Starting phenix.real_space_refine on Thu Feb 5 21:59:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cyi_46045/02_2026/9cyi_46045.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cyi_46045/02_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_46045/02_2026/9cyi_46045.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cyi_46045/02_2026/9cyi_46045.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cyi_46045/02_2026/9cyi_46045.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cyi_46045/02_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-2.0-5952/lib/python3.9/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, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.85, per 1000 atoms: 0.24 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: 1.75 Conformation dependent library (CDL) restraints added in 626.7 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: 0.77 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: 3.70 Time building geometry restraints manager: 2.27 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 2.510 nonbonded pdb=" O HIS C 347 " pdb="CA CA C 501 " model vdw 2.321 2.510 nonbonded pdb=" O HIS B 347 " pdb="CA CA B 501 " model vdw 2.321 2.510 nonbonded pdb=" O HIS A 347 " pdb="CA CA A 501 " model vdw 2.321 2.510 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: 0.06 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: 12.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.440 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 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 covalent geometry : bond 0.00628 (20696) covalent geometry : angle 0.94562 (28088) SS BOND : bond 0.00311 ( 44) SS BOND : angle 1.18475 ( 88) hydrogen bonds : bond 0.24742 ( 496) hydrogen bonds : angle 11.27358 ( 1380) link_ALPHA1-2 : bond 0.01387 ( 4) link_ALPHA1-2 : angle 4.12158 ( 12) link_ALPHA1-3 : bond 0.00322 ( 8) link_ALPHA1-3 : angle 2.44842 ( 24) link_ALPHA1-6 : bond 0.03024 ( 8) link_ALPHA1-6 : angle 6.79728 ( 24) link_BETA1-4 : bond 0.00824 ( 20) link_BETA1-4 : angle 5.33533 ( 60) link_NAG-ASN : bond 0.00162 ( 24) link_NAG-ASN : angle 2.81168 ( 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 : 0.805 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: 0.1477 time to fit residues: 71.7781 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 : 0.727 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 147 ASN A 273 GLN A 274 HIS A 336 HIS A 465 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 D 465 ASN G 73 ASN K 45 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.148808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.105691 restraints weight = 25659.181| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.57 r_work: 0.3097 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20804 Z= 0.191 Angle : 0.763 10.464 28368 Z= 0.369 Chirality : 0.050 0.196 3228 Planarity : 0.005 0.053 3524 Dihedral : 11.637 93.019 4044 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.08 % Allowed : 19.40 % Favored : 77.52 % 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: -1.26 (0.92), residues: 24 sheet: -1.43 (0.17), residues: 908 loop : -1.67 (0.14), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 18 TYR 0.013 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 A 184 Details of bonding type rmsd covalent geometry : bond 0.00433 (20696) covalent geometry : angle 0.72125 (28088) SS BOND : bond 0.00722 ( 44) SS BOND : angle 1.44333 ( 88) hydrogen bonds : bond 0.04433 ( 496) hydrogen bonds : angle 7.80468 ( 1380) link_ALPHA1-2 : bond 0.01353 ( 4) link_ALPHA1-2 : angle 4.21919 ( 12) link_ALPHA1-3 : bond 0.00919 ( 8) link_ALPHA1-3 : angle 1.90850 ( 24) link_ALPHA1-6 : bond 0.01307 ( 8) link_ALPHA1-6 : angle 3.20491 ( 24) link_BETA1-4 : bond 0.00775 ( 20) link_BETA1-4 : angle 3.42394 ( 60) link_NAG-ASN : bond 0.00203 ( 24) link_NAG-ASN : angle 2.51374 ( 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 369 