Starting phenix.real_space_refine on Mon Jul 6 08:57:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7fae_31502/07_2026/7fae_31502.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fae_31502/07_2026/7fae_31502.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7fae_31502/07_2026/7fae_31502.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fae_31502/07_2026/7fae_31502.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7fae_31502/07_2026/7fae_31502.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7fae_31502/07_2026/7fae_31502.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7fae_31502/07_2026/7fae_31502.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fae_31502/07_2026/7fae_31502.map" } resolution = 3.65 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 144 5.16 5 C 21774 2.51 5 N 5656 2.21 5 O 6778 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 89 residue(s): 0.04s 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: 34352 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 7853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1004, 7853 Classifications: {'peptide': 1004} Link IDs: {'PTRANS': 52, 'TRANS': 951} Chain breaks: 8 Chain: "B" Number of atoms: 7863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7863 Classifications: {'peptide': 1006} Link IDs: {'PTRANS': 53, 'TRANS': 952} Chain breaks: 8 Chain: "C" Number of atoms: 7866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1007, 7866 Classifications: {'peptide': 1007} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 52, 'TRANS': 954} Chain breaks: 8 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1670 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 11, 'TRANS': 210} Chain: "d" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1635 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 11, 'TRANS': 200} Chain: "e" Number of atoms: 1666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1666 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 210} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Chain: "g" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1635 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 11, 'TRANS': 200} Chain: "h" Number of atoms: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1661 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 11, 'TRANS': 209} Chain breaks: 1 Chain: "L" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1635 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 11, 'TRANS': 200} 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: "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: "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: "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: "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: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 7.07, per 1000 atoms: 0.21 Number of scatterers: 34352 At special positions: 0 Unit cell: (218.25, 188.18, 219.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 144 16.00 O 6778 8.00 N 5656 7.00 C 21774 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.17 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=1.98 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.05 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.05 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.05 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 149 " - pdb=" SG CYS H 205 " distance=2.04 Simple disulfide: pdb=" SG CYS d 23 " - pdb=" SG CYS d 88 " distance=2.04 Simple disulfide: pdb=" SG CYS d 134 " - pdb=" SG CYS d 194 " distance=2.04 Simple disulfide: pdb=" SG CYS e 22 " - pdb=" SG CYS e 96 " distance=2.03 Simple disulfide: pdb=" SG CYS e 149 " - pdb=" SG CYS e 205 " distance=2.04 Simple disulfide: pdb=" SG CYS g 23 " - pdb=" SG CYS g 88 " distance=2.04 Simple disulfide: pdb=" SG CYS g 134 " - pdb=" SG CYS g 194 " distance=2.04 Simple disulfide: pdb=" SG CYS h 22 " - pdb=" SG CYS h 96 " distance=2.03 Simple disulfide: pdb=" SG CYS h 149 " - pdb=" SG CYS h 205 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.04 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 C1410 " - " NAG C1411 " " NAG E 1 " - " NAG E 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 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 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-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 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 B 709 " " 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 343 " " NAG C1407 " - " ASN C 603 " " NAG C1408 " - " ASN C 616 " " NAG C1409 " - " ASN C 657 " " NAG C1410 " - " ASN C1074 " " NAG E 1 " - " ASN A 343 " " NAG I 1 " - " ASN A 709 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN A 801 " " NAG M 1 " - " ASN A1074 " " NAG N 1 " - " ASN A1098 " " NAG O 1 " - " ASN A1134 " " NAG Q 1 " - " ASN C 709 " " NAG R 1 " - " ASN C 717 " " NAG S 1 " - " ASN C 801 " " NAG T 1 " - " ASN C1098 " " NAG U 1 " - " ASN C1134 " " NAG X 1 " - " ASN B 717 " " NAG Y 1 " - " ASN B 801 " " NAG Z 1 " - " ASN B1074 " " NAG a 1 " - " ASN B1098 " " NAG b 1 " - " ASN B1134 " Time building additional restraints: 2.99 Conformation dependent library (CDL) restraints added in 1.1 seconds 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8046 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 75 sheets defined 19.6% alpha, 32.