Starting phenix.real_space_refine on Mon Apr 15 16:32:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cin_16680/04_2024/8cin_16680.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cin_16680/04_2024/8cin_16680.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cin_16680/04_2024/8cin_16680.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cin_16680/04_2024/8cin_16680.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cin_16680/04_2024/8cin_16680.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cin_16680/04_2024/8cin_16680.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 144 5.16 5 C 22335 2.51 5 N 5787 2.21 5 O 6909 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1116": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 35175 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1056, 8241 Classifications: {'peptide': 1056} Link IDs: {'PTRANS': 52, 'TRANS': 1003} Chain breaks: 6 Chain: "B" Number of atoms: 8241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1056, 8241 Classifications: {'peptide': 1056} Link IDs: {'PTRANS': 52, 'TRANS': 1003} Chain breaks: 6 Chain: "C" Number of atoms: 8241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1056, 8241 Classifications: {'peptide': 1056} Link IDs: {'PTRANS': 52, 'TRANS': 1003} Chain breaks: 6 Chain: "E" Number of atoms: 1664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1664 Classifications: {'peptide': 223} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 207} Chain: "F" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1582 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 199} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 1664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1664 Classifications: {'peptide': 223} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 207} Chain: "J" Number of atoms: 1664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1664 Classifications: {'peptide': 223} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 207} Chain: "K" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1582 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 199} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1582 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 199} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 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: 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: "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: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 18.07, per 1000 atoms: 0.51 Number of scatterers: 35175 At special positions: 0 Unit cell: (222.742, 216.899, 173.081, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 144 16.00 O 6909 8.00 N 5787 7.00 C 22335 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, symmetry=0 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 161 " distance=2.03 Simple disulfide: pdb=" SG CYS A 286 " - pdb=" SG CYS A 296 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 356 " distance=2.03 Simple disulfide: pdb=" SG CYS A 374 " - pdb=" SG CYS A 427 " distance=2.03 Simple disulfide: pdb=" SG CYS A 386 " - pdb=" SG CYS A 520 " distance=2.03 Simple disulfide: pdb=" SG CYS A 475 " - pdb=" SG CYS A 483 " distance=2.03 Simple disulfide: pdb=" SG CYS A 533 " - pdb=" SG CYS A 585 " distance=2.02 Simple disulfide: pdb=" SG CYS A 612 " - pdb=" SG CYS A 644 " distance=2.03 Simple disulfide: pdb=" SG CYS A 657 " - pdb=" SG CYS A 666 " distance=2.03 Simple disulfide: pdb=" SG CYS A 733 " - pdb=" SG CYS A 755 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 744 " distance=2.03 Simple disulfide: pdb=" SG CYS A 835 " - pdb=" SG CYS A 846 " distance=2.03 Simple disulfide: pdb=" SG CYS A1027 " - pdb=" SG CYS A1038 " distance=2.03 Simple disulfide: pdb=" SG CYS A1077 " - pdb=" SG CYS A1121 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 161 " distance=2.03 Simple disulfide: pdb=" SG CYS B 286 " - pdb=" SG CYS B 296 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 356 " distance=2.03 Simple disulfide: pdb=" SG CYS B 374 " - pdb=" SG CYS B 427 " distance=2.03 Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 520 " distance=2.03 Simple disulfide: pdb=" SG CYS B 475 " - pdb=" SG CYS B 483 " distance=2.03 Simple disulfide: pdb=" SG CYS B 533 " - pdb=" SG CYS B 585 " distance=2.02 Simple disulfide: pdb=" SG CYS B 612 " - pdb=" SG CYS B 644 " distance=2.03 Simple disulfide: pdb=" SG CYS B 657 " - pdb=" SG CYS B 666 " distance=2.03 Simple disulfide: pdb=" SG CYS B 733 " - pdb=" SG CYS B 755 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 744 " distance=2.03 Simple disulfide: pdb=" SG CYS B 835 " - pdb=" SG CYS B 846 " distance=2.03 Simple disulfide: pdb=" SG CYS B1027 " - pdb=" SG CYS B1038 " distance=2.03 Simple disulfide: pdb=" SG CYS B1077 " - pdb=" SG CYS B1121 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 161 " distance=2.03 Simple disulfide: pdb=" SG CYS C 286 " - pdb=" SG CYS C 296 " distance=2.03 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 356 " distance=2.03 Simple disulfide: pdb=" SG CYS C 374 " - pdb=" SG CYS C 427 " distance=2.03 Simple disulfide: pdb=" SG CYS C 386 " - pdb=" SG CYS C 520 " distance=2.03 Simple disulfide: pdb=" SG CYS C 475 " - pdb=" SG CYS C 483 " distance=2.03 Simple disulfide: pdb=" SG CYS C 533 " - pdb=" SG CYS C 585 " distance=2.02 Simple disulfide: pdb=" SG CYS C 612 " - pdb=" SG CYS C 644 " distance=2.03 Simple disulfide: pdb=" SG CYS C 657 " - pdb=" SG CYS C 666 " distance=2.03 Simple disulfide: pdb=" SG CYS C 733 " - pdb=" SG CYS C 755 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 744 " distance=2.03 Simple disulfide: pdb=" SG CYS C 835 " - pdb=" SG CYS C 846 " distance=2.03 Simple disulfide: pdb=" SG CYS C1027 " - pdb=" SG CYS C1038 " distance=2.03 Simple disulfide: pdb=" SG CYS C1077 " - pdb=" SG CYS C1121 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 148 " - pdb=" SG CYS E 204 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 