Starting phenix.real_space_refine on Tue Aug 26 13:18:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uxe_64582/08_2025/9uxe_64582.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uxe_64582/08_2025/9uxe_64582.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9uxe_64582/08_2025/9uxe_64582.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uxe_64582/08_2025/9uxe_64582.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9uxe_64582/08_2025/9uxe_64582.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uxe_64582/08_2025/9uxe_64582.map" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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 153 5.16 5 C 22736 2.51 5 N 5926 2.21 5 O 7070 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35885 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 8315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 8315 Classifications: {'peptide': 1062} Link IDs: {'PTRANS': 58, 'TRANS': 1003} Chain breaks: 5 Chain: "B" Number of atoms: 8325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1064, 8325 Classifications: {'peptide': 1064} Link IDs: {'PTRANS': 58, 'TRANS': 1005} Chain breaks: 5 Chain: "C" Number of atoms: 8307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8307 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 58, 'TRANS': 1002} Chain breaks: 5 Chain: "D" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1714 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 12, 'TRANS': 214} Chain: "E" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1617 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 199} Chain: "H" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1714 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 12, 'TRANS': 214} Chain: "L" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1617 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 199} Chain: "J" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1714 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 12, 'TRANS': 214} Chain: "K" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1617 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 199} Chain: "I" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" 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 Time building chain proxies: 7.93, per 1000 atoms: 0.22 Number of scatterers: 35885 At special positions: 0 Unit cell: (181.28, 146.26, 234.84, 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 153 16.00 O 7070 8.00 N 5926 7.00 C 22736 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 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=2.03 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 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.01 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 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 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 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=2.03 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=2.03 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 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " 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 Atom "HETATM35519 O5 NAG A1301 .*. O " rejected from bonding due to valence issues. 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 I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " BETA1-6 " NAG I 1 " - " FUC I 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG P 1 " - " FUC P 4 " " NAG V 1 " - " FUC V 4 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 603 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 125 " " NAG B1303 " - " ASN B 282 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1074 " " NAG F 1 " - " ASN C 234 " " NAG G 1 " - " ASN C 717 " " NAG I 1 " - " ASN C 343 " " NAG M 1 " - " ASN C 801 " " NAG N 1 " - " ASN C1098 " " NAG O 1 " - " ASN C1134 " " NAG P 1 " - " ASN A 343 " " NAG Q 1 " - " ASN A 234 " " NAG R 1 " - " ASN A 717 " " NAG S 1 " - " ASN A 801 " " NAG T 1 " - " ASN A1098 " " NAG U 1 " - " ASN A1134 " " NAG V 1 " - " ASN B 343 " " NAG W 1 " - " ASN B 234 " " NAG X 1 " - " ASN B 717 " " NAG Y 1 " - " ASN B 801 " " NAG Z 1 " - " ASN B1098 " " NAG a 1 " - " ASN B1134 " Time building additional restraints: 2.27 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 715.3 nanoseconds 8906 Ramachandran restraints generated. 4453 Oldfield, 0 Emsley, 4453 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8382 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 74 sheets defined 18.8% alpha, 32.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 344 removed outlier: 3.826A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.407A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.912A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 5.059A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.600A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.569A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.014A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.170A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.985A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.131A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.480A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 5.489A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.802A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.514A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.956A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.216A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.532A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.837A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.441A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.937A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.106A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 389 Processing helix chain 'C' and resid 405 through 410 removed outlier: 5.735A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.618A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.566A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.119A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.696A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 5.066A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 169 through 171 No H-bonds generated for 'chain 'D' and resid 169 through 171' Processing helix chain 'E' and resid 118 through 123 Processing helix chain 'E' and resid 180 through 186 removed outlier: 3.707A pdb=" N LYS E 185 " --> pdb=" O ALA E 181 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N HIS E 186 " --> pdb=" O ASP E 182 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 65 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.910A pdb=" N THR H 91 " --> pdb=" O THR H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 169 through 171 No H-bonds generated for 'chain 'H' and resid 169 through 171' Processing helix chain 'L' and resid 118 through 125 removed outlier: 3.979A pdb=" N GLY L 125 " --> pdb=" O GLN L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 180 through 186 removed outlier: 3.705A pdb=" N LYS L 185 " --> pdb=" O ALA L 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'J' and resid 169 through 171 No H-bonds generated for 'chain 'J' and resid 169 through 171' Processing helix chain 'K' and resid 118 through 125 removed outlier: 3.585A pdb=" N SER K 124 " --> pdb=" O GLU K 120 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLY K 125 " --> pdb=" O GLN K 121 " (cutoff:3.500A) Processing helix chain 'K' and resid 180 through 186 removed outlier: 3.968A pdb=" N LYS K 185 " --> pdb=" O ALA K 181 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N HIS K 186 " --> pdb=" O ASP K 182 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.912A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 6.892A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 55 removed outlier: 7.600A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.093A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.938A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.088A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.122A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N HIS A 146 " --> pdb=" O TRP A 152 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N TRP A 152 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 13.000A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 12.657A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 9.872A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG A 246 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.938A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.088A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.122A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N HIS A 146 " --> pdb=" O TRP A 152 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N TRP A 152 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.392A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.489A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.947A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.422A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.578A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 789 removed outlier: 5.289A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.704A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.146A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.214A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 42 through 43 removed outlier: 6.424A pdb=" N PHE B 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.823A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.525A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 151 through 160 removed outlier: 6.074A pdb=" N TRP B 152 " --> pdb=" O HIS B 146 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N HIS B 146 " --> pdb=" O TRP B 152 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 10.130A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.879A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.157A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 7.068A pdb=" N ASN B 437 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N PHE B 374 " --> pdb=" O ASN B 437 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.253A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.330A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.647A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD4, first strand: chain 'B' and resid 787 through 790 Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.655A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD7, first strand: chain 'C' and resid 27 through 29 removed outlier: 3.988A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 47 through 55 Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 12.873A pdb=" N PHE C 135 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 12.705A pdb=" N THR C 240 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 10.649A pdb=" N ASN C 137 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 11.307A pdb=" N LEU C 242 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 11.051A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.137A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.989A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.646A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.167A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 660 removed outlier: 6.048A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.472A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.472A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.481A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF2, first strand: chain 'D' and resid 3 through 8 Processing sheet with id=AF3, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.599A pdb=" N GLY D 10 " --> pdb=" O LEU D 121 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR D 123 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TRP D 33 " --> pdb=" O GLU D 99 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N MET D 34 " --> pdb=" O ARG D 50 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ARG D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.599A pdb=" N GLY D 10 " --> pdb=" O LEU D 121 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR D 123 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N CYS D 96 " --> pdb=" O TRP D 116 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N TRP D 116 " --> pdb=" O CYS D 96 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ARG D 98 " --> pdb=" O ASP D 114 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP D 114 " --> pdb=" O ARG D 98 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N TYR D 112 " --> pdb=" O ALA D 100 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 133 through 137 removed outlier: 3.609A pdb=" N PHE D 135 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU D 154 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU D 191 " --> pdb=" O VAL D 155 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ASP D 157 " --> pdb=" O TYR D 189 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N TYR D 189 " --> pdb=" O ASP D 157 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU D 188 " --> pdb=" O GLN D 184 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 164 through 167 removed outlier: 3.643A pdb=" N THR D 164 " --> pdb=" O ASN D 212 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.750A pdb=" N ALA E 19 " --> pdb=" O ILE E 76 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP E 71 " --> pdb=" O SER E 68 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.703A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 111 through 115 removed outlier: 3.613A pdb=" N ASN E 135 " --> pdb=" O TYR E 170 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N TYR E 170 " --> pdb=" O ASN E 135 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 150 through 151 removed outlier: 3.726A pdb=" N GLN E 144 " --> pdb=" O GLU E 192 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU E 192 " --> pdb=" O GLN E 144 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL E 193 " --> pdb=" O VAL E 202 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL E 202 " --> pdb=" O VAL E 193 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AG3, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.760A pdb=" N MET H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ARG H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'H' and resid 133 through 137 removed outlier: 3.933A pdb=" N PHE H 135 " --> pdb=" O LEU H 154 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU H 154 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU H 191 " --> pdb=" O VAL H 155 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ASP H 157 " --> pdb=" O TYR H 189 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N TYR H 189 " --> pdb=" O ASP H 157 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU H 188 " --> pdb=" O GLN H 184 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'H' and resid 164 through 167 removed outlier: 3.680A pdb=" N THR H 164 " --> pdb=" O ASN H 212 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL H 220 " --> pdb=" O VAL H 211 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AG7, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.808A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.504A pdb=" N SER L 94 " --> pdb=" O LEU L 91 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'L' and resid 111 through 115 removed outlier: 3.904A pdb=" N ASN L 135 " --> pdb=" O TYR L 170 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TYR L 170 " --> pdb=" O ASN L 135 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'L' and resid 150 through 152 removed outlier: 3.578A pdb=" N GLN L 152 " --> pdb=" O TRP L 145 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N TRP L 145 " --> pdb=" O GLN L 152 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'J' and resid 3 through 8 removed outlier: 3.592A pdb=" N GLN J 3 " --> pdb=" O SER J 25 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER J 25 " --> pdb=" O GLN J 3 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR J 78 " --> pdb=" O ASP J 73 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASP J 73 " --> pdb=" O THR J 78 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'J' and resid 11 through 12 removed outlier: 6.686A pdb=" N MET J 34 " --> pdb=" O ARG J 50 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ARG J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'J' and resid 133 through 137 removed outlier: 3.897A pdb=" N PHE J 135 " --> pdb=" O LEU J 154 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU J 154 " --> pdb=" O PHE J 135 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY J 152 " --> pdb=" O LEU J 137 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU J 191 " --> pdb=" O VAL J 155 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ASP J 157 " --> pdb=" O TYR J 189 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TYR J 189 " --> pdb=" O ASP J 157 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N VAL J 194 " --> pdb=" O HIS J 177 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS J 177 " --> pdb=" O VAL J 194 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'J' and resid 133 through 137 removed outlier: 3.897A pdb=" N PHE J 135 " --> pdb=" O LEU J 154 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU J 154 " --> pdb=" O PHE J 135 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY J 152 " --> pdb=" O LEU J 137 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU J 191 " --> pdb=" O VAL J 155 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ASP J 157 " --> pdb=" O TYR J 189 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TYR J 189 " --> pdb=" O ASP J 157 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU J 188 " --> pdb=" O GLN J 184 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'J' and resid 164 through 167 removed outlier: 3.794A pdb=" N THR J 164 " --> pdb=" O ASN J 212 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL J 220 " --> pdb=" O VAL J 211 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'K' and resid 4 through 7 removed outlier: 4.056A pdb=" N ALA K 19 " --> pdb=" O ILE K 76 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE K 76 " --> pdb=" O ALA K 19 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.510A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'K' and resid 10 through 13 removed outlier: 3.775A pdb=" N SER K 94 " --> pdb=" O LEU K 91 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'K' and resid 111 through 115 removed outlier: 3.575A pdb=" N ASN K 135 " --> pdb=" O TYR K 170 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N TYR K 170 " --> pdb=" O ASN K 135 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'K' and resid 150 through 152 removed outlier: 3.648A pdb=" N GLN K 152 " --> pdb=" O TRP K 145 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N TRP K 145 " --> pdb=" O GLN K 152 " (cutoff:3.500A) 1413 hydrogen bonds defined for protein. 