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.886A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.620A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.811A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.588A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.582A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.717A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (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: 3.562A pdb=" N ILE A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.604A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.590A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.354A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR A 961 " --> pdb=" O GLN A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 979 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.430A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.885A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.620A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 389 Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.812A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.588A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.631A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (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: 3.771A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN B 774 " --> pdb=" O ILE B 770 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 815 removed outlier: 3.633A pdb=" N LYS B 814 " --> pdb=" O LYS B 811 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG B 815 " --> pdb=" O PRO B 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 811 through 815' Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.647A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.574A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 918 removed outlier: 3.994A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.626A pdb=" N LYS B 933 " --> pdb=" O SER B 929 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 964 removed outlier: 3.879A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 981 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.632A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.647A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.886A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.621A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.812A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.587A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.965A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 823 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.544A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.603A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.011A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.372A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER C1021 " --> pdb=" O GLU C1017 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.664A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 140 Processing helix chain 'H' and resid 196 through 198 No H-bonds generated for 'chain 'H' and resid 196 through 198' Processing helix chain 'H' and resid 211 through 213 No H-bonds generated for 'chain 'H' and resid 211 through 213' Processing helix chain 'd' and resid 79 through 83 Processing helix chain 'd' and resid 121 through 128 removed outlier: 3.634A pdb=" N GLY d 128 " --> pdb=" O GLN d 124 " (cutoff:3.500A) Processing helix chain 'd' and resid 183 through 189 removed outlier: 3.503A pdb=" N GLU d 187 " --> pdb=" O LYS d 183 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS d 188 " --> pdb=" O ALA d 184 " (cutoff:3.500A) Processing helix chain 'e' and resid 87 through 91 removed outlier: 3.664A pdb=" N THR e 91 " --> pdb=" O SER e 88 " (cutoff:3.500A) Processing helix chain 'e' and resid 136 through 140 Processing helix chain 'e' and resid 196 through 198 No H-bonds generated for 'chain 'e' and resid 196 through 198' Processing helix chain 'e' and resid 210 through 213 Processing helix chain 'g' and resid 79 through 83 Processing helix chain 'g' and resid 121 through 128 removed outlier: 3.633A pdb=" N GLY g 128 " --> pdb=" O GLN g 124 " (cutoff:3.500A) Processing helix chain 'g' and resid 183 through 189 removed outlier: 3.503A pdb=" N GLU g 187 " --> pdb=" O LYS g 183 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS g 188 " --> pdb=" O ALA g 184 " (cutoff:3.500A) Processing helix chain 'h' and resid 87 through 91 removed outlier: 3.663A pdb=" N THR h 91 " --> pdb=" O SER h 88 " (cutoff:3.500A) Processing helix chain 'h' and resid 136 through 140 Processing helix chain 'h' and resid 196 through 198 No H-bonds generated for 'chain 'h' and resid 196 through 198' Processing helix chain 'h' and resid 210 through 213 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'L' and resid 121 through 128 removed outlier: 3.633A pdb=" N GLY L 128 " --> pdb=" O GLN L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 189 removed outlier: 3.502A pdb=" N GLU L 187 " --> pdb=" O LYS L 183 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS L 188 " --> pdb=" O ALA L 184 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 8.151A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 10.526A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.757A pdb=" N THR A 274 " --> pdb=" O CYS A 291 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N CYS A 291 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 128 through 131 removed outlier: 4.248A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.665A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 357 through 358 removed outlier: 3.618A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.973A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.664A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 538 through 543 Processing sheet with id=AB1, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.879A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.230A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 