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 303 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8576 (mt0) REVERT: H 19 ARG cc_start: 0.6536 (OUTLIER) cc_final: 0.6310 (tpt-90) REVERT: B 273 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8569 (mt0) REVERT: E 19 ARG cc_start: 0.6544 (OUTLIER) cc_final: 0.6313 (tpt-90) REVERT: E 102 LEU cc_start: 0.7354 (OUTLIER) cc_final: 0.6991 (mp) REVERT: C 273 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8576 (mt0) REVERT: F 19 ARG cc_start: 0.6524 (OUTLIER) cc_final: 0.6314 (tpt-90) REVERT: D 273 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8569 (mt0) REVERT: G 19 ARG cc_start: 0.6519 (OUTLIER) cc_final: 0.6310 (tpt-90) REVERT: G 102 LEU cc_start: 0.7345 (OUTLIER) cc_final: 0.6982 (mp) outliers start: 66 outliers final: 24 residues processed: 359 average time/residue: 0.1434 time to fit residues: 80.6815 Evaluate side-chains 313 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 279 time to evaluate : 0.747 ------------------------------------------------------------------------------- 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: 8.9990 chunk 227 optimal weight: 0.7980 chunk 176 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 194 optimal weight: 0.0980 chunk 28 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 217 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 199 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN A 391 GLN A 395 GLN A 465 ASN H 73 ASN L 45 ASN B 147 ASN B 391 GLN B 395 GLN B 465 ASN E 73 ASN I 45 ASN C 91 GLN C 147 ASN C 391 GLN C 395 GLN C 465 ASN J 45 ASN D 147 ASN D 391 GLN D 395 GLN D 465 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 = 0.3766 r_free = 0.3766 target = 0.147767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.104518 restraints weight = 25630.537| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.57 r_work: 0.3089 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 20804 Z= 0.186 Angle : 0.729 9.469 28368 Z= 0.356 Chirality : 0.048 0.203 3228 Planarity : 0.005 0.049 3524 Dihedral : 10.576 85.777 4036 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.17 % Allowed : 21.78 % Favored : 75.05 % 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: -1.99 (0.16), residues: 2480 helix: -0.61 (1.04), residues: 24 sheet: -1.22 (0.17), residues: 828 loop : -1.42 (0.14), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 18 TYR 0.016 0.002 TYR H 91 PHE 0.012 0.002 PHE D 354 TRP 0.015 0.001 TRP B 178 HIS 0.004 0.001 HIS C 184 Details of bonding type rmsd covalent geometry : bond 0.00434 (20696) covalent geometry : angle 0.69002 (28088) SS BOND : bond 0.00732 ( 44) SS BOND : angle 1.84182 ( 88) hydrogen bonds : bond 0.03956 ( 496) hydrogen bonds : angle 7.10472 ( 1380) link_ALPHA1-2 : bond 0.01151 ( 4) link_ALPHA1-2 : angle 3.93807 ( 12) link_ALPHA1-3 : bond 0.00962 ( 8) link_ALPHA1-3 : angle 1.70081 ( 24) link_ALPHA1-6 : bond 0.00700 ( 8) link_ALPHA1-6 : angle 2.43187 ( 24) link_BETA1-4 : bond 0.00957 ( 20) link_BETA1-4 : angle 3.06185 ( 60) link_NAG-ASN : bond 0.00185 ( 24) link_NAG-ASN : angle 2.44309 ( 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 350 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 282 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 TYR cc_start: 0.9351 (p90) cc_final: 0.8916 (p90) REVERT: A 273 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8641 (mt0) REVERT: H 95 THR cc_start: 0.7355 (m) cc_final: 0.6893 (p) REVERT: B 121 TYR cc_start: 0.9348 (p90) cc_final: 0.8919 (p90) REVERT: B 273 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.8621 (mt0) REVERT: E 95 THR cc_start: 0.7322 (m) cc_final: 0.6852 (p) REVERT: E 102 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.6976 (mp) REVERT: C 121 TYR cc_start: 0.9346 (p90) cc_final: 0.8912 (p90) REVERT: C 273 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8614 (mt0) REVERT: F 95 THR cc_start: 0.7327 (m) cc_final: 0.6864 (p) REVERT: D 121 TYR cc_start: 