Starting phenix.real_space_refine on Sun Jul 5 16:05:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7dx6_30897/07_2026/7dx6_30897.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dx6_30897/07_2026/7dx6_30897.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7dx6_30897/07_2026/7dx6_30897.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dx6_30897/07_2026/7dx6_30897.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7dx6_30897/07_2026/7dx6_30897.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dx6_30897/07_2026/7dx6_30897.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7dx6_30897/07_2026/7dx6_30897.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7dx6_30897/07_2026/7dx6_30897.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 133 5.16 5 C 18475 2.51 5 N 4720 2.21 5 O 5717 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29045 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 7872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1007, 7872 Classifications: {'peptide': 1007} Link IDs: {'PTRANS': 50, 'TRANS': 956} Chain breaks: 8 Chain: "B" Number of atoms: 7584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 971, 7584 Classifications: {'peptide': 971} Link IDs: {'PTRANS': 48, 'TRANS': 922} Chain breaks: 9 Chain: "C" Number of atoms: 7584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 971, 7584 Classifications: {'peptide': 971} Link IDs: {'PTRANS': 48, 'TRANS': 922} Chain breaks: 9 Chain: "D" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain: "E" 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 chiralities: 2 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 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 chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 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 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 chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 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 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 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 chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 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 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 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 chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" 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 chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" 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 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 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 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 chiralities: 8 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.71, per 1000 atoms: 0.20 Number of scatterers: 29045 At special positions: 0 Unit cell: (138.049, 195.66, 203.269, 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 133 16.00 O 5717 8.00 N 4720 7.00 C 18475 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 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=2.85 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.11 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=2.52 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.05 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 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=2.17 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.11 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=1.87 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.05 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.12 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 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=2.17 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.11 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.31 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.05 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 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=1.98 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.17 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B1409 " - " NAG B1410 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " 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 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 165 " " NAG A1404 " - " ASN A 234 " " NAG A1405 " - " ASN A 282 " " NAG A1406 " - " ASN A 603 " " NAG A1407 " - " ASN A 616 " " NAG A1408 " - " ASN A 657 " " NAG A1409 " - " ASN A 709 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 122 " " NAG B1403 " - " ASN B 165 " " NAG B1404 " - " ASN B 234 " " NAG B1405 " - " ASN B 282 " " NAG B1406 " - " ASN B 603 " " NAG B1407 " - " ASN B 616 " " NAG B1408 " - " ASN B 657 " " NAG B1409 " - " ASN B1074 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 122 " " NAG C1403 " - " ASN C 165 " " NAG C1404 " - " ASN C 234 " " NAG C1405 " - " ASN C 282 " " NAG C1406 " - " ASN C 603 " " NAG C1407 " - " ASN C 616 " " NAG C1408 " - " ASN C 657 " " NAG D 901 " - " ASN D 322 " " NAG E 1 " - " ASN A 331 " " NAG F 1 " - " ASN A 343 " " NAG G 1 " - " ASN A 717 " " NAG H 1 " - " ASN A 801 " " NAG I 1 " - " ASN A1074 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN A1134 " " NAG L 1 " - " ASN B 331 " " NAG M 1 " - " ASN B 343 " " NAG N 1 " - " ASN B 709 " " NAG O 1 " - " ASN B 717 " " NAG P 1 " - " ASN B 801 " " NAG Q 1 " - " ASN B1098 " " NAG R 1 " - " ASN B1134 " " NAG S 1 " - " ASN C 331 " " NAG T 1 " - " ASN C 343 " " NAG U 1 " - " ASN C 709 " " NAG V 1 " - " ASN C 717 " " NAG W 1 " - " ASN C 801 " " NAG X 1 " - " ASN C1074 " " NAG Y 1 " - " ASN C1098 " " NAG Z 1 " - " ASN C1134 " " NAG a 1 " - " ASN D 53 " " NAG b 1 " - " ASN D 90 " " NAG c 1 " - " ASN D 103 " " NAG d 1 " - " ASN D 432 " " NAG e 1 " - " ASN D 546 " Time building additional restraints: 2.33 Conformation dependent library (CDL) restraints added in 1.3 seconds 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6658 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 45 sheets defined 31.3% alpha, 24.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.073A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.258A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.623A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.738A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.629A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (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: 3.772A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 removed outlier: 3.634A pdb=" N LYS A 814 " --> pdb=" O LYS A 811 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A 815 " --> pdb=" O PRO A 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 811 through 815' Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.647A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.574A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 3.994A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.626A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.879A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 981 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.632A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.648A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.074A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.257A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.624A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.738A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 754 removed outlier: 3.695A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) 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: 3.964A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.544A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.603A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.010A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.244A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.074A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.257A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.624A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.737A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.717A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) 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: 3.561A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.605A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.634A 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 897 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.591A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.355A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR C 961 " --> pdb=" O GLN C 957 " (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 977 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.221A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 Processing helix chain 'D' and resid 22 through 53 removed outlier: 3.791A pdb=" N LYS D 31 " --> pdb=" O THR D 27 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU D 37 " --> pdb=" O ASN D 33 