90 " distance=2.03 Simple disulfide: pdb=" SG CYS F 138 " - pdb=" SG CYS F 197 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS H 148 " - pdb=" SG CYS H 204 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 95 " distance=2.03 Simple disulfide: pdb=" SG CYS J 148 " - pdb=" SG CYS J 204 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 90 " distance=2.03 Simple disulfide: pdb=" SG CYS K 138 " - pdb=" SG CYS K 197 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS L 138 " - pdb=" SG CYS L 197 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " 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 S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1201 " - " ASN A 58 " " NAG A1202 " - " ASN A 277 " " NAG A1203 " - " ASN A 598 " " NAG A1204 " - " ASN A 611 " " NAG A1205 " - " ASN A 652 " " NAG A1206 " - " ASN A 704 " " NAG A1207 " - " ASN A1069 " " NAG A1208 " - " ASN A 326 " " NAG A1209 " - " ASN A 338 " " NAG B1201 " - " ASN B 58 " " NAG B1202 " - " ASN B 277 " " NAG B1203 " - " ASN B 598 " " NAG B1204 " - " ASN B 611 " " NAG B1205 " - " ASN B 652 " " NAG B1206 " - " ASN B 704 " " NAG B1207 " - " ASN B1069 " " NAG B1208 " - " ASN B 326 " " NAG B1209 " - " ASN B 338 " " NAG C1201 " - " ASN C 58 " " NAG C1202 " - " ASN C 277 " " NAG C1203 " - " ASN C 598 " " NAG C1204 " - " ASN C 611 " " NAG C1205 " - " ASN C 652 " " NAG C1206 " - " ASN C 704 " " NAG C1207 " - " ASN C1069 " " NAG C1208 " - " ASN C 326 " " NAG C1209 " - " ASN C 338 " " NAG D 1 " - " ASN A 712 " " NAG G 1 " - " ASN A 796 " " NAG I 1 " - " ASN A1093 " " NAG M 1 " - " ASN A1129 " " NAG N 1 " - " ASN B 712 " " NAG O 1 " - " ASN B 796 " " NAG P 1 " - " ASN B1093 " " NAG Q 1 " - " ASN B1129 " " NAG R 1 " - " ASN C 712 " " NAG S 1 " - " ASN C 796 " " NAG T 1 " - " ASN C1093 " " NAG U 1 " - " ASN C1129 " Time building additional restraints: 13.79 Conformation dependent library (CDL) restraints added in 6.8 seconds 8850 Ramachandran restraints generated. 4425 Oldfield, 0 Emsley, 4425 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8328 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 87 sheets defined 21.7% alpha, 32.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.46 Creating SS restraints... Processing helix chain 'A' and resid 289 through 299 Processing helix chain 'A' and resid 333 through 338 Processing helix chain 'A' and resid 344 through 348 removed outlier: 3.523A pdb=" N TRP A 348 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 removed outlier: 4.050A pdb=" N TYR A 364 " --> pdb=" O SER A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 384 removed outlier: 4.587A pdb=" N ASN A 383 " --> pdb=" O THR A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 405 removed outlier: 4.109A pdb=" N SER A 403 " --> pdb=" O ASN A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 417 Processing helix chain 'A' and resid 433 through 438 removed outlier: 3.668A pdb=" N SER A 438 " --> pdb=" O ASN A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 500 Processing helix chain 'A' and resid 732 through 739 Processing helix chain 'A' and resid 741 through 750 removed outlier: 3.811A pdb=" N GLN A 750 " --> pdb=" O ASN A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 778 Processing helix chain 'A' and resid 811 through 821 Processing helix chain 'A' and resid 831 through 837 removed outlier: 3.831A pdb=" N CYS A 835 " --> pdb=" O GLN A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 851 Processing helix chain 'A' and resid 861 through 880 Processing helix chain 'A' and resid 881 through 885 Processing helix chain 'A' and resid 892 through 904 Processing helix chain 'A' and resid 907 through 914 removed outlier: 4.063A pdb=" N LEU A 911 " --> pdb=" O THR A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 936 Processing helix chain 'A' and resid 940 through 960 Processing helix chain 'A' and resid 961 through 963 No H-bonds generated for 'chain 'A' and resid 961 through 963' Processing helix chain 'A' and resid 971 through 979 Processing helix chain 'A' and resid 980 through 1028 removed outlier: 3.871A pdb=" N VAL A 986 " --> pdb=" O PRO A 982 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN A 987 " --> pdb=" O GLU A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 1135 through 1142 removed outlier: 4.176A pdb=" N GLU A1139 " --> pdb=" O PRO A1135 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 299 Processing helix chain 'B' and resid 333 through 338 Processing helix chain 'B' and resid 344 through 348 removed outlier: 3.519A pdb=" N TRP B 348 " --> pdb=" O VAL B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 removed outlier: 4.064A pdb=" N TYR B 364 " --> pdb=" O SER B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 384 removed outlier: 4.586A pdb=" N ASN B 383 " --> pdb=" O THR B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 405 removed outlier: 4.122A pdb=" N SER B 403 " --> pdb=" O ASN B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 417 Processing helix chain 'B' and resid 433 through 438 removed outlier: 3.663A pdb=" N SER B 438 " --> pdb=" O ASN B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 500 Processing helix chain 'B' and resid 732 through 739 Processing helix chain 'B' and resid 741 through 750 removed outlier: 3.810A pdb=" N GLN B 750 " --> pdb=" O ASN B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 753 through 778 Processing helix chain 'B' and resid 811 through 821 Processing helix chain 'B' and resid 831 through 837 removed outlier: 3.831A pdb=" N CYS B 835 " --> pdb=" O GLN B 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 851 Processing helix chain 'B' and resid 861 through 880 Processing helix chain 'B' and resid 881 through 885 Processing helix chain 'B' and resid 892 through 904 Processing helix chain 'B' and resid 907 through 914 removed outlier: 4.057A pdb=" N LEU B 911 " --> pdb=" O THR B 907 