3801 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: 9.09 Time building geometry restraints manager: 2.94 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: 11330 1.34 - 1.46: 8695 1.46 - 1.58: 16487 1.58 - 1.70: 0 1.70 - 1.83: 195 Bond restraints: 36707 Sorted by residual: bond pdb=" N ASP D 57 " pdb=" CA ASP D 57 " ideal model delta sigma weight residual 1.455 1.497 -0.043 1.25e-02 6.40e+03 1.16e+01 bond pdb=" N ASP D 62 " pdb=" CA ASP D 62 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.17e-02 7.31e+03 9.97e+00 bond pdb=" N VAL A 445 " pdb=" CA VAL A 445 " ideal model delta sigma weight residual 1.457 1.497 -0.039 1.25e-02 6.40e+03 9.83e+00 bond pdb=" N SER D 49 " pdb=" CA SER D 49 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.25e-02 6.40e+03 9.15e+00 bond pdb=" N VAL D 46 " pdb=" CA VAL D 46 " ideal model delta sigma weight residual 1.459 1.495 -0.035 1.19e-02 7.06e+03 8.81e+00 ... (remaining 36702 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 48865 2.05 - 4.10: 940 4.10 - 6.15: 117 6.15 - 8.20: 25 8.20 - 10.25: 8 Bond angle restraints: 49955 Sorted by residual: angle pdb=" N ARG D 53 " pdb=" CA ARG D 53 " pdb=" C ARG D 53 " ideal model delta sigma weight residual 111.28 104.10 7.18 1.09e+00 8.42e-01 4.34e+01 angle pdb=" C ARG D 50 " pdb=" N VAL D 51 " pdb=" CA VAL D 51 " ideal model delta sigma weight residual 123.14 115.32 7.82 1.31e+00 5.83e-01 3.56e+01 angle pdb=" N ASN D 52 " pdb=" CA ASN D 52 " pdb=" C ASN D 52 " ideal model delta sigma weight residual 110.53 104.26 6.27 1.29e+00 6.01e-01 2.36e+01 angle pdb=" CA ASP D 54 " pdb=" CB ASP D 54 " pdb=" CG ASP D 54 " ideal model delta sigma weight residual 112.60 117.15 -4.55 1.00e+00 1.00e+00 2.07e+01 angle pdb=" N VAL D 105 " pdb=" CA VAL D 105 " pdb=" C VAL D 105 " ideal model delta sigma weight residual 110.62 106.11 4.51 1.02e+00 9.61e-01 1.95e+01 ... (remaining 49950 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.32: 21630 24.32 - 48.64: 976 48.64 - 72.96: 134 72.96 - 97.29: 28 97.29 - 121.61: 5 Dihedral angle restraints: 22773 sinusoidal: 9725 harmonic: 13048 Sorted by residual: dihedral pdb=" CD ARG A 346 " pdb=" NE ARG A 346 " pdb=" CZ ARG A 346 " pdb=" NH1 ARG A 346 " ideal model delta sinusoidal sigma weight residual 0.00 53.83 -53.83 1 1.00e+01 1.00e-02 3.93e+01 dihedral pdb=" CA LYS A1073 " pdb=" C LYS A1073 " pdb=" N ASN A1074 " pdb=" CA ASN A1074 " ideal model delta harmonic sigma weight residual -180.00 -151.61 -28.39 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA VAL A 656 " pdb=" C VAL A 656 " pdb=" N ASN A 657 " pdb=" CA ASN A 657 " ideal model delta harmonic sigma weight residual -180.00 -156.35 -23.65 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 22770 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 5266 0.087 - 0.174: 532 0.174 - 0.261: 25 0.261 - 0.347: 7 0.347 - 0.434: 3 Chirality restraints: 5833 Sorted by residual: chirality pdb=" C1 BMA P 3 " pdb=" O4 NAG P 2 " pdb=" C2 BMA P 3 " pdb=" O5 BMA P 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-02 2.50e+03 1.77e+02 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-02 2.50e+03 1.42e+02 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.34 -0.06 2.00e-02 2.50e+03 8.63e+00 ... (remaining 5830 not shown) Planarity restraints: 6420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 346 " -0.890 9.50e-02 1.11e+02 3.99e-01 9.66e+01 pdb=" NE ARG A 346 " 0.053 2.00e-02 2.50e+03 pdb=" CZ ARG A 346 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 346 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 346 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG P 1 " -0.080 2.00e-02 2.50e+03 6.65e-02 5.52e+01 pdb=" C7 NAG P 1 " 0.022 2.00e-02 2.50e+03 pdb=" C8 NAG P 1 " -0.060 2.00e-02 2.50e+03 pdb=" N2 NAG P 1 " 0.107 2.00e-02 2.50e+03 pdb=" O7 NAG P 1 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 50 " -0.639 9.50e-02 1.11e+02 2.86e-01 5.00e+01 pdb=" NE ARG D 50 " 0.037 2.00e-02 2.50e+03 pdb=" CZ ARG D 50 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG D 50 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG D 50 " -0.021 2.00e-02 2.50e+03 ... (remaining 6417 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 10573 2.83 - 3.34: 32553 3.34 - 3.86: 58853 3.86 - 4.38: 66478 4.38 - 4.90: 115407 Nonbonded interactions: 283864 Sorted by model distance: nonbonded pdb=" O5 NAG I 1 " pdb=" O6 NAG I 1 " model vdw 2.308 2.432 nonbonded pdb=" O ASP J 90 " pdb=" OD1 ASP J 90 " model vdw 2.356 3.040 nonbonded pdb=" O ALA D 61 " pdb=" N LYS D 65 " model vdw 2.400 3.120 nonbonded pdb=" O5 NAG Y 1 " pdb=" O6 NAG Y 1 " model vdw 2.419 2.432 nonbonded pdb=" N THR A 345 " pdb=" OG1 THR A 345 " model vdw 2.440 2.496 ... (remaining 283859 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 14 through 827 or resid 855 through 1308)) selection = (chain 'B' and (resid 14 through 621 or resid 641 through 827 or resid 855 throu \ gh 1308)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' } ncs_group { reference = chain 'I' selection = chain 'P' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 32.250 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 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 0.049 36820 Z= 0.178 Angle : 0.776 33.507 50249 Z= 0.383 Chirality : 0.050 0.434 5833 Planarity : 0.008 0.399 6376 Dihedral : 13.202 121.607 14256 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.02 % Allowed : 12.35 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.12), residues: 4453 helix: 1.91 (0.20), residues: 716 sheet: 0.35 (0.15), residues: 1284 loop : -0.87 (0.12), residues: 2453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 46 TYR 0.026 0.001 TYR K 183 PHE 0.032 0.002 PHE C 201 TRP 0.055 0.002 TRP H 111 HIS 0.007 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00318 (36707) covalent geometry : angle 0.67474 (49955) SS BOND : bond 0.00338 ( 45) SS BOND : angle 1.09923 ( 90) hydrogen bonds : bond 0.13384 ( 1366) hydrogen bonds : angle 7.83749 ( 3801) link_BETA1-4 : bond 0.01366 ( 21) link_BETA1-4 : angle 2.69604 ( 63) link_BETA1-6 : bond 0.02184 ( 3) link_BETA1-6 : angle 3.49363 ( 9) link_NAG-ASN : bond 0.00908 ( 44) link_NAG-ASN : angle 7.20259 ( 132) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8906 Ramachandran restraints generated. 4453 Oldfield, 0 Emsley, 4453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8906 Ramachandran restraints generated. 4453 Oldfield, 0 Emsley, 4453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 335 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7664 (m-80) cc_final: 0.4510 (m-80) REVERT: A 196 ASN cc_start: 0.7888 (t0) cc_final: 0.7556 (p0) REVERT: A 207 HIS cc_start: 0.6568 (t-170) cc_final: 0.6284 (m-70) REVERT: A 269 TYR cc_start: 0.6875 (m-10) cc_final: 0.6546 (m-80) REVERT: A 354 ASN cc_start: 0.8345 (t0) cc_final: 0.7679 (p0) REVERT: A 394 ASN cc_start: 0.6797 (m-40) cc_final: 0.6527 (m-40) REVERT: A 515 PHE cc_start: 0.8307 (OUTLIER) cc_final: 0.7485 (m-80) REVERT: A 619 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8552 (tp30) REVERT: A 646 ARG cc_start: 0.8633 (ttm170) cc_final: 0.8126 (tpt-90) REVERT: A 985 ASP cc_start: 0.8490 (m-30) cc_final: 0.8265 (m-30) REVERT: B 130 VAL cc_start: 0.7945 (p) cc_final: 0.7722 (p) REVERT: B 191 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8370 (mt-10) REVERT: B 375 SER cc_start: 0.9339 (m) cc_final: 0.9042 (t) REVERT: B 400 PHE cc_start: 0.8538 (p90) cc_final: 0.8254 (p90) REVERT: B 453 TYR cc_start: 0.5630 (p90) cc_final: 0.5405 (p90) REVERT: B 489 TYR cc_start: 0.7875 (m-10) cc_final: 0.7594 (m-10) REVERT: B 821 LEU cc_start: 0.8583 (tt) cc_final: 0.8247 (mp) REVERT: B 936 ASP cc_start: 0.8443 (m-30) cc_final: 0.8116 (t0) REVERT: C 81 ASN cc_start: 0.7408 (p0) cc_final: 0.7107 (p0) REVERT: C 140 PHE cc_start: 0.7775 (p90) cc_final: 0.7531 (p90) REVERT: C 365 TYR cc_start: 0.7549 (m-80) cc_final: 0.7327 (m-80) REVERT: C 377 PHE cc_start: 0.7217 (t80) cc_final: 0.6771 (t80) REVERT: C 389 ASP cc_start: 0.8413 (m-30) cc_final: 0.7973 (p0) REVERT: C 558 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8350 (mmmt) REVERT: C 867 ASP cc_start: 0.8439 (m-30) cc_final: 0.8235 (p0) REVERT: C 950 ASP cc_start: 0.8998 (m-30) cc_final: 0.8789 (m-30) REVERT: D 83 MET cc_start: 0.4098 (OUTLIER) cc_final: 0.2941 (mmm) REVERT: D 209 CYS cc_start: -0.2052 (OUTLIER) cc_final: -0.3480 (p) REVERT: H 111 TRP cc_start: 0.3863 (t-100) cc_final: 0.2193 (m100) REVERT: L 46 ARG cc_start: 0.2653 (mmt180) cc_final: 0.1972 (mmt180) REVERT: K 13 LEU cc_start: 0.4331 (OUTLIER) cc_final: 0.3841 (tp) outliers start: 40 outliers final: 15 residues processed: 364 average time/residue: 0.2099 time to fit residues: 123.4818 Evaluate side-chains 308 residues out of total 3918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 287 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain K residue 13 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 432 optimal weight: 50.0000 chunk 197 optimal weight: 0.5980 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.7980 chunk 401 optimal weight: 30.0000 chunk 424 optimal weight: 50.0000 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 245 HIS A1005 GLN A1071 GLN B 66 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN B 658 ASN B 957 GLN C 14 GLN C 99 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 751 ASN C 755 GLN D 184 GLN E 121 GLN E 186 HIS L 121 GLN L 144 GLN J 39 GLN J 184 GLN K 39 GLN K 121 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.174896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.104063 restraints weight = 73785.966| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 3.14 r_work: 0.3203 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 36820 Z= 0.198 Angle : 0.685 26.023 50249 Z= 0.330 Chirality : 0.047 0.470 5833 Planarity : 0.004 0.069 6376 Dihedral : 7.756 113.973 6300 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.78 % Allowed : 12.10 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.12), residues: 4453 helix: 2.07 (0.20), residues: 718 sheet: 0.26 (0.14), residues: 1327 loop : -0.88 (0.12), residues: 2408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 355 TYR 0.042 0.001 TYR E 137 PHE 0.024 0.002 PHE J 68 TRP 0.020 0.002 TRP H 36 HIS 0.011 0.001 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00455 (36707) covalent geometry : angle 0.62266 (49955) SS BOND : bond 0.00197 ( 45) SS BOND : angle 0.85024 ( 90) hydrogen bonds : bond 0.04740 ( 1366) hydrogen bonds : angle 6.37396 ( 3801) link_BETA1-4 : bond 0.00410 ( 21) link_BETA1-4 : angle 1.94788 ( 63) link_BETA1-6 : bond 0.00161 ( 3) link_BETA1-6 : angle 1.54226 ( 9) link_NAG-ASN : bond 0.00775 ( 44) link_NAG-ASN : angle 5.42391 ( 132) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8906 Ramachandran restraints generated. 