removed outlier: 6.914A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.591A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.591A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.569A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.810A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, 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: 6.440A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.682A 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: 6.950A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.570A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC3, first strand: chain 'B' and resid 116 through 121 removed outlier: 3.731A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 7.661A 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: 4.588A 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=AC4, first strand: chain 'B' and resid 309 through 319 removed outlier: 6.679A pdb=" N GLU B 309 " --> pdb=" O GLY B 601 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N GLY B 601 " --> pdb=" O GLU B 309 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 327 through 328 removed outlier: 5.338A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 357 through 358 removed outlier: 3.618A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.622A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.255A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.623A 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=AC9, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.589A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.589A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.504A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.713A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.539A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.440A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 10.075A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.649A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.780A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU C 117 " --> pdb=" O PHE C 106 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.572A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.835A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 539 through 543 Processing sheet with id=AE3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.220A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.542A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.542A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.578A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE8, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.626A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.611A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AF2, first strand: chain 'H' and resid 129 through 133 removed outlier: 3.780A pdb=" N SER H 189 " --> pdb=" O CYS H 149 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N TYR H 185 " --> pdb=" O ASP H 153 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 129 through 133 removed outlier: 3.780A pdb=" N SER H 189 " --> pdb=" O CYS H 149 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N TYR H 185 " --> pdb=" O ASP H 153 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 159 through 163 removed outlier: 3.558A pdb=" N THR H 160 " --> pdb=" O ASN H 208 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N CYS H 205 " --> pdb=" O LYS H 218 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS H 218 " --> pdb=" O CYS H 205 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'd' and resid 4 through 6 removed outlier: 3.645A pdb=" N VAL d 19 " --> pdb=" O ILE d 75 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE d 75 " --> pdb=" O VAL d 19 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR d 72 " --> pdb=" O SER d 65 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'd' and resid 10 through 11 Processing sheet with id=AF7, first strand: chain 'd' and resid 53 through 54 removed outlier: 6.331A pdb=" N TRP d 35 " --> pdb=" O LEU d 47 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N TYR d 49 " --> pdb=" O LEU d 33 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU d 33 " --> pdb=" O TYR d 49 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN d 38 " --> pdb=" O THR d 85 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR d 85 " --> pdb=" O GLN d 38 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'd' and resid 114 through 118 removed outlier: 5.601A pdb=" N TYR d 173 " --> pdb=" O ASN d 138 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'd' and resid 154 through 155 removed outlier: 4.769A pdb=" N TRP d 148 " --> pdb=" O GLN d 155 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'e' and resid 3 through 6 removed outlier: 3.625A pdb=" N GLN e 3 " --> pdb=" O SER e 25 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER e 25 " --> pdb=" O GLN e 3 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'e' and resid 10 through 12 removed outlier: 6.612A pdb=" N TRP e 36 " --> pdb=" O MET e 48 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'e' and resid 10 through 12 Processing sheet with id=AG4, first strand: chain 'e' and resid 129 through 133 removed outlier: 3.779A pdb=" N SER e 189 " --> pdb=" O CYS e 149 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N TYR e 185 " --> pdb=" O ASP e 153 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'e' and resid 129 through 133 removed outlier: 3.779A pdb=" N SER e 189 " --> pdb=" O CYS e 149 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N TYR e 185 " --> pdb=" O ASP e 153 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'e' and resid 160 through 163 removed outlier: 