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 936 Processing helix chain 'B' and resid 940 through 960 Processing helix chain 'B' and resid 961 through 963 No H-bonds generated for 'chain 'B' and resid 961 through 963' Processing helix chain 'B' and resid 971 through 979 Processing helix chain 'B' and resid 980 through 1027 removed outlier: 3.871A pdb=" N VAL B 986 " --> pdb=" O PRO B 982 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN B 987 " --> pdb=" O GLU B 983 " (cutoff:3.500A) Processing helix chain 'B' and resid 1135 through 1142 removed outlier: 4.171A pdb=" N GLU B1139 " --> pdb=" O PRO B1135 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 299 Processing helix chain 'C' and resid 333 through 338 Processing helix chain 'C' and resid 344 through 348 removed outlier: 3.516A pdb=" N TRP C 348 " --> pdb=" O VAL C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 removed outlier: 4.056A pdb=" N TYR C 364 " --> pdb=" O SER C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 384 removed outlier: 4.589A pdb=" N ASN C 383 " --> pdb=" O THR C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 405 removed outlier: 4.095A pdb=" N SER C 403 " --> pdb=" O ASN C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 417 Processing helix chain 'C' and resid 433 through 438 removed outlier: 3.667A pdb=" N SER C 438 " --> pdb=" O ASN C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 500 Processing helix chain 'C' and resid 732 through 739 Processing helix chain 'C' and resid 741 through 750 removed outlier: 3.813A pdb=" N GLN C 750 " --> pdb=" O ASN C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 753 through 778 Processing helix chain 'C' and resid 811 through 821 Processing helix chain 'C' and resid 831 through 837 removed outlier: 3.832A pdb=" N CYS C 835 " --> pdb=" O GLN C 831 " (cutoff:3.500A) Processing helix chain 'C' and resid 842 through 851 Processing helix chain 'C' and resid 861 through 880 Processing helix chain 'C' and resid 881 through 885 Processing helix chain 'C' and resid 892 through 904 Processing helix chain 'C' and resid 907 through 914 removed outlier: 4.054A pdb=" N LEU C 911 " --> pdb=" O THR C 907 " (cutoff:3.500A) Processing helix chain 'C' and resid 914 through 936 Processing helix chain 'C' and resid 940 through 960 Processing helix chain 'C' and resid 961 through 963 No H-bonds generated for 'chain 'C' and resid 961 through 963' Processing helix chain 'C' and resid 971 through 979 Processing helix chain 'C' and resid 980 through 1028 removed outlier: 3.872A pdb=" N VAL C 986 " --> pdb=" O PRO C 982 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN C 987 " --> pdb=" O GLU C 983 " (cutoff:3.500A) Processing helix chain 'C' and resid 1135 through 1142 removed outlier: 4.172A pdb=" N GLU C1139 " --> pdb=" O PRO C1135 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 90 removed outlier: 3.501A pdb=" N THR E 90 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 140 Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'F' and resid 81 through 85 Processing helix chain 'F' and resid 125 through 131 Processing helix chain 'F' and resid 185 through 192 Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'H' and resid 135 through 140 Processing helix chain 'H' and resid 195 through 197 No H-bonds generated for 'chain 'H' and resid 195 through 197' Processing helix chain 'J' and resid 86 through 90 Processing helix chain 'J' and resid 135 through 140 Processing helix chain 'J' and resid 195 through 197 No H-bonds generated for 'chain 'J' and resid 195 through 197' Processing helix chain 'K' and resid 81 through 85 Processing helix chain 'K' and resid 125 through 131 Processing helix chain 'K' and resid 185 through 192 Processing helix chain 'L' and resid 81 through 85 Processing helix chain 'L' and resid 125 through 131 Processing helix chain 'L' and resid 185 through 192 Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 27 removed outlier: 7.363A pdb=" N ASN A 58 " --> pdb=" O TYR A 264 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N TYR A 264 " --> pdb=" O ASN A 58 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ALA A 259 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N THR A 90 " --> pdb=" O ALA A 259 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N SER A 200 " --> pdb=" O PRO A 220 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 40 removed outlier: 5.626A pdb=" N ASP B 569 " --> pdb=" O ILE B 582 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU B 319 " --> pdb=" O CYS B 533 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 44 through 52 removed outlier: 7.445A pdb=" N THR A 269 " --> pdb=" O ASP A 285 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ASP A 285 " --> pdb=" O THR A 269 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU A 271 " --> pdb=" O ALA A 283 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA A 283 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LYS A 273 " --> pdb=" O THR A 281 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 79 through 80 removed outlier: 6.639A pdb=" N ARG A 97 " --> pdb=" O ASN A 116 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ASN A 116 " --> pdb=" O ARG A 97 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 129 through 130 removed outlier: 6.473A pdb=" N GLN A 129 " --> pdb=" O SER A 156 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 306 through 314 removed outlier: 6.730A pdb=" N VAL A 590 " --> pdb=" O THR A 310 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ASN A 312 " --> pdb=" O GLY A 588 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLY A 588 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLY A 589 " --> pdb=" O GLN A 608 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 319 through 323 removed outlier: 4.210A pdb=" N GLU A 319 " --> pdb=" O CYS A 533 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ASP A 569 " --> pdb=" O ILE A 582 