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 81 removed outlier: 3.755A pdb=" N ASN D 64 " --> pdb=" O GLN D 60 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TRP D 69 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.640A pdb=" N GLN D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 130 removed outlier: 3.688A pdb=" N LYS D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 155 removed outlier: 3.527A pdb=" N ILE D 151 " --> pdb=" O GLY D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 172 removed outlier: 3.550A pdb=" N TRP D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 193 removed outlier: 3.834A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 204 Processing helix chain 'D' and resid 205 through 208 removed outlier: 3.564A pdb=" N GLU D 208 " --> pdb=" O GLY D 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 205 through 208' Processing helix chain 'D' and resid 220 through 231 removed outlier: 3.907A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 252 removed outlier: 3.595A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ASN D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 277 No H-bonds generated for 'chain 'D' and resid 275 through 277' Processing helix chain 'D' and resid 278 through 283 Processing helix chain 'D' and resid 294 through 299 removed outlier: 3.513A pdb=" N VAL D 298 " --> pdb=" O THR D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 319 removed outlier: 4.309A pdb=" N ILE D 307 " --> pdb=" O ASP D 303 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N PHE D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL D 318 " --> pdb=" O PHE D 314 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY D 319 " --> pdb=" O PHE D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 331 removed outlier: 3.760A pdb=" N SER D 331 " --> pdb=" O PHE D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 383 removed outlier: 3.636A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE D 379 " --> pdb=" O GLU D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 removed outlier: 3.548A pdb=" N ARG D 393 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.551A pdb=" N ALA D 403 " --> pdb=" O GLY D 399 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE D 407 " --> pdb=" O ALA D 403 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER D 411 " --> pdb=" O ILE D 407 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA D 412 " --> pdb=" O MET D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 removed outlier: 3.679A pdb=" N SER D 420 " --> pdb=" O LYS D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 444 removed outlier: 3.598A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE D 436 " --> pdb=" O ASN D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 465 Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.751A pdb=" N TRP D 478 " --> pdb=" O MET D 474 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG D 482 " --> pdb=" O TRP D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 502 removed outlier: 3.592A pdb=" N SER D 502 " --> pdb=" O ASP D 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 499 through 502' Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 533 removed outlier: 3.878A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA D 532 " --> pdb=" O ALA D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 548 through 559 removed outlier: 4.396A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG D 559 " --> pdb=" O PHE D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 removed outlier: 3.674A pdb=" N GLU D 571 " --> pdb=" O THR D 567 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASN D 572 " --> pdb=" O LEU D 568 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 588 removed outlier: 3.578A pdb=" N TYR D 587 " --> pdb=" O PRO D 583 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 599 removed outlier: 3.576A pdb=" N TRP D 594 " --> pdb=" O PRO D 590 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP D 597 " --> pdb=" O THR D 593 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.060A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 55 removed outlier: 3.856A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 116 through 121 removed outlier: 3.731A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN A 134 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 309 through 319 removed outlier: 6.547A pdb=" N GLU A 309 " --> pdb=" O GLY A 601 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N GLY A 601 " --> pdb=" O GLU A 309 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.543A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 448 through 454 removed outlier: 5.863A pdb=" N TYR A 449 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE A 497 " --> pdb=" O TYR A 449 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'A' and resid 539 through 543 removed outlier: 5.338A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.418A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.589A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.589A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.505A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.712A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.059A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 49 through 55 removed outlier: 3.855A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC1, first strand: chain 'B' and resid 116 through 121 removed outlier: 3.730A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN B 134 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 309 through 319 removed outlier: 6.059A pdb=" N LYS B 310 " --> pdb=" O GLY B 601 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLY B 601 " --> pdb=" O LYS B 310 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY B 593 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 326 removed outlier: 5.338A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.542A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 448 through 453 removed outlier: 5.864A pdb=" N TYR B 449 " --> pdb=" O PHE B 497 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE B 497 " --> pdb=" O TYR B 449 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR B 451 " --> pdb=" O TYR B 495 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.220A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.541A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.541A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.580A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD3, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.060A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 49 through 55 removed outlier: 3.857A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD6, first strand: chain 'C' and resid 116 through 121 removed outlier: 3.731A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE C 168 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN C 134 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.872A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.542A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 448 through 453 removed outlier: 5.864A pdb=" N TYR C 449 " --> pdb=" O PHE C 497 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE C 497 " --> pdb=" O TYR C 449 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 539 through 543 removed outlier: 5.338A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.271A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.591A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.591A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.568A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE7, first strand: chain 'D' and resid 132 through 133 Processing sheet with id=AE8, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.030A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'D' and resid 347 through 352 removed outlier: 3.582A pdb=" N LEU D 351 " --> pdb=" O ASP D 355 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) 1111 hydrogen bonds defined for protein. 3054 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: 6.04 Time building geometry restraints manager: 3.