3.558A pdb=" N THR e 160 " --> pdb=" O ASN e 208 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N CYS e 205 " --> pdb=" O LYS e 218 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS e 218 " --> pdb=" O CYS e 205 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'g' and resid 4 through 5 removed outlier: 3.645A pdb=" N VAL g 19 " --> pdb=" O ILE g 75 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE g 75 " --> pdb=" O VAL g 19 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR g 72 " --> pdb=" O SER g 65 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'g' and resid 11 through 13 Processing sheet with id=AG9, first strand: chain 'g' and resid 53 through 54 removed outlier: 6.331A pdb=" N TRP g 35 " --> pdb=" O LEU g 47 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR g 49 " --> pdb=" O LEU g 33 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU g 33 " --> pdb=" O TYR g 49 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN g 38 " --> pdb=" O THR g 85 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR g 85 " --> pdb=" O GLN g 38 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'g' and resid 114 through 118 Processing sheet with id=AH2, first strand: chain 'g' and resid 154 through 155 removed outlier: 4.770A pdb=" N TRP g 148 " --> pdb=" O GLN g 155 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'h' and resid 3 through 6 removed outlier: 3.625A pdb=" N GLN h 3 " --> pdb=" O SER h 25 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER h 25 " --> pdb=" O GLN h 3 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'h' and resid 10 through 12 removed outlier: 6.611A pdb=" N TRP h 36 " --> pdb=" O MET h 48 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'h' and resid 10 through 12 Processing sheet with id=AH6, first strand: chain 'h' and resid 129 through 133 removed outlier: 3.779A pdb=" N SER h 189 " --> pdb=" O CYS h 149 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N TYR h 185 " --> pdb=" O ASP h 153 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'h' and resid 129 through 133 removed outlier: 3.779A pdb=" N SER h 189 " --> pdb=" O CYS h 149 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N TYR h 185 " --> pdb=" O ASP h 153 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'h' and resid 160 through 163 removed outlier: 3.868A pdb=" N CYS h 205 " --> pdb=" O LYS h 218 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS h 218 " --> pdb=" O CYS h 205 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.646A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE L 75 " --> pdb=" O VAL L 19 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR L 72 " --> pdb=" O SER L 65 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.331A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN L 38 " --> pdb=" O THR L 85 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'L' and resid 114 through 118 Processing sheet with id=AI3, first strand: chain 'L' and resid 154 through 155 removed outlier: 4.769A pdb=" N TRP L 148 " --> pdb=" O GLN L 155 " (cutoff:3.500A) 1314 hydrogen bonds defined for protein. 3489 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: 8.14 Time building geometry restraints manager: 3.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 6044 1.32 - 1.45: 10852 1.45 - 1.58: 18039 1.58 - 1.72: 0 1.72 - 1.85: 183 Bond restraints: 35118 Sorted by residual: bond pdb=" N THR B 478 " pdb=" CA THR B 478 " ideal model delta sigma weight residual 1.458 1.491 -0.034 7.40e-03 1.83e+04 2.08e+01 bond pdb=" N THR A 478 " pdb=" CA THR A 478 " ideal model delta sigma weight residual 1.458 1.491 -0.033 7.40e-03 1.83e+04 1.99e+01 bond pdb=" C THR A 588 " pdb=" N PRO A 589 " ideal model delta sigma weight residual 1.332 1.388 -0.056 1.34e-02 5.57e+03 1.77e+01 bond pdb=" C HIS C1088 " pdb=" N PHE C1089 " ideal model delta sigma weight residual 1.331 1.265 0.066 1.59e-02 3.96e+03 1.74e+01 bond pdb=" N PHE B 329 " pdb=" CA PHE B 329 " ideal model delta sigma weight residual 1.453 1.487 -0.034 8.30e-03 1.45e+04 1.68e+01 ... (remaining 35113 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.69: 46449 2.69 - 5.39: 1196 5.39 - 8.08: 100 8.08 - 10.77: 10 10.77 - 13.47: 14 Bond angle restraints: 47769 Sorted by residual: angle pdb=" CA PRO L 8 " pdb=" N PRO L 8 " pdb=" CD PRO L 8 " ideal model delta sigma weight residual 112.00 98.58 13.42 1.40e+00 5.10e-01 9.19e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 122.26 -11.56 1.22e+00 6.72e-01 8.98e+01 angle pdb=" CA PRO A 899 " pdb=" N PRO A 899 " pdb=" CD PRO A 899 " ideal model delta sigma weight residual 112.00 99.28 12.72 1.40e+00 5.10e-01 8.26e+01 angle pdb=" CA PRO H 158 " pdb=" N PRO H 158 " pdb=" CD PRO H 158 " ideal model delta sigma weight residual 112.00 99.32 12.68 1.40e+00 5.10e-01 8.21e+01 angle pdb=" CA PRO C 899 " pdb=" N PRO C 899 " pdb=" CD PRO C 899 " ideal model delta sigma weight residual 112.00 99.49 12.51 1.40e+00 5.10e-01 7.98e+01 ... (remaining 47764 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 17937 17.91 - 35.82: 1846 35.82 - 53.73: 451 53.73 - 71.64: 154 71.64 - 89.55: 56 Dihedral angle restraints: 20444 sinusoidal: 7919 harmonic: 12525 Sorted by residual: dihedral pdb=" CA TYR d 94 " pdb=" C TYR d 94 " pdb=" N PRO d 95 " pdb=" CA PRO d 95 " ideal model delta harmonic sigma weight residual -180.00 -113.01 -66.99 0 5.00e+00 4.00e-02 1.80e+02 dihedral pdb=" CA TYR g 94 " pdb=" C TYR g 94 " pdb=" N PRO g 95 " pdb=" CA PRO g 95 " ideal model delta harmonic sigma weight residual -180.00 -113.02 -66.98 0 5.00e+00 4.00e-02 1.79e+02 dihedral pdb=" CA TYR L 94 " pdb=" C TYR L 94 " pdb=" N PRO L 95 " pdb=" CA PRO L 95 " ideal model delta harmonic