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N PHE A 560 " --> pdb=" O PHE C 40 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 349 through 353 Processing sheet with id=AA9, first strand: chain 'A' and resid 356 through 357 removed outlier: 6.729A pdb=" N CYS A 356 " --> pdb=" O CYS A 520 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 447 through 449 Processing sheet with id=AB2, first strand: chain 'A' and resid 468 through 469 Processing sheet with id=AB3, first strand: chain 'A' and resid 649 through 650 removed outlier: 6.328A pdb=" N ALA A 667 " --> pdb=" O PRO A 660 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 697 through 699 removed outlier: 3.652A pdb=" N LYS C 785 " --> pdb=" O ASN A 698 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 706 through 710 Processing sheet with id=AB6, first strand: chain 'A' and resid 713 through 723 removed outlier: 7.009A pdb=" N GLY A1054 " --> pdb=" O SER A1050 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N SER A1050 " --> pdb=" O GLY A1054 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL A1056 " --> pdb=" O PRO A1048 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU A1058 " --> pdb=" O SER A1046 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N SER A1046 " --> pdb=" O LEU A1058 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL A1060 " --> pdb=" O LEU A1044 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 728 through 731 removed outlier: 4.529A pdb=" N LYS A 728 " --> pdb=" O LEU A 856 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 783 through 785 removed outlier: 5.989A pdb=" N ILE A 783 " --> pdb=" O ASN B 698 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1115 through 1117 Processing sheet with id=AC1, first strand: chain 'A' and resid 1089 through 1092 Processing sheet with id=AC2, first strand: chain 'B' and resid 23 through 27 removed outlier: 7.366A pdb=" N ASN B 58 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N TYR B 264 " --> pdb=" O ASN B 58 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA B 259 " --> pdb=" O THR B 90 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N THR B 90 " --> pdb=" O ALA B 259 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N SER B 200 " --> pdb=" O PRO B 220 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 39 through 40 removed outlier: 5.627A pdb=" N ASP C 569 " --> pdb=" O ILE C 582 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLU C 319 " --> pdb=" O CYS C 533 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 44 through 52 removed outlier: 7.442A pdb=" N THR B 269 " --> pdb=" O ASP B 285 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ASP B 285 " --> pdb=" O THR B 269 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU B 271 " --> pdb=" O ALA B 283 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA B 283 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LYS B 273 " --> pdb=" O THR B 281 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 79 through 80 removed outlier: 6.637A pdb=" N ARG B 97 " --> pdb=" O ASN B 116 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ASN B 116 " --> pdb=" O ARG B 97 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 129 through 130 removed outlier: 6.474A pdb=" N GLN B 129 " --> pdb=" O SER B 156 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 306 through 314 removed outlier: 6.732A pdb=" N VAL B 590 " --> pdb=" O THR B 310 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ASN B 312 " --> pdb=" O GLY B 588 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N GLY B 588 " --> pdb=" O ASN B 312 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLY B 589 " --> pdb=" O GLN B 608 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 349 through 353 Processing sheet with id=AC9, first strand: chain 'B' and resid 356 through 357 removed outlier: 6.722A pdb=" N CYS B 356 " --> pdb=" O CYS B 520 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 447 through 449 Processing sheet with id=AD2, first strand: chain 'B' and resid 468 through 469 Processing sheet with id=AD3, first strand: chain 'B' and resid 649 through 650 removed outlier: 6.333A pdb=" N ALA B 667 " --> pdb=" O PRO B 660 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 706 through 710 Processing sheet with id=AD5, first strand: chain 'B' and resid 713 through 723 removed outlier: 7.007A pdb=" N GLY B1054 " --> pdb=" O SER B1050 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N SER B1050 " --> pdb=" O GLY B1054 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL B1056 " --> pdb=" O PRO B1048 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU B1058 " --> pdb=" O SER B1046 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N SER B1046 " --> pdb=" O LEU B1058 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL B1060 " --> pdb=" O LEU B1044 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 728 through 731 removed outlier: 4.539A pdb=" N LYS B 728 " --> pdb=" O LEU B 856 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 783 through 785 removed outlier: 5.987A pdb=" N ILE B 783 " --> pdb=" O ASN C 698 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'B' and resid 1115 through 1117 Processing sheet with id=AD9, first strand: chain 'B' and resid 1089 through 1092 Processing sheet with id=AE1, first strand: chain 'C' and resid 23 through 27 removed outlier: 7.369A pdb=" N ASN C 58 " --> pdb=" O TYR C 264 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N TYR C 264 " --> pdb=" O ASN C 58 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA C 259 " --> pdb=" O THR C 90 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N THR C 90 " --> pdb=" O ALA C 259 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N SER C 200 " --> pdb=" O PRO C 220 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 44 through 52 removed outlier: 7.445A pdb=" N THR C 269 " --> pdb=" O ASP C 285 