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6680 1.33 - 1.45: 7463 1.45 - 1.58: 15368 1.58 - 1.70: 0 1.70 - 1.83: 181 Bond restraints: 29692 Sorted by residual: bond pdb=" CA SER A 698 " pdb=" C SER A 698 " ideal model delta sigma weight residual 1.522 1.443 0.079 1.20e-02 6.94e+03 4.30e+01 bond pdb=" C HIS B1088 " pdb=" N PHE B1089 " ideal model delta sigma weight residual 1.331 1.263 0.068 1.59e-02 3.96e+03 1.82e+01 bond pdb=" N PRO D 426 " pdb=" CD PRO D 426 " ideal model delta sigma weight residual 1.473 1.533 -0.060 1.40e-02 5.10e+03 1.82e+01 bond pdb=" N PRO C 589 " pdb=" CD PRO C 589 " ideal model delta sigma weight residual 1.473 1.531 -0.058 1.40e-02 5.10e+03 1.72e+01 bond pdb=" N PRO D 346 " pdb=" CD PRO D 346 " ideal model delta sigma weight residual 1.473 1.528 -0.055 1.40e-02 5.10e+03 1.55e+01 ... (remaining 29687 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 39320 2.67 - 5.33: 972 5.33 - 8.00: 72 8.00 - 10.67: 9 10.67 - 13.34: 5 Bond angle restraints: 40378 Sorted by residual: angle pdb=" N THR D 362 " pdb=" CA THR D 362 " pdb=" C THR D 362 " ideal model delta sigma weight residual 109.76 119.35 -9.59 1.59e+00 3.96e-01 3.63e+01 angle pdb=" C PHE B 86 " pdb=" N ASN B 87 " pdb=" CA ASN B 87 " ideal model delta sigma weight residual 121.54 132.78 -11.24 1.91e+00 2.74e-01 3.46e+01 angle pdb=" C PHE C 86 " pdb=" N ASN C 87 " pdb=" CA ASN C 87 " ideal model delta sigma weight residual 121.54 132.78 -11.24 1.91e+00 2.74e-01 3.46e+01 angle pdb=" C PHE A 86 " pdb=" N ASN A 87 " pdb=" CA ASN A 87 " ideal model delta sigma weight residual 121.54 132.74 -11.20 1.91e+00 2.74e-01 3.44e+01 angle pdb=" N THR C 315 " pdb=" CA THR C 315 " pdb=" C THR C 315 " ideal model delta sigma weight residual 111.24 117.64 -6.40 1.29e+00 6.01e-01 2.46e+01 ... (remaining 40373 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 14671 17.94 - 35.88: 1669 35.88 - 53.82: 477 53.82 - 71.76: 144 71.76 - 89.70: 53 Dihedral angle restraints: 17014 sinusoidal: 6686 harmonic: 10328 Sorted by residual: dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.09 71.91 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.09 71.91 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.11 71.89 1 1.00e+01 1.00e-02 6.62e+01 ... (remaining 17011 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.330: 4768 0.330 - 0.660: 3 0.660 - 0.990: 5 0.990 - 1.320: 0 1.320 - 1.651: 1 Chirality restraints: 4777 Sorted by residual: chirality pdb=" C1 NAG B1410 " pdb=" O4 NAG B1409 " pdb=" C2 NAG B1410 " pdb=" O5 NAG B1410 " both_signs ideal model delta sigma weight residual False -2.40 -3.08 0.68 2.00e-02 2.50e+03 1.16e+03 chirality pdb=" C1 NAG Z 1 " pdb=" ND2 ASN C1134 " pdb=" C2 NAG Z 1 " pdb=" O5 NAG Z 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.75 -1.65 2.00e-01 2.50e+01 6.81e+01 chirality pdb=" C1 NAG c 1 " pdb=" ND2 ASN D 103 " pdb=" C2 NAG c 1 " pdb=" O5 NAG c 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.46 -0.94 2.00e-01 2.50e+01 2.21e+01 ... (remaining 4774 not shown) Planarity restraints: 5166 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG c 2 " 0.354 2.00e-02 2.50e+03 3.05e-01 1.17e+03 pdb=" C7 NAG c 2 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG c 2 " 0.107 2.00e-02 2.50e+03 pdb=" N2 NAG c 2 " -0.543 2.00e-02 2.50e+03 pdb=" O7 NAG c 2 " 0.166 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG c 1 " 0.285 2.00e-02 2.50e+03 2.39e-01 7.15e+02 pdb=" C7 NAG c 1 " -0.074 2.00e-02 2.50e+03 pdb=" C8 NAG c 1 " 0.185 2.00e-02 2.50e+03 pdb=" N2 NAG c 1 " -0.406 2.00e-02 2.50e+03 pdb=" O7 NAG c 1 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 331 " -0.099 2.00e-02 2.50e+03 1.30e-01 2.10e+02 pdb=" CG ASN B 331 " 0.037 2.00e-02 2.50e+03 pdb=" OD1 ASN B 331 " -0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN B 331 " 0.227 2.00e-02 2.50e+03 pdb=" C1 NAG L 1 " -0.145 2.00e-02 2.50e+03 ... (remaining 5163 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 249 2.53 - 3.12: 21280 3.12 - 3.71: 41441 3.71 - 4.31: 62824 4.31 - 4.90: 103717 Nonbonded interactions: 229511 Sorted by model distance: nonbonded pdb=" O SER D 105 " pdb=" OG SER D 106 " model vdw 1.932 3.040 nonbonded pdb=" NH1 ARG A 346 " pdb=" O PHE A 347 " model vdw 1.982 3.120 nonbonded pdb=" NH1 ARG B 346 " pdb=" O PHE B 347 " model vdw 1.983 3.120 nonbonded pdb=" NH1 ARG C 346 " pdb=" O PHE C 347 " model vdw 1.983 3.120 nonbonded pdb=" O SER C 316 " pdb=" ND2 ASN C 317 " model vdw 2.059 3.120 ... (remaining 229506 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 455 or resid 491 through 939 or resid 944 throu \ gh 1408)) selection = (chain 'B' and resid 27 through 1408) selection = chain 'C' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' } 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: 1.450 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: 0.380 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 25.300 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 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 : 0.013 0.818 29814 Z= 0.585 Angle : 1.293 71.320 40704 Z= 0.673 Chirality : 0.073 1.651 4777 Planarity : 0.009 0.305 5112 Dihedral : 17.829 89.696 10236 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 18.82 Ramachandran Plot: Outliers : 2.27 % Allowed : 9.24 % Favored : 88.49 % Rotamer: Outliers : 10.72 % Allowed : 15.93 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.35 (0.11), residues: 3484 helix: -2.96 (0.12), residues: 1000 sheet: -2.03 (0.17), residues: 755 loop : -3.27 (0.12), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1039 TYR 0.028 0.003 TYR B1067 PHE 0.025 0.003 PHE A 898 TRP 0.025 0.003 TRP C 104 HIS 0.009 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.01129 / 0.50 (29692) covalent geometry : angle 1.00755 / 0.58 (40378) SS BOND : bond 0.16599 / 8.43 ( 40) SS BOND : angle 13.85045 / 9.23 ( 80) hydrogen bonds : bond 0.22478 / 14.47 ( 1075) hydrogen bonds : angle 8.11377 / 5.50 ( 3054) link_BETA1-4 : bond 0.03731 / 2.48 ( 28) link_BETA1-4 : angle 4.22337 / 2.49 ( 84) link_NAG-ASN : bond 0.02607 / 1.62 ( 54) link_NAG-ASN : angle 7.92752 / 5.20 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 751 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 333 poor density : 418 time to evaluate : 0.962 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 81 ASN cc_start: 0.6689 (OUTLIER) cc_final: 0.6411 (t0) REVERT: A 153 MET cc_start: 0.0457 (mpp) cc_final: -0.0800 (ptt) REVERT: A 324 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6869 (pm20) REVERT: A 517 LEU cc_start: 0.4674 (OUTLIER) cc_final: 0.4303 (tt) REVERT: A 544 ASN cc_start: 0.8044 (p0) cc_final: 0.7568 (t0) REVERT: A 569 ILE cc_start: 0.8685 (mp) cc_final: 0.8062 (mt) REVERT: A 702 GLU cc_start: 0.4259 (OUTLIER) cc_final: 0.4056 (mm-30) REVERT: A 878 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8569 (tt) REVERT: A 1029 MET cc_start: 0.9052 (tpp) cc_final: 0.8845 (tpp) REVERT: B 133 PHE cc_start: 0.6087 (m-80) cc_final: 0.5805 (m-80) REVERT: B 153 MET cc_start: 0.2259 (mpp) cc_final: -0.1231 (ptt) REVERT: B 335 LEU cc_start: 0.6532 (OUTLIER) cc_final: 0.6150 (mt) REVERT: B 529 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7609 (mtpm) REVERT: C 153 MET cc_start: 0.2132 (mpp) cc_final: 0.1888 (mtm) REVERT: C 212 LEU cc_start: 0.5088 (tp) cc_final: 0.4254 (mt) REVERT: C 544 ASN cc_start: 0.7863 (p0) cc_final: 0.7588 (p0) REVERT: D 89 GLN cc_start: 0.2907 (mm110) cc_final: 0.2585 (pm20) REVERT: D 332 MET cc_start: 0.2508 (ttp) cc_final: 0.1684 (mpt) REVERT: D 338 ASN cc_start: 0.3067 (t0) cc_final: 0.2867 (m110) REVERT: D 345 HIS cc_start: 0.2863 (OUTLIER) cc_final: 0.2532 (p90) REVERT: D 474 MET cc_start: 0.2058 (mmm) cc_final: 0.1401 (mmt) REVERT: D 508 ASN cc_start: 0.1403 (m110) cc_final: 0.0061 (t0) REVERT: D 554 LEU cc_start: 0.3477 (tp) cc_final: 0.2776 (pp) REVERT: D 579 MET cc_start: 0.1379 (ptt) cc_final: 0.1114 (mtt) outliers start: 333 outliers final: 71 residues processed: 709 average time/residue: 0.5136 time to fit residues: 443.0506 Evaluate side-chains 278 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 199 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 537 LYS Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 345 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.5980 chunk 298 optimal weight: 9.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 ASN A 188 ASN A 334 ASN A 422 ASN A 440 ASN A 498 GLN A 644 GLN A 655 HIS A 751 ASN A 856 ASN A 901 GLN A 914 ASN A 919 ASN A 926 GLN A 955 ASN A 969 ASN A 992 GLN A1005 GLN A1101 HIS B 134 GLN B 137 ASN B 188 ASN B 207 HIS B 422 ASN B 440 ASN B 498 GLN B 542 ASN B 644 GLN B 655 HIS ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 914 ASN B 919 ASN B 920 GLN B 926 GLN B 992 GLN B1054 GLN C 134 GLN C 137 ASN C 188 ASN C 207 HIS C 317 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN C 607 GLN C 644 GLN C 703 ASN C 751 ASN C 784 GLN C 901 GLN C 914 ASN C 926 GLN C 935 GLN C 969 ASN C 992 GLN C1071 GLN C1101 HIS D 42 GLN D 58 ASN D 175 GLN D 195 HIS D 239 HIS D 277 ASN D 325 GLN D 378 HIS D 472 GLN D 505 HIS D 586 ASN Total number of N/Q/H flips: 66 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.182473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.121751 restraints weight = 47165.710| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 3.02 r_work: 0.3014 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 29814 Z= 0.166 Angle : 0.792 13.210 40704 Z= 0.385 Chirality : 0.050 0.560 4777 Planarity : 0.006 0.062 5112 Dihedral : 7.708 59.782 3909 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.77 % Favored : 92.88 % Rotamer: Outliers : 5.54 % Allowed : 21.15 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.13), residues: 3484 helix: -0.55 (0.16), residues: 986 sheet: -1.29 (0.18), residues: 719 loop : -2.61 (0.12), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 403 TYR 0.019 0.002 TYR A 495 PHE 0.022 0.002 PHE D 40 TRP 0.022 0.002 TRP D 566 HIS 0.004 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (29692) covalent geometry : angle 0.75700 / 0.38 (40378) SS BOND : bond 0.00416 / 0.24 ( 40) SS BOND : angle 1.84174 / 1.20 ( 80) hydrogen bonds : bond 0.05147 / 3.40 ( 1075) hydrogen bonds : angle 5.59040 / 3.76 ( 3054) link_BETA1-4 : bond 0.00533 / 0.30 ( 28) link_BETA1-4 : angle 2.28581 / 1.36 ( 84) link_NAG-ASN : bond 0.00582 / 0.30 ( 54) link_NAG-ASN : angle 3.24131 / 2.07 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 228 time to evaluate : 0.982 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 153 MET cc_start: -0.0476 (mpp) cc_final: -0.2449 (tmt) REVERT: A 158 ARG cc_start: 0.5532 (OUTLIER) cc_final: 0.4899 (mpp-170) REVERT: A 190 ARG cc_start: 0.7325 (mtt180) cc_final: 0.6868 (mtt90) REVERT: A 238 PHE cc_start: 0.6890 (p90) cc_final: 0.6659 (p90) REVERT: A 324 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.7087 (pm20) REVERT: A 544 ASN cc_start: 0.8692 (p0) cc_final: 0.7842 (t0) REVERT: A 856 ASN cc_start: 0.8631 (OUTLIER) cc_final: 0.8320 (p0) REVERT: A 878 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8923 (tp) REVERT: A 936 ASP cc_start: 0.7986 (m-30) cc_final: 0.7748 (m-30) REVERT: A 985 ASP cc_start: 0.8250 (OUTLIER) cc_final: 0.7511 (p0) REVERT: A 988 GLU cc_start: 0.8042 (mp0) cc_final: 0.7414 (mp0) REVERT: B 66 HIS cc_start: 0.6136 (OUTLIER) cc_final: 0.5910 (t-90) REVERT: B 141 LEU cc_start: 0.7101 (OUTLIER) cc_final: 0.6880 (pt) REVERT: B 153 MET cc_start: 0.0787 (mpp) cc_final: -0.2452 (ptt) REVERT: B 336 CYS cc_start: 0.5636 (OUTLIER) cc_final: 0.5398 (p) REVERT: B 437 ASN cc_start: 0.6983 (t0) cc_final: 0.6392 (p0) REVERT: B 529 LYS cc_start: 0.7681 (OUTLIER) cc_final: 0.7246 (mtpm) REVERT: B 532 ASN cc_start: 0.8448 (OUTLIER) cc_final: 0.8232 (m-40) REVERT: B 534 VAL cc_start: 0.8701 (m) cc_final: 0.8500 (p) REVERT: B 740 MET cc_start: 0.9134 (OUTLIER) cc_final: 0.8797 (ttp) REVERT: B 985 ASP cc_start: 0.8151 (OUTLIER) cc_final: 0.7932 (p0) REVERT: C 53 ASP cc_start: 0.8090 (t70) cc_final: 0.7860 (t0) REVERT: C 141 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7558 (pt) REVERT: C 153 MET cc_start: 0.1782 (mpp) cc_final: 0.1488 (mtm) REVERT: C 195 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7754 (mtmt) REVERT: C 212 LEU cc_start: 0.5590 (tp) cc_final: 0.4678 (mp) REVERT: C 336 CYS cc_start: 0.3536 (OUTLIER) cc_final: 0.2833 (p) REVERT: C 740 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.8580 (ttm) REVERT: C 787 GLN cc_start: 0.9212 (OUTLIER) cc_final: 0.8480 (mp10) REVERT: C 814 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.8053 (mptp) REVERT: D 39 LEU cc_start: 0.6325 (OUTLIER) cc_final: 0.6114 (tp) REVERT: D 72 PHE cc_start: 0.4650 (t80) cc_final: 0.4272 (m-10) REVERT: D 89 GLN cc_start: 0.3208 (mm110) cc_final: 0.2880 (pm20) REVERT: D 190 MET cc_start: 0.2781 (mtm) cc_final: 0.2254 (ttm) REVERT: D 231 GLU cc_start: 0.3222 (OUTLIER) cc_final: 0.3008 (mp0) REVERT: D 332 MET cc_start: 0.3219 (ttp) cc_final: 0.1676 (mpt) REVERT: D 338 ASN cc_start: 0.3622 (t0) cc_final: 0.3295 (m-40) REVERT: D 341 LYS cc_start: 0.3512 (OUTLIER) cc_final: 0.2689 (mptt) REVERT: D 439 LEU cc_start: 0.1150 (tp) cc_final: 0.0852 (tp) REVERT: D 474 MET cc_start: 0.2186 (mmm) cc_final: 0.1571 (mmt) REVERT: D 504 PHE cc_start: 0.4407 (t80) cc_final: 0.4061 (p90) REVERT: D 508 ASN cc_start: 0.4203 (m110) cc_final: 0.2995 (t0) REVERT: D 555 PHE cc_start: 0.4294 (OUTLIER) cc_final: 0.4080 (p90) REVERT: D 556 ASN cc_start: 0.1427 (t0) cc_final: 0.1122 (m110) REVERT: D 579 MET cc_start: 0.0580 (ptt) cc_final: 0.0015 (mpp) outliers start: 172 outliers final: 72 residues processed: 379 average time/residue: 0.4618 time to fit residues: 212.8617 Evaluate side-chains 260 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 166 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 192 ARG Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 341 LYS Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain D residue 555 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 75 optimal weight: 2.9990 chunk 12 optimal weight: 0.0060 chunk 307 optimal weight: 8.9990 chunk 112 optimal weight: 10.0000 chunk 148 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 159 optimal weight: 4.9990 chunk 252 optimal weight: 0.9990 chunk 348 optimal weight: 10.0000 chunk 35 optimal weight: 0.2980 chunk 53 optimal weight: 2.9990 overall best weight: 1.4602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 ASN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 762 GLN C 49 HIS C 115 GLN C 207 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 599 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.181916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.120236 restraints weight = 47279.527| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 4.29 r_work: 0.2974 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 29814 Z= 0.149 Angle : 0.730 12.503 40704 Z= 0.347 Chirality : 0.048 0.442 4777 Planarity : 0.005 0.056 5112 Dihedral : 6.530 58.691 3838 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.69 % Favored : 93.17 % Rotamer: Outliers : 4.92 % Allowed : 22.08 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.13), residues: 3484 helix: 0.32 (0.17), residues: 991 sheet: -0.95 (0.18), residues: 734 loop : -2.25 (0.13), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 115 TYR 0.044 0.001 TYR D 521 PHE 0.030 0.001 PHE D 523 TRP 0.021 0.001 TRP D 566 HIS 0.004 0.001 HIS D 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (29692) covalent geometry : angle 0.69737 / 0.34 (40378) SS BOND : bond 0.00549 / 0.39 ( 40) SS BOND : angle 1.75280 / 1.20 ( 80) hydrogen bonds : bond 0.04509 / 2.97 ( 1075) hydrogen bonds : angle 5.20856 / 3.50 ( 3054) link_BETA1-4 : bond 0.00519 / 0.31 ( 28) link_BETA1-4 : angle 2.18610 / 1.32 ( 84) link_NAG-ASN : bond 0.00444 / 0.25 ( 54) link_NAG-ASN : angle 2.95464 / 2.02 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 207 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.7560 (m110) cc_final: 0.7243 (p0) REVERT: A 131 CYS cc_start: 0.3778 (m) cc_final: 0.3293 (m) REVERT: A 153 MET cc_start: -0.0524 (mpp) cc_final: -0.2402 (tmt) REVERT: A 155 SER cc_start: 0.6462 (OUTLIER) cc_final: 0.6107 (p) REVERT: A 190 ARG cc_start: 0.7087 (mtt180) cc_final: 0.6557 (mtt90) REVERT: A 200 TYR cc_start: 0.8269 (m-80) cc_final: 0.7921 (m-80) REVERT: A 238 PHE cc_start: 0.6793 (p90) cc_final: 0.6532 (p90) REVERT: A 544 ASN cc_start: 0.8689 (p0) cc_final: 0.7733 (t0) REVERT: A 692 ILE cc_start: 0.9263 (OUTLIER) cc_final: 0.8827 (mm) REVERT: A 878 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8950 (tp) REVERT: A 985 ASP cc_start: 0.8142 (OUTLIER) cc_final: 0.7895 (p0) REVERT: A 1019 ARG cc_start: 0.8839 (tpt170) cc_final: 0.8440 (ttm110) REVERT: B 66 HIS cc_start: 0.6202 (OUTLIER) cc_final: 0.5990 (t-90) REVERT: B 140 PHE cc_start: 0.8281 (p90) cc_final: 0.8024 (p90) REVERT: B 141 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.7032 (pp) REVERT: B 153 MET cc_start: 0.0552 (mpp) cc_final: -0.3122 (ppp) REVERT: B 212 LEU cc_start: 0.4860 (tp) cc_final: 0.4327 (pp) REVERT: B 437 ASN cc_start: 0.6898 (t0) cc_final: 0.6650 (p0) REVERT: B 529 LYS cc_start: 0.7495 (OUTLIER) cc_final: 0.7043 (mtpm) REVERT: B 740 MET cc_start: 0.9162 (OUTLIER) cc_final: 0.8827 (ttp) REVERT: B 916 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.9089 (tp) REVERT: C 45 SER cc_start: 0.7554 (t) cc_final: 0.7158 (m) REVERT: C 141 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7630 (pt) REVERT: C 153 MET cc_start: 0.1420 (mpp) cc_final: 0.1220 (mtm) REVERT: C 195 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7629 (mtmt) REVERT: C 207 HIS cc_start: 0.7749 (OUTLIER) cc_final: 0.6921 (m170) REVERT: C 212 LEU cc_start: 0.5532 (tp) cc_final: 0.4590 (mp) REVERT: C 239 GLN cc_start: 0.7586 (tt0) cc_final: 0.7280 (mt0) REVERT: C 336 CYS cc_start: 0.3977 (OUTLIER) cc_final: 0.3045 (p) REVERT: C 534 VAL cc_start: 0.7847 (OUTLIER) cc_final: 0.7599 (p) REVERT: C 646 ARG cc_start: 0.8659 (tmt170) cc_final: 0.8267 (tmt-80) REVERT: C 740 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8578 (ttm) REVERT: C 787 GLN cc_start: 0.9250 (OUTLIER) cc_final: 0.8520 (mp10) REVERT: C 814 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7977 (mmtt) REVERT: C 1144 GLU cc_start: 0.8657 (tp30) cc_final: 0.8240 (tt0) REVERT: D 39 LEU cc_start: 0.6229 (OUTLIER) cc_final: 0.6016 (tp) REVERT: D 72 PHE cc_start: 0.4635 (t80) cc_final: 0.4242 (m-10) REVERT: D 89 GLN cc_start: 0.3201 (mm110) cc_final: 0.2898 (pm20) REVERT: D 190 MET cc_start: 0.2792 (mtm) cc_final: 0.2293 (ttm) REVERT: D 233 ILE cc_start: -0.0889 (OUTLIER) cc_final: -0.1140 (tp) REVERT: D 332 MET cc_start: 0.2954 (ttp) cc_final: 0.1460 (mpt) REVERT: D 474 MET cc_start: 0.2269 (mmm) cc_final: 0.1916 (mmp) REVERT: D 504 PHE