Starting phenix.real_space_refine on Sun Jun 29 06:52:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zbz_39917/06_2025/8zbz_39917.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zbz_39917/06_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_39917/06_2025/8zbz_39917.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zbz_39917/06_2025/8zbz_39917.map" model { file = "/net/cci-nas-00/data/ceres_data/8zbz_39917/06_2025/8zbz_39917.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zbz_39917/06_2025/8zbz_39917.cif" } resolution = 4.71 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 20.95, per 1000 atoms: 0.62 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: 8.44 Conformation dependent library (CDL) restraints added in 4.4 seconds 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: 4.92 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: 17.00 Time building geometry restraints manager: 10.14 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 1147 or resid 1301 through 1305)) selection = (chain 'B' and (resid 27 through 95 or resid 100 through 245 or resid 263 throug \ h 1147 or resid 1301 through 1305)) selection = (chain 'C' and (resid 27 through 142 or resid 155 through 210 or resid 216 throu \ gh 245 or resid 263 through 1147 or resid 1301 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: 2.670 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: 0.060 Extract box with map and model: 1.410 Check model and map are aligned: 0.250 Set scattering table: 0.340 Process input model: 82.100 Find NCS groups from input model: 2.290 Set up NCS constraints: 0.320 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.450 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (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 TRP 0.020 0.001 TRP M 196 HIS 0.006 0.001 HIS E 35 PHE 0.042 0.001 PHE C 55 TYR 0.025 0.001 TYR D 37 ARG 0.012 0.000 ARG R 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00588 ( 41) link_NAG-ASN : angle 2.84772 ( 123) link_BETA1-4 : bond 0.00566 ( 19) link_BETA1-4 : angle 2.20755 ( 57) hydrogen bonds : bond 0.23992 ( 907) hydrogen bonds : angle 9.05284 ( 2547) SS BOND : bond 0.00342 ( 51) SS BOND : angle 0.86858 ( 102) covalent geometry : bond 0.00349 (34803) covalent geometry : angle 0.68765 (47386) *********************** 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 : 3.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.7775 (mm) cc_final: 0.7413 (mm) REVERT: A 985 ASP cc_start: 0.9151 (m-30) cc_final: 0.8797 (t0) REVERT: B 238 PHE cc_start: 0.8320 (t80) cc_final: 0.8023 (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: 0.4810 (mmp80) REVERT: B 562 PHE cc_start: 0.7341 (p90) cc_final: 0.7092 (p90) REVERT: B 712 ILE cc_start: 0.8725 (tt) cc_final: 0.8467 (tt) REVERT: B 868 GLU cc_start: 0.8145 (pm20) cc_final: 0.7881 (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: 0.6889 (t0) REVERT: D 150 PHE cc_start: 0.6463 (p90) cc_final: 0.5813 (p90) REVERT: E 73 ASP cc_start: 0.6237 (t0) cc_final: 0.5985 (t0) REVERT: E 215 LYS cc_start: 0.7390 (pttp) cc_final: 0.6408 (tttp) outliers start: 4 outliers final: 1 residues processed: 211 average time/residue: 0.4167 time to fit residues: 151.1591 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 : 3.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 359 optimal weight: 8.9990 chunk 322 optimal weight: 7.9990 chunk 179 optimal weight: 6.9990 chunk 110 optimal weight: 10.0000 chunk 217 optimal weight: 0.7980 chunk 172 optimal weight: 0.5980 chunk 333 optimal weight: 20.0000 chunk 129 optimal weight: 20.0000 chunk 203 optimal weight: 6.9990 chunk 248 optimal weight: 5.9990 chunk 386 optimal weight: 30.0000 overall best weight: 4.2786 ------------------------------------------------------------------------------- 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** N 28 ASN N 38 GLN Q 6 GLN R 43 GLN R 65 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.082576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.063803 restraints weight = 216780.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.062278 restraints weight = 182475.