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ASP C 285 " --> pdb=" O THR C 269 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU C 271 " --> pdb=" O ALA C 283 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ALA C 283 " --> pdb=" O LEU C 271 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LYS C 273 " --> pdb=" O THR C 281 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 79 through 80 removed outlier: 6.636A pdb=" N ARG C 97 " --> pdb=" O ASN C 116 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ASN C 116 " --> pdb=" O ARG C 97 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 129 through 130 removed outlier: 6.470A pdb=" N GLN C 129 " --> pdb=" O SER C 156 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 306 through 314 removed outlier: 6.732A pdb=" N VAL C 590 " --> pdb=" O THR C 310 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ASN C 312 " --> pdb=" O GLY C 588 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N GLY C 588 " --> pdb=" O ASN C 312 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLY C 589 " --> pdb=" O GLN C 608 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 349 through 353 Processing sheet with id=AE7, first strand: chain 'C' and resid 356 through 357 removed outlier: 6.725A pdb=" N CYS C 356 " --> pdb=" O CYS C 520 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 447 through 449 Processing sheet with id=AE9, first strand: chain 'C' and resid 468 through 469 Processing sheet with id=AF1, first strand: chain 'C' and resid 649 through 650 removed outlier: 6.338A pdb=" N ALA C 667 " --> pdb=" O PRO C 660 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 706 through 710 Processing sheet with id=AF3, first strand: chain 'C' and resid 713 through 723 removed outlier: 7.006A pdb=" N GLY C1054 " --> pdb=" O SER C1050 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N SER C1050 " --> pdb=" O GLY C1054 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL C1056 " --> pdb=" O PRO C1048 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU C1058 " --> pdb=" O SER C1046 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N SER C1046 " --> pdb=" O LEU C1058 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL C1060 " --> pdb=" O LEU C1044 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 728 through 731 removed outlier: 4.536A pdb=" N LYS C 728 " --> pdb=" O LEU C 856 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 1115 through 1117 Processing sheet with id=AF6, first strand: chain 'C' and resid 1089 through 1092 Processing sheet with id=AF7, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AF8, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.563A pdb=" N TRP E 34 " --> pdb=" O ASN E 50 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ASN E 50 " --> pdb=" O TRP E 34 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N TYR E 52 " --> pdb=" O SER E 56 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N SER E 56 " --> pdb=" O TYR E 52 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 11 through 12 Processing sheet with id=AG1, first strand: chain 'E' and resid 128 through 132 removed outlier: 5.114A pdb=" N ALA E 145 " --> pdb=" O VAL E 192 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL E 192 " --> pdb=" O ALA E 145 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLY E 147 " --> pdb=" O VAL E 190 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL E 190 " --> pdb=" O GLY E 147 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N LEU E 149 " --> pdb=" O SER E 188 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N SER E 188 " --> pdb=" O LEU E 149 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LYS E 151 " --> pdb=" O LEU E 186 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N LEU E 186 " --> pdb=" O LYS E 151 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 128 through 132 removed outlier: 5.114A pdb=" N ALA E 145 " --> pdb=" O VAL E 192 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL E 192 " --> pdb=" O ALA E 145 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLY E 147 " --> pdb=" O VAL E 190 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL E 190 " --> pdb=" O GLY E 147 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N LEU E 149 " --> pdb=" O SER E 188 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N SER E 188 " --> pdb=" O LEU E 149 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LYS E 151 " --> pdb=" O LEU E 186 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N LEU E 186 " --> pdb=" O LYS E 151 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 159 through 162 removed outlier: 4.607A pdb=" N TYR E 202 " --> pdb=" O VAL E 219 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 9 through 12 removed outlier: 6.365A pdb=" N TRP F 37 " --> pdb=" O MET F 49 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 9 through 12 Processing sheet with id=AG6, first strand: chain 'F' and resid 18 through 23 Processing sheet with id=AG7, first strand: chain 'F' and resid 118 through 122 removed outlier: 5.945A pdb=" N TYR F 176 " --> pdb=" O ASP F 142 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 118 through 122 removed outlier: 5.945A pdb=" N TYR F 176 " --> pdb=" O ASP F 142 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'F' and resid 157 through 159 removed outlier: 4.231A pdb=" N TRP F 152 " --> pdb=" O VAL F 159 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AH2, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.563A pdb=" N TRP H 34 " --> pdb=" O ASN H 50 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ASN H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N TYR H 52 " --> pdb=" O SER H 56 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N SER H 56 " --> pdb=" O TYR H 52 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AH4, first strand: chain 'H' and resid 128 through 132 removed outlier: 5.931A pdb=" N TYR H 184 " --> pdb=" O ASP H 