4453 Oldfield, 0 Emsley, 4453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8906 Ramachandran restraints generated. 4453 Oldfield, 0 Emsley, 4453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 3918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 303 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 ASN cc_start: 0.7926 (t0) cc_final: 0.7626 (p0) REVERT: A 207 HIS cc_start: 0.6638 (t-170) cc_final: 0.6267 (m-70) REVERT: A 239 GLN cc_start: 0.7149 (OUTLIER) cc_final: 0.6848 (mt0) REVERT: A 269 TYR cc_start: 0.7045 (m-10) cc_final: 0.6678 (m-80) REVERT: A 356 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.8048 (tppt) REVERT: A 394 ASN cc_start: 0.7387 (m-40) cc_final: 0.7154 (m-40) REVERT: A 587 ILE cc_start: 0.8364 (mt) cc_final: 0.8135 (mm) REVERT: A 619 GLU cc_start: 0.8980 (OUTLIER) cc_final: 0.8678 (mp0) REVERT: A 646 ARG cc_start: 0.8724 (ttm170) cc_final: 0.8297 (tpt-90) REVERT: A 985 ASP cc_start: 0.8576 (m-30) cc_final: 0.8355 (m-30) REVERT: B 64 TRP cc_start: 0.7699 (t-100) cc_final: 0.7214 (t-100) REVERT: B 104 TRP cc_start: 0.8548 (m-90) cc_final: 0.7992 (m-90) REVERT: B 191 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8424 (mt-10) REVERT: B 400 PHE cc_start: 0.8510 (p90) cc_final: 0.8280 (p90) REVERT: B 453 TYR cc_start: 0.5696 (p90) cc_final: 0.5431 (p90) REVERT: B 619 GLU cc_start: 0.9084 (mt-10) cc_final: 0.8772 (mp0) REVERT: B 808 ASP cc_start: 0.8723 (t0) cc_final: 0.8502 (t0) REVERT: B 821 LEU cc_start: 0.8508 (tt) cc_final: 0.8163 (mp) REVERT: B 936 ASP cc_start: 0.8626 (m-30) cc_final: 0.8202 (t0) REVERT: C 81 ASN cc_start: 0.7565 (p0) cc_final: 0.7185 (p0) REVERT: C 177 MET cc_start: 0.1373 (mmt) cc_final: 0.1089 (tpp) REVERT: C 207 HIS cc_start: 0.6315 (OUTLIER) cc_final: 0.5899 (m-70) REVERT: C 338 PHE cc_start: 0.8605 (m-80) cc_final: 0.8382 (m-80) REVERT: C 389 ASP cc_start: 0.8538 (m-30) cc_final: 0.8086 (p0) REVERT: C 461 LEU cc_start: 0.3921 (OUTLIER) cc_final: 0.3490 (mp) REVERT: C 558 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8685 (mtpt) REVERT: C 867 ASP cc_start: 0.8663 (m-30) cc_final: 0.8319 (p0) REVERT: C 950 ASP cc_start: 0.9082 (m-30) cc_final: 0.8796 (m-30) REVERT: D 29 PHE cc_start: 0.7792 (t80) cc_final: 0.7172 (t80) REVERT: D 36 TRP cc_start: 0.5900 (m100) cc_final: 0.4979 (m100) REVERT: D 65 LYS cc_start: 0.6507 (pttp) cc_final: 0.5985 (ptpt) REVERT: D 77 ASN cc_start: 0.5082 (t0) cc_final: 0.4515 (p0) REVERT: D 99 GLU cc_start: 0.6760 (tt0) cc_final: 0.6387 (tt0) REVERT: D 115 LEU cc_start: 0.6700 (OUTLIER) cc_final: 0.6419 (pt) REVERT: D 209 CYS cc_start: -0.1152 (OUTLIER) cc_final: -0.2953 (p) REVERT: E 4 MET cc_start: 0.5601 (ttm) cc_final: 0.4327 (ptm) REVERT: E 24 ARG cc_start: 0.7005 (mmm160) cc_final: 0.6697 (mmm-85) REVERT: E 137 TYR cc_start: 0.4922 (t80) cc_final: 0.4489 (t80) REVERT: H 50 ARG cc_start: 0.6076 (ttt-90) cc_final: 0.5098 (mtp-110) REVERT: J 108 MET cc_start: 0.6099 (tmm) cc_final: 0.5659 (mtt) REVERT: J 184 GLN cc_start: 0.2167 (OUTLIER) cc_final: 0.1325 (tt0) REVERT: K 13 LEU cc_start: 0.2599 (OUTLIER) cc_final: 0.2192 (tp) outliers start: 109 outliers final: 66 residues processed: 394 average time/residue: 0.2096 time to fit residues: 135.0785 Evaluate side-chains 355 residues out of total 3918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 279 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 939 SER Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 62 ARG Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 182 ASP Chi-restraints excluded: chain L residue 188 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 71 SER Chi-restraints excluded: chain J residue 184 GLN Chi-restraints excluded: chain J residue 222 LYS Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 130 VAL Chi-restraints excluded: chain K residue 188 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 376 optimal weight: 20.0000 chunk 17 optimal weight: 0.8980 chunk 218 optimal weight: 0.2980 chunk 73 optimal weight: 0.8980 chunk 433 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 132 optimal weight: 0.9980 chunk 291 optimal weight: 0.9990 chunk 61 optimal weight: 0.0030 chunk 174 optimal weight: 0.9990 chunk 171 optimal weight: 1.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN B 487 ASN B 957 GLN C 14 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 GLN L 195 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.176542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.109261 restraints weight = 73704.395| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 3.84 r_work: 0.3208 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 36820 Z= 0.109 Angle : 0.611 23.769 50249 Z= 0.292 Chirality : 0.045 0.482 5833 Planarity : 0.004 0.068 6376 Dihedral : 7.245 108.969 6287 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.76 % Allowed : 12.40 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.12), residues: 4453 helix: 2.30 (0.20), residues: 720 sheet: 0.25 (0.14), residues: 1339 loop : -0.86 (0.12), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 765 TYR 0.021 0.001 TYR D 112 PHE 0.017 0.001 PHE H 29 TRP 0.031 0.001 TRP H 111 HIS 0.009 0.001 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00233 (36707) covalent geometry : angle 0.55351 (49955) SS BOND : bond 0.00176 ( 45) SS BOND : angle 0.82035 ( 90) hydrogen bonds : bond 0.04091 ( 1366) hydrogen bonds : angle 5.98619 ( 3801) link_BETA1-4 : bond 0.00469 ( 21) link_BETA1-4 : angle 1.71355 ( 63) link_BETA1-6 : bond 0.00148 ( 3) link_BETA1-6 : angle 1.53683 ( 9) link_NAG-ASN : bond 0.00715 ( 44) link_NAG-ASN : angle 4.93606 ( 132) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8906 Ramachandran restraints generated. 4453 Oldfield, 0 Emsley, 4453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8906 Ramachandran restraints generated. 4453 Oldfield, 0 Emsley, 4453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 301 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8396 (p) cc_final: 0.7997 (t) REVERT: A 196 ASN cc_start: 0.7830 (t0) cc_final: 0.7510 (p0) REVERT: A 207 HIS cc_start: 0.6651 (t-170) cc_final: 0.6207 (m-70) REVERT: A 239 GLN cc_start: 0.6737 (OUTLIER) cc_final: 0.6474 (mt0) REVERT: A 269 TYR cc_start: 0.6783 (m-10) cc_final: 0.6393 (m-80) REVERT: A 394 ASN cc_start: 0.7177 (m-40) cc_final: 0.6850 (m-40) REVERT: A 498 GLN cc_start: 0.8614 (mm-40) cc_final: 0.8412 (mm-40) REVERT: A 587 ILE cc_start: 0.8322 (mt) cc_final: 0.8087 (mm) REVERT: A 619 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8525 (mp0) REVERT: A 646 ARG cc_start: 0.8734 (ttm170) cc_final: 0.8294 (tpt-90) REVERT: A 985 ASP cc_start: 0.8418 (m-30) cc_final: 0.7928 (m-30) REVERT: A 988 GLU cc_start: 0.8474 (pm20) cc_final: 0.8045 (pm20) REVERT: B 104 TRP cc_start: 0.8363 (m-90) cc_final: 0.7808 (m-90) REVERT: B 400 PHE cc_start: 0.8353 (p90) cc_final: 0.8055 (p90) REVERT: B 453 TYR cc_start: 0.5599 (p90) cc_final: 0.5266 (p90) REVERT: B 808 ASP cc_start: 0.8559 (t0) cc_final: 0.8252 (t0) REVERT: B 821 LEU cc_start: 0.8377 (tt) cc_final: 0.8047 (mp) REVERT: B 936 ASP cc_start: 0.8469 (m-30) cc_final: 0.8086 (t0) REVERT: C 140 PHE cc_start: 0.7851 (p90) cc_final: 0.7595 (p90) REVERT: C 177 MET cc_start: 0.1604 (mmt) cc_final: 0.1294 (tpp) REVERT: C 207 HIS cc_start: 0.6137 (OUTLIER) cc_final: 0.5551 (m170) REVERT: C 389 ASP cc_start: 0.8519 (m-30) cc_final: 0.8027 (p0) REVERT: C 461 LEU cc_start: 0.3888 (OUTLIER) cc_final: 0.3569 (mp) REVERT: C 558 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8667 (mtpp) REVERT: C 867 ASP cc_start: 0.8375 (m-30) cc_final: 0.8071 (p0) REVERT: C 950 ASP cc_start: 0.8918 (m-30) cc_final: 0.8577 (m-30) REVERT: D 34 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.7456 (tpp) REVERT: D 35 HIS cc_start: 0.6197 (m-70) cc_final: 0.5658 (m170) REVERT: D 36 TRP cc_start: 0.5677 (m100) cc_final: 0.5025 (m100) REVERT: D 83 MET cc_start: 0.4702 (OUTLIER) cc_final: 0.3640 (mmm) REVERT: D 115 LEU cc_start: 0.6796 (OUTLIER) cc_final: 0.6510 (pt) REVERT: D 209 CYS cc_start: -0.0954 (OUTLIER) cc_final: -0.2754 (p) REVERT: E 24 ARG cc_start: 0.6906 (mmm160) cc_final: 0.6608 (mmm-85) REVERT: E 76 ILE cc_start: 0.3447 (OUTLIER) cc_final: 0.3173 (pt) REVERT: H 34 MET cc_start: 0.6733 (mmm) cc_final: 0.6519 (mmm) REVERT: H 65 LYS cc_start: 0.3564 (tppt) cc_final: 0.2995 (mttm) REVERT: H 111 TRP cc_start: 0.5412 (t-100) cc_final: 0.4612 (m-90) outliers start: 108 outliers final: 58 residues processed: 388 average time/residue: 0.2015 time to fit residues: 128.4056 Evaluate side-chains 343 residues out of total 3918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 275 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 189 TYR Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain L residue 62 ARG Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 182 ASP Chi-restraints excluded: chain L residue 188 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 222 LYS Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 130 VAL Chi-restraints excluded: chain K residue 188 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 216 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 293 optimal weight: 0.2980 chunk 284 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 6 optimal weight: 9.9990 chunk 86 optimal weight: 0.3980 chunk 241 optimal weight: 4.9990 chunk 331 optimal weight: 1.9990 chunk 377 optimal weight: 20.0000 chunk 11 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS B 487 ASN B 957 GLN B1135 ASN C 14 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.175530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.107603 restraints weight = 73339.676| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 3.62 r_work: 0.3204 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 36820 Z= 0.130 Angle : 0.606 22.826 50249 Z= 0.288 Chirality : 0.045 0.500 5833 Planarity : 0.004 0.068 6376 Dihedral : 6.889 106.549 6282 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.81 % Allowed : 12.99 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.12), residues: 4453 helix: 2.35 (0.20), residues: 718 sheet: 0.25 (0.14), residues: 1331 loop : -0.86 (0.12), residues: 2404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 87 TYR 0.019 0.001 TYR A1067 PHE 0.023 0.001 PHE C 201 TRP 0.021 0.001 TRP A 104 HIS 0.007 0.001 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00292 (36707) covalent geometry : angle 0.54959 (49955) SS BOND : bond 0.00152 ( 45) SS BOND : angle 0.72141 ( 90) hydrogen bonds : bond 0.03936 ( 1366) hydrogen bonds : angle 5.77692 ( 3801) link_BETA1-4 : bond 0.00427 ( 21) link_BETA1-4 : angle 1.69508 ( 63) link_BETA1-6 : bond 0.00104 ( 3) link_BETA1-6 : angle 1.54516 ( 9) link_NAG-ASN : bond 0.00673 ( 44) link_NAG-ASN : angle 4.83816 ( 132) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8906 Ramachandran restraints generated. 