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.062182 restraints weight = 201834.705| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 34914 Z= 0.223 Angle : 0.671 10.566 47668 Z= 0.339 Chirality : 0.047 0.444 5536 Planarity : 0.005 0.079 6009 Dihedral : 6.841 59.894 5818 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.08 % Allowed : 6.30 % Favored : 93.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.13), residues: 4192 helix: 0.55 (0.21), residues: 656 sheet: -0.18 (0.18), residues: 812 loop : -1.53 (0.11), residues: 2724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 353 HIS 0.007 0.001 HIS B 66 PHE 0.023 0.002 PHE C 92 TYR 0.022 0.002 TYR C 313 ARG 0.007 0.001 ARG C1000 Details of bonding type rmsd link_NAG-ASN : bond 0.00562 ( 41) link_NAG-ASN : angle 2.53548 ( 123) link_BETA1-4 : bond 0.00366 ( 19) link_BETA1-4 : angle 1.90219 ( 57) hydrogen bonds : bond 0.04979 ( 907) hydrogen bonds : angle 6.48160 ( 2547) SS BOND : bond 0.00442 ( 51) SS BOND : angle 1.38945 ( 102) covalent geometry : bond 0.00481 (34803) covalent geometry : angle 0.65380 (47386) *********************** 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 166 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 163 time to evaluate : 3.420 Fit side-chains REVERT: A 429 PHE cc_start: 0.7452 (t80) cc_final: 0.6875 (t80) REVERT: A 1033 VAL cc_start: 0.8992 (t) cc_final: 0.8648 (t) REVERT: B 238 PHE cc_start: 0.8385 (t80) cc_final: 0.7975 (t80) REVERT: B 562 PHE cc_start: 0.7571 (p90) cc_final: 0.7271 (p90) REVERT: B 1050 MET cc_start: 0.8249 (tmm) cc_final: 0.8034 (tmm) REVERT: C 533 LEU cc_start: 0.8678 (mt) cc_final: 0.8473 (mt) REVERT: C 613 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.7600 (pp30) REVERT: C 1041 ASP cc_start: 0.7731 (t0) cc_final: 0.7418 (t70) REVERT: E 210 CYS cc_start: 0.3842 (t) cc_final: 0.3430 (t) REVERT: N 188 TYR cc_start: 0.1634 (m-80) cc_final: 0.0644 (t80) REVERT: R 64 PHE cc_start: 0.6872 (m-80) cc_final: 0.6556 (m-80) REVERT: R 159 TYR cc_start: 0.5597 (p90) cc_final: 0.5226 (p90) outliers start: 3 outliers final: 0 residues processed: 166 average time/residue: 0.4429 time to fit residues: 127.4107 Evaluate side-chains 121 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 120 time to evaluate : 3.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 199 optimal weight: 5.9990 chunk 27 optimal weight: 0.0000 chunk 227 optimal weight: 4.9990 chunk 153 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 242 optimal weight: 9.9990 chunk 378 optimal weight: 20.0000 chunk 320 optimal weight: 9.9990 chunk 393 optimal weight: 20.0000 chunk 67 optimal weight: 2.9990 chunk 256 optimal weight: 3.9990 overall best weight: 3.5992 ------------------------------------------------------------------------------- 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 901 GLN B 907 ASN ** 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 178 HIS ** M 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN Q 3 GLN Q 6 GLN ** Q 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 43 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.081925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.062645 restraints weight = 216734.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.061476 restraints weight = 181952.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.061635 restraints weight = 165329.245| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 34914 Z= 0.176 Angle : 0.599 10.282 47668 Z= 0.302 Chirality : 0.045 0.402 5536 Planarity : 0.005 0.072 6009 Dihedral : 6.304 59.875 5818 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.05 % Allowed : 4.82 % Favored : 95.