0.9350 (p90) cc_final: 0.8918 (p90) REVERT: D 273 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.8635 (mt0) REVERT: G 95 THR cc_start: 0.7340 (m) cc_final: 0.6873 (p) REVERT: G 102 LEU cc_start: 0.7384 (OUTLIER) cc_final: 0.6977 (mp) outliers start: 68 outliers final: 38 residues processed: 326 average time/residue: 0.1332 time to fit residues: 68.0479 Evaluate side-chains 308 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 264 time to evaluate : 0.644 ------------------------------------------------------------------------------- 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: 3.9990 chunk 226 optimal weight: 0.8980 chunk 173 optimal weight: 5.9990 chunk 164 optimal weight: 0.1980 chunk 197 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 137 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN A 168 HIS A 465 ASN B 147 ASN B 168 HIS B 465 ASN C 147 ASN C 168 HIS C 465 ASN D 147 ASN D 168 HIS D 465 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.148922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.107367 restraints weight = 24913.900| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.15 r_work: 0.3150 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1994 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= 0.181 Angle : 0.711 9.336 28368 Z= 0.346 Chirality : 0.048 0.199 3228 Planarity : 0.005 0.047 3524 Dihedral : 9.979 75.041 4036 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.08 % Allowed : 21.97 % Favored : 74.95 % 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: -1.92 (0.16), residues: 2480 helix: -0.61 (1.04), residues: 24 sheet: -1.26 (0.17), residues: 884 loop : -1.29 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 18 TYR 0.022 0.002 TYR H 91 PHE 0.013 0.002 PHE C 354 TRP 0.016 0.001 TRP C 178 HIS 0.003 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00423 (20696) covalent geometry : angle 0.67762 (28088) SS BOND : bond 0.00628 ( 44) SS BOND : angle 1.65100 ( 88) hydrogen bonds : bond 0.03674 ( 496) hydrogen bonds : angle 6.80009 ( 1380) link_ALPHA1-2 : bond 0.01232 ( 4) link_ALPHA1-2 : angle 3.70998 ( 12) link_ALPHA1-3 : bond 0.00873 ( 8) link_ALPHA1-3 : angle 1.97726 ( 24) link_ALPHA1-6 : bond 0.00362 ( 8) link_ALPHA1-6 : angle 1.73899 ( 24) link_BETA1-4 : bond 0.00875 ( 20) link_BETA1-4 : angle 2.78862 ( 60) link_NAG-ASN : bond 0.00193 ( 24) link_NAG-ASN : angle 2.41717 ( 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 332 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 266 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 TYR cc_start: 0.9357 (p90) cc_final: 0.9085 (p90) REVERT: H 4 LEU cc_start: 0.8150 (mp) cc_final: 0.7719 (mt) REVERT: H 91 TYR cc_start: 0.6659 (m-80) cc_final: 0.6443 (m-80) REVERT: H 95 THR cc_start: 0.7429 (m) cc_final: 0.7058 (p) REVERT: L 46 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8663 (tp) REVERT: B 121 TYR cc_start: 0.9351 (p90) cc_final: 0.9083 (p90) REVERT: E 4 LEU cc_start: 0.8156 (mp) cc_final: 0.7682 (mt) REVERT: E 91 TYR cc_start: 0.6667 (m-80) cc_final: 0.6445 (m-80) REVERT: E 95 THR cc_start: 0.7416 (m) cc_final: 0.7034 (p) REVERT: E 102 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.7001 (mp) REVERT: I 46 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8665 (tp) REVERT: C 121 TYR cc_start: 0.9351 (p90) cc_final: 0.9081 (p90) REVERT: F 4 LEU cc_start: 0.8140 (mp) cc_final: 0.7707 (mt) REVERT: F 91 TYR cc_start: 0.6665 (m-80) cc_final: 0.6448 (m-80) REVERT: F 95 THR cc_start: 0.7410 (m) cc_final: 0.7035 (p) REVERT: J 46 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8665 (tp) REVERT: D 121 TYR cc_start: 0.9349 (p90) cc_final: 0.9080 (p90) REVERT: G 4 LEU cc_start: 0.8152 (mp) cc_final: 0.7682 (mt) REVERT: G 91 TYR cc_start: 0.6655 (m-80) cc_final: 0.6444 (m-80) REVERT: G 95 THR cc_start: 0.7413 (m) cc_final: 0.7035 (p) REVERT: G 102 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.6994 (mp) REVERT: K 46 