sigma weight residual -180.00 -113.05 -66.95 0 5.00e+00 4.00e-02 1.79e+02 ... (remaining 20441 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.328: 5569 0.328 - 0.655: 9 0.655 - 0.983: 3 0.983 - 1.311: 0 1.311 - 1.639: 1 Chirality restraints: 5582 Sorted by residual: chirality pdb=" C1 NAG C1411 " pdb=" O4 NAG C1410 " pdb=" C2 NAG C1411 " pdb=" O5 NAG C1411 " 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 O 1 " pdb=" ND2 ASN A1134 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.76 -1.64 2.00e-01 2.50e+01 6.71e+01 chirality pdb=" C1 NAG Z 1 " pdb=" ND2 ASN B1074 " pdb=" C2 NAG Z 1 " pdb=" O5 NAG Z 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.64 -0.76 2.00e-01 2.50e+01 1.43e+01 ... (remaining 5579 not shown) Planarity restraints: 6124 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 343 " -0.195 2.00e-02 2.50e+03 2.12e-01 5.62e+02 pdb=" CG ASN A 343 " 0.068 2.00e-02 2.50e+03 pdb=" OD1 ASN A 343 " 0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN A 343 " 0.351 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " -0.242 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER L 7 " -0.118 5.00e-02 4.00e+02 1.64e-01 4.30e+01 pdb=" N PRO L 8 " 0.283 5.00e-02 4.00e+02 pdb=" CA PRO L 8 " -0.085 5.00e-02 4.00e+02 pdb=" CD PRO L 8 " -0.080 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 816 " -0.113 5.00e-02 4.00e+02 1.59e-01 4.03e+01 pdb=" N PRO C 817 " 0.274 5.00e-02 4.00e+02 pdb=" CA PRO C 817 " -0.084 5.00e-02 4.00e+02 pdb=" CD PRO C 817 " -0.076 5.00e-02 4.00e+02 ... (remaining 6121 not shown) Histogram of nonbonded interaction distances: 1.04 - 1.81: 1 1.81 - 2.58: 411 2.58 - 3.36: 42599 3.36 - 4.13: 80648 4.13 - 4.90: 146395 Nonbonded interactions: 270054 Sorted by model distance: nonbonded pdb=" NH1 ARG A 357 " pdb=" OG1 THR B 167 " model vdw 1.041 3.120 nonbonded pdb=" NH1 ARG A 357 " pdb=" CB THR B 167 " model vdw 1.838 3.550 nonbonded pdb=" O GLN A 804 " pdb=" CD PRO A 817 " model vdw 1.904 3.440 nonbonded pdb=" NH1 ARG A 357 " pdb=" CG2 THR B 167 " model vdw 2.017 3.540 nonbonded pdb=" O PRO H 156 " pdb=" CD PRO H 158 " model vdw 2.040 3.440 ... (remaining 270049 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 385 or (resid 386 and (name N or name CA or nam \ e C or name O or name CB )) or resid 387 through 826 or resid 855 through 1408)) \ selection = (chain 'B' and (resid 27 through 385 or (resid 386 and (name N or name CA or nam \ e C or name O or name CB )) or resid 387 through 620 or resid 641 through 939 or \ resid 944 through 1408)) selection = (chain 'C' and (resid 27 through 620 or resid 641 through 826 or resid 855 throu \ gh 1408)) } ncs_group { reference = chain 'E' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' } ncs_group { reference = (chain 'H' and (resid 1 through 155 or (resid 156 and (name N or name CA or name \ C or name O or name CB )) or (resid 158 and (name N or name CA or name C or nam \ e O or name CB )) or resid 159 through 222)) selection = (chain 'e' and (resid 1 through 156 or resid 158 through 222)) selection = (chain 'h' and (resid 1 through 155 or (resid 156 through 158 and (name N or nam \ e CA or name C or name O or name CB )) or resid 159 through 222)) } ncs_group { reference = chain 'L' selection = chain 'd' selection = chain 'g' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.980 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: 0.040 Extract box with map and model: 0.880 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 29.990 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 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 : 0.010 0.231 35231 Z= 0.500 Angle : 1.156 49.058 48057 Z= 0.649 Chirality : 0.071 1.639 5582 Planarity : 0.008 0.164 6080 Dihedral : 16.708 89.552 12245 Min Nonbonded Distance : 1.041 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.71 % Allowed : 9.15 % Favored : 90.14 % Rotamer: Outliers : 7.89 % Allowed : 10.58 % Favored : 81.53 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.35 % 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: -3.13 (0.11), residues: 4250 helix: -2.21 (0.16), residues: 696 sheet: -1.49 (0.14), residues: 1222 loop : -2.40 (0.11), residues: 2332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B1039 TYR 0.038 0.003 TYR H 32 PHE 0.034 0.003 PHE d 71 TRP 0.025 0.003 TRP B 104 HIS 0.009 0.002 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.01026 / 0.49 (35118) covalent geometry : angle 1.03678 / 0.62 (47769) SS BOND : bond 0.02190 / 1.69 ( 51) SS BOND : angle 6.58848 / 4.54 ( 102) hydrogen bonds : bond 0.24085 / 15.73 ( 1213) hydrogen bonds : angle 8.82071 / 6.13 ( 3489) link_BETA1-4 : bond 0.04634 / 2.21 ( 18) link_BETA1-4 : angle 4.61329 / 3.11 ( 54) link_NAG-ASN : bond 0.04043 / 2.90 ( 44) link_NAG-ASN : angle 7.45422 / 4.72 ( 132) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 938 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 296 poor density : 642 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 ASP cc_start: 0.0880 (OUTLIER) cc_final: 0.0216 (t70) REVERT: A 976 VAL cc_start: 0.8973 (OUTLIER) cc_final: 0.8447 (m) REVERT: B 369 TYR cc_start: 0.5943 (t80) cc_final: 0.5496 (t80) REVERT: B 697 MET cc_start: 0.8827 (ptm) cc_final: 0.8486 (ptm) REVERT: C 95 THR cc_start: 0.6110 (OUTLIER) cc_final: 0.5829 (m) REVERT: C 158 ARG cc_start: 0.6466 (OUTLIER) cc_final: 0.5487 (tpt-90) REVERT: C 357 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.7704 (tpp-160) REVERT: C 567 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7864 (ptp-170) REVERT: C 786 LYS cc_start: 0.7562 (mtmt) cc_final: 0.7323 (mttm) REVERT: H 180 GLN cc_start: -0.1784 (mt0) cc_final: -0.2846 (tp40) REVERT: d 141 PRO cc_start: 0.5015 (Cg_exo) cc_final: 0.4767 (Cg_endo) REVERT: d 204 PRO cc_start: 0.2173 (Cg_exo) cc_final: 0.1921 (Cg_endo) REVERT: e 81 MET cc_start: 0.3621 (tmm) cc_final: 0.2934 (tpp) REVERT: g 54 LEU cc_start: 0.7990 (tp) cc_final: 0.7670 (mm) REVERT: g 83 PHE cc_start: 0.6353 (m-10) cc_final: 0.5974 (m-80) REVERT: g 140 TYR cc_start: 0.4841 (t80) cc_final: 0.4520 (t80) REVERT: h 72 ARG cc_start: 0.7261 (pmt-80) cc_final: 0.7032 (ptt90) REVERT: h 110 ASP cc_start: 0.6833 (p0) cc_final: 0.6313 (p0) outliers start: 296 outliers final: 54 residues processed: 874 average time/residue: 0.2018 time to fit residues: 284.3863 Evaluate side-chains 329 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 269 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 939 SER Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 9.