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.13), residues: 4192 helix: 0.74 (0.21), residues: 663 sheet: -0.12 (0.17), residues: 861 loop : -1.52 (0.12), residues: 2668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 886 HIS 0.005 0.001 HIS A 954 PHE 0.017 0.002 PHE C 275 TYR 0.033 0.001 TYR D 50 ARG 0.011 0.001 ARG C 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00438 ( 41) link_NAG-ASN : angle 2.49518 ( 123) link_BETA1-4 : bond 0.00387 ( 19) link_BETA1-4 : angle 1.85675 ( 57) hydrogen bonds : bond 0.04790 ( 907) hydrogen bonds : angle 5.95635 ( 2547) SS BOND : bond 0.00385 ( 51) SS BOND : angle 1.35215 ( 102) covalent geometry : bond 0.00381 (34803) covalent geometry : angle 0.58056 (47386) *********************** 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 167 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 165 time to evaluate : 3.418 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.8209 (p90) cc_final: 0.7718 (p90) REVERT: A 429 PHE cc_start: 0.7277 (t80) cc_final: 0.6768 (t80) REVERT: A 731 MET cc_start: 0.8926 (pmm) cc_final: 0.8635 (pmm) REVERT: B 238 PHE cc_start: 0.8438 (t80) cc_final: 0.7979 (t80) REVERT: B 562 PHE cc_start: 0.7686 (p90) cc_final: 0.7347 (p90) REVERT: C 1041 ASP cc_start: 0.7572 (t0) cc_final: 0.7183 (t70) REVERT: D 26 ARG cc_start: 0.6931 (tpm170) cc_final: 0.6680 (tpm170) REVERT: E 210 CYS cc_start: 0.3293 (t) cc_final: 0.2908 (t) REVERT: R 159 TYR cc_start: 0.5742 (p90) cc_final: 0.5225 (p90) outliers start: 2 outliers final: 0 residues processed: 167 average time/residue: 0.4090 time to fit residues: 118.4663 Evaluate side-chains 111 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 3.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 193 optimal weight: 1.9990 chunk 223 optimal weight: 2.9990 chunk 410 optimal weight: 5.9990 chunk 152 optimal weight: 9.9990 chunk 239 optimal weight: 10.0000 chunk 272 optimal weight: 1.9990 chunk 253 optimal weight: 1.9990 chunk 362 optimal weight: 0.0470 chunk 8 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 351 optimal weight: 10.0000 overall best weight: 1.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN A1005 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN C 394 ASN C 613 GLN C 777 ASN C1005 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 3 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 = 0.3722 r_free = 0.3722 target = 0.083003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.063970 restraints weight = 215980.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.062439 restraints weight = 191536.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.062577 restraints weight = 173372.043| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 34914 Z= 0.103 Angle : 0.539 11.339 47668 Z= 0.268 Chirality : 0.044 0.404 5536 Planarity : 0.004 0.074 6009 Dihedral : 5.682 55.904 5818 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.03 % Allowed : 2.34 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.13), residues: 4192 helix: 0.96 (0.21), residues: 663 sheet: -0.10 (0.17), residues: 890 loop : -1.40 (0.12), residues: 2639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP M 196 HIS 0.010 0.001 HIS A 954 PHE 0.029 0.001 PHE C 275 TYR 0.011 0.001 TYR C1067 ARG 0.003 0.000 ARG R 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00411 ( 41) link_NAG-ASN : angle 2.38427 ( 123) link_BETA1-4 : bond 0.00311 ( 19) link_BETA1-4 : angle 1.75163 ( 57) hydrogen bonds : bond 0.03861 ( 907) hydrogen bonds : angle 5.51474 ( 2547) SS BOND : bond 0.00312 ( 51) SS BOND : angle 1.24614 ( 102) covalent geometry : bond 0.00226 (34803) covalent geometry : angle 0.52009 (47386) *********************** 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 181 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 180 time to evaluate : 5.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.8243 (p90) cc_final: 0.7797 (p90) REVERT: A 429 PHE cc_start: 0.7155 (t80) cc_final: 0.6595 (t80) REVERT: B 238 PHE cc_start: 0.8363 (t80) cc_final: 0.7920 (t80) REVERT: B 562 PHE cc_start: 0.7601 (p90) cc_final: 0.7327 (p90) REVERT: B 868 GLU cc_start: 0.8580 (pm20) cc_final: 0.8190 (mp0) REVERT: C 1041 ASP cc_start: 0.7384 (t0) cc_final: 0.7034 (t0) REVERT: D 150 PHE cc_start: 0.6565 (p90) cc_final: 0.6291 (p90) REVERT: E 210 CYS cc_start: 0.3500 (t) cc_final: 0.3224 (t) REVERT: R 159 TYR cc_start: 0.5774 (p90) cc_final: 0.5100 (p90) outliers start: 1 outliers final: 0 residues processed: 181 average time/residue: 0.4696 time to fit residues: 146.3490 Evaluate side-chains 125 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 4.