cc_start: 0.4348 (t80) cc_final: 0.3976 (p90) REVERT: D 508 ASN cc_start: 0.4310 (m110) cc_final: 0.3286 (t0) REVERT: D 579 MET cc_start: 0.0325 (ptt) cc_final: 0.0101 (mtp) outliers start: 153 outliers final: 65 residues processed: 339 average time/residue: 0.4881 time to fit residues: 203.6143 Evaluate side-chains 252 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 168 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 477 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 293 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 259 optimal weight: 2.9990 chunk 265 optimal weight: 0.0980 chunk 183 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 309 optimal weight: 10.0000 chunk 256 optimal weight: 0.9990 chunk 299 optimal weight: 10.0000 chunk 9 optimal weight: 20.0000 chunk 296 optimal weight: 30.0000 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 762 GLN A 957 GLN A1005 GLN B 164 ASN B 762 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.180427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.119091 restraints weight = 46930.118| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 3.80 r_work: 0.2960 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 29814 Z= 0.168 Angle : 0.716 10.739 40704 Z= 0.341 Chirality : 0.048 0.502 4777 Planarity : 0.004 0.054 5112 Dihedral : 6.146 59.132 3824 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.60 % Favored : 93.23 % Rotamer: Outliers : 4.80 % Allowed : 22.69 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.14), residues: 3484 helix: 0.60 (0.17), residues: 997 sheet: -0.68 (0.18), residues: 738 loop : -2.12 (0.13), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1039 TYR 0.053 0.001 TYR D 521 PHE 0.022 0.001 PHE D 523 TRP 0.021 0.001 TRP D 566 HIS 0.010 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (29692) covalent geometry : angle 0.68800 / 0.33 (40378) SS BOND : bond 0.00538 / 0.37 ( 40) SS BOND : angle 1.70348 / 1.15 ( 80) hydrogen bonds : bond 0.04438 / 2.95 ( 1075) hydrogen bonds : angle 5.13564 / 3.46 ( 3054) link_BETA1-4 : bond 0.00544 / 0.30 ( 28) link_BETA1-4 : angle 2.11400 / 1.28 ( 84) link_NAG-ASN : bond 0.00376 / 0.21 ( 54) link_NAG-ASN : angle 2.65162 / 1.73 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 192 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.7626 (m110) cc_final: 0.7280 (p0) REVERT: A 131 CYS cc_start: 0.3606 (m) cc_final: 0.2970 (m) REVERT: A 153 MET cc_start: -0.0211 (mpp) cc_final: -0.2272 (tmt) REVERT: A 188 ASN cc_start: 0.5998 (m-40) cc_final: 0.5499 (p0) REVERT: A 190 ARG cc_start: 0.7038 (mtt180) cc_final: 0.6494 (mpt-90) REVERT: A 238 PHE cc_start: 0.6847 (p90) cc_final: 0.6548 (p90) REVERT: A 324 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.7105 (pm20) REVERT: A 544 ASN cc_start: 0.8743 (p0) cc_final: 0.7714 (t0) REVERT: A 692 ILE cc_start: 0.9247 (OUTLIER) cc_final: 0.8886 (mm) REVERT: A 878 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.9002 (tp) REVERT: B 66 HIS cc_start: 0.6327 (OUTLIER) cc_final: 0.6103 (t-90) REVERT: B 140 PHE cc_start: 0.8370 (p90) cc_final: 0.8035 (p90) REVERT: B 141 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.7084 (pp) REVERT: B 153 MET cc_start: 0.1089 (mpp) cc_final: -0.2500 (ppp) REVERT: B 212 LEU cc_start: 0.5065 (tp) cc_final: 0.4635 (pp) REVERT: B 336 CYS cc_start: 0.5317 (t) cc_final: 0.5099 (p) REVERT: B 387 LEU cc_start: 0.8290 (mt) cc_final: 0.7934 (mp) REVERT: B 437 ASN cc_start: 0.6884 (t0) cc_final: 0.6580 (p0) REVERT: B 529 LYS cc_start: 0.7300 (OUTLIER) cc_final: 0.6872 (mtpm) REVERT: B 654 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8583 (pt0) REVERT: B 740 MET cc_start: 0.9167 (OUTLIER) cc_final: 0.8822 (ttp) REVERT: B 900 MET cc_start: 0.9425 (OUTLIER) cc_final: 0.9214 (mtp) REVERT: B 916 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9125 (tp) REVERT: C 141 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7548 (pt) REVERT: C 195 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7672 (mtmt) REVERT: C 207 HIS cc_start: 0.7589 (t-170) cc_final: 0.7022 (m-70) REVERT: C 239 GLN cc_start: 0.7663 (tt0) cc_final: 0.7380 (mt0) REVERT: C 336 CYS cc_start: 0.4016 (OUTLIER) cc_final: 0.3290 (p) REVERT: C 740 MET cc_start: 0.8938 (OUTLIER) cc_final: 0.8671 (ttm) REVERT: C 787 GLN cc_start: 0.9219 (OUTLIER) cc_final: 0.8495 (mp10) REVERT: C 1144 GLU cc_start: 0.8755 (tp30) cc_final: 0.8526 (tp30) REVERT: D 72 PHE cc_start: 0.4647 (t80) cc_final: 0.4335 (m-10) REVERT: D 89 GLN cc_start: 0.3613 (mm110) cc_final: 0.3059 (pm20) REVERT: D 123 MET cc_start: -0.0819 (OUTLIER) cc_final: -0.1454 (ptm) REVERT: D 131 LYS cc_start: 0.4245 (mttm) cc_final: 0.4014 (tmmt) REVERT: D 190 MET cc_start: 0.2583 (mtm) cc_final: 0.1974 (ttm) REVERT: D 233 ILE cc_start: -0.0863 (OUTLIER) cc_final: -0.1123 (tp) REVERT: D 332 MET cc_start: 0.2972 (ttp) cc_final: 0.2039 (pmm) REVERT: D 474 MET cc_start: 0.1938 (mmm) cc_final: 0.1559 (mmp) REVERT: D 504 PHE cc_start: 0.4412 (t80) cc_final: 0.4037 (p90) REVERT: D 508 ASN cc_start: 0.4243 (m110) cc_final: 0.3435 (t0) REVERT: D 579 MET cc_start: 0.0391 (ptt) cc_final: -0.0272 (mpp) outliers start: 149 outliers final: 66 residues processed: 321 average time/residue: 0.4879 time to fit residues: 191.7758 Evaluate side-chains 249 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 166 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 343 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 189 optimal weight: 2.9990 chunk 151 optimal weight: 4.9990 chunk 294 optimal weight: 1.9990 chunk 159 optimal weight: 0.9990 chunk 198 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 304 optimal weight: 20.0000 chunk 40 optimal weight: 9.9990 chunk 214 optimal weight: 10.0000 chunk 147 optimal weight: 8.9990 chunk 150 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 957 GLN B 164 ASN C 207 HIS C 542 ASN D 24 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.178730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.119434 restraints weight = 46804.753| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.96 r_work: 0.2948 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 29814 Z= 0.229 Angle : 0.752 12.967 40704 Z= 0.360 Chirality : 0.050 0.526 4777 Planarity : 0.004 0.073 5112 Dihedral : 6.131 59.204 3820 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.09 % Favored : 92.74 % Rotamer: Outliers : 5.37 % Allowed : 22.34 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.14), residues: 3484 helix: 0.67 (0.17), residues: 983 sheet: -0.59 (0.18), residues: 752 loop : -2.02 (0.13), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 158 TYR 0.019 0.002 TYR A 160 PHE 0.019 0.002 PHE A 86 TRP 0.017 0.002 TRP D 48 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00558 / 0.23 (29692) covalent geometry : angle 0.72223 / 0.35 (40378) SS BOND : bond 0.00584 / 0.42 ( 40) SS BOND : angle 1.95709 / 1.40 ( 80) hydrogen bonds : bond 0.04886 / 3.24 ( 1075) hydrogen bonds : angle 5.24664 / 3.53 ( 3054) link_BETA1-4 : bond 0.00494 / 0.27 ( 28) link_BETA1-4 : angle 2.17638 / 1.32 ( 84) link_NAG-ASN : bond 0.00371 / 0.20 ( 54) link_NAG-ASN : angle 2.78751 / 1.80 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 176 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 CYS cc_start: 0.3915 (m) cc_final: 0.3141 (m) REVERT: A 153 MET cc_start: -0.0224 (mpp) cc_final: -0.2231 (tmt) REVERT: A 188 ASN cc_start: 0.6217 (m-40) cc_final: 0.5689 (p0) REVERT: A 190 ARG cc_start: 0.7193 (OUTLIER) cc_final: 0.6604 (mpt-90) REVERT: A 216 LEU cc_start: 0.6734 (OUTLIER) cc_final: 0.6447 (tt) REVERT: A 238 PHE cc_start: 0.7003 (p90) cc_final: 0.6728 (p90) REVERT: A 355 ARG cc_start: 0.5163 (OUTLIER) cc_final: 0.4732 (ttt90) REVERT: A 544 ASN cc_start: 0.8668 (p0) cc_final: 0.7679 (t0) REVERT: A 614 ASP cc_start: 0.8719 (p0) cc_final: 0.8506 (p0) REVERT: A 692 ILE cc_start: 0.9221 (OUTLIER) cc_final: 0.8899 (mm) REVERT: A 854 LYS cc_start: 0.6638 (OUTLIER) cc_final: 0.5616 (pptt) REVERT: A 1142 GLN cc_start: 0.8413 (tp40) cc_final: 0.7999 (tm-30) REVERT: B 66 HIS cc_start: 0.6599 (OUTLIER) cc_final: 0.6344 (t-90) REVERT: B 140 PHE cc_start: 0.8472 (p90) cc_final: 0.8144 (p90) REVERT: B 141 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.7145 (pp) REVERT: B 153 MET cc_start: 0.1451 (mpp) cc_final: -0.1637 (ptp) REVERT: B 212 LEU cc_start: 0.5335 (tp) cc_final: 0.4940 (pp) REVERT: B 387 LEU cc_start: 0.8340 (mt) cc_final: 0.7933 (mp) REVERT: B 529 LYS cc_start: 0.7042 (OUTLIER) cc_final: 0.6745 (mtpm) REVERT: B 581 THR cc_start: 0.8880 (OUTLIER) cc_final: 0.8659 (t) REVERT: B 654 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8557 (pt0) REVERT: B 740 MET cc_start: 0.9186 (OUTLIER) cc_final: 0.8857 (ttp) REVERT: B 900 MET cc_start: 0.9434 (OUTLIER) cc_final: 0.9193 (mtp) REVERT: B 916 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.9061 (tt) REVERT: C 141 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7729 (pt) REVERT: C 207 HIS cc_start: 0.7609 (OUTLIER) cc_final: 0.6882 (m170) REVERT: C 239 GLN cc_start: 0.7746 (tt0) cc_final: 0.7415 (mt0) REVERT: C 336 CYS cc_start: 0.4019 (OUTLIER) cc_final: 0.3143 (p) REVERT: C 740 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8715 (ttm) REVERT: C 787 GLN cc_start: 0.9272 (OUTLIER) cc_final: 0.8551 (mp10) REVERT: D 81 GLN cc_start: 0.3296 (OUTLIER) cc_final: 0.2345 (tt0) REVERT: D 89 GLN cc_start: 0.3615 (mm110) cc_final: 0.3146 (pm20) REVERT: D 190 MET cc_start: 0.2553 (mtm) cc_final: 0.2047 (ttm) REVERT: D 332 MET cc_start: 0.2787 (ttp) cc_final: 0.1288 (mpt) REVERT: D 474 MET cc_start: 0.1374 (mmm) cc_final: 0.1136 (mmp) REVERT: D 504 PHE cc_start: 0.4229 (t80) cc_final: 0.3886 (p90) REVERT: D 508 ASN cc_start: 0.3441 (m110) cc_final: 0.2467 (t0) outliers start: 167 outliers final: 74 residues processed: 319 average time/residue: 0.4621 time to fit residues: 181.6115 Evaluate side-chains 254 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 161 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 48 TRP Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 343 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 202 optimal weight: 0.9990 chunk 160 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 chunk 294 optimal weight: 9.9990 chunk 90 optimal weight: 0.9990 chunk 236 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 308 optimal weight: 1.9990 chunk 221 optimal weight: 4.9990 chunk 272 optimal weight: 2.9990 chunk 295 optimal weight: 20.0000 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 957 GLN B 690 GLN C 207 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.179480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.117299 restraints weight = 46883.870| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 3.45 r_work: 0.2966 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 29814 Z= 0.152 Angle : 0.692 11.305 40704 Z= 0.329 Chirality : 0.048 0.503 4777 Planarity : 0.004 0.055 5112 Dihedral : 5.711 59.512 3812 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.11 % Favored : 93.71 % Rotamer: Outliers : 4.47 % Allowed : 23.33 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.14), residues: 3484 helix: 0.86 (0.17), residues: 988 sheet: -0.44 (0.18), residues: 754 loop : -1.88 (0.13), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 460 TYR 0.018 0.001 TYR A 160 PHE 0.019 0.001 PHE C 140 TRP 0.014 0.001 TRP D 477 HIS 0.024 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (29692) covalent geometry : angle 0.66365 / 0.32 (40378) SS BOND : bond 0.00518 / 0.38 ( 40) SS BOND : angle 1.99081 / 1.41 ( 80) hydrogen bonds : bond 0.04124 / 2.75 ( 1075) hydrogen bonds : angle 5.06773 / 3.42 ( 3054) link_BETA1-4 : bond 0.00542 / 0.30 ( 28) link_BETA1-4 : angle 2.02020 / 1.23 ( 84) link_NAG-ASN : bond 0.00361 / 0.20 ( 54) link_NAG-ASN : angle 2.53385 / 1.65 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 169 time to evaluate : 0.957 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: A 131 CYS cc_start: 0.3617 (m) cc_final: 0.2883 (m) REVERT: A 153 MET cc_start: -0.0262 (mpp) cc_final: -0.2017 (tmt) REVERT: A 188 ASN cc_start: 0.6191 (m-40) cc_final: 0.5710 (p0) REVERT: A 190 ARG cc_start: 0.7015 (mtt180) cc_final: 0.6510 (mpt-90) REVERT: A 216 LEU cc_start: 0.6493 (OUTLIER) cc_final: 0.6252 (tt) REVERT: A 355 ARG cc_start: 0.5255 (OUTLIER) cc_final: 0.4719 (ttt90) REVERT: A 544 ASN cc_start: 0.8636 (p0) cc_final: 0.7614 (t0) REVERT: A 692 ILE cc_start: 0.9203 (OUTLIER) cc_final: 0.8885 (mm) REVERT: A 854 LYS cc_start: 0.6610 (OUTLIER) cc_final: 0.5578 (pptt) REVERT: B 66 HIS cc_start: 0.6558 (OUTLIER) cc_final: 0.6305 (t-90) REVERT: B 140 PHE cc_start: 0.8412 (p90) cc_final: 0.8057 (p90) REVERT: B 153 MET cc_start: 0.1519 (mpp) cc_final: -0.2242 (ppp) REVERT: B 212 LEU cc_start: 0.5315 (tp) cc_final: 0.4947 (pp) REVERT: B 387 LEU cc_start: 0.8285 (mt) cc_final: 0.7900 (mp) REVERT: B 654 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8510 (pt0) REVERT: B 740 MET cc_start: 0.9187 (OUTLIER) cc_final: 0.8842 (ttp) REVERT: B 900 MET cc_start: 0.9420 (OUTLIER) cc_final: 0.9141 (mtp) REVERT: B 916 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9115 (tp) REVERT: C 141 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7714 (pt) REVERT: C 207 HIS cc_start: 0.7720 (OUTLIER) cc_final: 0.6845 (m170) REVERT: C 239 GLN cc_start: 0.7666 (tt0) cc_final: 0.7338 (mt0) REVERT: C 336 CYS cc_start: 0.3912 (OUTLIER) cc_final: 0.3109 (p) REVERT: C 740 MET cc_start: 0.8933 (OUTLIER) cc_final: 0.8670 (ttm) REVERT: C 787 GLN cc_start: 0.9245 (OUTLIER) cc_final: 0.8559 (mp10) REVERT: C 1144 GLU cc_start: 0.8668 (tp30) cc_final: 0.8376 (tt0) REVERT: D 72 PHE cc_start: 0.4602 (t80) cc_final: 0.4237 (m-10) REVERT: D 81 GLN cc_start: 0.3392 (OUTLIER) cc_final: 0.2383 (tt0) REVERT: D 89 GLN cc_start: 0.3661 (mm110) cc_final: 0.3230 (pm20) REVERT: D 123 MET cc_start: -0.0791 (OUTLIER) cc_final: -0.1481 (ptm) REVERT: D 190 MET cc_start: 0.2429 (mtm) cc_final: 0.1927 (ttm) REVERT: D 233 ILE cc_start: -0.0825 (OUTLIER) cc_final: -0.1116 (tp) REVERT: D 332 MET cc_start: 0.2609 (ttp) cc_final: 0.1217 (mpt) REVERT: D 504 PHE cc_start: 0.4370 (t80) cc_final: 0.3997 (p90) REVERT: D 508 ASN cc_start: 0.4103 (m110) cc_final: 0.3275 (t0) REVERT: D 566 TRP cc_start: 0.0502 (p-90) cc_final: -0.0148 (p-90) outliers start: 139 outliers final: 77 residues processed: 293 average time/residue: 0.4660 time to fit residues: 169.1031 Evaluate side-chains 250 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 156 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 48 TRP Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 344 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 76 optimal weight: 0.5980 chunk 266 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 339 optimal weight: 7.9990 chunk 311 optimal weight: 10.0000 chunk 309 optimal weight: 20.0000 chunk 181 optimal weight: 1.9990 chunk 325 optimal weight: 0.5980 chunk 264 optimal weight: 4.9990 chunk 178 optimal weight: 1.9990 chunk 234 optimal weight: 20.0000 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 762 GLN A 957 GLN B 703 ASN B 969 ASN C 207 HIS C1002 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.180273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.118109 restraints weight = 47000.261| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 4.36 r_work: 0.2963 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.4366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29814 Z= 0.126 Angle : 0.669 10.174 40704 Z= 0.317 Chirality : 0.046 0.474 4777 Planarity : 0.004 0.053 5112 Dihedral : 5.192 59.956 3803 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.49 % Favored : 93.37 % Rotamer: Outliers : 3.67 % Allowed : 23.88 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.14), residues: 3484 helix: 1.03 (0.17), residues: 993 sheet: -0.32 (0.18), residues: 750 loop : -1.77 (0.13), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 190 TYR 0.017 0.001 TYR B1067 PHE 0.021 0.001 PHE A 192 TRP 0.015 0.001 TRP D 477 HIS 0.017 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (29692) covalent geometry : angle 0.64270 / 0.31 (40378) SS BOND : bond 0.00510 / 0.35 ( 40) SS BOND : angle 1.98606 / 1.24 ( 80) hydrogen bonds : bond 0.03775 / 2.52 ( 1075) hydrogen bonds : angle 4.95922 / 3.34 ( 3054) link_BETA1-4 : bond 0.00533 / 0.30 ( 28) link_BETA1-4 : angle 1.94228 / 1.19 ( 84) link_NAG-ASN : bond 0.00341 / 0.20 ( 54) link_NAG-ASN : angle 2.36526 / 1.55 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 168 time to evaluate : 1.024 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 95 THR cc_start: 0.7468 (p) cc_final: 0.7134 (t) REVERT: A 131 CYS cc_start: 0.3353 (m) cc_final: 0.2639 (m) REVERT: A 188 ASN cc_start: 0.6168 (m-40) cc_final: 0.5497 (p0) REVERT: A 190 ARG cc_start: 0.6913 (OUTLIER) cc_final: 0.6370 (mpt-90) REVERT: A 355 ARG cc_start: 0.4992 (OUTLIER) cc_final: 0.4672 (ttt90) REVERT: A 544 ASN cc_start: 0.8621 (p0) cc_final: 0.7589 (t0) REVERT: A 646 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.8663 (ttm-80) REVERT: A 692 ILE cc_start: 0.9173 (OUTLIER) cc_final: 0.8858 (mm) REVERT: A 1019 ARG cc_start: 0.8849 (tpt170) cc_final: 0.8448 (ttp-110) REVERT: B 66 HIS cc_start: 0.6414 (OUTLIER) cc_final: 0.6154 (t-90) REVERT: B 140 PHE cc_start: 0.8391 (p90) cc_final: 0.7944 (p90) REVERT: B 153 MET cc_start: 0.1118 (mpp) cc_final: -0.2417 (ppp) REVERT: B 212 LEU cc_start: 0.5403 (tp) cc_final: 0.4959 (pp) REVERT: B 387 LEU cc_start: 0.8225 (mt) cc_final: 0.7839 (mp) REVERT: B 569 ILE cc_start: 0.7229 (mp) cc_final: 0.7008 (mp) REVERT: B 654 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8502 (pt0) REVERT: B 916 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.9071 (tp) REVERT: B 985 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.8086 (p0) REVERT: C 141 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7742 (pt) REVERT: C 207 HIS cc_start: 0.7655 (OUTLIER) cc_final: 0.6796 (m-70) REVERT: C 239 GLN cc_start: 0.7637 (tt0) cc_final: 0.7306 (mt0) REVERT: C 336 CYS cc_start: 0.4007 (OUTLIER) cc_final: 0.3135 (p) REVERT: C 740 MET cc_start: 0.8870 (OUTLIER) cc_final: 0.8615 (ttm) REVERT: C 787 GLN cc_start: 0.9285 (OUTLIER) cc_final: 0.8602 (mp10) REVERT: C 1005 GLN cc_start: 0.9113 (OUTLIER) cc_final: 0.8840 (mt0) REVERT: D 72 PHE cc_start: 0.4634 (t80) cc_final: 0.4255 (m-10) REVERT: D 81 GLN cc_start: 0.3425 (OUTLIER) cc_final: 0.2547 (tt0) REVERT: D 89 GLN cc_start: 0.3612 (mm110) cc_final: 0.3260 (pm20) REVERT: D 190 MET cc_start: 0.2433 (mtm) cc_final: 0.1934 (ttm) REVERT: D 233 ILE cc_start: -0.1128 (OUTLIER) cc_final: -0.1396 (tp) REVERT: D 332 MET cc_start: 0.2928 (ttp) cc_final: 0.1346 (mpt) REVERT: D 504 PHE cc_start: 0.4558 (t80) cc_final: 0.4151 (p90) REVERT: D 508 ASN cc_start: 0.3836 (m110) cc_final: 0.3048 (t0) REVERT: D 566 TRP cc_start: 0.0579 (p-90) cc_final: 0.0045 (p-90) outliers start: 114 outliers final: 66 residues processed: 266 average time/residue: 0.5146 time to fit residues: 167.9531 Evaluate side-chains 237 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 155 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 48 TRP Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 343 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 188 optimal weight: 0.9980 chunk 278 optimal weight: 0.8980 chunk 347 optimal weight: 6.9990 chunk 68 optimal weight: 0.0030 chunk 225 optimal weight: 5.9990 chunk 348 optimal weight: 4.9990 chunk 216 optimal weight: 8.9990 chunk 191 optimal weight: 0.7980 chunk 222 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 341 optimal weight: 8.9990 overall best weight: 1.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 957 GLN C 207 HIS C1002 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.180040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.118106 restraints weight = 46868.372| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 4.40 r_work: 0.2962 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.4499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 29814 Z= 0.139 Angle : 0.671 10.542 40704 Z= 0.318 Chirality : 0.047 0.447 4777 Planarity : 0.004 0.054 5112 Dihedral : 5.059 58.770 3801 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.23 % Favored : 93.63 % Rotamer: Outliers : 3.83 % Allowed : 23.95 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.14), residues: 3484 helix: 1.10 (0.17), residues: 998 sheet: -0.19 (0.19), residues: 753 loop : -1.74 (0.14), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 190 TYR 0.017 0.001 TYR B1067 PHE 0.021 0.001 PHE A 140 TRP 0.027 0.001 TRP D 302 HIS 0.017 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (29692) covalent geometry : angle 0.64548 / 0.31 (40378) SS BOND : bond 0.00448 / 0.32 ( 40) SS BOND : angle 1.89192 / 1.17 ( 80) hydrogen bonds : bond 0.03859 / 2.58 ( 1075) hydrogen bonds : angle 4.92728 / 3.32 ( 3054) link_BETA1-4 : bond 0.00548 / 0.31 ( 28) link_BETA1-4 : angle 1.92350 / 1.18 ( 84) link_NAG-ASN : bond 0.00328 / 0.18 ( 54) link_NAG-ASN : angle 2.35611 / 1.53 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 161 time to evaluate : 1.101 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 95 THR cc_start: 0.7366 (p) cc_final: 0.7074 (t) REVERT: A 131 CYS cc_start: 0.3421 (m) cc_final: 0.2703 (m) REVERT: A 188 ASN cc_start: 0.6225 (m-40) cc_final: 0.5572 (p0) REVERT: A 190 ARG cc_start: 0.6864 (OUTLIER) cc_final: 0.6240 (mpt-90) REVERT: A 310 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8720 (ttpp) REVERT: A 355 ARG cc_start: 0.5019 (OUTLIER) cc_final: 0.4520 (ttt90) REVERT: A 544 ASN cc_start: 0.8619 (p0) cc_final: 0.7571 (t0) REVERT: A 646 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.8608 (ttm-80) REVERT: A 692 ILE cc_start: 0.9178 (OUTLIER) cc_final: 0.8863 (mm) REVERT: A 854 LYS cc_start: 0.6614 (OUTLIER) cc_final: 0.5322 (pptt) REVERT: A 1019 ARG cc_start: 0.8832 (tpt170) cc_final: 0.8446 (ttp-110) REVERT: B 66 HIS cc_start: 0.6398 (OUTLIER) cc_final: 0.6112 (t-90) REVERT: B 140 PHE cc_start: 0.8438 (p90) cc_final: 0.7957 (p90) REVERT: B 153 MET cc_start: 0.1303 (mpp) cc_final: -0.2154 (ppp) REVERT: B 212 LEU cc_start: 0.5397 (tp) cc_final: 0.4972 (pp) REVERT: B 387 LEU cc_start: 0.8178 (mt) cc_final: 0.7780 (mp) REVERT: B 569 ILE cc_start: 0.7162 (mp) cc_final: 0.6954 (mp) REVERT: B 654 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8439 (pt0) REVERT: B 861 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9080 (mt) REVERT: B 916 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.9093 (tp) REVERT: C 141 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7651 (pt) REVERT: C 239 GLN cc_start: 0.7698 (tt0) cc_final: 0.7398 (mt0) REVERT: C 336 CYS cc_start: 0.4462 (OUTLIER) cc_final: 0.3659 (p) REVERT: C 544 ASN cc_start: 0.7859 (OUTLIER) cc_final: 0.7133 (p0) REVERT: C 740 MET cc_start: 0.8884 (OUTLIER) cc_final: 0.8633 (ttm) REVERT: C 787 GLN cc_start: 0.9285 (OUTLIER) cc_final: 0.8627 (mp10) REVERT: D 48 TRP cc_start: 0.3443 (OUTLIER) cc_final: 0.3021 (m100) REVERT: D 72 PHE cc_start: 0.4693 (t80) cc_final: 0.4290 (m-10) REVERT: D 81 GLN cc_start: 0.3211 (OUTLIER) cc_final: 0.2435 (tt0) REVERT: D 89 GLN cc_start: 0.3602 (mm110) cc_final: 0.3247 (pm20) REVERT: D 123 MET cc_start: -0.0361 (OUTLIER) cc_final: -0.1167 (ptm) REVERT: D 190 MET cc_start: 0.2431 (mtm) cc_final: 0.1932 (ttm) REVERT: D 233 ILE cc_start: -0.0985 (OUTLIER) cc_final: -0.1212 (tp) REVERT: D 332 MET cc_start: 0.2811 (ttp) cc_final: 0.1343 (mpt) REVERT: D 504 PHE cc_start: 0.4547 (t80) cc_final: 0.4137 (p90) REVERT: D 508 ASN cc_start: 0.3597 (m110) cc_final: 0.2812 (t0) REVERT: D 566 TRP cc_start: 0.0741 (p-90) cc_final: 0.0331 (p-90) outliers start: 119 outliers final: 73 residues processed: 263 average time/residue: 0.4836 time to fit residues: 156.5596 Evaluate side-chains 242 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 150 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 577 ARG Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 48 TRP Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 344 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 193 optimal weight: 3.9990 chunk 313 optimal weight: 0.9980 chunk 41 optimal weight: 20.0000 chunk 90 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 263 optimal weight: 8.9990 chunk 176 optimal weight: 2.9990 chunk 233 optimal weight: 30.0000 chunk 238 optimal weight: 0.0170 chunk 136 optimal weight: 10.0000 overall best weight: 2.0024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 957 GLN C 207 HIS C1002 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.179471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.118062 restraints weight = 46618.819| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 4.37 r_work: 0.2949 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.4593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 29814 Z= 0.161 Angle : 0.683 10.928 40704 Z= 0.324 Chirality : 0.048 0.456 4777 Planarity : 0.004 0.054 5112 Dihedral : 5.065 57.628 3800 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.34 % Favored : 93.54 % Rotamer: Outliers : 3.67 % Allowed : 24.07 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.14), residues: 3484 helix: 1.13 (0.17), residues: 998 sheet: -0.19 (0.18), residues: 759 loop : -1.74 (0.14), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 190 TYR 0.018 0.001 TYR B1067 PHE 0.025 0.001 PHE B 855 TRP 0.019 0.001 TRP D 302 HIS 0.011 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 (29692) covalent geometry : angle 0.65891 / 0.32 (40378) SS BOND : bond 0.00445 / 0.31 ( 40) SS BOND : angle 1.73904 / 1.10 ( 80) hydrogen bonds : bond 0.04056 / 2.70 ( 1075) hydrogen bonds : angle 4.96340 / 3.35 ( 3054) link_BETA1-4 : bond 0.00509 / 0.28 ( 28) link_BETA1-4 : angle 1.94296 / 1.19 ( 84) link_NAG-ASN : bond 0.00319 / 0.17 ( 54) link_NAG-ASN : angle 2.38767 / 1.54 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 157 time to evaluate : 1.110 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 95 THR cc_start: 0.7377 (p) cc_final: 0.7085 (t) REVERT: A 131 CYS cc_start: 0.3365 (m) cc_final: 0.2618 (m) REVERT: A 188 ASN cc_start: 0.6198 (m-40) cc_final: 0.5537 (p0) REVERT: A 190 ARG cc_start: 0.6827 (OUTLIER) cc_final: 0.6212 (mpt-90) REVERT: A 355 ARG cc_start: 0.5086 (OUTLIER) cc_final: 0.4594 (ttt180) REVERT: A 544 ASN cc_start: 0.8631 (p0) cc_final: 0.7550 (t0) REVERT: A 646 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.8605 (ttm-80) REVERT: A 692 ILE cc_start: 0.9179 (OUTLIER) cc_final: 0.8869 (mm) REVERT: A 1005 GLN cc_start: 0.9086 (tt0) cc_final: 0.8843 (mt0) REVERT: A 1142 GLN cc_start: 0.8366 (tp-100) cc_final: 0.7967 (tm-30) REVERT: B 66 HIS cc_start: 0.6276 (OUTLIER) cc_final: 0.6022 (t-90) REVERT: B 140 PHE cc_start: 0.8455 (p90) cc_final: 0.7970 (p90) REVERT: B 153 MET cc_start: 0.1550 (mpp) cc_final: -0.2108 (ppp) REVERT: B 212 LEU cc_start: 0.5345 (tp) cc_final: 0.4966 (pp) REVERT: B 335 LEU cc_start: 0.6680 (mp) cc_final: 0.6402 (tt) REVERT: B 387 LEU cc_start: 0.8103 (mt) cc_final: 0.7696 (mp) REVERT: B 569 ILE cc_start: 0.7253 (mp) cc_final: 0.7050 (mp) REVERT: B 654 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8494 (pt0) REVERT: B 861 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9081 (mt) REVERT: B 900 MET cc_start: 0.9427 (OUTLIER) cc_final: 0.9164 (mtm) REVERT: B 916 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.8984 (tt) REVERT: C 141 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7468 (pt) REVERT: C 208 THR cc_start: 0.8054 (m) cc_final: 0.7638 (p) REVERT: C 239 GLN cc_start: 0.7649 (tt0) cc_final: 0.7360 (mt0) REVERT: C 336 CYS cc_start: 0.4704 (OUTLIER) cc_final: 0.3692 (p) REVERT: C 544 ASN cc_start: 0.7862 (OUTLIER) cc_final: 0.7137 (p0) REVERT: C 740 MET cc_start: 0.8914 (OUTLIER) cc_final: 0.8653 (ttm) REVERT: C 787 GLN cc_start: 0.9299 (OUTLIER) cc_final: 0.8589 (mp10) REVERT: D 48 TRP cc_start: 0.3406 (OUTLIER) cc_final: 0.3022 (m100) REVERT: D 72 PHE cc_start: 0.4688 (t80) cc_final: 0.4330 (m-10) REVERT: D 81 GLN cc_start: 0.3047 (OUTLIER) cc_final: 0.2360 (tt0) REVERT: D 89 GLN cc_start: 0.3625 (mm110) cc_final: 0.3281 (pm20) REVERT: D 123 MET cc_start: -0.0433 (OUTLIER) cc_final: -0.1182 (ptm) REVERT: D 190 MET cc_start: 0.2342 (mtm) cc_final: 0.1928 (ttm) REVERT: D 233 ILE cc_start: -0.0815 (OUTLIER) cc_final: -0.1060 (tp) REVERT: D 297 MET cc_start: -0.1326 (mmt) cc_final: -0.1707 (mmm) REVERT: D 332 MET cc_start: 0.3002 (ttp) cc_final: 0.1546 (mpt) REVERT: D 504 PHE cc_start: 0.4613 (t80) cc_final: 0.4184 (p90) REVERT: D 508 ASN cc_start: 0.3390 (m110) cc_final: 0.2920 (t0) REVERT: D 566 TRP cc_start: 0.0852 (p-90) cc_final: 0.0439 (p-90) outliers start: 114 outliers final: 79 residues processed: 256 average time/residue: 0.5112 time to fit residues: 160.2665 Evaluate side-chains 248 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 151 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 577 ARG Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 48 TRP Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 344 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 115 optimal weight: 7.9990 chunk 300 optimal weight: 6.9990 chunk 157 optimal weight: 0.9990 chunk 260 optimal weight: 0.5980 chunk 312 optimal weight: 7.9990 chunk 223 optimal weight: 8.9990 chunk 305 optimal weight: 5.9990 chunk 317 optimal weight: 1.9990 chunk 320 optimal weight: 0.2980 chunk 321 optimal weight: 0.5980 chunk 18 optimal weight: 10.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 957 GLN B 239 GLN C 207 HIS C1002 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.180597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.119108 restraints weight = 46649.440| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 4.22 r_work: 0.2982 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.4711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 29814 Z= 0.115 Angle : 0.658 10.084 40704 Z= 0.312 Chirality : 0.046 0.427 4777 Planarity : 0.004 0.052 5112 Dihedral : 4.857 55.808 3799 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.83 % Favored : 94.06 % Rotamer: Outliers : 2.83 % Allowed : 24.85 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.14), residues: 3484 helix: 1.27 (0.17), residues: 998 sheet: -0.04 (0.19), residues: 746 loop : -1.66 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 190 TYR 0.017 0.001 TYR C1067 PHE 0.026 0.001 PHE D 32 TRP 0.022 0.001 TRP D 477 HIS 0.018 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (29692) covalent geometry : angle 0.63549 / 0.31 (40378) SS BOND : bond 0.00399 / 0.28 ( 40) SS BOND : angle 1.62311 / 1.06 ( 80) hydrogen bonds : bond 0.03497 / 2.33 ( 1075) hydrogen bonds : angle 4.82349 / 3.26 ( 3054) link_BETA1-4 : bond 0.00546 / 0.30 ( 28) link_BETA1-4 : angle 1.85260 / 1.14 ( 84) link_NAG-ASN : bond 0.00337 / 0.20 ( 54) link_NAG-ASN : angle 2.22245 / 1.45 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 164 time to evaluate : 1.128 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: A 95 THR cc_start: 0.7312 (p) cc_final: 0.6994 (t) REVERT: A 131 CYS cc_start: 0.3244 (m) cc_final: 0.2579 (m) REVERT: A 188 ASN cc_start: 0.6229 (m-40) cc_final: 0.5553 (p0) REVERT: A 190 ARG cc_start: 0.6683 (OUTLIER) cc_final: 0.6031 (mpt-90) REVERT: A 310 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8718 (ttpp) REVERT: A 355 ARG cc_start: 0.5220 (OUTLIER) cc_final: 0.4822 (ttt90) REVERT: A 544 ASN cc_start: 0.8636 (p0) cc_final: 0.7565 (t0) REVERT: A 646 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.8595 (ttm-80) REVERT: A 770 ILE cc_start: 0.8676 (OUTLIER) cc_final: 0.8182 (mt) REVERT: A 1005 GLN cc_start: 0.9023 (tt0) cc_final: 0.8803 (mt0) REVERT: A 1019 ARG cc_start: 0.8824 (tpt170) cc_final: 0.8464 (ttp-110) REVERT: B 66 HIS cc_start: 0.6473 (m-70) cc_final: 0.6143 (t-90) REVERT: B 140 PHE cc_start: 0.8465 (p90) cc_final: 0.8012 (p90) REVERT: B 153 MET cc_start: 0.1489 (mpp) cc_final: -0.2119 (ppp) REVERT: B 212 LEU cc_start: 0.5311 (tp) cc_final: 0.5005 (pp) REVERT: B 335 LEU cc_start: 0.6654 (mp) cc_final: 0.6379 (tt) REVERT: B 387 LEU cc_start: 0.8127 (mt) cc_final: 0.7719 (mp) REVERT: B 654 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8450 (pt0) REVERT: B 861 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9074 (mt) REVERT: B 900 MET cc_start: 0.9429 (OUTLIER) cc_final: 0.9121 (mtm) REVERT: B 916 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.9027 (tp) REVERT: C 141 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7632 (pt) REVERT: C 208 THR cc_start: 0.7977 (m) cc_final: 0.7527 (p) REVERT: C 239 GLN cc_start: 0.7643 (tt0) cc_final: 0.7393 (mt0) REVERT: C 246 ARG cc_start: 0.4776 (mmt90) cc_final: 0.4556 (mmt180) REVERT: C 336 CYS cc_start: 0.4534 (OUTLIER) cc_final: 0.3529 (p) REVERT: C 740 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8619 (ttm) REVERT: C 787 GLN cc_start: 0.9285 (OUTLIER) cc_final: 0.8614 (mp10) REVERT: C 1005 GLN cc_start: 0.9101 (OUTLIER) cc_final: 0.8849 (mt0) REVERT: D 48 TRP cc_start: 0.3258 (OUTLIER) cc_final: 0.2977 (m100) REVERT: D 72 PHE cc_start: 0.4866 (t80) cc_final: 0.4506 (m-10) REVERT: D 81 GLN cc_start: 0.3277 (OUTLIER) cc_final: 0.2511 (tt0) REVERT: D 89 GLN cc_start: 0.3635 (mm110) cc_final: 0.3294 (pm20) REVERT: D 123 MET cc_start: -0.0438 (OUTLIER) cc_final: -0.1156 (ptm) REVERT: D 190 MET cc_start: 0.2347 (mtm) cc_final: 0.1895 (ttm) REVERT: D 233 ILE cc_start: -0.0982 (OUTLIER) cc_final: -0.1245 (tp) REVERT: D 332 MET cc_start: 0.2947 (ttp) cc_final: 0.1502 (mpt) REVERT: D 504 PHE cc_start: 0.4500 (t80) cc_final: 0.4100 (p90) REVERT: D 508 ASN cc_start: 0.3744 (m110) cc_final: 0.3168 (t0) REVERT: D 566 TRP cc_start: 0.0847 (p-90) cc_final: 0.0438 (p-90) outliers start: 88 outliers final: 60 residues processed: 241 average time/residue: 0.5480 time to fit residues: 162.0044 Evaluate side-chains 228 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 150 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 48 TRP Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 344 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 69 optimal weight: 0.0000 chunk 348 optimal weight: 9.9990 chunk 337 optimal weight: 7.9990 chunk 270 optimal weight: 4.9990 chunk 267 optimal weight: 4.9990 chunk 146 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 191 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 112 optimal weight: 9.9990 chunk 275 optimal weight: 0.8980 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 957 GLN C 207 HIS C1002 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.180131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.117776 restraints weight = 46848.369| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 4.04 r_work: 0.2977 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.4766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 29814 Z= 0.131 Angle : 0.663 10.112 40704 Z= 0.314 Chirality : 0.047 0.423 4777 Planarity : 0.004 0.053 5112 Dihedral : 4.831 54.233 3799 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.31 % Favored : 93.57 % Rotamer: Outliers : 2.90 % Allowed : 24.81 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.14), residues: 3484 helix: 1.29 (0.17), residues: 998 sheet: -0.06 (0.19), residues: 752 loop : -1.62 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 190 TYR 0.018 0.001 TYR A 369 PHE 0.025 0.001 PHE B 855 TRP 0.017 0.001 TRP D 271 HIS 0.016 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (29692) covalent geometry : angle 0.64141 / 0.31 (40378) SS BOND : bond 0.00404 / 0.28 ( 40) SS BOND : angle 1.58940 / 1.03 ( 80) hydrogen bonds : bond 0.03689 / 2.46 ( 1075) hydrogen bonds : angle 4.81683 / 3.25 ( 3054) link_BETA1-4 : bond 0.00513 / 0.28 ( 28) link_BETA1-4 : angle 1.85519 / 1.14 ( 84) link_NAG-ASN : bond 0.00314 / 0.18 ( 54) link_NAG-ASN : angle 2.23442 / 1.45 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13391.25 seconds wall clock time: 227 minutes 36.16 seconds (13656.16 seconds total)