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8654 (tp) outliers start: 66 outliers final: 46 residues processed: 320 average time/residue: 0.1405 time to fit residues: 71.0593 Evaluate side-chains 306 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 254 time to evaluate : 0.805 ------------------------------------------------------------------------------- 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 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 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 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 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: 7.9990 chunk 122 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 228 optimal weight: 9.9990 chunk 93 optimal weight: 0.7980 chunk 139 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 220 optimal weight: 0.0370 chunk 168 optimal weight: 9.9990 chunk 140 optimal weight: 0.7980 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN A 465 ASN B 147 ASN B 465 ASN C 91 GLN C 147 ASN C 465 ASN D 147 ASN D 465 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.150899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.109355 restraints weight = 24842.364| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.16 r_work: 0.3179 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 20804 Z= 0.139 Angle : 0.684 10.040 28368 Z= 0.331 Chirality : 0.047 0.210 3228 Planarity : 0.004 0.048 3524 Dihedral : 8.923 55.254 4024 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.36 % Allowed : 21.92 % Favored : 74.72 % 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: -1.76 (0.16), residues: 2480 helix: -0.32 (1.06), residues: 24 sheet: -1.22 (0.16), residues: 892 loop : -1.13 (0.15), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 18 TYR 0.020 0.002 TYR H 91 PHE 0.011 0.001 PHE B 354 TRP 0.014 0.001 TRP C 178 HIS 0.003 0.001 HIS K 90 Details of bonding type rmsd covalent geometry : bond 0.00318 (20696) covalent geometry : angle 0.65193 (28088) SS BOND : bond 0.00546 ( 44) SS BOND : angle 1.49706 ( 88) hydrogen bonds : bond 0.03330 ( 496) hydrogen bonds : angle 6.49675 ( 1380) link_ALPHA1-2 : bond 0.01495 ( 4) link_ALPHA1-2 : angle 3.81285 ( 12) link_ALPHA1-3 : bond 0.00915 ( 8) link_ALPHA1-3 : angle 2.01261 ( 24) link_ALPHA1-6 : bond 0.00469 ( 8) link_ALPHA1-6 : angle 1.62759 ( 24) link_BETA1-4 : bond 0.00933 ( 20) link_BETA1-4 : angle 2.54087 ( 60) link_NAG-ASN : bond 0.00174 ( 24) link_NAG-ASN : angle 2.37352 ( 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 343 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 271 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 TYR cc_start: 0.9350 (p90) cc_final: 0.9123 (p90) REVERT: H 21 SER cc_start: 0.7985 (m) cc_final: 0.7545 (t) REVERT: H 46 GLU cc_start: 0.6525 (mt-10) cc_final: 0.4984 (mm-30) REVERT: H 95 THR cc_start: 0.7471 (m) cc_final: 0.7250 (p) REVERT: L 46 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8626 (tp) REVERT: E 21 SER cc_start: 0.7982 (m) cc_final: 0.7539 (t) REVERT: E 46 GLU cc_start: 0.6542 (mt-10) cc_final: 0.4983 (mm-30) REVERT: E 95 THR cc_start: 0.7469 (m) cc_final: 0.7229 (p) REVERT: E 102 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.6987 (mp) REVERT: I 46 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8626 (tp) REVERT: F 21 SER cc_start: 0.7990 (m) cc_final: 0.7553 (t) REVERT: F 46 GLU cc_start: 0.6552 (mt-10) cc_final: 0.4990 (mm-30) REVERT: F 95 THR cc_start: 0.7462 (m) cc_final: 0.7224 (p) REVERT: J 46 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8623 (tp) REVERT: G 21 SER cc_start: 0.8001 (m) cc_final: 0.7569 (t) REVERT: G 46 GLU cc_start: 0.6519 (mt-10) cc_final: 0.4969 (mm-30) REVERT: G 95 THR cc_start: 0.7456 (m) cc_final: 0.7234 (p) REVERT: G 102 LEU cc_start: 0.7416 (OUTLIER) cc_final: 0.7008 (mp) REVERT: K 46 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8621 (tp) outliers start: 72 outliers final: 48 residues processed: 331 average time/residue: 