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 89 optimal weight: 2.9990 chunk 387 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 408 optimal weight: 6.9990 chunk 143 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 384 optimal weight: 40.0000 chunk 83 optimal weight: 8.9990 chunk 182 optimal weight: 6.9990 chunk 188 optimal weight: 9.9990 chunk 219 optimal weight: 0.2980 overall best weight: 4.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** A1048 HIS ** 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** C 613 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN ** D 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 GLN ** 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 = 0.3665 r_free = 0.3665 target = 0.080586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.061425 restraints weight = 216503.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.060310 restraints weight = 190955.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.060512 restraints weight = 160326.424| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 34914 Z= 0.209 Angle : 0.649 13.388 47668 Z= 0.324 Chirality : 0.046 0.421 5536 Planarity : 0.005 0.070 6009 Dihedral : 6.046 57.684 5818 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 0.05 % Allowed : 3.71 % Favored : 96.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.13), residues: 4192 helix: 0.72 (0.20), residues: 654 sheet: -0.30 (0.18), residues: 856 loop : -1.52 (0.12), residues: 2682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 50 HIS 0.011 0.002 HIS A1048 PHE 0.022 0.002 PHE A 782 TYR 0.020 0.002 TYR A 660 ARG 0.023 0.001 ARG C 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00566 ( 41) link_NAG-ASN : angle 2.64467 ( 123) link_BETA1-4 : bond 0.00336 ( 19) link_BETA1-4 : angle 1.97549 ( 57) hydrogen bonds : bond 0.04539 ( 907) hydrogen bonds : angle 5.74398 ( 2547) SS BOND : bond 0.00496 ( 51) SS BOND : angle 1.62907 ( 102) covalent geometry : bond 0.00458 (34803) covalent geometry : angle 0.62814 (47386) *********************** 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 153 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 151 time to evaluate : 4.112 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 562 PHE cc_start: 0.7839 (p90) cc_final: 0.7401 (p90) REVERT: C 55 PHE cc_start: 0.7901 (m-10) cc_final: 0.7609 (m-10) REVERT: C 697 MET cc_start: 0.7752 (ttt) cc_final: 0.7424 (ttt) REVERT: C 1041 ASP cc_start: 0.7282 (t0) cc_final: 0.6927 (t0) REVERT: E 210 CYS cc_start: 0.2907 (t) cc_final: 0.2698 (t) REVERT: N 101 PHE cc_start: 0.8498 (m-10) cc_final: 0.7586 (p90) REVERT: R 98 ARG cc_start: 0.8517 (ttp80) cc_final: 0.8174 (ttp80) outliers start: 2 outliers final: 0 residues processed: 153 average time/residue: 0.4618 time to fit residues: 122.2435 Evaluate side-chains 108 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 3.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 311 optimal weight: 20.0000 chunk 238 optimal weight: 6.9990 chunk 158 optimal weight: 1.9990 chunk 166 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 3 optimal weight: 0.2980 chunk 62 optimal weight: 0.9990 chunk 207 optimal weight: 0.1980 chunk 342 optimal weight: 6.9990 chunk 375 optimal weight: 8.9990 chunk 21 optimal weight: 0.6980 overall best weight: 0.6384 ------------------------------------------------------------------------------- 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 613 GLN C 641 ASN C 777 ASN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 R 43 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.082769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.063953 restraints weight = 213271.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.062464 restraints weight = 183305.