152 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'H' and resid 128 through 132 removed outlier: 5.931A pdb=" N TYR H 184 " --> pdb=" O ASP H 152 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'H' and resid 159 through 162 removed outlier: 4.623A pdb=" N TYR H 202 " --> pdb=" O VAL H 219 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AH8, first strand: chain 'J' and resid 11 through 12 removed outlier: 6.565A pdb=" N TRP J 34 " --> pdb=" O ASN J 50 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ASN J 50 " --> pdb=" O TRP J 34 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N TYR J 52 " --> pdb=" O SER J 56 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N SER J 56 " --> pdb=" O TYR J 52 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'J' and resid 11 through 12 Processing sheet with id=AI1, first strand: chain 'J' and resid 128 through 132 removed outlier: 5.107A pdb=" N ALA J 145 " --> pdb=" O VAL J 192 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL J 192 " --> pdb=" O ALA J 145 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N GLY J 147 " --> pdb=" O VAL J 190 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL J 190 " --> pdb=" O GLY J 147 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N LEU J 149 " --> pdb=" O SER J 188 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N SER J 188 " --> pdb=" O LEU J 149 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N LYS J 151 " --> pdb=" O LEU J 186 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N LEU J 186 " --> pdb=" O LYS J 151 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'J' and resid 128 through 132 removed outlier: 5.107A pdb=" N ALA J 145 " --> pdb=" O VAL J 192 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL J 192 " --> pdb=" O ALA J 145 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N GLY J 147 " --> pdb=" O VAL J 190 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL J 190 " --> pdb=" O GLY J 147 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N LEU J 149 " --> pdb=" O SER J 188 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N SER J 188 " --> pdb=" O LEU J 149 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N LYS J 151 " --> pdb=" O LEU J 186 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N LEU J 186 " --> pdb=" O LYS J 151 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'J' and resid 159 through 162 removed outlier: 4.616A pdb=" N TYR J 202 " --> pdb=" O VAL J 219 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'K' and resid 9 through 12 removed outlier: 6.362A pdb=" N TRP K 37 " --> pdb=" O MET K 49 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'K' and resid 9 through 12 Processing sheet with id=AI6, first strand: chain 'K' and resid 18 through 23 Processing sheet with id=AI7, first strand: chain 'K' and resid 118 through 122 removed outlier: 5.947A pdb=" N TYR K 176 " --> pdb=" O ASP K 142 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'K' and resid 118 through 122 removed outlier: 5.947A pdb=" N TYR K 176 " --> pdb=" O ASP K 142 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'K' and resid 157 through 159 removed outlier: 4.231A pdb=" N TRP K 152 " --> pdb=" O VAL K 159 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.366A pdb=" N TRP L 37 " --> pdb=" O MET L 49 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AJ3, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AJ4, first strand: chain 'L' and resid 118 through 122 removed outlier: 5.947A pdb=" N TYR L 176 " --> pdb=" O ASP L 142 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'L' and resid 118 through 122 removed outlier: 5.947A pdb=" N TYR L 176 " --> pdb=" O ASP L 142 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'L' and resid 157 through 159 removed outlier: 4.230A pdb=" N TRP L 152 " --> pdb=" O VAL L 159 " (cutoff:3.500A) 1595 hydrogen bonds defined for protein. 4155 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: 21.32 Time building geometry restraints manager: 14.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11157 1.34 - 1.46: 8324 1.46 - 1.58: 16333 1.58 - 1.70: 0 1.70 - 1.81: 171 Bond restraints: 35985 Sorted by residual: bond pdb=" C1 NAG B1207 " pdb=" O5 NAG B1207 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.75e+00 bond pdb=" C1 NAG C1207 " pdb=" O5 NAG C1207 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.75e+00 bond pdb=" C1 NAG A1207 " pdb=" O5 NAG A1207 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.54e+00 bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.24e+00 bond pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.22e+00 ... (remaining 35980 not shown) Histogram of bond angle deviations from ideal: 99.99 - 106.79: 1163 106.79 - 113.60: 20130 113.60 - 120.40: 12568 120.40 - 127.21: 14792 127.21 - 134.01: 370 Bond angle restraints: 49023 Sorted by residual: angle pdb=" N ILE B 839 " pdb=" CA ILE B 839 " pdb=" C ILE B 839 " ideal model delta sigma weight residual 113.47 108.23 5.24 1.01e+00 9.80e-01 2.69e+01 angle pdb=" N ILE A 839 " pdb=" CA ILE A 839 " pdb=" C ILE A 839 " ideal model delta sigma weight residual 113.47 108.25 5.22 1.01e+00 9.80e-01 2.67e+01 angle pdb=" N ILE C 839 " pdb=" CA ILE C 839 " pdb=" C ILE C 839 " ideal model delta sigma weight residual 113.47 108.30 5.17 1.01e+00 9.80e-01 2.62e+01 angle pdb=" C THR B 310 " pdb=" N SER B 311 " pdb=" CA SER B 311 " ideal model delta sigma weight residual 122.08 117.33 4.75 1.84e+00 2.95e-01 6.65e+00 angle pdb=" C THR C 310 " pdb=" N SER C 311 " pdb=" CA SER C 311 " ideal model delta sigma weight residual 122.08 117.37 4.71 1.84e+00 2.95e-01 6.57e+00 ... (remaining 49018 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 21171 17.90 - 35.79: 733 35.79 - 53.69: 154 53.69 - 71.59: 25 71.59 - 89.49: 15 Dihedral angle restraints: 22098 sinusoidal: 9111 harmonic: 12987 Sorted by residual: dihedral pdb=" CA THR A 594 " pdb=" C THR A 594 " pdb=" N PRO A 595 " pdb=" CA PRO A 595 " ideal model delta harmonic sigma weight residual 180.00 160.25 19.75 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA THR B 594 " pdb=" C THR B 594 " pdb=" N PRO B 595 " pdb=" CA PRO B 595 " ideal model delta harmonic sigma weight residual 180.00 160.25 19.75 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA THR C 594 " pdb=" C THR C 594 " pdb=" N PRO C 595 " pdb=" CA PRO C 595 " ideal model delta harmonic sigma weight residual 180.00 160.41 19.59 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 22095 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 3502 0.032 - 0.063: 1434 0.063 - 0.095: 447 0.095 - 0.127: 317 0.127 - 0.159: 36 Chirality restraints: 5736 Sorted by residual: chirality pdb=" C1 NAG C1203 " pdb=" ND2 ASN C 598 " pdb=" C2 NAG C1203 " pdb=" O5 NAG C1203 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.28e-01 chirality pdb=" C1 NAG A1203 " pdb=" ND2 ASN A 598 " pdb=" C2 NAG A1203 " pdb=" O5 NAG A1203 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.22e-01 chirality pdb=" C1 NAG B1203 " pdb=" ND2 ASN B 598 " pdb=" C2 NAG B1203 " pdb=" O5 NAG B1203 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.15e-01 ... (remaining 5733 not shown) Planarity restraints: 6279 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU J 156 " 0.030 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO J 157 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO J 157 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO J 157 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU E 156 " -0.030 5.00e-02 4.00e+02 4.44e-02 3.16e+00 pdb=" N PRO E 157 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO E 157 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 157 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU H 156 " 0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO H 157 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO H 157 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO H 157 " 0.022 5.00e-02 4.00e+02 ... (remaining 6276 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 6173 2.77 - 3.30: 31759 3.30 - 3.84: 57175 3.84 - 4.37: 69651 4.37 - 4.90: 121486 Nonbonded interactions: 286244 Sorted by model distance: nonbonded pdb=" O THR C 388 " pdb=" OG1 THR C 518 " model vdw 2.238 2.440 nonbonded pdb=" O THR A 388 " pdb=" OG1 THR A 518 " model vdw 2.240 2.440 nonbonded pdb=" O THR B 388 " pdb=" OG1 THR B 518 " model vdw 2.240 2.440 nonbonded pdb=" O THR B 103 " pdb=" NH1 ARG B 232 " model vdw 2.256 2.520 nonbonded pdb=" O THR C 103 " pdb=" NH1 ARG C 232 " model vdw 2.260 2.520 ... (remaining 286239 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'I' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'F' selection = chain 'K' selection = chain 'L' } 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: 5.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 21.230 Check model and map are aligned: 0.630 Set scattering table: 0.290 Process input model: 100.770 Find NCS groups from input model: 2.320 Set up NCS constraints: 0.400 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 143.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 35985 Z= 0.261 Angle : 0.519 6.261 49023 Z= 0.269 Chirality : 0.044 0.159 5736 Planarity : 0.004 0.045 6240 Dihedral : 9.970 89.486 13608 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.70 % Allowed : 3.21 % Favored : 96.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.13), residues: 4425 helix: 1.92 (0.19), residues: 759 sheet: 0.63 (0.14), residues: 1290 loop : -0.62 (0.13), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 431 HIS 0.003 0.000 HIS B1059 PHE 0.014 0.001 PHE A 372 TYR 0.016 0.001 TYR A1062 ARG 0.003 0.000 ARG C1009 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8850 Ramachandran restraints generated. 4425 Oldfield, 0 Emsley, 4425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8850 Ramachandran restraints generated. 4425 Oldfield, 0 Emsley, 4425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 325 time to evaluate : 4.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLN cc_start: 0.8836 (tt0) cc_final: 0.8580 (tm-30) REVERT: A 152 PHE cc_start: 0.6813 (p90) cc_final: 0.6575 (p90) REVERT: A 352 ARG cc_start: 0.8681 (ttp80) cc_final: 0.8440 (ttt-90) REVERT: A 569 ASP cc_start: 0.8297 (t70) cc_final: 0.7859 (t0) REVERT: A 656 GLU cc_start: 0.8269 (mt-10) cc_final: 0.8022 (mp0) REVERT: A 1137 GLN cc_start: 0.9029 (tp40) cc_final: 0.8607 (tm-30) REVERT: B 49 GLN cc_start: 0.8861 (tt0) cc_final: 0.8486 (tm-30) REVERT: B 152 PHE cc_start: 0.6780 (p90) cc_final: 0.6534 (p90) REVERT: B 352 ARG cc_start: 0.8662 (ttp80) cc_final: 0.8421 (ttt-90) REVERT: B 569 ASP cc_start: 0.8246 (t70) cc_final: 0.7795 (t0) REVERT: B 656 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7954 (mp0) REVERT: B 1137 GLN cc_start: 0.9023 (tp40) cc_final: 0.8560 (tm-30) REVERT: C 49 GLN cc_start: 0.8821 (tt0) cc_final: 0.8528 (tm-30) REVERT: C 152 PHE cc_start: 0.6684 (p90) cc_final: 0.6444 (p90) REVERT: C 569 ASP cc_start: 0.8376 (t70) cc_final: 0.8035 (t0) REVERT: C 656 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7962 (mp0) REVERT: C 775 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8199 (mm-30) REVERT: C 1137 GLN cc_start: 0.9028 (tp40) cc_final: 0.8557 (tm-30) REVERT: E 162 TRP cc_start: 0.7455 (m100) cc_final: 0.7158 (m100) REVERT: E 205 ASN cc_start: 0.7024 (t0) cc_final: 0.6765 (m110) REVERT: F 195 TYR cc_start: 0.5216 (m-80) cc_final: 0.4740 (m-80) REVERT: J 205 ASN cc_start: 0.6956 (t0) cc_final: 0.6717 (m110) REVERT: K 195 TYR cc_start: 0.5404 (m-80) cc_final: 0.5069 (m-80) REVERT: L 85 GLU cc_start: 0.8614 (tt0) cc_final: 0.8389 (mt-10) outliers start: 27 outliers final: 10 residues processed: 343 average time/residue: 1.4252 time to fit residues: 595.6712 Evaluate side-chains 185 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 175 time to evaluate : 4.