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 10.0000 chunk 401 optimal weight: 7.9990 chunk 424 optimal weight: 20.0000 chunk 155 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN A 188 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN A 321 GLN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 ASN A 606 ASN A 641 ASN A 690 GLN ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN A 901 GLN A 914 ASN A 926 GLN A 969 ASN A 992 GLN A1010 GLN A1071 GLN A1101 HIS A1106 GLN B 134 GLN B 137 ASN B 188 ASN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN B 690 GLN B 703 ASN B 856 ASN B 901 GLN B 914 ASN B 926 GLN B 969 ASN B 992 GLN B1005 GLN C 66 HIS C 115 GLN C 188 ASN C 360 ASN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN C 501 ASN C 540 ASN C 563 GLN C 690 GLN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 913 GLN C 914 ASN C 919 ASN C 920 GLN C 926 GLN C 992 GLN C1054 GLN H 57 ASN d 37 GLN e 39 GLN e 57 ASN ** e 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 37 GLN h 1 GLN h 57 ASN h 208 ASN L 37 GLN Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.127934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.100866 restraints weight = 117470.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.092450 restraints weight = 150735.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.090915 restraints weight = 117877.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.088998 restraints weight = 104265.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.089337 restraints weight = 111397.876| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 35231 Z= 0.275 Angle : 0.892 14.098 48057 Z= 0.442 Chirality : 0.052 0.441 5582 Planarity : 0.006 0.115 6080 Dihedral : 7.364 66.899 4708 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.95 % Favored : 93.88 % Rotamer: Outliers : 4.50 % Allowed : 15.43 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.80 % Twisted General : 0.05 % 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: -1.96 (0.12), residues: 4250 helix: -0.30 (0.19), residues: 686 sheet: -0.92 (0.14), residues: 1272 loop : -1.86 (0.12), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 357 TYR 0.023 0.002 TYR A 789 PHE 0.027 0.002 PHE A 392 TRP 0.046 0.003 TRP d 35 HIS 0.011 0.002 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00631 / 0.27 (35118) covalent geometry : angle 0.86629 / 0.44 (47769) SS BOND : bond 0.00840 / 0.60 ( 51) SS BOND : angle 2.22282 / 1.62 ( 102) hydrogen bonds : bond 0.04654 / 3.07 ( 1213) hydrogen bonds : angle 6.50698 / 4.53 ( 3489) link_BETA1-4 : bond 0.00699 / 0.43 ( 18) link_BETA1-4 : angle 2.28840 / 1.54 ( 54) link_NAG-ASN : bond 0.00860 / 0.52 ( 44) link_NAG-ASN : angle 3.46424 / 2.28 ( 132) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 278 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 131 CYS cc_start: 0.0808 (OUTLIER) cc_final: -0.0460 (m) REVERT: A 902 MET cc_start: 0.9064 (tpp) cc_final: 0.8643 (tpt) REVERT: B 369 TYR cc_start: 0.6807 (t80) cc_final: 0.6556 (m-10) REVERT: C 167 THR cc_start: 0.2906 (OUTLIER) cc_final: 0.1690 (m) REVERT: H 153 ASP cc_start: 0.7149 (m-30) cc_final: 0.6911 (m-30) REVERT: H 180 GLN cc_start: -0.1053 (mt0) cc_final: -0.2759 (tp40) REVERT: d 116 PHE cc_start: 0.3558 (m-80) cc_final: 0.2507 (m-80) REVERT: e 36 TRP cc_start: 0.4370 (m100) cc_final: 0.3771 (m100) REVERT: e 81 MET cc_start: 0.1577 (tmm) cc_final: 0.1324 (tpp) REVERT: g 83 PHE cc_start: 0.7402 (m-10) cc_final: 0.6712 (m-80) REVERT: g 189 HIS cc_start: 0.7129 (m-70) cc_final: 0.6918 (m-70) REVERT: h 72 ARG cc_start: 0.7514 (pmt-80) cc_final: 0.6921 (ptt90) REVERT: h 110 ASP cc_start: 0.8119 (p0) cc_final: 0.7512 (p0) REVERT: h 111 TYR cc_start: 0.7859 (m-80) cc_final: 0.7285 (m-80) REVERT: h 154 TYR cc_start: 0.4761 (p90) cc_final: 0.4385 (p90) outliers start: 169 outliers final: 102 residues processed: 433 average time/residue: 0.1973 time to fit residues: 140.4158 Evaluate side-chains 313 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 209 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain d residue 27 GLN Chi-restraints excluded: chain e residue 11 VAL Chi-restraints excluded: chain e residue 50 TRP Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain g residue 75 ILE Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain g residue 94 TYR Chi-restraints excluded: chain g residue 138 ASN Chi-restraints excluded: chain h residue 93 VAL Chi-restraints excluded: chain L residue 52 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 221 optimal weight: 2.9990 chunk 382 optimal weight: 40.0000 chunk 63 optimal weight: 2.9990 chunk 350 optimal weight: 8.9990 chunk 134 optimal weight: 40.0000 chunk 427 optimal weight: 6.9990 chunk 154 optimal weight: 10.0000 chunk 236 optimal weight: 20.0000 chunk 409 optimal weight: 30.0000 chunk 379 optimal weight: 10.0000 chunk 112 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 ASN A 540 ASN A1088 HIS B 239 GLN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN B 450 ASN B 498 GLN B 580 GLN B 755 GLN B1011 GLN C 188 ASN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 655 HIS C 784 GLN C1071 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 38 GLN ** e 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 138 ASN ** h 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 62 GLN L 166 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.123201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.094499 restraints weight = 118409.