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.062571 restraints weight = 168272.248| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 34914 Z= 0.098 Angle : 0.554 10.994 47668 Z= 0.273 Chirality : 0.045 0.391 5536 Planarity : 0.004 0.068 6009 Dihedral : 5.369 56.294 5818 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.05 % Allowed : 1.91 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.13), residues: 4192 helix: 0.98 (0.21), residues: 655 sheet: -0.13 (0.18), residues: 883 loop : -1.37 (0.12), residues: 2654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 886 HIS 0.010 0.001 HIS A 954 PHE 0.030 0.001 PHE D 101 TYR 0.020 0.001 TYR D 202 ARG 0.004 0.000 ARG D 26 Details of bonding type rmsd link_NAG-ASN : bond 0.00437 ( 41) link_NAG-ASN : angle 2.38880 ( 123) link_BETA1-4 : bond 0.00435 ( 19) link_BETA1-4 : angle 1.83514 ( 57) hydrogen bonds : bond 0.03757 ( 907) hydrogen bonds : angle 5.32602 ( 2547) SS BOND : bond 0.00287 ( 51) SS BOND : angle 1.22093 ( 102) covalent geometry : bond 0.00210 (34803) covalent geometry : angle 0.53573 (47386) *********************** 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 178 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 176 time to evaluate : 3.847 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 712 ILE cc_start: 0.9331 (tp) cc_final: 0.9128 (tp) REVERT: A 731 MET cc_start: 0.8930 (pmm) cc_final: 0.8315 (pmm) REVERT: B 238 PHE cc_start: 0.8633 (t80) cc_final: 0.8154 (t80) REVERT: B 562 PHE cc_start: 0.7550 (p90) cc_final: 0.7260 (p90) REVERT: B 1058 HIS cc_start: 0.8446 (m90) cc_final: 0.7969 (m-70) REVERT: C 55 PHE cc_start: 0.8202 (m-10) cc_final: 0.7859 (m-10) REVERT: C 697 MET cc_start: 0.8145 (ttt) cc_final: 0.7729 (ttt) REVERT: C 1041 ASP cc_start: 0.7662 (t0) cc_final: 0.7170 (t70) REVERT: D 150 PHE cc_start: 0.6466 (p90) cc_final: 0.6206 (p90) REVERT: E 210 CYS cc_start: 0.3586 (t) cc_final: 0.3142 (t) REVERT: N 101 PHE cc_start: 0.8444 (m-10) cc_final: 0.7584 (p90) REVERT: R 35 HIS cc_start: 0.8741 (m-70) cc_final: 0.8367 (m90) REVERT: R 70 MET cc_start: 0.6930 (mmp) cc_final: 0.6679 (mmm) REVERT: R 98 ARG cc_start: 0.8584 (ttp80) cc_final: 0.8280 (ttp80) REVERT: R 159 TYR cc_start: 0.5951 (p90) cc_final: 0.5066 (p90) outliers start: 2 outliers final: 1 residues processed: 178 average time/residue: 0.4311 time to fit residues: 132.5325 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 : 3.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 318 optimal weight: 8.9990 chunk 222 optimal weight: 2.9990 chunk 358 optimal weight: 8.9990 chunk 362 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 331 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 246 optimal weight: 0.8980 chunk 97 optimal weight: 7.9990 chunk 59 optimal weight: 7.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** 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** C 422 ASN ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.082115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.063281 restraints weight = 215809.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.061864 restraints weight = 179151.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.061838 restraints weight = 161126.754| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 34914 Z= 0.120 Angle : 0.561 9.878 47668 Z= 0.276 Chirality : 0.045 0.404 5536 Planarity : 0.004 0.074 6009 Dihedral : 5.282 56.827 5818 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.13), residues: 4192 helix: 1.02 (0.21), residues: 657 sheet: -0.14 (0.18), residues: 867 loop : -1.35 (0.12), residues: 2668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.001 TRP D 196 HIS 0.009 0.001 HIS A 954 PHE 0.018 0.001 PHE C 275 TYR 0.016 0.001 TYR D 50 ARG 0.004 0.000 ARG A1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00402 ( 41) link_NAG-ASN : angle 2.52448 ( 123) link_BETA1-4 : bond 0.00305 ( 19) link_BETA1-4 : angle 1.85008 ( 57) hydrogen bonds : bond 0.03804 ( 907) hydrogen bonds : angle 5.30130 ( 2547) SS BOND : bond 0.00326 ( 51) SS BOND : angle 1.18596 ( 102) covalent geometry : bond 0.00266 (34803) covalent geometry : angle 0.54132 (47386) *********************** 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 159 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 3.