4453 Oldfield, 0 Emsley, 4453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8906 Ramachandran restraints generated. 4453 Oldfield, 0 Emsley, 4453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 283 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8678 (p) cc_final: 0.8221 (t) REVERT: A 196 ASN cc_start: 0.7729 (t0) cc_final: 0.7487 (p0) REVERT: A 207 HIS cc_start: 0.6666 (OUTLIER) cc_final: 0.6179 (m-70) REVERT: A 239 GLN cc_start: 0.6803 (OUTLIER) cc_final: 0.6573 (mt0) REVERT: A 269 TYR cc_start: 0.6859 (m-10) cc_final: 0.6478 (m-80) REVERT: A 394 ASN cc_start: 0.7130 (m-40) cc_final: 0.6783 (m-40) REVERT: A 403 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7684 (ptt-90) REVERT: A 587 ILE cc_start: 0.8294 (mt) cc_final: 0.8044 (mm) REVERT: A 619 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8484 (mp0) REVERT: A 646 ARG cc_start: 0.8663 (ttm170) cc_final: 0.8306 (tpt-90) REVERT: A 988 GLU cc_start: 0.8470 (pm20) cc_final: 0.8146 (pm20) REVERT: B 64 TRP cc_start: 0.7309 (t-100) cc_final: 0.6961 (t-100) REVERT: B 104 TRP cc_start: 0.8499 (m-90) cc_final: 0.8027 (m-90) REVERT: B 400 PHE cc_start: 0.8445 (p90) cc_final: 0.8137 (p90) REVERT: B 453 TYR cc_start: 0.5435 (p90) cc_final: 0.5188 (p90) REVERT: B 808 ASP cc_start: 0.8581 (t0) cc_final: 0.8242 (t0) REVERT: B 821 LEU cc_start: 0.8387 (tt) cc_final: 0.8049 (mp) REVERT: B 936 ASP cc_start: 0.8481 (m-30) cc_final: 0.8104 (t0) REVERT: C 140 PHE cc_start: 0.8047 (p90) cc_final: 0.7777 (p90) REVERT: C 177 MET cc_start: 0.1858 (mmt) cc_final: 0.1549 (tpp) REVERT: C 389 ASP cc_start: 0.8585 (m-30) cc_final: 0.8032 (p0) REVERT: C 461 LEU cc_start: 0.3688 (OUTLIER) cc_final: 0.3384 (mp) REVERT: C 558 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8621 (mtpt) REVERT: C 867 ASP cc_start: 0.8384 (m-30) cc_final: 0.8112 (p0) REVERT: C 950 ASP cc_start: 0.8887 (m-30) cc_final: 0.8545 (m-30) REVERT: D 34 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.7510 (tpp) REVERT: D 35 HIS cc_start: 0.5927 (m-70) cc_final: 0.5573 (m-70) REVERT: D 36 TRP cc_start: 0.5688 (m100) cc_final: 0.4948 (m100) REVERT: D 65 LYS cc_start: 0.6245 (OUTLIER) cc_final: 0.5792 (ptmt) REVERT: D 83 MET cc_start: 0.4266 (pmm) cc_final: 0.3567 (mmm) REVERT: D 115 LEU cc_start: 0.6881 (OUTLIER) cc_final: 0.6627 (pt) REVERT: D 209 CYS cc_start: -0.0775 (OUTLIER) cc_final: -0.2671 (p) REVERT: E 24 ARG cc_start: 0.6914 (mmm160) cc_final: 0.6699 (mmm-85) REVERT: E 76 ILE cc_start: 0.3428 (OUTLIER) cc_final: 0.3209 (pt) REVERT: H 111 TRP cc_start: 0.5818 (OUTLIER) cc_final: 0.4830 (m-90) REVERT: J 184 GLN cc_start: 0.2406 (OUTLIER) cc_final: 0.1532 (tt0) REVERT: J 222 LYS cc_start: 0.0899 (OUTLIER) cc_final: -0.0146 (ttpt) outliers start: 110 outliers final: 70 residues processed: 367 average time/residue: 0.2143 time to fit residues: 129.1146 Evaluate side-chains 352 residues out of total 3918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 268 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 182 ASP Chi-restraints excluded: chain L residue 188 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 71 SER Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 184 GLN Chi-restraints excluded: chain J residue 222 LYS Chi-restraints excluded: chain K residue 130 VAL Chi-restraints excluded: chain K residue 188 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 208 optimal weight: 3.9990 chunk 329 optimal weight: 7.9990 chunk 224 optimal weight: 20.0000 chunk 108 optimal weight: 4.9990 chunk 381 optimal weight: 0.0020 chunk 75 optimal weight: 0.5980 chunk 353 optimal weight: 0.9990 chunk 173 optimal weight: 0.9990 chunk 260 optimal weight: 9.9990 chunk 261 optimal weight: 7.9990 chunk 230 optimal weight: 7.9990 overall best weight: 1.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 957 GLN C 14 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.175077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.106436 restraints weight = 73434.971| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 3.51 r_work: 0.3195 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 36820 Z= 0.138 Angle : 0.604 22.009 50249 Z= 0.287 Chirality : 0.045 0.524 5833 Planarity : 0.004 0.067 6376 Dihedral : 6.678 105.263 6279 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.96 % Allowed : 13.37 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.12), residues: 4453 helix: 2.57 (0.20), residues: 700 sheet: 0.26 (0.14), residues: 1332 loop : -0.87 (0.12), residues: 2421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 765 TYR 0.022 0.001 TYR D 112 PHE 0.019 0.001 PHE H 29 TRP 0.022 0.001 TRP A 104 HIS 0.019 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00315 (36707) covalent geometry : angle 0.55107 (49955) SS BOND : bond 0.00163 ( 45) SS BOND : angle 0.71173 ( 90) hydrogen bonds : bond 0.03923 ( 1366) hydrogen bonds : angle 5.67534 ( 3801) link_BETA1-4 : bond 0.00403 ( 21) link_BETA1-4 : angle 1.63994 ( 63) link_BETA1-6 : bond 0.00125 ( 3) link_BETA1-6 : angle 1.52710 ( 9) link_NAG-ASN : bond 0.00676 ( 44) link_NAG-ASN : angle 4.72329 ( 132) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8906 Ramachandran restraints generated. 4453 Oldfield, 0 Emsley, 4453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8906 Ramachandran restraints generated. 4453 Oldfield, 0 Emsley, 4453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 288 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8681 (p) cc_final: 0.8218 (t) REVERT: A 133 PHE cc_start: 0.8121 (m-80) cc_final: 0.7884 (m-80) REVERT: A 140 PHE cc_start: 0.8308 (p90) cc_final: 0.8076 (p90) REVERT: A 196 ASN cc_start: 0.7760 (t0) cc_final: 0.7513 (p0) REVERT: A 207 HIS cc_start: 0.6395 (t-170) cc_final: 0.6079 (m-70) REVERT: A 269 TYR cc_start: 0.6939 (m-10) cc_final: 0.6520 (m-80) REVERT: A 394 ASN cc_start: 0.7138 (m-40) cc_final: 0.6750 (m-40) REVERT: A 403 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.7727 (tmm-80) REVERT: A 587 ILE cc_start: 0.8386 (mt) cc_final: 0.8131 (mm) REVERT: A 619 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.8482 (mp0) REVERT: A 646 ARG cc_start: 0.8675 (ttm170) cc_final: 0.8320 (tpt-90) REVERT: A 988 GLU cc_start: 0.8456 (pm20) cc_final: 0.8103 (pm20) REVERT: B 64 TRP cc_start: 0.7255 (t-100) cc_final: 0.6838 (t-100) REVERT: B 104 TRP cc_start: 0.8386 (m-90) cc_final: 0.7823 (m-90) REVERT: B 287 ASP cc_start: 0.7985 (OUTLIER) cc_final: 0.7731 (m-30) REVERT: B 365 TYR cc_start: 0.8258 (m-80) cc_final: 0.7815 (m-80) REVERT: B 400 PHE cc_start: 0.8505 (p90) cc_final: 0.8218 (p90) REVERT: B 453 TYR cc_start: 0.5369 (p90) cc_final: 0.5075 (p90) REVERT: B 808 ASP cc_start: 0.8571 (t0) cc_final: 0.8210 (t0) REVERT: B 821 LEU cc_start: 0.8377 (tt) cc_final: 0.8045 (mp) REVERT: B 936 ASP cc_start: 0.8499 (m-30) cc_final: 0.8130 (t0) REVERT: C 140 PHE cc_start: 0.8052 (p90) cc_final: 0.7759 (p90) REVERT: C 177 MET cc_start: 0.1799 (mmt) cc_final: 0.1501 (tpp) REVERT: C 389 ASP cc_start: 0.8574 (m-30) cc_final: 0.8049 (p0) REVERT: C 452 LEU cc_start: 0.6124 (tp) cc_final: 0.5789 (tt) REVERT: C 461 LEU cc_start: 0.3844 (OUTLIER) cc_final: 0.3509 (mp) REVERT: C 558 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8702 (mtpp) REVERT: C 867 ASP cc_start: 0.8363 (m-30) cc_final: 0.8135 (p0) REVERT: C 950 ASP cc_start: 0.8892 (m-30) cc_final: 0.8535 (m-30) REVERT: C 957 GLN cc_start: 0.8296 (tt0) cc_final: 0.7958 (tt0) REVERT: D 34 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.7356 (tpp) REVERT: D 35 HIS cc_start: 0.6258 (m-70) cc_final: 0.5463 (m-70) REVERT: D 118 ARG cc_start: 0.6815 (OUTLIER) cc_final: 0.5671 (mmm160) REVERT: D 209 CYS cc_start: -0.0937 (OUTLIER) cc_final: -0.2756 (p) REVERT: E 4 MET cc_start: 0.6192 (ptm) cc_final: 0.3236 (pmm) REVERT: E 76 ILE cc_start: 0.3573 (OUTLIER) cc_final: 0.3369 (pt) REVERT: H 111 TRP cc_start: 0.5730 (OUTLIER) cc_final: 0.4900 (m-90) REVERT: J 73 ASP cc_start: 0.3911 (OUTLIER) cc_final: 0.3610 (p0) REVERT: J 184 GLN cc_start: 0.2362 (OUTLIER) cc_final: 0.1229 (tt0) outliers start: 116 outliers final: 79 residues processed: 376 average time/residue: 0.1924 time to fit residues: 118.7384 Evaluate side-chains 366 residues out of total 3918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 275 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 118 ARG Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 182 ASP