Dihedral : 10.270 76.337 4036 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.40 % Allowed : 21.83 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.16), residues: 2480 helix: -0.63 (1.04), residues: 24 sheet: -1.18 (0.17), residues: 912 loop : -1.37 (0.15), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 18 TYR 0.023 0.002 TYR G 91 PHE 0.014 0.002 PHE C 354 TRP 0.017 0.002 TRP C 178 HIS 0.004 0.001 HIS B 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00603 / 0.26 (20696) covalent geometry : angle 0.72212 / 0.36 (28088) SS BOND : bond 0.00772 / 0.33 ( 44) SS BOND : angle 1.84848 / 1.23 ( 88) hydrogen bonds : bond 0.03951 / 2.67 ( 496) hydrogen bonds : angle 6.92508 / 4.95 ( 1380) link_ALPHA1-2 : bond 0.01085 / 0.54 ( 4) link_ALPHA1-2 : angle 3.71134 / 2.01 ( 12) link_ALPHA1-3 : bond 0.00748 / 0.48 ( 8) link_ALPHA1-3 : angle 2.13379 / 1.29 ( 24) link_ALPHA1-6 : bond 0.00185 / 0.10 ( 8) link_ALPHA1-6 : angle 1.82481 / 1.10 ( 24) link_BETA1-4 : bond 0.00818 / 0.54 ( 20) link_BETA1-4 : angle 2.86489 / 1.79 ( 60) link_NAG-ASN : bond 0.00309 / 0.16 ( 24) link_NAG-ASN : angle 2.50280 / 1.60 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 253 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 TYR cc_start: 0.9364 (p90) cc_final: 0.9082 (p90) REVERT: H 4 LEU cc_start: 0.8160 (mp) cc_final: 0.7380 (tp) REVERT: H 91 TYR cc_start: 0.6753 (m-80) cc_final: 0.6505 (m-80) REVERT: H 95 THR cc_start: 0.7566 (m) cc_final: 0.7189 (p) REVERT: L 46 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8728 (tp) REVERT: B 121 TYR cc_start: 0.9364 (p90) cc_final: 0.9079 (p90) REVERT: E 4 LEU cc_start: 0.8168 (mp) cc_final: 0.7700 (mt) REVERT: E 91 TYR cc_start: 0.6749 (m-80) cc_final: 0.6498 (m-80) REVERT: E 95 THR cc_start: 0.7555 (m) cc_final: 0.7169 (p) REVERT: E 102 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.7008 (mp) REVERT: I 46 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8725 (tp) REVERT: C 121 TYR cc_start: 0.9364 (p90) cc_final: 0.9081 (p90) REVERT: F 4 LEU cc_start: 0.8153 (mp) cc_final: 0.7716 (mt) REVERT: F 91 TYR cc_start: 0.6726 (m-80) cc_final: 0.6424 (m-80) REVERT: F 95 THR cc_start: 0.7544 (m) cc_final: 0.7166 (p) REVERT: J 46 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8722 (tp) REVERT: D 121 TYR cc_start: 0.9362 (p90) cc_final: 0.9081 (p90) REVERT: G 4 LEU cc_start: 0.8161 (mp) cc_final: 0.7359 (tp) REVERT: G 91 TYR cc_start: 0.6716 (m-80) cc_final: 0.6412 (m-80) REVERT: G 95 THR cc_start: 0.7556 (m) cc_final: 0.7175 (p) REVERT: G 102 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.6883 (mp) REVERT: K 46 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8724 (tp) outliers start: 73 outliers final: 50 residues processed: 314 average time/residue: 0.1378 time to fit residues: 68.8419 Evaluate side-chains 301 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 245 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain E residue 32 TYR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain F residue 32 TYR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 97 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 111 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 228 optimal weight: 10.0000 chunk 93 optimal weight: 0.8980 chunk 139 optimal weight: 0.7980 chunk 153 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 220 optimal weight: 2.9990 chunk 168 optimal weight: 8.9990 chunk 140 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 ASN A 465 ASN L 45 ASN B 147 ASN B 465 ASN I 45 ASN C 147 ASN C 465 ASN J 45 ASN D 147 ASN D 465 ASN K 45 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.149934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.108288 restraints weight = 24820.304| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.17 r_work: 0.3163 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 20804 Z= 0.151 Angle : 0.697 10.019 28368 Z= 0.338 Chirality : 0.047 0.205 3228 Planarity : 0.004 0.046 3524 Dihedral : 9.128 57.372 4024 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.12 % Allowed : 22.11 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.16), residues: 2480 helix: -0.49 (1.04), residues: 24 sheet: -1.18 (0.16), residues: 880 loop : -1.26 (0.15), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 18 TYR 0.019 