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 527 PRO cc_start: 0.7803 (Cg_endo) cc_final: 0.7578 (Cg_exo) REVERT: A 712 ILE cc_start: 0.9380 (tp) cc_final: 0.9171 (tp) REVERT: B 238 PHE cc_start: 0.8662 (t80) cc_final: 0.8176 (t80) REVERT: B 562 PHE cc_start: 0.7641 (p90) cc_final: 0.7285 (p90) REVERT: C 55 PHE cc_start: 0.8143 (m-10) cc_final: 0.7848 (m-10) REVERT: C 429 PHE cc_start: 0.7799 (t80) cc_final: 0.7580 (t80) REVERT: C 1041 ASP cc_start: 0.7684 (t0) cc_final: 0.7244 (t70) REVERT: E 210 CYS cc_start: 0.3430 (t) cc_final: 0.3007 (t) REVERT: N 101 PHE cc_start: 0.8440 (m-10) cc_final: 0.7529 (p90) REVERT: R 35 HIS cc_start: 0.8771 (m-70) cc_final: 0.8403 (m90) REVERT: R 70 MET cc_start: 0.7133 (mmp) cc_final: 0.6871 (mmm) REVERT: R 159 TYR cc_start: 0.5971 (p90) cc_final: 0.5107 (p90) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.4058 time to fit residues: 111.2585 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 : 3.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 74 optimal weight: 2.9990 chunk 302 optimal weight: 0.0010 chunk 57 optimal weight: 6.9990 chunk 218 optimal weight: 0.7980 chunk 41 optimal weight: 10.0000 chunk 338 optimal weight: 7.9990 chunk 372 optimal weight: 10.0000 chunk 147 optimal weight: 7.9990 chunk 291 optimal weight: 3.9990 chunk 137 optimal weight: 0.0670 chunk 258 optimal weight: 6.9990 overall best weight: 1.5728 ------------------------------------------------------------------------------- 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** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 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 777 ASN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 ASN ** M 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 6 GLN R 43 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.082378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.064465 restraints weight = 212544.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.062563 restraints weight = 186934.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.063105 restraints weight = 170917.702| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 34914 Z= 0.106 Angle : 0.549 9.736 47668 Z= 0.270 Chirality : 0.045 0.400 5536 Planarity : 0.004 0.068 6009 Dihedral : 5.123 56.478 5818 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.13), residues: 4192 helix: 1.18 (0.21), residues: 651 sheet: -0.02 (0.18), residues: 850 loop : -1.34 (0.12), residues: 2691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP D 196 HIS 0.009 0.001 HIS A 954 PHE 0.027 0.001 PHE C 275 TYR 0.013 0.001 TYR D 50 ARG 0.003 0.000 ARG R 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00402 ( 41) link_NAG-ASN : angle 2.42604 ( 123) link_BETA1-4 : bond 0.00332 ( 19) link_BETA1-4 : angle 1.79975 ( 57) hydrogen bonds : bond 0.03668 ( 907) hydrogen bonds : angle 5.18802 ( 2547) SS BOND : bond 0.00314 ( 51) SS BOND : angle 1.15422 ( 102) covalent geometry : bond 0.00238 (34803) covalent geometry : angle 0.52989 (47386) *********************** 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 153 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 3.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 527 PRO cc_start: 0.7734 (Cg_endo) cc_final: 0.7499 (Cg_exo) REVERT: A 712 ILE cc_start: 0.9348 (tp) cc_final: 0.9143 (tp) REVERT: A 731 MET cc_start: 0.8851 (pmm) cc_final: 0.8238 (pmm) REVERT: B 238 PHE cc_start: 0.8570 (t80) cc_final: 0.8073 (t80) REVERT: B 562 PHE cc_start: 0.7555 (p90) cc_final: 0.7260 (p90) REVERT: C 55 PHE cc_start: 0.8149 (m-10) cc_final: 0.7738 (m-10) REVERT: C 429 PHE cc_start: 0.7760 (t80) cc_final: 0.7553 (t80) REVERT: C 697 MET cc_start: 0.8109 (ttt) cc_final: 0.7675 (ttt) REVERT: C 1041 ASP cc_start: 0.7564 (t0) cc_final: 0.7130 (t70) REVERT: N 101 PHE cc_start: 0.8495 (m-10) cc_final: 0.7579 (p90) REVERT: R 35 HIS cc_start: 0.8719 (m-70) cc_final: 0.8283 (m90) REVERT: R 70 MET cc_start: 0.7049 (mmp) cc_final: 0.4924 (mmp) REVERT: R 98 ARG cc_start: 0.8604 (ttp80) cc_final: 0.8239 (ttp80) REVERT: R 159 TYR cc_start: 0.6247 (p90) cc_final: 0.5260 (p90) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.4342 time to fit residues: 116.4864 Evaluate side-chains 118 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 3.