Chi-restraints excluded: chain L residue 188 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 71 SER Chi-restraints excluded: chain J residue 73 ASP Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 184 GLN Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 130 VAL Chi-restraints excluded: chain K residue 188 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 331 optimal weight: 0.0270 chunk 434 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 243 optimal weight: 1.9990 chunk 138 optimal weight: 7.9990 chunk 218 optimal weight: 10.0000 chunk 268 optimal weight: 0.8980 chunk 223 optimal weight: 9.9990 chunk 315 optimal weight: 0.7980 chunk 177 optimal weight: 3.9990 chunk 262 optimal weight: 1.9990 overall best weight: 1.1442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS C 14 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 GLN J 184 GLN K 144 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.175106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.107044 restraints weight = 73245.340| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 3.77 r_work: 0.3183 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 36820 Z= 0.129 Angle : 0.594 21.451 50249 Z= 0.282 Chirality : 0.045 0.538 5833 Planarity : 0.004 0.067 6376 Dihedral : 6.509 103.802 6278 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.16 % Allowed : 13.83 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.12), residues: 4453 helix: 2.60 (0.20), residues: 701 sheet: 0.29 (0.14), residues: 1318 loop : -0.86 (0.12), residues: 2434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 346 TYR 0.020 0.001 TYR E 137 PHE 0.027 0.001 PHE C 201 TRP 0.024 0.001 TRP A 104 HIS 0.004 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00289 (36707) covalent geometry : angle 0.54202 (49955) SS BOND : bond 0.00153 ( 45) SS BOND : angle 0.68436 ( 90) hydrogen bonds : bond 0.03809 ( 1366) hydrogen bonds : angle 5.56421 ( 3801) link_BETA1-4 : bond 0.00418 ( 21) link_BETA1-4 : angle 1.54624 ( 63) link_BETA1-6 : bond 0.00047 ( 3) link_BETA1-6 : angle 1.51260 ( 9) link_NAG-ASN : bond 0.00672 ( 44) link_NAG-ASN : angle 4.63200 ( 132) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8906 Ramachandran restraints generated. 4453 Oldfield, 0 Emsley, 4453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8906 Ramachandran restraints generated. 4453 Oldfield, 0 Emsley, 4453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 3918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 294 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8677 (p) cc_final: 0.8218 (t) REVERT: A 133 PHE cc_start: 0.8144 (m-80) cc_final: 0.7916 (m-80) REVERT: A 140 PHE cc_start: 0.8325 (p90) cc_final: 0.8096 (p90) REVERT: A 196 ASN cc_start: 0.7751 (t0) cc_final: 0.7520 (p0) REVERT: A 207 HIS cc_start: 0.6580 (t-170) cc_final: 0.6216 (m-70) REVERT: A 241 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7808 (mt) REVERT: A 269 TYR cc_start: 0.6961 (m-10) cc_final: 0.6541 (m-80) REVERT: A 394 ASN cc_start: 0.7191 (m-40) cc_final: 0.6814 (m-40) REVERT: A 403 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7746 (tmm-80) REVERT: A 515 PHE cc_start: 0.8722 (OUTLIER) cc_final: 0.8148 (m-80) REVERT: A 587 ILE cc_start: 0.8392 (mt) cc_final: 0.8127 (mm) REVERT: A 619 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8517 (mp0) REVERT: A 646 ARG cc_start: 0.8718 (ttm170) cc_final: 0.8322 (tpt-90) REVERT: A 988 GLU cc_start: 0.8536 (pm20) cc_final: 0.8179 (pm20) REVERT: B 64 TRP cc_start: 0.7287 (t-100) cc_final: 0.6970 (t-100) REVERT: B 104 TRP cc_start: 0.8347 (m-90) cc_final: 0.7749 (m-90) REVERT: B 287 ASP cc_start: 0.8038 (OUTLIER) cc_final: 0.7741 (m-30) REVERT: B 365 TYR cc_start: 0.8273 (m-80) cc_final: 0.7885 (m-80) REVERT: B 400 PHE cc_start: 0.8418 (p90) cc_final: 0.8099 (p90) REVERT: B 436 TRP cc_start: 0.7880 (p90) cc_final: 0.7353 (p90) REVERT: B 619 GLU cc_start: 0.8950 (mp0) cc_final: 0.8684 (mp0) REVERT: B 808 ASP cc_start: 0.8589 (t0) cc_final: 0.8208 (t0) REVERT: B 821 LEU cc_start: 0.8374 (tt) cc_final: 0.8043 (mp) REVERT: B 936 ASP cc_start: 0.8514 (m-30) cc_final: 0.8136 (t0) REVERT: C 14 GLN cc_start: 0.4788 (OUTLIER) cc_final: 0.4513 (pm20) REVERT: C 140 PHE cc_start: 0.8041 (p90) cc_final: 0.7710 (p90) REVERT: C 177 MET cc_start: 0.1781 (mmt) cc_final: 0.1480 (tpp) REVERT: C 389 ASP cc_start: 0.8627 (m-30) cc_final: 0.8099 (p0) REVERT: C 398 ASP cc_start: 0.6073 (OUTLIER) cc_final: 0.5841 (p0) REVERT: C 452 LEU cc_start: 0.6027 (tp) cc_final: 0.5701 (tt) REVERT: C 558 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8726 (mtpp) REVERT: C 867 ASP cc_start: 0.8331 (m-30) cc_final: 0.8124 (p0) REVERT: C 950 ASP cc_start: 0.8920 (m-30) cc_final: 0.8570 (m-30) REVERT: C 957 GLN cc_start: 0.8351 (tt0) cc_final: 0.8003 (tt0) REVERT: D 34 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.7384 (tpp) REVERT: D 35 HIS cc_start: 0.6043 (m-70) cc_final: 0.5135 (m-70) REVERT: D 83 MET cc_start: 0.4681 (pmm) cc_final: 0.3357 (mmm) REVERT: D 99 GLU cc_start: 0.6338 (mt-10) cc_final: 0.6012 (mt-10) REVERT: D 118 ARG cc_start: 0.6949 (OUTLIER) cc_final: 0.5799 (mmm160) REVERT: D 209 CYS cc_start: -0.0584 (OUTLIER) cc_final: -0.2407 (p) REVERT: E 4 MET cc_start: 0.6308 (ptm) cc_final: 0.3572 (pmm) REVERT: H 52 ASN cc_start: 0.6614 (t0) cc_final: 0.5871 (p0) REVERT: H 111 TRP cc_start: 0.5659 (OUTLIER) cc_final: 0.4601 (m-90) REVERT: J 73 ASP cc_start: 0.3991 (OUTLIER) cc_final: 0.3692 (p0) REVERT: J 184 GLN cc_start: 0.2106 (OUTLIER) cc_final: 0.1417 (tp40) outliers start: 124 outliers final: 83 residues processed: 385 average time/residue: 0.1944 time to fit residues: 123.9412 Evaluate side-chains 380 residues out of total 3918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 283 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 118 ARG Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 182 ASP Chi-restraints excluded: chain L residue 188 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 71 SER Chi-restraints excluded: chain J residue 73 ASP Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 184 GLN Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 84 PHE Chi-restraints excluded: chain K residue 130 VAL Chi-restraints excluded: chain K residue 188 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 234 optimal weight: 0.9990 chunk 315 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 196 optimal weight: 4.9990 chunk 338 optimal weight: 9.9990 chunk 310 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 173 optimal weight: 0.7980 chunk 346 optimal weight: 40.0000 chunk 418 optimal weight: 0.0770 chunk 396 optimal weight: 20.0000 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN A 207 HIS C 14 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.175179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.107362 restraints weight = 73212.517| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 3.71 r_work: 0.3195 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 36820 Z= 0.117 Angle : 0.591 21.118 50249 Z= 0.281 Chirality : 0.045 0.555 5833 Planarity : 0.004 0.067 6376 Dihedral : 6.368 102.564 6276 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.06 % Allowed : 14.11 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.12), residues: 4453 helix: 2.64 (0.20), residues: 701 sheet: 0.29 (0.14), residues: 1318 loop : -0.84 (0.12), residues: 2434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 24 TYR 0.023 0.001 TYR E 137 PHE 0.014 0.001 PHE A 374 TRP 0.025 0.001 TRP H 36 HIS 0.004 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00261 (36707) covalent geometry : angle 0.53955 (49955) SS BOND : bond 0.00174 ( 45) SS BOND : angle 1.13714 ( 90) hydrogen bonds : bond 0.03716 ( 1366) hydrogen bonds : angle 5.49516 ( 3801) link_BETA1-4 : bond 0.00425 ( 21) link_BETA1-4 : angle 1.49085 ( 63) link_BETA1-6 : bond 0.00141 ( 3) link_BETA1-6 : angle 1.56025 ( 9) link_NAG-ASN : bond 0.00679 ( 44) link_NAG-ASN : angle 4.55993 ( 132) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8906 Ramachandran restraints generated. 4453 Oldfield, 0 Emsley, 4453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8906 Ramachandran restraints generated. 4453 Oldfield, 0 Emsley, 4453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 3918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 295 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8718 (p) cc_final: 0.8272 (t) REVERT: A 81 ASN cc_start: 0.6369 (OUTLIER) cc_final: 0.5907 (p0) REVERT: A 133 PHE cc_start: 0.8090 (m-80) cc_final: 0.7847 (m-80) REVERT: A 140 PHE cc_start: 0.8343 (p90) cc_final: 0.8074 (p90) REVERT: A 196 ASN cc_start: 0.7746 (t0) cc_final: 0.7499 (p0) REVERT: A 207 HIS cc_start: 0.6622 (OUTLIER) cc_final: 0.6284 (m-70) REVERT: A 269 TYR cc_start: 0.6949 (m-10) cc_final: 0.6555 (m-80) REVERT: A 394 ASN cc_start: 0.7146 (m-40) cc_final: 0.6836 (m-40) REVERT: A 515 PHE cc_start: 0.8679 (OUTLIER) cc_final: 0.8114 (m-80) REVERT: A 587 ILE cc_start: 0.8345 (mt) cc_final: 0.8079 (mm) REVERT: A 619 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8471 (mp0) REVERT: A 646 ARG cc_start: 0.8710 (ttm170) cc_final: 0.8324 (tpt-90) REVERT: A 988 GLU cc_start: 0.8540 (pm20) cc_final: 0.8153 (pm20) REVERT: B 64 TRP cc_start: 0.7230 (t-100) cc_final: 0.6944 (t-100) REVERT: B 104 TRP cc_start: 0.8391 (m-90) cc_final: 0.7766 (m-90) REVERT: B 287 ASP cc_start: 0.8041 (OUTLIER) cc_final: 0.7735 (m-30) REVERT: B 365 TYR cc_start: 0.8271 (m-80) cc_final: 0.7889 (m-80) REVERT: B 400 PHE cc_start: 0.8463 (p90) cc_final: 0.8151 (p90) REVERT: B 436 TRP cc_start: 0.7848 (p90) cc_final: 0.7349 (p90) REVERT: B 619 GLU cc_start: 0.8963 (mp0) cc_final: 0.8718 (mp0) REVERT: B 808 ASP cc_start: 0.8605 (t0) cc_final: 0.8216 (t0) REVERT: B 821 LEU cc_start: 0.8368 (tt) cc_final: 0.8040 (mp) REVERT: B 936 ASP cc_start: 0.8517 (m-30) cc_final: 0.8140 (t0) REVERT: C 118 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8377 (tm) REVERT: C 140 PHE cc_start: 0.8056 (p90) cc_final: 0.7725 (p90) REVERT: C 177 MET cc_start: 0.1935 (mmt) cc_final: 0.1606 (tpp) REVERT: C 389 ASP cc_start: 0.8660 (m-30) cc_final: 0.8150 (p0) REVERT: C 398 ASP cc_start: 0.6102 (OUTLIER) cc_final: 0.5842 (p0) REVERT: C 452 LEU cc_start: 0.6139 (tp) cc_final: 0.5829 (tt) REVERT: C 558 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8714 (mtpp) REVERT: C 867 ASP cc_start: 0.8344 (m-30) cc_final: 0.8126 (p0) REVERT: C 950 ASP cc_start: 0.8884 (m-30) cc_final: 0.8583 (m-30) REVERT: C 957 GLN cc_start: 0.8314 (tt0) cc_final: 0.7968 (tt0) REVERT: D 34 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.7491 (tpp) REVERT: D 35 HIS cc_start: 0.5978 (OUTLIER) cc_final: 0.5142 (m-70) REVERT: D 83 MET cc_start: 0.3845 (pmm) cc_final: 0.3274 (mmm) REVERT: D 118 ARG cc_start: 0.6918 (OUTLIER) cc_final: 0.5761 (mmm160) REVERT: D 209 CYS cc_start: -0.0916 (OUTLIER) cc_final: -0.2528 (p) REVERT: E 4 MET cc_start: 0.6318 (ptm) cc_final: 0.3707 (pmm) REVERT: E 132 LEU cc_start: 0.1870 (OUTLIER) cc_final: 0.1540 (mp) REVERT: H 35 HIS cc_start: 0.7014 (m-70) cc_final: 0.6277 (m90) REVERT: H 111 TRP cc_start: 0.5798 (OUTLIER) cc_final: 0.4819 (m-90) REVERT: J 73 ASP cc_start: 0.3995 (OUTLIER) cc_final: 0.3689 (p0) REVERT: J 184 GLN cc_start: 0.1875 (OUTLIER) cc_final: 0.1214 (tp40) outliers start: 120 outliers final: 80 residues processed: 383 average time/residue: 0.2047 time to fit residues: 127.9822 Evaluate side-chains 381 residues out of total 3918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 285 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 35 HIS Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 118 ARG Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 209 CYS Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 188 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 73 ASP Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 184 GLN Chi-restraints excluded: chain J residue 222 LYS Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 130 VAL Chi-restraints excluded: chain K residue 188 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 106 optimal weight: 20.0000 chunk 113 optimal weight: 8.9990 chunk 228 optimal weight: 20.0000 chunk 204 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 218 optimal weight: 10.0000 chunk 422 optimal weight: 7.9990 chunk 158 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 445 optimal weight: 20.0000 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN A 540 ASN A 655 HIS B 87 ASN B 907 ASN ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C1005 GLN ** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 177 HIS J 184 GLN K 163 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.171576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.099559 restraints weight = 72842.403| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 3.12 r_work: 0.3139 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 36820 Z= 0.265 Angle : 0.693 21.059 50249 Z= 0.334 Chirality : 0.048 0.570 5833 Planarity : 0.005 0.074 6376 Dihedral : 6.807 107.268 6276 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.01 % Allowed : 14.27 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.12), residues: 4453 helix: 2.25 (0.20), residues: 704 sheet: 0.21 (0.14), residues: 1297 loop : -1.05 (0.12), residues: 2452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 24 TYR 0.022 0.002 TYR A1067 PHE 0.026 0.002 PHE H 29 TRP 0.021 0.002 TRP E 36 HIS 0.024 0.002 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00623 (36707) covalent geometry : angle 0.64662 (49955) SS BOND : bond 0.00326 ( 45) SS BOND : angle 1.13110 ( 90) hydrogen bonds : bond 0.04705 ( 1366) hydrogen bonds : angle 5.77297 ( 3801) link_BETA1-4 : bond 0.00380 ( 21) link_BETA1-4 : angle 1.69502 ( 63) link_BETA1-6 : bond 0.00201 ( 3) link_BETA1-6 : angle 1.59371 ( 9) link_NAG-ASN : bond 0.00699 ( 44) link_NAG-ASN : angle 4.71592 ( 132) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8906 Ramachandran restraints generated. 4453 Oldfield, 0 Emsley, 4453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8906 Ramachandran restraints generated. 4453 Oldfield, 0 Emsley, 4453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 3918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 292 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8818 (p) cc_final: 0.8378 (t) REVERT: A 269 TYR cc_start: 0.7539 (m-10) cc_final: 0.7132 (m-80) REVERT: A 314 GLN cc_start: 0.8710 (mp10) cc_final: 0.8495 (mp10) REVERT: A 394 ASN cc_start: 0.7592 (m-40) cc_final: 0.7238 (m-40) REVERT: A 587 ILE cc_start: 0.8441 (mt) cc_final: 0.8168 (mm) REVERT: A 619 GLU cc_start: 0.9019 (OUTLIER) cc_final: 0.8597 (mp0) REVERT: A 990 GLU cc_start: 0.8484 (tt0) cc_final: 0.8160 (tm-30) REVERT: B 64 TRP cc_start: 0.7452 (t-100) cc_final: 0.7203 (t-100) REVERT: B 104 TRP cc_start: 0.8601 (m-90) cc_final: 0.8061 (m-90) REVERT: B 400 PHE cc_start: 0.8430 (p90) cc_final: 0.8055 (p90) REVERT: B 619 GLU cc_start: 0.9119 (mp0) cc_final: 0.8863 (mp0) REVERT: B 808 ASP cc_start: 0.8789 (t0) cc_final: 0.8393 (t0) REVERT: B 821 LEU cc_start: 0.8546 (tt) cc_final: 0.8192 (mp) REVERT: B 936 ASP cc_start: 0.8771 (m-30) cc_final: 0.8299 (t0) REVERT: B 976 VAL cc_start: 0.8818 (OUTLIER) cc_final: 0.8547 (m) REVERT: C 118 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8340 (tm) REVERT: C 140 PHE cc_start: 0.8057 (p90) cc_final: 0.7677 (p90) REVERT: C 360 ASN cc_start: 0.8591 (t0) cc_final: 0.8383 (m-40) REVERT: C 452 LEU cc_start: 0.6365 (tp) cc_final: 0.6064 (tt) REVERT: C 558 LYS cc_start: 0.9124 (OUTLIER) cc_final: 0.8859 (mtpp) REVERT: C 867 ASP cc_start: 0.8672 (m-30) cc_final: 0.8450 (p0) REVERT: C 950 ASP cc_start: 0.9141 (m-30) cc_final: 0.8814 (m-30) REVERT: C 957 GLN cc_start: 0.8466 (tt0) cc_final: 0.8100 (tt0) REVERT: C 1019 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.7773 (ttm-80) REVERT: D 34 MET cc_start: 0.8400 (mmp) cc_final: 0.7470 (tpp) REVERT: D 116 TRP cc_start: 0.5820 (m100) cc_final: 0.5424 (m100) REVERT: D 118 ARG cc_start: 0.6974 (OUTLIER) cc_final: 0.5873 (mmm160) REVERT: E 4 MET cc_start: 0.6397 (ptm) cc_final: 0.3731 (pmm) REVERT: E 34 LEU cc_start: 0.7200 (OUTLIER) cc_final: 0.6799 (tm) REVERT: E 132 LEU cc_start: 0.1695 (OUTLIER) cc_final: 0.1425 (mp) REVERT: H 111 TRP cc_start: 0.6017 (OUTLIER) cc_final: 0.4811 (m-90) REVERT: L 82 GLU cc_start: 0.4805 (OUTLIER) cc_final: 0.4599 (pm20) REVERT: L 95 PHE cc_start: 0.5313 (OUTLIER) cc_final: 0.5095 (m-10) REVERT: J 73 ASP cc_start: 0.3854 (OUTLIER) cc_final: 0.3525 (p0) REVERT: J 184 GLN cc_start: 0.2132 (OUTLIER) cc_final: 0.1497 (tp40) outliers start: 118 outliers final: 85 residues processed: 381 average time/residue: 0.2060 time to fit residues: 129.6787 Evaluate side-chains 370 residues out of total 3918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 272 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 1019 ARG Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 35 HIS Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 118 ARG Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain L residue 95 PHE Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 182 ASP Chi-restraints excluded: chain L residue 188 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 73 ASP Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 184 GLN Chi-restraints excluded: chain J residue 222 LYS Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 130 VAL Chi-restraints excluded: chain K residue 188 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 375 optimal weight: 9.9990 chunk 302 optimal weight: 0.9990 chunk 257 optimal weight: 7.9990 chunk 243 optimal weight: 2.9990 chunk 413 optimal weight: 0.9990 chunk 22 optimal weight: 8.9990 chunk 226 optimal weight: 7.9990 chunk 426 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 225 optimal weight: 8.9990 chunk 160 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN A 207 HIS B 388 ASN ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN J 184 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.169889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.100549 restraints weight = 73124.649| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 4.09 r_work: 0.3083 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 36820 Z= 0.267 Angle : 0.691 21.255 50249 Z= 0.334 Chirality : 0.048 0.574 5833 Planarity : 0.004 0.067 6376 Dihedral : 7.053 109.915 6273 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.83 % Allowed : 14.70 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.12), residues: 4453 helix: 2.23 (0.20), residues: 691 sheet: 0.13 (0.14), residues: 1297 loop : -1.15 (0.12), residues: 2465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 24 TYR 0.022 0.002 TYR A1067 PHE 0.030 0.002 PHE H 29 TRP 0.024 0.002 TRP A 104 HIS 0.007 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00627 (36707) covalent geometry : angle 0.64469 (49955) SS BOND : bond 0.00300 ( 45) SS BOND : angle 1.18109 ( 90) hydrogen bonds : bond 0.04633 ( 1366) hydrogen bonds : angle 5.78968 ( 3801) link_BETA1-4 : bond 0.00397 ( 21) link_BETA1-4 : angle 1.65167 ( 63) link_BETA1-6 : bond 0.00282 ( 3) link_BETA1-6 : angle 1.62117 ( 9) link_NAG-ASN : bond 0.00674 ( 44) link_NAG-ASN : angle 4.68266 ( 132) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8906 Ramachandran restraints generated. 4453 Oldfield, 0 Emsley, 4453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8906 Ramachandran restraints generated. 