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.088378 restraints weight = 141557.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.085443 restraints weight = 111906.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.083905 restraints weight = 115914.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.083728 restraints weight = 111935.104| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.5138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.136 35231 Z= 0.380 Angle : 0.916 16.788 48057 Z= 0.449 Chirality : 0.054 0.536 5582 Planarity : 0.006 0.105 6080 Dihedral : 6.868 63.818 4655 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.46 % Favored : 92.38 % Rotamer: Outliers : 5.84 % Allowed : 17.11 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.35 % Twisted General : 0.05 % 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: -1.78 (0.12), residues: 4250 helix: 0.22 (0.20), residues: 693 sheet: -0.73 (0.14), residues: 1338 loop : -1.96 (0.12), residues: 2219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 577 TYR 0.028 0.003 TYR A1067 PHE 0.027 0.003 PHE C 464 TRP 0.037 0.003 TRP h 163 HIS 0.040 0.003 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00880 / 0.38 (35118) covalent geometry : angle 0.89137 / 0.44 (47769) SS BOND : bond 0.00562 / 0.36 ( 51) SS BOND : angle 2.27920 / 1.68 ( 102) hydrogen bonds : bond 0.05213 / 3.42 ( 1213) hydrogen bonds : angle 6.30059 / 4.38 ( 3489) link_BETA1-4 : bond 0.00550 / 0.31 ( 18) link_BETA1-4 : angle 2.19248 / 1.42 ( 54) link_NAG-ASN : bond 0.00585 / 0.41 ( 44) link_NAG-ASN : angle 3.41189 / 2.22 ( 132) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 219 poor density : 212 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 TYR cc_start: 0.6759 (m-80) cc_final: 0.6537 (m-80) REVERT: A 902 MET cc_start: 0.9120 (tpp) cc_final: 0.8647 (tpt) REVERT: C 357 ARG cc_start: 0.8171 (tmt170) cc_final: 0.7651 (tpp-160) REVERT: H 153 ASP cc_start: 0.7134 (m-30) cc_final: 0.6930 (m-30) REVERT: H 180 GLN cc_start: -0.1098 (mt0) cc_final: -0.2814 (tp40) REVERT: g 83 PHE cc_start: 0.7682 (m-10) cc_final: 0.6957 (m-80) REVERT: g 87 TYR cc_start: 0.7379 (m-80) cc_final: 0.7034 (m-10) REVERT: g 140 TYR cc_start: 0.5438 (t80) cc_final: 0.5035 (t80) REVERT: h 13 LYS cc_start: 0.8445 (ptpp) cc_final: 0.7843 (mmtm) REVERT: h 32 TYR cc_start: 0.5772 (OUTLIER) cc_final: 0.2598 (t80) REVERT: h 110 ASP cc_start: 0.8106 (p0) cc_final: 0.7251 (p0) REVERT: h 111 TYR cc_start: 0.8051 (m-80) cc_final: 0.7245 (m-80) REVERT: h 153 ASP cc_start: 0.7697 (m-30) cc_final: 0.7083 (p0) REVERT: L 169 LYS cc_start: 0.7259 (pttm) cc_final: 0.6796 (tptp) REVERT: L 188 LYS cc_start: 0.4631 (pttt) cc_final: 0.3939 (mttt) outliers start: 219 outliers final: 138 residues processed: 410 average time/residue: 0.1801 time to fit residues: 124.4908 Evaluate side-chains 312 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 173 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 976 VAL 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 1116 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain d residue 27 GLN Chi-restraints excluded: chain d residue 94 TYR Chi-restraints excluded: chain e residue 11 VAL Chi-restraints excluded: chain e residue 50 TRP Chi-restraints excluded: chain e residue 174 THR Chi-restraints excluded: chain e residue 185 TYR Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain g residue 75 ILE Chi-restraints excluded: chain g residue 94 TYR Chi-restraints excluded: chain h residue 32 TYR Chi-restraints excluded: chain h residue 51 ILE Chi-restraints excluded: chain h residue 206 ASN Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 42 LYS Chi-restraints excluded: chain L residue 109 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 141 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 155 optimal weight: 4.9990 chunk 184 optimal weight: 4.9990 chunk 223 optimal weight: 4.9990 chunk 370 optimal weight: 10.0000 chunk 166 optimal weight: 3.9990 chunk 112 optimal weight: 9.9990 chunk 127 optimal weight: 5.9990 chunk 396 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN C 188 ASN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 914 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 38 GLN d 147 GLN ** e 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 208 ASN ** e 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 166 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.123905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.093913 restraints weight = 114996.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.087815 restraints weight = 142327.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.085103 restraints weight = 101935.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.083235 restraints weight = 123950.