0.1472 time to fit residues: 77.2190 Evaluate side-chains 308 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 254 time to evaluate : 0.768 ------------------------------------------------------------------------------- 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 242 THR 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 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 242 THR Chi-restraints excluded: chain B residue 275 VAL 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 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 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 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 97 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 34 optimal weight: 1.9990 chunk 173 optimal weight: 0.3980 chunk 40 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 220 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 152 optimal weight: 4.9990 chunk 204 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3792 r_free = 0.3792 target = 0.150481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.108884 restraints weight = 24637.136| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.14 r_work: 0.3172 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 20804 Z= 0.152 Angle : 0.678 9.174 28368 Z= 0.330 Chirality : 0.047 0.222 3228 Planarity : 0.004 0.049 3524 Dihedral : 8.472 54.233 4024 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.68 % Allowed : 22.48 % Favored : 73.83 % 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: -1.73 (0.16), residues: 2480 helix: -0.26 (1.07), residues: 24 sheet: -1.27 (0.16), residues: 908 loop : -1.06 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 18 TYR 0.014 0.001 TYR L 87 PHE 0.012 0.001 PHE C 354 TRP 0.013 0.001 TRP A 178 HIS 0.003 0.001 HIS C 184 Details of bonding type rmsd covalent geometry : bond 0.00355 (20696) covalent geometry : angle 0.64426 (28088) SS BOND : bond 0.00634 ( 44) SS BOND : angle 1.58380 ( 88) hydrogen bonds : bond 0.03315 ( 496) hydrogen bonds : angle 6.37973 ( 1380) link_ALPHA1-2 : bond 0.01610 ( 4) link_ALPHA1-2 : angle 4.23769 ( 12) link_ALPHA1-3 : bond 0.00830 ( 8) link_ALPHA1-3 : angle 2.29221 ( 24) link_ALPHA1-6 : bond 0.00438 ( 8) link_ALPHA1-6 : angle 1.62098 ( 24) link_BETA1-4 : bond 0.00868 ( 20) link_BETA1-4 : angle 2.45001 ( 60) link_NAG-ASN : bond 0.00159 ( 24) link_NAG-ASN : angle 2.33749 ( 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 322 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 243 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 21 SER cc_start: 0.8009 (m) cc_final: 0.7594 (t) REVERT: H 46 GLU cc_start: 0.6570 (mt-10) cc_final: 0.5050 (mm-30) REVERT: H 102 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.6984 (mp) REVERT: L 46 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8606 (tp) REVERT: E 21 SER cc_start: 0.8085 (m) cc_final: 0.7669 (t) REVERT: E 46 GLU cc_start: 0.6584 (mt-10) cc_final: 0.5056 (mm-30) REVERT: E 95 THR cc_start: 0.7537 (m) cc_final: 0.7324 (p) REVERT: E 102 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.7019 (mp) REVERT: I 46 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8619 (tp) REVERT: F 21 SER cc_start: 0.8020 (m) cc_final: 0.7597 (t) REVERT: F 46 GLU cc_start: 0.6574 (mt-10) cc_final: 0.5047 (mm-30) REVERT: F 102 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.6995 (mp) REVERT: J 46 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8608 (tp) REVERT: G 21 SER cc_start: 0.8017 (m) cc_final: 0.7603 (t) REVERT: G 46 GLU cc_start: 0.6549 (mt-10) cc_final: 0.5015 (mm-30) REVERT: G 102 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.7032 (mp) REVERT: K 46 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8627 (tp) outliers start: 79 outliers final: 54 residues processed: 308 average time/residue: 0.1284 time to fit residues: 62.4658 Evaluate side-chains 287 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 225 time to evaluate : 