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 161 optimal weight: 9.9990 chunk 125 optimal weight: 6.9990 chunk 261 optimal weight: 7.9990 chunk 186 optimal weight: 4.9990 chunk 166 optimal weight: 6.9990 chunk 81 optimal weight: 0.7980 chunk 127 optimal weight: 2.9990 chunk 168 optimal weight: 5.9990 chunk 129 optimal weight: 8.9990 chunk 265 optimal weight: 0.2980 chunk 312 optimal weight: 0.0000 overall best weight: 1.8188 ------------------------------------------------------------------------------- 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** ** A1048 HIS ** 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** C 613 GLN ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN Q 6 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 = 0.3704 r_free = 0.3704 target = 0.082133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.063579 restraints weight = 213410.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.062047 restraints weight = 196384.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.062494 restraints weight = 159350.501| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.3212 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= 0.114 Angle : 0.551 9.784 47668 Z= 0.271 Chirality : 0.045 0.402 5536 Planarity : 0.004 0.068 6009 Dihedral : 5.091 56.632 5818 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.03 % Allowed : 0.48 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.13), residues: 4192 helix: 1.18 (0.21), residues: 650 sheet: 0.00 (0.18), residues: 854 loop : -1.33 (0.12), residues: 2688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 196 HIS 0.009 0.001 HIS A 954 PHE 0.019 0.001 PHE C 275 TYR 0.034 0.001 TYR C 796 ARG 0.005 0.000 ARG B 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00394 ( 41) link_NAG-ASN : angle 2.43128 ( 123) link_BETA1-4 : bond 0.00301 ( 19) link_BETA1-4 : angle 1.79493 ( 57) hydrogen bonds : bond 0.03665 ( 907) hydrogen bonds : angle 5.13015 ( 2547) SS BOND : bond 0.00312 ( 51) SS BOND : angle 1.16868 ( 102) covalent geometry : bond 0.00255 (34803) covalent geometry : angle 0.53211 (47386) *********************** 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 156 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 155 time to evaluate : 3.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 527 PRO cc_start: 0.7800 (Cg_endo) cc_final: 0.7567 (Cg_exo) REVERT: A 731 MET cc_start: 0.8821 (pmm) cc_final: 0.8230 (pmm) REVERT: A 869 MET cc_start: 0.8562 (ptt) cc_final: 0.8334 (ppp) REVERT: B 238 PHE cc_start: 0.8616 (t80) cc_final: 0.8070 (t80) REVERT: B 562 PHE cc_start: 0.7658 (p90) cc_final: 0.7295 (p90) REVERT: B 1058 HIS cc_start: 0.8338 (m90) cc_final: 0.7888 (m-70) REVERT: C 55 PHE cc_start: 0.8040 (m-10) cc_final: 0.7772 (m-10) REVERT: C 429 PHE cc_start: 0.7838 (t80) cc_final: 0.7616 (t80) REVERT: C 1041 ASP cc_start: 0.7710 (t0) cc_final: 0.7281 (t70) REVERT: E 70 MET cc_start: -0.1043 (mtt) cc_final: -0.1270 (mtm) REVERT: E 73 ASP cc_start: 0.6538 (t0) cc_final: 0.6245 (t0) REVERT: N 101 PHE cc_start: 0.8270 (m-10) cc_final: 0.7615 (p90) REVERT: R 159 TYR cc_start: 0.6205 (p90) cc_final: 0.5265 (p90) outliers start: 1 outliers final: 0 residues processed: 156 average time/residue: 0.4123 time to fit residues: 112.8357 Evaluate side-chains 116 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 3.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 166 optimal weight: 0.4980 chunk 317 optimal weight: 30.0000 chunk 383 optimal weight: 3.9990 chunk 246 optimal weight: 9.9990 chunk 57 optimal weight: 10.0000 chunk 33 optimal weight: 0.1980 chunk 323 optimal weight: 9.9990 chunk 242 optimal weight: 7.9990 chunk 219 optimal weight: 0.0570 chunk 368 optimal weight: 10.0000 chunk 324 optimal weight: 6.9990 overall best weight: 2.3502 ------------------------------------------------------------------------------- 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** ** A1048 HIS ** 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** C 613 GLN ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 ASN ** M 16 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 = 0.3689 r_free = 0.3689 target = 0.081526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.063162 restraints weight = 213599.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.061530 restraints weight = 184543.