0.002 TYR F 91 PHE 0.012 0.001 PHE C 354 TRP 0.015 0.001 TRP C 178 HIS 0.003 0.001 HIS J 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (20696) covalent geometry : angle 0.66195 / 0.33 (28088) SS BOND : bond 0.00751 / 0.30 ( 44) SS BOND : angle 1.81915 / 1.19 ( 88) hydrogen bonds : bond 0.03420 / 2.33 ( 496) hydrogen bonds : angle 6.59647 / 4.69 ( 1380) link_ALPHA1-2 : bond 0.01460 / 0.73 ( 4) link_ALPHA1-2 : angle 3.79785 / 2.03 ( 12) link_ALPHA1-3 : bond 0.00911 / 0.58 ( 8) link_ALPHA1-3 : angle 2.03950 / 1.23 ( 24) link_ALPHA1-6 : bond 0.00449 / 0.28 ( 8) link_ALPHA1-6 : angle 1.68152 / 1.02 ( 24) link_BETA1-4 : bond 0.00923 / 0.61 ( 20) link_BETA1-4 : angle 2.59007 / 1.64 ( 60) link_NAG-ASN : bond 0.00176 / 0.11 ( 24) link_NAG-ASN : angle 2.41904 / 1.53 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 264 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 21 SER cc_start: 0.7999 (m) cc_final: 0.7550 (t) REVERT: H 46 GLU cc_start: 0.6634 (mt-10) cc_final: 0.4996 (mm-30) REVERT: H 91 TYR cc_start: 0.6684 (m-80) cc_final: 0.6420 (m-80) REVERT: H 95 THR cc_start: 0.7528 (m) cc_final: 0.7248 (p) REVERT: H 102 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.6981 (mp) REVERT: L 46 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8672 (tp) REVERT: E 21 SER cc_start: 0.7995 (m) cc_final: 0.7542 (t) REVERT: E 46 GLU cc_start: 0.6567 (mt-10) cc_final: 0.4977 (mm-30) REVERT: E 91 TYR cc_start: 0.6674 (m-80) cc_final: 0.6398 (m-80) REVERT: E 95 THR cc_start: 0.7537 (m) cc_final: 0.7254 (p) REVERT: E 102 LEU cc_start: 0.7417 (OUTLIER) cc_final: 0.7000 (mp) REVERT: I 46 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8671 (tp) REVERT: F 46 GLU cc_start: 0.6566 (mt-10) cc_final: 0.4978 (mm-30) REVERT: F 91 TYR cc_start: 0.6710 (m-80) cc_final: 0.6359 (m-80) REVERT: F 95 THR cc_start: 0.7518 (m) cc_final: 0.7234 (p) REVERT: F 102 LEU cc_start: 0.7340 (OUTLIER) cc_final: 0.6985 (mp) REVERT: J 46 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8668 (tp) REVERT: G 21 SER cc_start: 0.8015 (m) cc_final: 0.7568 (t) REVERT: G 46 GLU cc_start: 0.6542 (mt-10) cc_final: 0.4965 (mm-30) REVERT: G 91 TYR cc_start: 0.6706 (m-80) cc_final: 0.6355 (m-80) REVERT: G 95 THR cc_start: 0.7529 (m) cc_final: 0.7247 (p) REVERT: G 102 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.7029 (mp) REVERT: K 46 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8668 (tp) outliers start: 67 outliers final: 44 residues processed: 317 average time/residue: 0.1411 time to fit residues: 70.5271 Evaluate side-chains 287 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 235 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain E residue 32 TYR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain F residue 32 TYR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 97 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 34 optimal weight: 0.9980 chunk 173 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 44 optimal weight: 0.8980 chunk 220 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 152 optimal weight: 0.6980 chunk 204 optimal weight: 2.9990 chunk 109 optimal weight: 6.9990 chunk 98 optimal weight: 0.9980 chunk 37 optimal weight: 0.0020 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 ASN A 465 ASN L 45 ASN B 147 ASN B 465 ASN I 45 ASN C 147 ASN C 465 ASN J 45 ASN D 147 ASN D 465 ASN K 45 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.150928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.109577 restraints weight = 24555.102| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.14 r_work: 0.3186 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 20804 Z= 0.138 Angle : 0.673 9.224 28368 Z= 0.327 Chirality : 0.047 0.225 3228 Planarity : 0.004 0.047 3524 Dihedral : 8.383 53.993 4024 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.50 % Allowed : 22.15 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.16), residues: 2480 helix: -0.30 (1.06), residues: 24 sheet: -1.17 (0.16), residues: 920 loop : -1.05 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 18 TYR 0.016 0.001 TYR G 91 PHE 0.011 0.001 PHE D 354 TRP 0.013 0.001 TRP C 178 HIS 0.003 0.001 HIS J 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (20696) covalent geometry : angle 0.63878 / 0.32 (28088) SS BOND : bond 