0.759 ------------------------------------------------------------------------------- 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 204 SER Chi-restraints excluded: chain A residue 213 ASP 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 A residue 325 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 47 PHE 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 204 SER 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 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 204 SER 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 97 THR Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 213 ASP 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 47 PHE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 167 optimal weight: 10.0000 chunk 222 optimal weight: 0.0970 chunk 56 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 238 optimal weight: 3.9990 chunk 242 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3787 r_free = 0.3787 target = 0.149799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.108243 restraints weight = 24885.466| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.16 r_work: 0.3166 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 20804 Z= 0.163 Angle : 0.677 9.243 28368 Z= 0.330 Chirality : 0.047 0.223 3228 Planarity : 0.004 0.049 3524 Dihedral : 8.383 54.653 4024 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 4.06 % Allowed : 21.55 % Favored : 74.39 % 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: -1.62 (0.16), residues: 2480 helix: -0.30 (1.06), residues: 24 sheet: -1.14 (0.16), residues: 916 loop : -1.01 (0.16), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 18 TYR 0.014 0.002 TYR L 87 PHE 0.013 0.001 PHE C 354 TRP 0.013 0.001 TRP B 178 HIS 0.003 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00383 (20696) covalent geometry : angle 0.64350 (28088) SS BOND : bond 0.00662 ( 44) SS BOND : angle 1.46739 ( 88) hydrogen bonds : bond 0.03325 ( 496) hydrogen bonds : angle 6.31099 ( 1380) link_ALPHA1-2 : bond 0.01573 ( 4) link_ALPHA1-2 : angle 4.36865 ( 12) link_ALPHA1-3 : bond 0.00829 ( 8) link_ALPHA1-3 : angle 2.36910 ( 24) link_ALPHA1-6 : bond 0.00391 ( 8) link_ALPHA1-6 : angle 1.62287 ( 24) link_BETA1-4 : bond 0.00850 ( 20) link_BETA1-4 : angle 2.39474 ( 60) link_NAG-ASN : bond 0.00177 ( 24) link_NAG-ASN : angle 2.33804 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 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 330 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 243 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 21 SER cc_start: 0.8076 (m) cc_final: 0.7673 (t) REVERT: H 46 GLU cc_start: 0.6552 (mt-10) cc_final: 0.5060 (mm-30) REVERT: H 102 LEU cc_start: 0.7296 (OUTLIER) cc_final: 0.6948 (mp) REVERT: L 46 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8576 (tp) REVERT: E 46 GLU cc_start: 0.6573 (mt-10) cc_final: 0.5072 (mm-30) REVERT: E 102 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.7004 (mp) REVERT: I 46 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8619 (tp) REVERT: F 21 SER cc_start: 0.8075 (m) cc_final: 0.7677 (t) REVERT: F 46 GLU cc_start: 0.6560 (mt-10) cc_final: 0.5066 (mm-30) REVERT: F 102 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.6942 (mp) REVERT: J 46 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8571 (tp) REVERT: G 21 SER cc_start: 0.8088 (m) cc_final: 0.7690 (t) REVERT: G 46 GLU cc_start: 0.6525 (mt-10) cc_final: 0.5032 (mm-30) REVERT: G 102 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.7016 (mp) REVERT: K 46 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8576 (tp) outliers start: 87 outliers final: 63 residues processed: 315 average time/residue: 0.1434 time to fit residues: 71.7550 Evaluate side-chains 295 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 224 time to evaluate : 0.838 ------------------------------------------------------------------------------- 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 