4453 Oldfield, 0 Emsley, 4453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 3918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 281 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8834 (p) cc_final: 0.8360 (t) REVERT: A 201 PHE cc_start: 0.7871 (t80) cc_final: 0.7663 (t80) REVERT: A 239 GLN cc_start: 0.7602 (tt0) cc_final: 0.7213 (tt0) REVERT: A 394 ASN cc_start: 0.7421 (m-40) cc_final: 0.7054 (m-40) REVERT: A 587 ILE cc_start: 0.8402 (mt) cc_final: 0.8117 (mm) REVERT: A 979 ASP cc_start: 0.8564 (t70) cc_final: 0.8209 (t0) REVERT: A 990 GLU cc_start: 0.8274 (tt0) cc_final: 0.7970 (tm-30) REVERT: B 104 TRP cc_start: 0.8553 (m-90) cc_final: 0.8140 (m-90) REVERT: B 400 PHE cc_start: 0.8169 (p90) cc_final: 0.7766 (p90) REVERT: B 619 GLU cc_start: 0.9010 (mp0) cc_final: 0.8704 (mp0) REVERT: B 821 LEU cc_start: 0.8373 (tt) cc_final: 0.8007 (mp) REVERT: B 936 ASP cc_start: 0.8710 (m-30) cc_final: 0.8268 (t0) REVERT: B 976 VAL cc_start: 0.8589 (OUTLIER) cc_final: 0.8309 (m) REVERT: C 118 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8210 (tm) REVERT: C 140 PHE cc_start: 0.8037 (p90) cc_final: 0.7658 (p90) REVERT: C 191 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8309 (mt-10) REVERT: C 360 ASN cc_start: 0.8596 (t0) cc_final: 0.8367 (m110) REVERT: C 398 ASP cc_start: 0.6332 (OUTLIER) cc_final: 0.5844 (p0) REVERT: C 452 LEU cc_start: 0.6252 (tp) cc_final: 0.5967 (tt) REVERT: C 558 LYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8810 (mtpp) REVERT: C 950 ASP cc_start: 0.8968 (m-30) cc_final: 0.8595 (m-30) REVERT: C 957 GLN cc_start: 0.8313 (tt0) cc_final: 0.7934 (tt0) REVERT: C 1019 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.7564 (ttm-80) REVERT: D 34 MET cc_start: 0.8437 (mmp) cc_final: 0.7581 (tpp) REVERT: D 83 MET cc_start: 0.4280 (pmm) cc_final: 0.3705 (mmm) REVERT: D 116 TRP cc_start: 0.5679 (m100) cc_final: 0.5049 (m-90) REVERT: D 118 ARG cc_start: 0.7113 (OUTLIER) cc_final: 0.6002 (mmm160) REVERT: E 4 MET cc_start: 0.6393 (ptm) cc_final: 0.4489 (pmm) REVERT: E 132 LEU cc_start: 0.1689 (OUTLIER) cc_final: 0.1410 (mp) REVERT: H 73 ASP cc_start: 0.7157 (p0) cc_final: 0.6639 (p0) REVERT: H 111 TRP cc_start: 0.5870 (OUTLIER) cc_final: 0.4931 (m-90) REVERT: J 73 ASP cc_start: 0.3767 (OUTLIER) cc_final: 0.3438 (p0) REVERT: J 184 GLN cc_start: 0.2540 (OUTLIER) cc_final: 0.1823 (tt0) outliers start: 111 outliers final: 87 residues processed: 362 average time/residue: 0.2039 time to fit residues: 120.3196 Evaluate side-chains 367 residues out of total 3918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 270 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 1019 ARG Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 35 HIS Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 118 ARG Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 182 ASP Chi-restraints excluded: chain L residue 188 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 73 ASP Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 184 GLN Chi-restraints excluded: chain J residue 222 LYS Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 130 VAL Chi-restraints excluded: chain K residue 188 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 282 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 258 optimal weight: 5.9990 chunk 388 optimal weight: 0.0170 chunk 387 optimal weight: 5.9990 chunk 421 optimal weight: 50.0000 chunk 302 optimal weight: 0.0040 chunk 67 optimal weight: 0.6980 chunk 424 optimal weight: 0.4980 chunk 50 optimal weight: 0.5980 chunk 122 optimal weight: 10.0000 overall best weight: 0.3630 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN D 84 ASN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.174327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.106515 restraints weight = 72884.011| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 3.42 r_work: 0.3201 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 36820 Z= 0.105 Angle : 0.612 20.568 50249 Z= 0.292 Chirality : 0.046 0.567 5833 Planarity : 0.004 0.071 6376 Dihedral : 6.631 107.656 6270 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.86 % Allowed : 15.77 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.12), residues: 4453 helix: 2.57 (0.20), residues: 692 sheet: 0.23 (0.14), residues: 1279 loop : -0.99 (0.12), residues: 2482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 346 TYR 0.022 0.001 TYR E 137 PHE 0.046 0.001 PHE A 374 TRP 0.026 0.002 TRP A 104 HIS 0.006 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00223 (36707) covalent geometry : angle 0.56505 (49955) SS BOND : bond 0.00181 ( 45) SS BOND : angle 1.05553 ( 90) hydrogen bonds : bond 0.03668 ( 1366) hydrogen bonds : angle 5.46780 ( 3801) link_BETA1-4 : bond 0.00490 ( 21) link_BETA1-4 : angle 1.38452 ( 63) link_BETA1-6 : bond 0.00077 ( 3) link_BETA1-6 : angle 1.70497 ( 9) link_NAG-ASN : bond 0.00710 ( 44) link_NAG-ASN : angle 4.44413 ( 132) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8906 Ramachandran restraints generated. 4453 Oldfield, 0 Emsley, 4453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8906 Ramachandran restraints generated. 4453 Oldfield, 0 Emsley, 4453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 292 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8755 (p) cc_final: 0.8345 (t) REVERT: A 64 TRP cc_start: 0.6636 (t60) cc_final: 0.6319 (t60) REVERT: A 239 GLN cc_start: 0.7808 (tt0) cc_final: 0.7514 (tt0) REVERT: A 394 ASN cc_start: 0.7516 (m-40) cc_final: 0.7167 (m-40) REVERT: A 587 ILE cc_start: 0.8402 (mt) cc_final: 0.8100 (mm) REVERT: A 646 ARG cc_start: 0.8882 (ttm170) cc_final: 0.8510 (tpt-90) REVERT: A 979 ASP cc_start: 0.8583 (t70) cc_final: 0.8225 (t0) REVERT: B 104 TRP cc_start: 0.8575 (m-90) cc_final: 0.8151 (m-90) REVERT: B 365 TYR cc_start: 0.8313 (m-80) cc_final: 0.7868 (m-80) REVERT: B 369 TYR cc_start: 0.8985 (t80) cc_final: 0.8757 (t80) REVERT: B 388 ASN cc_start: 0.8128 (t0) cc_final: 0.7495 (p0) REVERT: B 400 PHE cc_start: 0.8268 (p90) cc_final: 0.7845 (p90) REVERT: B 436 TRP cc_start: 0.7975 (p90) cc_final: 0.7436 (p90) REVERT: B 619 GLU cc_start: 0.9100 (mp0) cc_final: 0.8820 (mp0) REVERT: B 808 ASP cc_start: 0.8687 (t0) cc_final: 0.8268 (t0) REVERT: B 821 LEU cc_start: 0.8441 (tt) cc_final: 0.8169 (mp) REVERT: B 936 ASP cc_start: 0.8676 (m-30) cc_final: 0.8313 (t0) REVERT: C 118 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8445 (tm) REVERT: C 140 PHE cc_start: 0.8035 (p90) cc_final: 0.7698 (p90) REVERT: C 168 PHE cc_start: 0.8077 (t80) cc_final: 0.7809 (t80) REVERT: C 191 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8376 (mt-10) REVERT: C 360 ASN cc_start: 0.8581 (t0) cc_final: 0.8357 (m110) REVERT: C 389 ASP cc_start: 0.8887 (m-30) cc_final: 0.8395 (p0) REVERT: C 398 ASP cc_start: 0.6181 (OUTLIER) cc_final: 0.5831 (p0) REVERT: C 452 LEU cc_start: 0.6037 (tp) cc_final: 0.5759 (tt) REVERT: C 950 ASP cc_start: 0.9099 (m-30) cc_final: 0.8789 (m-30) REVERT: C 957 GLN cc_start: 0.8419 (tt0) cc_final: 0.8080 (tt0) REVERT: C 1019 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.7690 (ttm-80) REVERT: D 34 MET cc_start: 0.8426 (mmp) cc_final: 0.7514 (tpp) REVERT: E 4 MET cc_start: 0.6458 (ptm) cc_final: 0.3951 (pmm) REVERT: E 36 TRP cc_start: 0.5535 (m-10) cc_final: 0.5264 (m-10) REVERT: E 132 LEU cc_start: 0.1495 (OUTLIER) cc_final: 0.1233 (mp) REVERT: H 73 ASP cc_start: 0.6723 (p0) cc_final: 0.6471 (p0) REVERT: H 111 TRP cc_start: 0.5787 (OUTLIER) cc_final: 0.5006 (m-90) REVERT: J 73 ASP cc_start: 0.3723 (OUTLIER) cc_final: 0.3376 (p0) outliers start: 73 outliers final: 57 residues processed: 343 average time/residue: 0.1964 time to fit residues: 110.4761 Evaluate side-chains 340 residues out of total 3918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 277 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 1019 ARG Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain D residue 35 HIS Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain L residue 95 PHE Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 73 ASP Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 130 VAL Chi-restraints excluded: chain K residue 188 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 62 optimal weight: 0.5980 chunk 16 optimal weight: 9.9990 chunk 152 optimal weight: 7.9990 chunk 429 optimal weight: 20.0000 chunk 184 optimal weight: 0.9980 chunk 432 optimal weight: 0.0980 chunk 395 optimal weight: 9.9990 chunk 200 optimal weight: 3.9990 chunk 222 optimal weight: 10.0000 chunk 171 optimal weight: 3.9990 chunk 314 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 77 ASN J 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.171322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.099215 restraints weight = 72668.030| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 3.24 r_work: 0.3155 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 36820 Z= 0.167 Angle : 0.633 20.598 50249 Z= 0.302 Chirality : 0.046 0.579 5833 Planarity : 0.004 0.070 6376 Dihedral : 6.646 107.419 6266 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.94 % Allowed : 15.88 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.12), residues: 4453 helix: 2.59 (0.20), residues: 695 sheet: 0.26 (0.14), residues: 1279 loop : -0.98 (0.12), residues: 2479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 46 TYR 0.020 0.001 TYR A1067 PHE 0.032 0.001 PHE A 374 TRP 0.019 0.002 TRP A 104 HIS 0.006 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00390 (36707) covalent geometry : angle 0.58704 (49955) SS BOND : bond 0.00192 ( 45) SS BOND : angle 1.04033 ( 90) hydrogen bonds : bond 0.04020 ( 1366) hydrogen bonds : angle 5.49769 ( 3801) link_BETA1-4 : bond 0.00389 ( 21) link_BETA1-4 : angle 1.48382 ( 63) link_BETA1-6 : bond 0.00170 ( 3) link_BETA1-6 : angle 1.64895 ( 9) link_NAG-ASN : bond 0.00654 ( 44) link_NAG-ASN : angle 4.46188 ( 132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13558.63 seconds wall clock time: 231 minutes 4.71 seconds (13864.71 seconds total)