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 704 ASN Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain B residue 704 ASN Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain C residue 704 ASN Chi-restraints excluded: chain C residue 1117 VAL Chi-restraints excluded: chain F residue 91 CYS Chi-restraints excluded: chain K residue 91 CYS Chi-restraints excluded: chain L residue 91 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 374 optimal weight: 0.0000 chunk 336 optimal weight: 10.0000 chunk 186 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 chunk 227 optimal weight: 10.0000 chunk 179 optimal weight: 0.8980 chunk 348 optimal weight: 40.0000 chunk 134 optimal weight: 0.0000 chunk 211 optimal weight: 6.9990 chunk 259 optimal weight: 7.9990 chunk 403 optimal weight: 9.9990 overall best weight: 2.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 HIS A 309 GLN A 400 ASN A 757 GLN A1000 GLN B 309 GLN B 400 ASN B 608 GLN B 757 GLN B1000 GLN C 202 HIS C 400 ASN C 757 GLN C1000 GLN E 50 ASN E 58 ASN ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 200 GLN E 207 ASN F 39 GLN ** F 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 ASN H 58 ASN H 200 GLN ** H 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 50 ASN J 58 ASN ** J 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 200 GLN J 207 ASN K 16 GLN K 39 GLN ** K 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN ** L 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 188 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.0950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 35985 Z= 0.272 Angle : 0.513 6.309 49023 Z= 0.268 Chirality : 0.044 0.170 5736 Planarity : 0.004 0.050 6240 Dihedral : 5.936 55.428 5878 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.63 % Allowed : 6.63 % Favored : 91.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.13), residues: 4425 helix: 2.10 (0.19), residues: 759 sheet: 0.69 (0.14), residues: 1263 loop : -0.57 (0.13), residues: 2403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP H 162 HIS 0.003 0.001 HIS B1059 PHE 0.024 0.001 PHE F 122 TYR 0.018 0.001 TYR K 176 ARG 0.008 0.000 ARG C 232 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8850 Ramachandran restraints generated. 4425 Oldfield, 0 Emsley, 4425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8850 Ramachandran restraints generated. 4425 Oldfield, 0 Emsley, 4425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 192 time to evaluate : 4.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLN cc_start: 0.8839 (tt0) cc_final: 0.8581 (tm-30) REVERT: A 152 PHE cc_start: 0.6836 (p90) cc_final: 0.6606 (p90) REVERT: A 466 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7856 (mp0) REVERT: A 569 ASP cc_start: 0.8303 (t70) cc_final: 0.7819 (t0) REVERT: A 656 GLU cc_start: 0.8273 (mt-10) cc_final: 0.8031 (mp0) REVERT: A 1137 GLN cc_start: 0.9046 (tp40) cc_final: 0.8599 (tm-30) REVERT: B 49 GLN cc_start: 0.8867 (tt0) cc_final: 0.8516 (tm-30) REVERT: B 352 ARG cc_start: 0.8749 (ttp80) cc_final: 0.8505 (ttt-90) REVERT: B 466 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7961 (mp0) REVERT: B 472 ASN cc_start: 0.8532 (OUTLIER) cc_final: 0.8245 (m-40) REVERT: B 569 ASP cc_start: 0.8311 (t70) cc_final: 0.7924 (t0) REVERT: B 656 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7942 (mp0) REVERT: B 1137 GLN cc_start: 0.9037 (tp40) cc_final: 0.8580 (tm-30) REVERT: C 49 GLN cc_start: 0.8830 (tt0) cc_final: 0.8519 (tm-30) REVERT: C 152 PHE cc_start: 0.6713 (p90) cc_final: 0.6455 (p90) REVERT: C 466 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7834 (mp0) REVERT: C 569 ASP cc_start: 0.8417 (t70) cc_final: 0.8074 (t0) REVERT: C 656 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7969 (mp0) REVERT: C 775 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8230 (mm-30) REVERT: C 1137 GLN cc_start: 0.9058 (tp40) cc_final: 0.8591 (tm-30) REVERT: E 205 ASN cc_start: 0.6987 (t0) cc_final: 0.6771 (m110) REVERT: F 195 TYR cc_start: 0.5230 (m-80) cc_final: 0.4568 (m-80) REVERT: J 205 ASN cc_start: 0.6916 (t0) cc_final: 0.6696 (m110) REVERT: K 85 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8502 (mt-10) REVERT: K 195 TYR cc_start: 0.5179 (m-80) cc_final: 0.4781 (m-80) REVERT: L 128 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7674 (pp20) outliers start: 63 outliers final: 24 residues processed: 235 average time/residue: 1.3641 time to fit residues: 397.9285 Evaluate side-chains 195 residues out of total 3864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 166 time to evaluate : 4.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 472 ASN Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 704 ASN Chi-restraints excluded: chain B residue 1076 ILE Chi-restraints excluded: chain B residue 1087 GLU Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain C residue 466 GLU Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 704 ASN Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1117 VAL Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 207 ASN Chi-restraints excluded: chain F residue 91 CYS Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 205 ASN Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain J residue 207 ASN Chi-restraints excluded: chain K residue 91 CYS Chi-restraints excluded: chain K residue 140 ILE Chi-restraints excluded: chain L residue 91 CYS Chi-restraints excluded: chain L residue 128 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 224 optimal weight: 6.9990 chunk 125 optimal weight: 0.0770 chunk 335 optimal weight: 10.0000 chunk 274 optimal weight: 4.9990 chunk 111 optimal weight: 10.0000 chunk 403 optimal weight: 7.9990 chunk 436 optimal weight: 40.0000 chunk 359 optimal weight: 30.0000 chunk 400 optimal weight: 20.0000 chunk 137 optimal weight: 3.9990 chunk 324 optimal weight: 10.0000 overall best weight: 4.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: