Starting phenix.real_space_refine on Tue Aug 26 06:11:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zbz_39917/08_2025/8zbz_39917.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zbz_39917/08_2025/8zbz_39917.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zbz_39917/08_2025/8zbz_39917.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zbz_39917/08_2025/8zbz_39917.map" model { file = "/net/cci-nas-00/data/ceres_data/8zbz_39917/08_2025/8zbz_39917.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zbz_39917/08_2025/8zbz_39917.cif" } resolution = 4.71 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= 0.004 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 21647 2.51 5 N 5562 2.21 5 O 6646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33999 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 7781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7781 Classifications: {'peptide': 993} Link IDs: {'PTRANS': 55, 'TRANS': 937} Chain breaks: 10 Chain: "B" Number of atoms: 7793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 994, 7793 Classifications: {'peptide': 994} Link IDs: {'PTRANS': 55, 'TRANS': 938} Chain breaks: 10 Chain: "C" Number of atoms: 7781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7781 Classifications: {'peptide': 993} Link IDs: {'PTRANS': 55, 'TRANS': 937} Chain breaks: 10 Chain: "D" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1591 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 195} Chain breaks: 1 Chain: "E" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1679 Classifications: {'peptide': 221} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 208} Chain breaks: 1 Chain: "M" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1591 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 195} Chain breaks: 1 Chain: "N" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1591 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 195} Chain breaks: 1 Chain: "Q" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1679 Classifications: {'peptide': 221} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 208} Chain breaks: 1 Chain: "R" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1679 Classifications: {'peptide': 221} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 208} Chain breaks: 1 Chain: "F" 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: "H" 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" 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: "K" 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: "L" 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} 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: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 6.85, per 1000 atoms: 0.20 Number of scatterers: 33999 At special positions: 0 Unit cell: (174.24, 162.36, 241.56, 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 6646 8.00 N 5562 7.00 C 21647 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.04 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 145 " - pdb=" SG CYS D 204 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 103 " - pdb=" SG CYS E 108 " distance=2.03 Simple disulfide: pdb=" SG CYS E 154 " - pdb=" SG CYS E 210 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 89 " distance=2.03 Simple disulfide: pdb=" SG CYS M 145 " - pdb=" SG CYS M 204 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 89 " distance=2.03 Simple disulfide: pdb=" SG CYS N 145 " - pdb=" SG CYS N 204 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 96 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 103 " - pdb=" SG CYS Q 108 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 154 " - pdb=" SG CYS Q 210 " distance=2.03 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 103 " - pdb=" SG CYS R 108 " distance=2.03 Simple disulfide: pdb=" SG CYS R 154 " - pdb=" SG CYS R 210 " 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 BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " 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 W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A 61 " " NAG A1308 " - " ASN A 234 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 343 " " NAG C1301 " - " ASN C 331 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 122 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C 343 " " NAG C1310 " - " ASN C 282 " " NAG C1311 " - " ASN C 603 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG H 1 " - " ASN A1074 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN A1134 " " NAG K 1 " - " ASN B 122 " " NAG L 1 " - " ASN B 709 " " NAG O 1 " - " ASN B 717 " " NAG P 1 " - " ASN B 801 " " NAG S 1 " - " ASN B1074 " " NAG T 1 " - " ASN B1098 " " NAG U 1 " - " ASN B1134 " " NAG V 1 " - " ASN B 331 " " NAG W 1 " - " ASN C 717 " " NAG X 1 " - " ASN C 801 " " NAG Y 1 " - " ASN C1098 " " NAG Z 1 " - " ASN C1134 " Time building additional restraints: 3.03 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 715.3 nanoseconds 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8000 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 76 sheets defined 17.2% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 366 through 370 removed outlier: 4.328A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASN A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 366 through 370' Processing helix chain 'A' and resid 738 through 743 Processing helix chain 'A' and resid 746 through 753 removed outlier: 4.070A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 783 removed outlier: 3.729A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 883 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 918 removed outlier: 3.549A pdb=" N VAL A 915 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU A 916 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N TYR A 917 " --> pdb=" O ASN A 914 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU A 918 " --> pdb=" O VAL A 915 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 912 through 918' Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.839A pdb=" N SER A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.594A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 984 removed outlier: 3.788A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG A 983 " --> pdb=" O ASP A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.159A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 344 Processing helix chain 'B' and resid 364 through 369 removed outlier: 4.279A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.543A pdb=" N LYS B 386 " --> pdb=" O SER B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 5.070A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.633A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 757 removed outlier: 3.991A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 781 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.507A pdb=" N ILE B 870 " --> pdb=" O THR B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.896A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 916 removed outlier: 3.679A pdb=" N VAL B 915 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU B 916 " --> pdb=" O GLN B 913 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 912 through 916' Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 966 removed outlier: 3.725A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.064A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1142 through 1147 removed outlier: 3.695A pdb=" N ASP B1146 " --> pdb=" O PRO B1143 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER B1147 " --> pdb=" O GLU B1144 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.841A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 371 removed outlier: 3.689A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE C 371 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.638A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 743 Processing helix chain 'C' and resid 746 through 753 removed outlier: 3.656A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 754 through 757 Processing helix chain 'C' and resid 758 through 781 removed outlier: 4.220A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 910 removed outlier: 3.541A pdb=" N GLN C 901 " --> pdb=" O PRO C 897 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 918 removed outlier: 3.511A pdb=" N VAL C 915 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR C 917 " --> pdb=" O ASN C 914 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU C 918 " --> pdb=" O VAL C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 967 removed outlier: 3.525A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 979 through 984 Processing helix chain 'C' and resid 989 through 1033 Processing helix chain 'D' and resid 132 through 137 removed outlier: 3.800A pdb=" N LEU D 136 " --> pdb=" O SER D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 199 removed outlier: 3.751A pdb=" N HIS D 199 " --> pdb=" O GLN D 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 112 removed outlier: 3.771A pdb=" N ARG E 110 " --> pdb=" O SER E 107 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET E 112 " --> pdb=" O GLN E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 172 No H-bonds generated for 'chain 'E' and resid 170 through 172' Processing helix chain 'E' and resid 199 through 204 removed outlier: 3.699A pdb=" N LEU E 203 " --> pdb=" O PRO E 199 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY E 204 " --> pdb=" O SER E 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 199 through 204' Processing helix chain 'M' and resid 134 through 139 removed outlier: 3.716A pdb=" N GLN M 137 " --> pdb=" O GLU M 134 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN M 139 " --> pdb=" O LEU M 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 192 through 197 removed outlier: 3.508A pdb=" N LYS M 197 " --> pdb=" O PRO M 193 " (cutoff:3.500A) Processing helix chain 'N' and resid 132 through 137 removed outlier: 3.608A pdb=" N LEU N 136 " --> pdb=" O SER N 132 " (cutoff:3.500A) Processing helix chain 'N' and resid 192 through 198 Processing helix chain 'Q' and resid 87 through 91 removed outlier: 3.796A pdb=" N THR Q 91 " --> pdb=" O SER Q 88 " (cutoff:3.500A) Processing helix chain 'Q' and resid 170 through 172 No H-bonds generated for 'chain 'Q' and resid 170 through 172' Processing helix chain 'R' and resid 105 through 109 removed outlier: 3.747A pdb=" N GLN R 109 " --> pdb=" O ASN R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 170 through 172 No H-bonds generated for 'chain 'R' and resid 170 through 172' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.400A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.568A pdb=" N PHE A 43 " --> pdb=" O PHE B 565 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL B 576 " --> pdb=" O LEU B 585 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 49 through 55 removed outlier: 3.528A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.851A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG A 237 " --> pdb=" O GLY A 107 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRP A 104 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ILE A 119 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 140 through 141 removed outlier: 3.912A pdb=" N PHE A 140 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG A 158 " --> pdb=" O PHE A 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 314 through 317 removed outlier: 6.843A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLN A 613 " --> pdb=" O GLY A 594 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.598A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 585 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL A 576 " --> pdb=" O LEU A 585 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 355 through 358 removed outlier: 3.845A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL A 510 " --> pdb=" O PHE A 400 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 355 through 358 removed outlier: 3.845A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE A 392 " --> pdb=" O VAL A 524 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.685A pdb=" N TYR A 453 " --> pdb=" O ARG A 493 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 660 removed outlier: 4.953A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 712 through 719 removed outlier: 7.147A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 722 through 728 removed outlier: 3.736A pdb=" N THR A 723 " --> pdb=" O HIS A1064 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N HIS A1064 " --> pdb=" O THR A 723 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL A1061 " --> pdb=" O GLN A1054 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 3.760A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 789 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 removed outlier: 3.578A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.573A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 49 through 55 removed outlier: 4.050A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE B 275 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS B 278 " --> pdb=" O ASP B 287 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.916A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 119 through 121 removed outlier: 4.191A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL B 127 " --> pdb=" O VAL B 120 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.031A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY B 593 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 356 through 357 removed outlier: 3.530A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TRP B 436 " --> pdb=" O ARG B 509 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 656 removed outlier: 5.447A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE B 666 " --> pdb=" O ILE B 670 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE B 664 " --> pdb=" O ALA B 672 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 713 through 728 removed outlier: 6.942A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL B1061 " --> pdb=" O GLN B1054 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AC9, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AD1, first strand: chain 'B' and resid 1076 through 1077 removed outlier: 3.640A pdb=" N VAL B1094 " --> pdb=" O THR B1105 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR B1105 " --> pdb=" O VAL B1094 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1121 removed outlier: 3.615A pdb=" N PHE B1121 " --> pdb=" O PHE B1089 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE B1089 " --> pdb=" O PHE B1121 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 28 through 31 removed outlier: 4.053A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 48 through 49 removed outlier: 3.850A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 48 through 49 removed outlier: 3.641A pdb=" N LYS C 278 " --> pdb=" O ASP C 287 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.835A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER C 116 " --> pdb=" O CYS C 131 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 207 through 209 removed outlier: 4.071A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS C 202 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE C 197 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 207 through 209 removed outlier: 3.729A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 313 through 317 removed outlier: 6.885A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.806A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.489A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 399 through 402 removed outlier: 3.543A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL C 510 " --> pdb=" O PHE C 400 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE C 402 " --> pdb=" O TYR C 508 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR C 508 " --> pdb=" O ILE C 402 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 539 through 543 removed outlier: 3.693A pdb=" N VAL C 539 " --> pdb=" O GLY C 550 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 655 through 656 removed outlier: 4.295A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE C 693 " --> pdb=" O SER C 673 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY C 667 " --> pdb=" O ILE C 670 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 712 through 713 removed outlier: 3.515A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR C1105 " --> pdb=" O VAL C1094 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 717 through 719 removed outlier: 3.759A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 717 through 719 removed outlier: 3.759A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 734 through 735 Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1122 removed outlier: 3.656A pdb=" N PHE C1121 " --> pdb=" O PHE C1089 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 17 through 22 removed outlier: 3.733A pdb=" N ALA D 72 " --> pdb=" O CYS D 22 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE D 64 " --> pdb=" O ALA D 75 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 46 through 50 removed outlier: 3.776A pdb=" N LEU D 48 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP D 93 " --> pdb=" O GLY D 98 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY D 98 " --> pdb=" O ASP D 93 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 125 through 129 removed outlier: 3.795A pdb=" N SER D 148 " --> pdb=" O SER D 125 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL D 144 " --> pdb=" O PHE D 129 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N TYR D 183 " --> pdb=" O ASP D 149 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU D 171 " --> pdb=" O TYR D 188 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 206 through 207 removed outlier: 4.709A pdb=" N VAL D 206 " --> pdb=" O VAL D 213 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL D 213 " --> pdb=" O VAL D 206 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'E' and resid 5 through 7 removed outlier: 3.887A pdb=" N VAL E 5 " --> pdb=" O LYS E 23 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS E 23 " --> pdb=" O VAL E 5 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL E 18 " --> pdb=" O LEU E 83 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET E 81 " --> pdb=" O VAL E 20 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.897A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N TRP E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ILE E 34 " --> pdb=" O TRP E 50 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL E 37 " --> pdb=" O PHE E 95 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN E 39 " --> pdb=" O VAL E 93 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL E 93 " --> pdb=" O GLN E 39 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N CYS E 96 " --> pdb=" O GLY E 118 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY E 118 " --> pdb=" O CYS E 96 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 150 through 153 Processing sheet with id=AG1, first strand: chain 'E' and resid 156 through 157 removed outlier: 4.035A pdb=" N VAL E 156 " --> pdb=" O LEU E 192 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU E 192 " --> pdb=" O VAL E 156 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N SER E 191 " --> pdb=" O VAL E 183 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL E 183 " --> pdb=" O SER E 191 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'E' and resid 166 through 168 removed outlier: 3.866A pdb=" N SER E 167 " --> pdb=" O ASN E 211 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN E 211 " --> pdb=" O SER E 167 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N CYS E 210 " --> pdb=" O LYS E 223 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS E 223 " --> pdb=" O CYS E 210 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'M' and resid 9 through 12 removed outlier: 4.289A pdb=" N THR M 108 " --> pdb=" O ALA M 10 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLY M 12 " --> pdb=" O THR M 108 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP M 86 " --> pdb=" O GLN M 39 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N TRP M 36 " --> pdb=" O LEU M 48 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'M' and resid 9 through 12 removed outlier: 4.289A pdb=" N THR M 108 " --> pdb=" O ALA M 10 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLY M 12 " --> pdb=" O THR M 108 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'M' and resid 18 through 23 removed outlier: 3.622A pdb=" N PHE M 64 " --> pdb=" O ALA M 75 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'M' and resid 128 through 129 removed outlier: 3.541A pdb=" N PHE M 129 " --> pdb=" O VAL M 144 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL M 144 " --> pdb=" O PHE M 129 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS M 145 " --> pdb=" O SER M 187 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N TYR M 183 " --> pdb=" O ASP M 149 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'M' and resid 141 through 142 Processing sheet with id=AG8, first strand: chain 'M' and resid 157 through 160 removed outlier: 3.900A pdb=" N LYS M 160 " --> pdb=" O SER M 203 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER M 203 " --> pdb=" O LYS M 160 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N CYS M 204 " --> pdb=" O LYS M 215 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LYS M 215 " --> pdb=" O CYS M 204 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL M 206 " --> pdb=" O VAL M 213 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL M 213 " --> pdb=" O VAL M 206 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'N' and resid 18 through 23 removed outlier: 3.836A pdb=" N ILE N 76 " --> pdb=" O VAL N 18 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE N 20 " --> pdb=" O LEU N 74 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'N' and resid 45 through 50 removed outlier: 7.019A pdb=" N TRP N 36 " --> pdb=" O LEU N 48 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN N 39 " --> pdb=" O ASP N 86 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASP N 86 " --> pdb=" O GLN N 39 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP N 93 " --> pdb=" O GLY N 98 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLY N 98 " --> pdb=" O ASP N 93 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'N' and resid 45 through 50 removed outlier: 7.019A pdb=" N TRP N 36 " --> pdb=" O LEU N 48 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN N 39 " --> pdb=" O ASP N 86 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASP N 86 " --> pdb=" O GLN N 39 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR N 105 " --> pdb=" O TYR N 87 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'N' and resid 125 through 129 removed outlier: 3.787A pdb=" N PHE N 129 " --> pdb=" O VAL N 144 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL N 144 " --> pdb=" O PHE N 129 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA N 184 " --> pdb=" O SER N 176 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'N' and resid 141 through 142 Processing sheet with id=AH5, first strand: chain 'N' and resid 171 through 172 Processing sheet with id=AH6, first strand: chain 'Q' and resid 46 through 47 removed outlier: 3.616A pdb=" N VAL Q 37 " --> pdb=" O PHE Q 95 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR Q 116 " --> pdb=" O ARG Q 98 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'Q' and resid 46 through 47 removed outlier: 3.616A pdb=" N VAL Q 37 " --> pdb=" O PHE Q 95 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA Q 92 " --> pdb=" O VAL Q 123 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL Q 123 " --> pdb=" O ALA Q 92 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR Q 94 " --> pdb=" O ALA Q 121 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA Q 121 " --> pdb=" O TYR Q 94 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'Q' and resid 68 through 70 removed outlier: 3.503A pdb=" N THR Q 69 " --> pdb=" O GLU Q 82 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU Q 82 " --> pdb=" O THR Q 69 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH8 Processing sheet with id=AH9, first strand: chain 'Q' and resid 165 through 168 removed outlier: 4.076A pdb=" N THR Q 165 " --> pdb=" O ASN Q 213 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL Q 212 " --> pdb=" O VAL Q 221 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL Q 221 " --> pdb=" O VAL Q 212 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N HIS Q 214 " --> pdb=" O THR Q 219 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR Q 219 " --> pdb=" O HIS Q 214 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'R' and resid 58 through 60 removed outlier: 3.822A pdb=" N ASN R 59 " --> pdb=" O TRP R 50 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TRP R 50 " --> pdb=" O ASN R 59 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N TRP R 36 " --> pdb=" O MET R 48 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N TRP R 50 " --> pdb=" O ILE R 34 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE R 34 " --> pdb=" O TRP R 50 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL R 93 " --> pdb=" O GLN R 39 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR R 116 " --> pdb=" O ARG R 98 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'R' and resid 71 through 72 removed outlier: 4.385A pdb=" N THR R 71 " --> pdb=" O TYR R 80 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR R 80 " --> pdb=" O THR R 71 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI2 Processing sheet with id=AI3, first strand: chain 'R' and resid 135 through 137 removed outlier: 4.361A pdb=" N LEU R 152 " --> pdb=" O VAL R 196 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL R 196 " --> pdb=" O LEU R 152 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'R' and resid 165 through 168 932 hydrogen bonds defined for protein. 2547 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: 7.91 Time building geometry restraints manager: 3.99 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: 10684 1.34 - 1.47: 8724 1.47 - 1.59: 15215 1.59 - 1.71: 0 1.71 - 1.84: 180 Bond restraints: 34803 Sorted by residual: bond pdb=" C PRO B 986 " pdb=" N PRO B 987 " ideal model delta sigma weight residual 1.335 1.382 -0.047 1.38e-02 5.25e+03 1.15e+01 bond pdb=" CG PRO Q 163 " pdb=" CD PRO Q 163 " ideal model delta sigma weight residual 1.512 1.446 0.066 2.70e-02 1.37e+03 5.96e+00 bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.71e+00 bond pdb=" C1 NAG A1308 " pdb=" O5 NAG A1308 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.03e+00 bond pdb=" C1 NAG L 1 " pdb=" O5 NAG L 1 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.88e+00 ... (remaining 34798 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 46172 2.01 - 4.02: 1059 4.02 - 6.03: 115 6.03 - 8.04: 32 8.04 - 10.05: 8 Bond angle restraints: 47386 Sorted by residual: angle pdb=" N PRO Q 163 " pdb=" CD PRO Q 163 " pdb=" CG PRO Q 163 " ideal model delta sigma weight residual 103.80 97.92 5.88 1.20e+00 6.94e-01 2.40e+01 angle pdb=" N THR A 470 " pdb=" CA THR A 470 " pdb=" C THR A 470 " ideal model delta sigma weight residual 114.56 109.52 5.04 1.27e+00 6.20e-01 1.57e+01 angle pdb=" CA PRO Q 163 " pdb=" N PRO Q 163 " pdb=" CD PRO Q 163 " ideal model delta sigma weight residual 111.50 105.97 5.53 1.40e+00 5.10e-01 1.56e+01 angle pdb=" CB PRO Q 163 " pdb=" CG PRO Q 163 " pdb=" CD PRO Q 163 " ideal model delta sigma weight residual 105.40 96.74 8.66 2.30e+00 1.89e-01 1.42e+01 angle pdb=" C GLU Q 162 " pdb=" N PRO Q 163 " pdb=" CD PRO Q 163 " ideal model delta sigma weight residual 120.60 112.42 8.18 2.20e+00 2.07e-01 1.38e+01 ... (remaining 47381 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.80: 20005 21.80 - 43.60: 1272 43.60 - 65.40: 146 65.40 - 87.21: 76 87.21 - 109.01: 13 Dihedral angle restraints: 21512 sinusoidal: 9083 harmonic: 12429 Sorted by residual: dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual 93.00 9.77 83.23 1 1.00e+01 1.00e-02 8.47e+01 dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 12.77 80.23 1 1.00e+01 1.00e-02 7.97e+01 dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual -86.00 -8.43 -77.57 1 1.00e+01 1.00e-02 7.53e+01 ... (remaining 21509 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 5490 0.130 - 0.260: 38 0.260 - 0.390: 5 0.390 - 0.521: 1 0.521 - 0.651: 2 Chirality restraints: 5536 Sorted by residual: chirality pdb=" C1 NAG S 1 " pdb=" ND2 ASN B1074 " pdb=" C2 NAG S 1 " pdb=" O5 NAG S 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.75 -0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN A1134 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-01 2.50e+01 9.61e+00 chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN B 122 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.56e+00 ... (remaining 5533 not shown) Planarity restraints: 6050 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1304 " 0.336 2.00e-02 2.50e+03 2.92e-01 1.07e+03 pdb=" C7 NAG C1304 " -0.075 2.00e-02 2.50e+03 pdb=" C8 NAG C1304 " 0.087 2.00e-02 2.50e+03 pdb=" N2 NAG C1304 " -0.520 2.00e-02 2.50e+03 pdb=" O7 NAG C1304 " 0.171 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1305 " 0.327 2.00e-02 2.50e+03 2.84e-01 1.01e+03 pdb=" C7 NAG B1305 " -0.073 2.00e-02 2.50e+03 pdb=" C8 NAG B1305 " 0.054 2.00e-02 2.50e+03 pdb=" N2 NAG B1305 " -0.501 2.00e-02 2.50e+03 pdb=" O7 NAG B1305 " 0.193 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU Q 162 " -0.069 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO Q 163 " 0.173 5.00e-02 4.00e+02 pdb=" CA PRO Q 163 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO Q 163 " -0.045 5.00e-02 4.00e+02 ... (remaining 6047 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 192 2.54 - 3.13: 23570 3.13 - 3.72: 50526 3.72 - 4.31: 66147 4.31 - 4.90: 110919 Nonbonded interactions: 251354 Sorted by model distance: nonbonded pdb=" OG SER Q 126 " pdb=" CZ PHE Q 160 " model vdw 1.945 3.340 nonbonded pdb=" OG1 THR A 323 " pdb=" OE1 GLU A 324 " model vdw 2.222 3.040 nonbonded pdb=" OG SER Q 126 " pdb=" CE1 PHE Q 160 " model vdw 2.252 3.340 nonbonded pdb=" OH TYR B 756 " pdb=" OD1 ASP B 994 " model vdw 2.257 3.040 nonbonded pdb=" OG SER A1030 " pdb=" OD2 ASP B1041 " model vdw 2.259 3.040 ... (remaining 251349 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 142 or resid 155 through 210 or resid 216 throu \ gh 245 or resid 263 through 1305)) selection = (chain 'B' and (resid 27 through 95 or resid 100 through 245 or resid 263 throug \ h 1305)) selection = (chain 'C' and (resid 27 through 142 or resid 155 through 210 or resid 216 throu \ gh 245 or resid 263 through 1305)) } ncs_group { reference = chain 'D' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'E' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Z' } ncs_group { reference = chain 'I' selection = chain 'Y' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 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: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 31.120 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.120 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 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 : 0.003 0.066 34914 Z= 0.182 Angle : 0.706 12.724 47668 Z= 0.355 Chirality : 0.050 0.651 5536 Planarity : 0.008 0.292 6009 Dihedral : 14.174 109.008 13359 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.11 % Allowed : 0.43 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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 aren not related in a simple way. whole: -1.66 (0.12), residues: 4192 helix: -0.17 (0.19), residues: 645 sheet: 0.07 (0.20), residues: 701 loop : -1.75 (0.11), residues: 2846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG R 98 TYR 0.025 0.001 TYR D 37 PHE 0.042 0.001 PHE C 55 TRP 0.020 0.001 TRP M 196 HIS 0.006 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00349 (34803) covalent geometry : angle 0.68765 (47386) SS BOND : bond 0.00342 ( 51) SS BOND : angle 0.86858 ( 102) hydrogen bonds : bond 0.23992 ( 907) hydrogen bonds : angle 9.05284 ( 2547) link_BETA1-4 : bond 0.00566 ( 19) link_BETA1-4 : angle 2.20755 ( 57) link_NAG-ASN : bond 0.00588 ( 41) link_NAG-ASN : angle 2.84772 ( 123) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 207 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.7775 (mm) cc_final: 0.7414 (mm) REVERT: A 984 LEU cc_start: 0.7664 (mm) cc_final: 0.7121 (tp) REVERT: A 985 ASP cc_start: 0.9151 (m-30) cc_final: 0.8774 (t0) REVERT: B 238 PHE cc_start: 0.8320 (t80) cc_final: 0.8024 (t80) REVERT: B 497 PHE cc_start: 0.4958 (m-10) cc_final: 0.4532 (m-10) REVERT: B 498 ARG cc_start: 0.6442 (mmt-90) cc_final: 0.4804 (mmp80) REVERT: B 562 PHE cc_start: 0.7341 (p90) cc_final: 0.7091 (p90) REVERT: B 712 ILE cc_start: 0.8725 (tt) cc_final: 0.8468 (tt) REVERT: B 868 GLU cc_start: 0.8145 (pm20) cc_final: 0.7880 (mp0) REVERT: C 141 LEU cc_start: 0.8375 (mm) cc_final: 0.8031 (tp) REVERT: C 1018 ILE cc_start: 0.8841 (tp) cc_final: 0.8487 (tp) REVERT: C 1041 ASP cc_start: 0.7391 (t0) cc_final: 0.6888 (t0) REVERT: D 150 PHE cc_start: 0.6463 (p90) cc_final: 0.5812 (p90) REVERT: E 73 ASP cc_start: 0.6237 (t0) cc_final: 0.5984 (t0) REVERT: E 215 LYS cc_start: 0.7390 (pttp) cc_final: 0.6407 (tttp) outliers start: 4 outliers final: 1 residues processed: 211 average time/residue: 0.1776 time to fit residues: 64.6257 Evaluate side-chains 134 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 133 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 50.0000 chunk 424 optimal weight: 8.9990 chunk 155 optimal weight: 7.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN A 774 GLN B 66 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1108 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 644 GLN C 954 HIS ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 ASN ** D 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 GLN M 16 GLN N 28 ASN N 38 GLN Q 6 GLN R 43 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.081923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.061784 restraints weight = 213483.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.061343 restraints weight = 159818.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.061366 restraints weight = 127272.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.061431 restraints weight = 123556.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.061579 restraints weight = 109254.252| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 34914 Z= 0.237 Angle : 0.686 11.387 47668 Z= 0.346 Chirality : 0.047 0.464 5536 Planarity : 0.005 0.077 6009 Dihedral : 6.911 58.953 5818 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.11 % Allowed : 6.35 % Favored : 93.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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 aren not related in a simple way. whole: -1.31 (0.13), residues: 4192 helix: 0.57 (0.21), residues: 656 sheet: -0.16 (0.18), residues: 836 loop : -1.56 (0.12), residues: 2700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C1000 TYR 0.023 0.002 TYR C 313 PHE 0.021 0.002 PHE C 92 TRP 0.015 0.002 TRP C 353 HIS 0.008 0.002 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00512 (34803) covalent geometry : angle 0.66935 (47386) SS BOND : bond 0.00440 ( 51) SS BOND : angle 1.43631 ( 102) hydrogen bonds : bond 0.05009 ( 907) hydrogen bonds : angle 6.51997 ( 2547) link_BETA1-4 : bond 0.00417 ( 19) link_BETA1-4 : angle 1.93594 ( 57) link_NAG-ASN : bond 0.00648 ( 41) link_NAG-ASN : angle 2.52413 ( 123) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 164 time to evaluate : 1.154 Fit side-chains REVERT: A 429 PHE cc_start: 0.7379 (t80) cc_final: 0.6844 (t80) REVERT: A 1033 VAL cc_start: 0.9010 (t) cc_final: 0.8747 (t) REVERT: B 238 PHE cc_start: 0.8422 (t80) cc_final: 0.7995 (t80) REVERT: B 562 PHE cc_start: 0.7588 (p90) cc_final: 0.7264 (p90) REVERT: B 1050 MET cc_start: 0.8490 (tmm) cc_final: 0.8272 (tmm) REVERT: C 613 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.7714 (pp30) REVERT: C 1041 ASP cc_start: 0.7516 (t0) cc_final: 0.7230 (t70) REVERT: D 52 ASN cc_start: 0.4829 (t160) cc_final: 0.4572 (m-40) REVERT: E 210 CYS cc_start: 0.3786 (t) cc_final: 0.3336 (t) REVERT: N 188 TYR cc_start: 0.1701 (m-80) cc_final: 0.0658 (t80) REVERT: R 64 PHE cc_start: 0.6863 (m-80) cc_final: 0.6534 (m-80) REVERT: R 159 TYR cc_start: 0.5419 (p90) cc_final: 0.5027 (p90) outliers start: 4 outliers final: 0 residues processed: 168 average time/residue: 0.1859 time to fit residues: 54.4150 Evaluate side-chains 118 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 117 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 235 optimal weight: 2.9990 chunk 394 optimal weight: 5.9990 chunk 200 optimal weight: 8.9990 chunk 221 optimal weight: 20.0000 chunk 241 optimal weight: 5.9990 chunk 401 optimal weight: 30.0000 chunk 276 optimal weight: 3.9990 chunk 266 optimal weight: 8.9990 chunk 391 optimal weight: 9.9990 chunk 114 optimal weight: 8.9990 chunk 293 optimal weight: 0.4980 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 907 ASN B 957 GLN ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 613 GLN ** C 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 GLN E 178 HIS ** M 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN Q 6 GLN R 43 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.081442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.062211 restraints weight = 216223.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.061131 restraints weight = 201293.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.061139 restraints weight = 180501.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.061425 restraints weight = 158406.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.061504 restraints weight = 137595.996| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 34914 Z= 0.189 Angle : 0.621 10.422 47668 Z= 0.314 Chirality : 0.046 0.403 5536 Planarity : 0.005 0.072 6009 Dihedral : 6.395 57.420 5818 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.05 % Allowed : 5.22 % Favored : 94.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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 aren not related in a simple way. whole: -1.31 (0.13), residues: 4192 helix: 0.64 (0.20), residues: 663 sheet: -0.22 (0.17), residues: 866 loop : -1.57 (0.12), residues: 2663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 346 TYR 0.035 0.002 TYR D 50 PHE 0.019 0.002 PHE R 29 TRP 0.026 0.002 TRP A 886 HIS 0.016 0.001 HIS C 954 Details of bonding type rmsd covalent geometry : bond 0.00411 (34803) covalent geometry : angle 0.60261 (47386) SS BOND : bond 0.00437 ( 51) SS BOND : angle 1.36217 ( 102) hydrogen bonds : bond 0.04972 ( 907) hydrogen bonds : angle 6.01489 ( 2547) link_BETA1-4 : bond 0.00384 ( 19) link_BETA1-4 : angle 1.90003 ( 57) link_NAG-ASN : bond 0.00458 ( 41) link_NAG-ASN : angle 2.54402 ( 123) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 164 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.8208 (p90) cc_final: 0.7698 (p90) REVERT: A 731 MET cc_start: 0.8952 (pmm) cc_final: 0.8644 (pmm) REVERT: B 238 PHE cc_start: 0.8445 (t80) cc_final: 0.7989 (t80) REVERT: B 562 PHE cc_start: 0.7763 (p90) cc_final: 0.7415 (p90) REVERT: C 55 PHE cc_start: 0.8131 (m-10) cc_final: 0.7792 (m-10) REVERT: C 390 LEU cc_start: 0.8503 (mm) cc_final: 0.8228 (tp) REVERT: C 1041 ASP cc_start: 0.7655 (t0) cc_final: 0.7300 (t70) REVERT: E 210 CYS cc_start: 0.3148 (t) cc_final: 0.2780 (t) REVERT: R 98 ARG cc_start: 0.8426 (ttp80) cc_final: 0.7956 (ttp80) REVERT: R 159 TYR cc_start: 0.5786 (p90) cc_final: 0.5237 (p90) outliers start: 2 outliers final: 0 residues processed: 166 average time/residue: 0.2024 time to fit residues: 57.6666 Evaluate side-chains 113 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 409 optimal weight: 10.0000 chunk 425 optimal weight: 7.9990 chunk 172 optimal weight: 0.9990 chunk 117 optimal weight: 0.6980 chunk 77 optimal weight: 6.9990 chunk 170 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 159 optimal weight: 4.9990 chunk 258 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 347 optimal weight: 40.0000 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN B 710 ASN B 907 ASN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 613 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 178 GLN Q 6 GLN R 43 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.081313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.061756 restraints weight = 216312.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.060554 restraints weight = 174245.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.060766 restraints weight = 162782.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.060894 restraints weight = 141271.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.061041 restraints weight = 127063.601| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 34914 Z= 0.171 Angle : 0.599 11.569 47668 Z= 0.300 Chirality : 0.045 0.418 5536 Planarity : 0.004 0.073 6009 Dihedral : 6.132 58.047 5818 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.03 % Allowed : 3.26 % Favored : 96.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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 aren not related in a simple way. whole: -1.29 (0.13), residues: 4192 helix: 0.74 (0.21), residues: 657 sheet: -0.27 (0.17), residues: 861 loop : -1.55 (0.12), residues: 2674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1107 TYR 0.022 0.001 TYR A 660 PHE 0.031 0.001 PHE C 275 TRP 0.017 0.001 TRP E 50 HIS 0.008 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00373 (34803) covalent geometry : angle 0.57872 (47386) SS BOND : bond 0.00426 ( 51) SS BOND : angle 1.39872 ( 102) hydrogen bonds : bond 0.04325 ( 907) hydrogen bonds : angle 5.78913 ( 2547) link_BETA1-4 : bond 0.00259 ( 19) link_BETA1-4 : angle 1.89224 ( 57) link_NAG-ASN : bond 0.00447 ( 41) link_NAG-ASN : angle 2.55721 ( 123) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 174 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.8229 (p90) cc_final: 0.7793 (p90) REVERT: B 238 PHE cc_start: 0.8471 (t80) cc_final: 0.7999 (t80) REVERT: B 562 PHE cc_start: 0.7701 (p90) cc_final: 0.7361 (p90) REVERT: C 55 PHE cc_start: 0.8140 (m-10) cc_final: 0.7712 (m-10) REVERT: C 697 MET cc_start: 0.7961 (ttt) cc_final: 0.7662 (ttt) REVERT: C 1041 ASP cc_start: 0.7570 (t0) cc_final: 0.7205 (t0) REVERT: D 26 ARG cc_start: 0.7220 (tpm170) cc_final: 0.6839 (tpm170) REVERT: D 62 ARG cc_start: 0.5054 (ttt180) cc_final: 0.4826 (ttt-90) REVERT: E 210 CYS cc_start: 0.3297 (t) cc_final: 0.2776 (t) REVERT: R 159 TYR cc_start: 0.5626 (p90) cc_final: 0.5096 (p90) outliers start: 1 outliers final: 0 residues processed: 175 average time/residue: 0.2039 time to fit residues: 61.1381 Evaluate side-chains 115 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 74 optimal weight: 0.9990 chunk 32 optimal weight: 20.0000 chunk 15 optimal weight: 1.9990 chunk 168 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 chunk 391 optimal weight: 10.0000 chunk 132 optimal weight: 1.9990 chunk 401 optimal weight: 50.0000 chunk 123 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 777 ASN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN ** D 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 6 GLN R 43 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.082018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.062183 restraints weight = 215620.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.061403 restraints weight = 174634.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.061678 restraints weight = 147934.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.061708 restraints weight = 131962.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.061858 restraints weight = 120444.999| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 34914 Z= 0.120 Angle : 0.563 13.767 47668 Z= 0.278 Chirality : 0.045 0.402 5536 Planarity : 0.004 0.069 6009 Dihedral : 5.698 57.097 5818 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.05 % Allowed : 3.07 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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 aren not related in a simple way. whole: -1.12 (0.13), residues: 4192 helix: 0.95 (0.21), residues: 657 sheet: -0.22 (0.18), residues: 876 loop : -1.43 (0.12), residues: 2659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 346 TYR 0.018 0.001 TYR C 396 PHE 0.019 0.001 PHE C 275 TRP 0.026 0.001 TRP M 196 HIS 0.009 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00265 (34803) covalent geometry : angle 0.54363 (47386) SS BOND : bond 0.00331 ( 51) SS BOND : angle 1.32889 ( 102) hydrogen bonds : bond 0.03928 ( 907) hydrogen bonds : angle 5.50720 ( 2547) link_BETA1-4 : bond 0.00338 ( 19) link_BETA1-4 : angle 1.85426 ( 57) link_NAG-ASN : bond 0.00439 ( 41) link_NAG-ASN : angle 2.46341 ( 123) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 168 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.8240 (p90) cc_final: 0.7838 (p90) REVERT: A 429 PHE cc_start: 0.7022 (t80) cc_final: 0.6489 (t80) REVERT: A 712 ILE cc_start: 0.9357 (tp) cc_final: 0.9154 (tp) REVERT: B 238 PHE cc_start: 0.8503 (t80) cc_final: 0.8007 (t80) REVERT: B 562 PHE cc_start: 0.7706 (p90) cc_final: 0.7356 (p90) REVERT: B 740 MET cc_start: 0.8574 (ttt) cc_final: 0.8286 (ttt) REVERT: B 868 GLU cc_start: 0.8602 (pm20) cc_final: 0.8248 (mp0) REVERT: B 1029 MET cc_start: 0.8901 (tpp) cc_final: 0.8636 (tpp) REVERT: C 55 PHE cc_start: 0.8044 (m-10) cc_final: 0.7714 (m-10) REVERT: C 697 MET cc_start: 0.8005 (ttt) cc_final: 0.7638 (ttt) REVERT: C 1041 ASP cc_start: 0.7567 (t0) cc_final: 0.7169 (t70) REVERT: E 210 CYS cc_start: 0.3499 (t) cc_final: 0.2918 (t) REVERT: N 101 PHE cc_start: 0.8457 (m-10) cc_final: 0.7583 (p90) REVERT: R 5 VAL cc_start: 0.8424 (p) cc_final: 0.7932 (p) REVERT: R 159 TYR cc_start: 0.5624 (p90) cc_final: 0.5040 (p90) outliers start: 2 outliers final: 0 residues processed: 170 average time/residue: 0.2098 time to fit residues: 59.6912 Evaluate side-chains 121 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 359 optimal weight: 20.0000 chunk 139 optimal weight: 2.9990 chunk 390 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 chunk 246 optimal weight: 4.9990 chunk 8 optimal weight: 8.9990 chunk 367 optimal weight: 7.9990 chunk 418 optimal weight: 7.9990 chunk 248 optimal weight: 8.9990 chunk 225 optimal weight: 4.9990 chunk 301 optimal weight: 0.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN D 32 ASN D 52 ASN ** D 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 43 GLN R 178 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.080043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.060451 restraints weight = 215465.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.059437 restraints weight = 181235.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.059846 restraints weight = 161831.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.059860 restraints weight = 138429.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.060085 restraints weight = 122445.341| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 34914 Z= 0.214 Angle : 0.661 10.784 47668 Z= 0.331 Chirality : 0.047 0.430 5536 Planarity : 0.005 0.066 6009 Dihedral : 6.107 57.222 5818 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 0.03 % Allowed : 2.66 % Favored : 97.