204 SER Chi-restraints excluded: chain A residue 213 ASP 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 A residue 325 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 47 PHE 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 143 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 213 ASP 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 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 143 VAL Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 213 ASP 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 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 159 LEU Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 213 ASP 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 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 85 THR Chi-restraints excluded: chain K residue 97 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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-2.0-5952/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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-2.0-5952/lib/python3.9/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-2.0-5952/lib/python3.9/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-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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-2.0-5952/lib/python3.9/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-2.0-5952/lib/python3.9/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-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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-2.0-5952/lib/python3.9/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-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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-2.0-5952/lib/python3.9/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-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.6929 > 50: distance: 33 - 125: 18.509 distance: 36 - 122: 19.772 distance: 48 - 108: 5.761 distance: 79 - 81: 27.264 distance: 81 - 82: 10.308 distance: 82 - 83: 21.830 distance: 82 - 85: 33.431 distance: 83 - 84: 12.302 distance: 83 - 90: 16.750 distance: 85 - 86: 41.063 distance: 86 - 87: 25.770 distance: 87 - 88: 26.202 distance: 88 - 89: 33.920 distance: 90 - 91: 10.575 distance: 91 - 92: 11.252 distance: 91 - 94: 21.643 distance: 92 - 93: 28.710 distance: 92 - 98: 26.117 distance: 94 - 95: 36.425 distance: 94 - 96: 27.882 distance: 95 - 97: 27.244 distance: 98 - 99: 16.834 distance: 99 - 100: 15.959 distance: 99 - 102: 23.393 distance: 100 - 101: 25.856 distance: 100 - 105: 17.554 distance: 102 - 103: 13.416 distance: 102 - 104: 25.254 distance: 105 - 106: 12.391 distance: 106 - 107: 4.646 distance: 106 - 109: 8.913 distance: 107 - 108: 6.859 distance: 107 - 115: 5.624 distance: 109 - 110: 5.489 distance: 110 - 111: 3.134 distance: 110 - 112: 3.576 distance: 111 - 113: 3.374 distance: 112 - 114: 3.263 distance: 116 - 117: 12.119 distance: 116 - 119: 5.451 distance: 117 - 118: 9.773 distance: 117 - 122: 14.676 distance: 119 - 120: 5.682 distance: 119 - 121: 6.489 distance: 122 - 123: 6.935 distance: 123 - 124: 14.084 distance: 124 - 125: 14.139 distance: 124 - 128: 10.123 distance: 126 - 127: 15.210 distance: 128 - 129: 10.516 distance: 129 - 130: 12.529 distance: 129 - 132: 14.062 distance: 130 - 131: 42.512 distance: 130 - 137: 10.709 distance: 132 - 133: 10.676 distance: 133 - 134: 12.995 distance: 134 - 135: 4.379 distance: 135 - 136: 15.098 distance: 137 - 138: 4.387 distance: 138 - 139: 16.608 distance: 138 - 141: 14.327 distance: 139 - 140: 20.486 distance: 139 - 145: 36.001 distance: 141 - 142: 26.993 distance: 142 - 143: 18.695 distance: 142 - 144: 20.002 distance: 145 - 146: 21.181 distance: 146 - 147: 21.418 distance: 146 - 149: 19.828 distance: 147 - 148: 19.710 distance: 147 - 151: 36.529 distance: 149 - 150: 45.939 distance: 151 - 152: 28.913 distance: 152 - 153: 7.470 distance: 153 - 154: 20.974 distance: 153 - 155: 25.002