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.061695 restraints weight = 160455.610| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.3381 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= 0.130 Angle : 0.570 9.844 47668 Z= 0.282 Chirality : 0.045 0.408 5536 Planarity : 0.004 0.069 6009 Dihedral : 5.176 56.638 5818 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.03 % Allowed : 0.35 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.13), residues: 4192 helix: 1.07 (0.21), residues: 654 sheet: -0.06 (0.18), residues: 868 loop : -1.32 (0.12), residues: 2670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 196 HIS 0.011 0.001 HIS A 954 PHE 0.018 0.001 PHE C 275 TYR 0.021 0.001 TYR A 873 ARG 0.006 0.000 ARG B 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00412 ( 41) link_NAG-ASN : angle 2.43068 ( 123) link_BETA1-4 : bond 0.00291 ( 19) link_BETA1-4 : angle 1.81846 ( 57) hydrogen bonds : bond 0.03776 ( 907) hydrogen bonds : angle 5.13912 ( 2547) SS BOND : bond 0.00344 ( 51) SS BOND : angle 1.20342 ( 102) covalent geometry : bond 0.00289 (34803) covalent geometry : angle 0.55195 (47386) ********************** 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 155 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 154 time to evaluate : 3.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 527 PRO cc_start: 0.7842 (Cg_endo) cc_final: 0.7606 (Cg_exo) REVERT: A 731 MET cc_start: 0.8790 (pmm) cc_final: 0.8247 (pmm) REVERT: A 869 MET cc_start: 0.8554 (ptt) cc_final: 0.8341 (ppp) REVERT: B 238 PHE cc_start: 0.8598 (t80) cc_final: 0.8068 (t80) REVERT: B 562 PHE cc_start: 0.7635 (p90) cc_final: 0.7303 (p90) REVERT: B 1058 HIS cc_start: 0.8342 (m90) cc_final: 0.7906 (m-70) REVERT: C 562 PHE cc_start: 0.8783 (p90) cc_final: 0.8458 (p90) REVERT: C 697 MET cc_start: 0.7865 (ttt) cc_final: 0.7536 (ttt) REVERT: C 1041 ASP cc_start: 0.7746 (t0) cc_final: 0.7330 (t70) REVERT: E 70 MET cc_start: -0.1028 (mtt) cc_final: -0.1257 (mtm) REVERT: E 119 GLN cc_start: 0.6073 (pm20) cc_final: 0.5702 (mm-40) REVERT: N 101 PHE cc_start: 0.8210 (m-10) cc_final: 0.7513 (p90) REVERT: R 159 TYR cc_start: 0.6121 (p90) cc_final: 0.5183 (p90) outliers start: 1 outliers final: 0 residues processed: 155 average time/residue: 0.4236 time to fit residues: 115.1032 Evaluate side-chains 116 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 3.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 375 optimal weight: 0.9990 chunk 251 optimal weight: 9.9990 chunk 260 optimal weight: 8.9990 chunk 364 optimal weight: 10.0000 chunk 336 optimal weight: 5.9990 chunk 266 optimal weight: 5.9990 chunk 107 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 268 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 78 optimal weight: 0.1980 overall best weight: 2.6386 ------------------------------------------------------------------------------- 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 394 ASN C 613 GLN ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.081086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.061648 restraints weight = 215279.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.060376 restraints weight = 191674.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.060790 restraints weight = 177609.940| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34914 Z= 0.141 Angle : 0.583 13.048 47668 Z= 0.288 Chirality : 0.045 0.410 5536 Planarity : 0.004 0.069 6009 Dihedral : 5.312 56.744 5818 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.03 % Allowed : 0.35 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.13), residues: 4192 helix: 0.98 (0.21), residues: 658 sheet: -0.11 (0.18), residues: 871 loop : -1.37 (0.12), residues: 2663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 196 HIS 0.009 0.001 HIS A 954 PHE 0.022 0.001 PHE C 275 TYR 0.017 0.001 TYR C 873 ARG 0.006 0.000 ARG B 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00408 ( 41) link_NAG-ASN : angle 2.47100 ( 123) link_BETA1-4 : bond 0.00276 ( 19) link_BETA1-4 : angle 1.85271 ( 57) hydrogen bonds : bond 0.03877 ( 907) hydrogen bonds : angle 5.18693 ( 2547) SS BOND : bond 0.00378 ( 51) SS BOND : angle 1.22255 ( 102) covalent geometry : bond 0.00312 (34803) covalent geometry : angle 0.56424 (47386) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8859.72 seconds wall clock time: 157 minutes 26.36 seconds (9446.36 seconds total)