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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 aren not related in a simple way. whole: -1.41 (0.13), residues: 4192 helix: 0.62 (0.20), residues: 653 sheet: -0.42 (0.18), residues: 807 loop : -1.58 (0.12), residues: 2732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1039 TYR 0.017 0.002 TYR B 756 PHE 0.027 0.002 PHE B 759 TRP 0.017 0.002 TRP E 50 HIS 0.011 0.002 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00469 (34803) covalent geometry : angle 0.64067 (47386) SS BOND : bond 0.00438 ( 51) SS BOND : angle 1.39701 ( 102) hydrogen bonds : bond 0.04549 ( 907) hydrogen bonds : angle 5.76666 ( 2547) link_BETA1-4 : bond 0.00315 ( 19) link_BETA1-4 : angle 2.10796 ( 57) link_NAG-ASN : bond 0.00568 ( 41) link_NAG-ASN : angle 2.78174 ( 123) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 141 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 712 ILE cc_start: 0.9452 (tp) cc_final: 0.9250 (tp) REVERT: A 731 MET cc_start: 0.8908 (pmm) cc_final: 0.8314 (pmm) REVERT: B 562 PHE cc_start: 0.7890 (p90) cc_final: 0.7500 (p90) REVERT: B 740 MET cc_start: 0.8600 (ttt) cc_final: 0.8229 (ttt) REVERT: C 429 PHE cc_start: 0.8001 (t80) cc_final: 0.7732 (t80) REVERT: C 1041 ASP cc_start: 0.7862 (t0) cc_final: 0.7417 (t70) REVERT: D 26 ARG cc_start: 0.7176 (tpm170) cc_final: 0.6886 (tpm170) REVERT: E 210 CYS cc_start: 0.2937 (t) cc_final: 0.2520 (t) outliers start: 1 outliers final: 1 residues processed: 142 average time/residue: 0.1832 time to fit residues: 44.7351 Evaluate side-chains 111 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 206 optimal weight: 7.9990 chunk 222 optimal weight: 4.9990 chunk 347 optimal weight: 30.0000 chunk 121 optimal weight: 0.7980 chunk 225 optimal weight: 4.9990 chunk 383 optimal weight: 9.9990 chunk 284 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 170 optimal weight: 0.7980 chunk 234 optimal weight: 9.9990 chunk 85 optimal weight: 3.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN B 907 ASN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 HIS ** M 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 6 GLN R 43 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.080631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.062653 restraints weight = 214760.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.060999 restraints weight = 186969.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.061200 restraints weight = 163503.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.061356 restraints weight = 155717.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.061491 restraints weight = 135641.716| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 34914 Z= 0.163 Angle : 0.608 10.146 47668 Z= 0.303 Chirality : 0.046 0.416 5536 Planarity : 0.004 0.065 6009 Dihedral : 5.923 56.833 5818 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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 aren not related in a simple way. whole: -1.33 (0.13), residues: 4192 helix: 0.74 (0.21), residues: 646 sheet: -0.47 (0.17), residues: 859 loop : -1.50 (0.12), residues: 2687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1039 TYR 0.014 0.001 TYR D 50 PHE 0.025 0.001 PHE C 275 TRP 0.055 0.002 TRP D 196 HIS 0.008 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00360 (34803) covalent geometry : angle 0.58794 (47386) SS BOND : bond 0.00379 ( 51) SS BOND : angle 1.34945 ( 102) hydrogen bonds : bond 0.04261 ( 907) hydrogen bonds : angle 5.60367 ( 2547) link_BETA1-4 : bond 0.00299 ( 19) link_BETA1-4 : angle 2.03133 ( 57) link_NAG-ASN : bond 0.00436 ( 41) link_NAG-ASN : angle 2.58648 ( 123) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 731 MET cc_start: 0.8863 (pmm) cc_final: 0.8500 (pmm) REVERT: B 238 PHE cc_start: 0.8648 (t80) cc_final: 0.8176 (t80) REVERT: B 562 PHE cc_start: 0.7740 (p90) cc_final: 0.7296 (p90) REVERT: B 740 MET cc_start: 0.8468 (ttt) cc_final: 0.8142 (ttt) REVERT: C 429 PHE cc_start: 0.8023 (t80) cc_final: 0.7731 (t80) REVERT: C 697 MET cc_start: 0.7739 (ttt) cc_final: 0.7385 (ttt) REVERT: C 1041 ASP cc_start: 0.7956 (t0) cc_final: 0.7531 (t70) REVERT: E 210 CYS cc_start: 0.2784 (t) cc_final: 0.2450 (t) REVERT: R 35 HIS cc_start: 0.8741 (m-70) cc_final: 0.8343 (m90) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.1813 time to fit residues: 45.3242 Evaluate side-chains 105 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 358 optimal weight: 0.8980 chunk 13 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 chunk 387 optimal weight: 8.9990 chunk 37 optimal weight: 7.9990 chunk 352 optimal weight: 10.0000 chunk 128 optimal weight: 7.9990 chunk 226 optimal weight: 6.9990 chunk 189 optimal weight: 7.9990 chunk 193 optimal weight: 10.0000 chunk 172 optimal weight: 0.6980 overall best weight: 4.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN B 907 ASN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 954 HIS C1011 GLN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 ASN ** M 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 33 ASN R 43 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.079158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.060963 restraints weight = 214986.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.059422 restraints weight = 183878.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.059436 restraints weight = 163280.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.059683 restraints weight = 144953.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.059738 restraints weight = 130579.390| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 34914 Z= 0.235 Angle : 0.705 10.602 47668 Z= 0.353 Chirality : 0.048 0.450 5536 Planarity : 0.005 0.064 6009 Dihedral : 6.449 57.244 5818 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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 aren not related in a simple way. whole: -1.64 (0.13), residues: 4192 helix: 0.38 (0.20), residues: 649 sheet: -0.65 (0.17), residues: 836 loop : -1.70 (0.12), residues: 2707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 237 TYR 0.034 0.002 TYR B 756 PHE 0.043 0.002 PHE B 759 TRP 0.039 0.002 TRP E 50 HIS 0.010 0.002 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00515 (34803) covalent geometry : angle 0.68448 (47386) SS BOND : bond 0.00570 ( 51) SS BOND : angle 1.59386 ( 102) hydrogen bonds : bond 0.04760 ( 907) hydrogen bonds : angle 5.88303 ( 2547) link_BETA1-4 : bond 0.00320 ( 19) link_BETA1-4 : angle 2.24564 ( 57) link_NAG-ASN : bond 0.00570 ( 41) link_NAG-ASN : angle 2.76486 ( 123) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 1.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 712 ILE cc_start: 0.9438 (tp) cc_final: 0.9235 (tp) REVERT: A 731 MET cc_start: 0.8895 (pmm) cc_final: 0.8385 (pmm) REVERT: B 238 PHE cc_start: 0.8697 (t80) cc_final: 0.8493 (t80) REVERT: B 740 MET cc_start: 0.8578 (ttt) cc_final: 0.8238 (ttt) REVERT: C 429 PHE cc_start: 0.8137 (t80) cc_final: 0.7870 (t80) REVERT: C 697 MET cc_start: 0.7991 (ttt) cc_final: 0.7670 (ttt) REVERT: D 26 ARG cc_start: 0.7174 (tpm170) cc_final: 0.6950 (tpm170) REVERT: D 54 GLN cc_start: 0.8172 (tm-30) cc_final: 0.7840 (pm20) REVERT: E 210 CYS cc_start: 0.2322 (t) cc_final: 0.1934 (t) REVERT: R 98 ARG cc_start: 0.8244 (ttp80) cc_final: 0.6917 (ttp80) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.1819 time to fit residues: 43.8306 Evaluate side-chains 101 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 329 optimal weight: 5.9990 chunk 31 optimal weight: 20.0000 chunk 319 optimal weight: 0.0470 chunk 272 optimal weight: 0.8980 chunk 217 optimal weight: 7.9990 chunk 305 optimal weight: 20.0000 chunk 85 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 258 optimal weight: 2.9990 chunk 173 optimal weight: 0.6980 chunk 290 optimal weight: 5.9990 overall best weight: 1.5282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 ASN B 907 ASN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN C 777 ASN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 3 GLN Q 6 GLN R 43 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.081147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.062359 restraints weight = 212744.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.061096 restraints weight = 186262.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.061433 restraints weight = 157042.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.061542 restraints weight = 144265.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.061628 restraints weight = 131446.346| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 34914 Z= 0.116 Angle : 0.592 10.066 47668 Z= 0.293 Chirality : 0.046 0.397 5536 Planarity : 0.004 0.061 6009 Dihedral : 5.801 56.500 5818 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.03 % Allowed : 0.62 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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 aren not related in a simple way. whole: -1.30 (0.13), residues: 4192 helix: 0.84 (0.21), residues: 641 sheet: -0.53 (0.17), residues: 879 loop : -1.48 (0.12), residues: 2672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C1039 TYR 0.019 0.001 TYR A 873 PHE 0.027 0.001 PHE C 275 TRP 0.028 0.001 TRP D 196 HIS 0.008 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00260 (34803) covalent geometry : angle 0.57211 (47386) SS BOND : bond 0.00366 ( 51) SS BOND : angle 1.23638 ( 102) hydrogen bonds : bond 0.03970 ( 907) hydrogen bonds : angle 5.39499 ( 2547) link_BETA1-4 : bond 0.00401 ( 19) link_BETA1-4 : angle 2.06606 ( 57) link_NAG-ASN : bond 0.00432 ( 41) link_NAG-ASN : angle 2.54122 ( 123) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 146 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 712 ILE cc_start: 0.9377 (tp) cc_final: 0.9176 (tp) REVERT: A 731 MET cc_start: 0.8921 (pmm) cc_final: 0.8349 (pmm) REVERT: B 562 PHE cc_start: 0.7708 (p90) cc_final: 0.7271 (p90) REVERT: B 740 MET cc_start: 0.8389 (ttt) cc_final: 0.8026 (ttt) REVERT: C 55 PHE cc_start: 0.8195 (m-10) cc_final: 0.7965 (m-10) REVERT: C 429 PHE cc_start: 0.8025 (t80) cc_final: 0.7764 (t80) REVERT: C 697 MET cc_start: 0.7953 (ttt) cc_final: 0.7714 (ttt) REVERT: D 26 ARG cc_start: 0.7149 (tpm170) cc_final: 0.6947 (tpm170) REVERT: D 52 ASN cc_start: 0.5654 (t0) cc_final: 0.5447 (t0) REVERT: D 54 GLN cc_start: 0.8189 (tm-30) cc_final: 0.7971 (pm20) REVERT: E 210 CYS cc_start: 0.2667 (t) cc_final: 0.2327 (t) REVERT: R 35 HIS cc_start: 0.8850 (m-70) cc_final: 0.8243 (m90) REVERT: R 98 ARG cc_start: 0.8379 (ttp80) cc_final: 0.7211 (ttp80) outliers start: 1 outliers final: 0 residues processed: 147 average time/residue: 0.2051 time to fit residues: 52.1855 Evaluate side-chains 109 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 215 optimal weight: 9.9990 chunk 346 optimal weight: 0.0040 chunk 175 optimal weight: 0.7980 chunk 333 optimal weight: 4.9990 chunk 369 optimal weight: 7.9990 chunk 409 optimal weight: 8.9990 chunk 245 optimal weight: 0.2980 chunk 85 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 109 optimal weight: 20.0000 chunk 88 optimal weight: 5.9990 overall best weight: 2.0196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 3 GLN ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 43 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.080940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.063005 restraints weight = 213312.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.061140 restraints weight = 181446.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.061344 restraints weight = 159746.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.061584 restraints weight = 139053.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.061627 restraints weight = 126410.866| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34914 Z= 0.126 Angle : 0.585 9.748 47668 Z= 0.289 Chirality : 0.045 0.401 5536 Planarity : 0.004 0.058 6009 Dihedral : 5.641 56.805 5818 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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 aren not related in a simple way. whole: -1.25 (0.13), residues: 4192 helix: 0.86 (0.21), residues: 645 sheet: -0.45 (0.18), residues: 866 loop : -1.45 (0.12), residues: 2681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1000 TYR 0.020 0.001 TYR B1067 PHE 0.023 0.001 PHE C 275 TRP 0.026 0.001 TRP D 196 HIS 0.009 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00283 (34803) covalent geometry : angle 0.56482 (47386) SS BOND : bond 0.00345 ( 51) SS BOND : angle 1.21196 ( 102) hydrogen bonds : bond 0.03924 ( 907) hydrogen bonds : angle 5.33373 ( 2547) link_BETA1-4 : bond 0.00303 ( 19) link_BETA1-4 : angle 2.02934 ( 57) link_NAG-ASN : bond 0.00409 ( 41) link_NAG-ASN : angle 2.53294 ( 123) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 527 PRO cc_start: 0.7904 (Cg_endo) cc_final: 0.7674 (Cg_exo) REVERT: A 731 MET cc_start: 0.9017 (pmm) cc_final: 0.8424 (pmm) REVERT: B 238 PHE cc_start: 0.8530 (t80) cc_final: 0.8028 (t80) REVERT: B 562 PHE cc_start: 0.7578 (p90) cc_final: 0.7198 (p90) REVERT: B 740 MET cc_start: 0.8354 (ttt) cc_final: 0.7994 (ttt) REVERT: B 902 MET cc_start: 0.8662 (tpp) cc_final: 0.8411 (mpp) REVERT: C 429 PHE cc_start: 0.7994 (t80) cc_final: 0.7775 (t80) REVERT: D 26 ARG cc_start: 0.7153 (tpm170) cc_final: 0.6901 (tpm170) REVERT: D 52 ASN cc_start: 0.5899 (t0) cc_final: 0.5677 (t0) REVERT: E 210 CYS cc_start: 0.2738 (t) cc_final: 0.2279 (t) REVERT: R 35 HIS cc_start: 0.8969 (m-70) cc_final: 0.8330 (m90) REVERT: R 159 TYR cc_start: 0.6102 (p90) cc_final: 0.5188 (p90) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.1890 time to fit residues: 46.2314 Evaluate side-chains 106 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 246 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 50 optimal weight: 9.9990 chunk 135 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 271 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 216 optimal weight: 3.9990 chunk 380 optimal weight: 3.9990 chunk 202 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 3 GLN R 43 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.077771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.059372 restraints weight = 216561.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.059386 restraints weight = 166876.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.059585 restraints weight = 132524.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.059919 restraints weight = 115724.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.059979 restraints weight = 101564.822| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 34914 Z= 0.281 Angle : 0.760 12.327 47668 Z= 0.381 Chirality : 0.050 0.466 5536 Planarity : 0.005 0.058 6009 Dihedral : 6.651 57.138 5818 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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 aren not related in a simple way. whole: -1.76 (0.13), residues: 4192 helix: 0.24 (0.20), residues: 652 sheet: -0.76 (0.18), residues: 810 loop : -1.75 (0.12), residues: 2730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C1000 TYR 0.030 0.002 TYR B 756 PHE 0.032 0.002 PHE A 562 TRP 0.030 0.003 TRP Q 113 HIS 0.008 0.002 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00614 (34803) covalent geometry : angle 0.74013 (47386) SS BOND : bond 0.00521 ( 51) SS BOND : angle 1.57445 ( 102) hydrogen bonds : bond 0.05001 ( 907) hydrogen bonds : angle 5.92771 ( 2547) link_BETA1-4 : bond 0.00380 ( 19) link_BETA1-4 : angle 2.30995 ( 57) link_NAG-ASN : bond 0.00645 ( 41) link_NAG-ASN : angle 2.83381 ( 123) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4428.31 seconds wall clock time: 78 minutes 14.61 seconds (4694.61 seconds total)