0.00646 / 0.26 ( 44) SS BOND : angle 1.58607 / 1.04 ( 88) hydrogen bonds : bond 0.03231 / 2.22 ( 496) hydrogen bonds : angle 6.36504 / 4.53 ( 1380) link_ALPHA1-2 : bond 0.01709 / 0.86 ( 4) link_ALPHA1-2 : angle 4.42657 / 2.32 ( 12) link_ALPHA1-3 : bond 0.00893 / 0.57 ( 8) link_ALPHA1-3 : angle 2.27637 / 1.37 ( 24) link_ALPHA1-6 : bond 0.00504 / 0.32 ( 8) link_ALPHA1-6 : angle 1.57595 / 0.95 ( 24) link_BETA1-4 : bond 0.00889 / 0.59 ( 20) link_BETA1-4 : angle 2.43880 / 1.55 ( 60) link_NAG-ASN : bond 0.00181 / 0.11 ( 24) link_NAG-ASN : angle 2.38390 / 1.50 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 238 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 21 SER cc_start: 0.7999 (m) cc_final: 0.7580 (t) REVERT: H 46 GLU cc_start: 0.6568 (mt-10) cc_final: 0.5037 (mm-30) REVERT: H 91 TYR cc_start: 0.6625 (m-80) cc_final: 0.6376 (m-80) REVERT: H 95 THR cc_start: 0.7535 (m) cc_final: 0.7333 (p) REVERT: H 102 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.6971 (mp) REVERT: L 46 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8605 (tp) REVERT: E 21 SER cc_start: 0.7993 (m) cc_final: 0.7575 (t) REVERT: E 46 GLU cc_start: 0.6606 (mt-10) cc_final: 0.5079 (mm-30) REVERT: E 91 TYR cc_start: 0.6635 (m-80) cc_final: 0.6374 (m-80) REVERT: E 102 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.6992 (mp) REVERT: I 46 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8607 (tp) REVERT: F 21 SER cc_start: 0.7994 (m) cc_final: 0.7568 (t) REVERT: F 46 GLU cc_start: 0.6589 (mt-10) cc_final: 0.5067 (mm-30) REVERT: F 91 TYR cc_start: 0.6662 (m-80) cc_final: 0.6343 (m-80) REVERT: F 102 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.6977 (mp) REVERT: J 46 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8626 (tp) REVERT: G 21 SER cc_start: 0.8010 (m) cc_final: 0.7594 (t) REVERT: G 46 GLU cc_start: 0.6575 (mt-10) cc_final: 0.5049 (mm-30) REVERT: G 91 TYR cc_start: 0.6660 (m-80) cc_final: 0.6341 (m-80) REVERT: G 102 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.7021 (mp) REVERT: K 46 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8596 (tp) outliers start: 75 outliers final: 50 residues processed: 295 average time/residue: 0.1452 time to fit residues: 67.8027 Evaluate side-chains 280 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 222 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain E residue 32 TYR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain F residue 32 TYR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 46 LEU Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 97 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.2895 > 50: distance: 33 - 125: 34.924 distance: 36 - 122: 36.520 distance: 48 - 108: 26.901 distance: 79 - 81: 34.415 distance: 81 - 82: 40.190 distance: 82 - 83: 39.044 distance: 83 - 90: 40.111 distance: 87 - 88: 56.579 distance: 88 - 89: 56.443 distance: 90 - 91: 32.264 distance: 91 - 92: 31.190 distance: 91 - 94: 8.537 distance: 92 - 93: 40.073 distance: 92 - 98: 40.578 distance: 94 - 95: 39.126 distance: 94 - 96: 39.894 distance: 98 - 99: 14.125 distance: 99 - 100: 15.269 distance: 99 - 102: 24.853 distance: 100 - 101: 40.616 distance: 100 - 105: 55.800 distance: 102 - 103: 38.676 distance: 102 - 104: 56.142 distance: 106 - 107: 40.478 distance: 106 - 109: 8.516 distance: 107 - 108: 49.065 distance: 107 - 115: 22.788 distance: 109 - 110: 14.984 distance: 110 - 111: 3.762 distance: 110 - 112: 16.717 distance: 111 - 113: 40.612 distance: 112 - 114: 28.068 distance: 115 - 116: 15.676 distance: 116 - 117: 43.891 distance: 116 - 119: 29.085 distance: 117 - 118: 43.277 distance: 117 - 122: 22.781 distance: 119 - 120: 42.105 distance: 119 - 121: 7.403 distance: 123 - 124: 45.975 distance: 124 - 125: 18.230 distance: 124 - 128: 43.693 distance: 128 - 129: 13.186 distance: 129 - 130: 40.280 distance: 129 - 132: 14.381 distance: 130 - 131: 50.223 distance: 130 - 137: 48.760 distance: 132 - 133: 6.298 distance: 133 - 134: 38.487 distance: 134 - 135: 26.165 distance: 135 - 136: 41.544 distance: 137 - 138: 40.442 distance: 138 - 139: 36.960 distance: 138 - 141: 53.767 distance: 139 - 145: 39.747 distance: 142 - 143: 39.197 distance: 145 - 146: 56.370 distance: 146 - 149: 39.355 distance: 147 - 148: 56.869 distance: 149 - 150: 57.136 distance: 153 - 155: 35.691