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.083721 restraints weight = 100560.908| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.5424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 35231 Z= 0.211 Angle : 0.750 16.037 48057 Z= 0.360 Chirality : 0.049 0.512 5582 Planarity : 0.005 0.096 6080 Dihedral : 6.216 63.727 4645 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.27 % Favored : 94.61 % Rotamer: Outliers : 4.80 % Allowed : 18.63 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.35 % Twisted General : 0.02 % 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: -1.46 (0.12), residues: 4250 helix: 0.80 (0.20), residues: 693 sheet: -0.61 (0.14), residues: 1315 loop : -1.80 (0.12), residues: 2242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 403 TYR 0.022 0.002 TYR A1067 PHE 0.026 0.002 PHE A 92 TRP 0.017 0.002 TRP h 163 HIS 0.007 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.21 (35118) covalent geometry : angle 0.72954 / 0.35 (47769) SS BOND : bond 0.00435 / 0.28 ( 51) SS BOND : angle 1.73244 / 1.28 ( 102) hydrogen bonds : bond 0.03928 / 2.59 ( 1213) hydrogen bonds : angle 5.88773 / 4.11 ( 3489) link_BETA1-4 : bond 0.00559 / 0.34 ( 18) link_BETA1-4 : angle 1.96653 / 1.30 ( 54) link_NAG-ASN : bond 0.00407 / 0.29 ( 44) link_NAG-ASN : angle 2.89412 / 1.87 ( 132) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 206 time to evaluate : 1.274 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: A 131 CYS cc_start: 0.1969 (OUTLIER) cc_final: 0.1669 (m) REVERT: A 902 MET cc_start: 0.9070 (tpp) cc_final: 0.8621 (tpt) REVERT: B 161 SER cc_start: 0.8368 (OUTLIER) cc_final: 0.7585 (p) REVERT: C 266 TYR cc_start: 0.7925 (OUTLIER) cc_final: 0.7398 (m-80) REVERT: C 455 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8381 (tp) REVERT: C 474 GLN cc_start: 0.7682 (mt0) cc_final: 0.7229 (tp40) REVERT: C 969 ASN cc_start: 0.8573 (OUTLIER) cc_final: 0.8372 (m110) REVERT: H 81 MET cc_start: 0.2406 (tpp) cc_final: 0.2001 (tpp) REVERT: H 153 ASP cc_start: 0.7096 (m-30) cc_final: 0.6888 (m-30) REVERT: H 180 GLN cc_start: -0.0800 (mt0) cc_final: -0.2751 (tp40) REVERT: d 55 GLU cc_start: 0.2812 (tt0) cc_final: 0.2492 (tt0) REVERT: e 32 TYR cc_start: 0.2330 (OUTLIER) cc_final: 0.1866 (t80) REVERT: e 110 ASP cc_start: 0.5829 (OUTLIER) cc_final: 0.4645 (p0) REVERT: g 87 TYR cc_start: 0.7573 (m-80) cc_final: 0.7074 (m-10) REVERT: h 13 LYS cc_start: 0.8442 (ptpp) cc_final: 0.7775 (mmtm) REVERT: h 32 TYR cc_start: 0.5685 (OUTLIER) cc_final: 0.2944 (t80) REVERT: h 72 ARG cc_start: 0.7896 (pmt-80) cc_final: 0.7495 (ppt170) REVERT: h 81 MET cc_start: 0.6629 (tmm) cc_final: 0.6224 (tmm) REVERT: L 42 LYS cc_start: 0.5318 (OUTLIER) cc_final: 0.4820 (ptmm) REVERT: L 94 TYR cc_start: 0.3001 (m-10) cc_final: 0.2191 (m-80) REVERT: L 169 LYS cc_start: 0.7302 (pttm) cc_final: 0.6795 (tptp) REVERT: L 188 LYS cc_start: 0.4564 (pttt) cc_final: 0.3879 (mttt) outliers start: 180 outliers final: 114 residues processed: 368 average time/residue: 0.1867 time to fit residues: 114.8249 Evaluate side-chains 302 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 179 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 963 VAL 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 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain d residue 27 GLN Chi-restraints excluded: chain d residue 52 SER Chi-restraints excluded: chain d residue 94 TYR Chi-restraints excluded: chain d residue 178 THR Chi-restraints excluded: chain e residue 32 TYR Chi-restraints excluded: chain e residue 35 HIS Chi-restraints excluded: chain e residue 50 TRP Chi-restraints excluded: chain e residue 110 ASP Chi-restraints excluded: chain e residue 174 THR Chi-restraints excluded: chain e residue 178 VAL Chi-restraints excluded: chain g residue 58 VAL Chi-restraints excluded: chain g residue 75 ILE Chi-restraints excluded: chain h residue 32 TYR Chi-restraints excluded: chain h residue 206 ASN Chi-restraints excluded: chain L residue 42 LYS Chi-restraints excluded: chain L residue 52 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 40 optimal weight: 0.9990 chunk 364 optimal weight: 9.9990 chunk 218 optimal weight: 5.9990 chunk 155 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 400 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 304 optimal weight: 0.7980 chunk 268 optimal weight: 3.9990 chunk 166 optimal weight: 0.7980 chunk 126 optimal weight: 8.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS B 409 GLN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.124098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.095638 restraints weight = 115123.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.087351 restraints weight = 133466.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.084526 restraints weight = 104257.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.083868 restraints weight = 94460.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.083862 restraints weight = 92504.733| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.5667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 35231 Z= 0.171 Angle : 0.703 15.730 48057 Z= 0.336 Chirality : 0.048 0.457 5582 Planarity : 0.005 0.099 6080 Dihedral : 5.802 64.536 4638 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.46 % Favored : 94.42 % Rotamer: Outliers : 4.69 % Allowed : 19.13 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.35 % 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: -1.20 (0.13), residues: 4250 helix: 1.19 (0.21), residues: 691 sheet: -0.52 (0.14), residues: 1337 loop : -1.65 (0.12), residues: 2222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG h 87 TYR 0.027 0.002 TYR g 94 PHE 0.017 0.002 PHE C 86 TRP 0.016 0.001 TRP H 50 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 (35118) covalent geometry : angle 0.68564 / 0.33 (47769) SS BOND : bond 0.00430 / 0.28 ( 51) SS BOND : angle 1.55135 / 1.12 ( 102) hydrogen bonds : bond 0.03645 / 2.40 ( 1213) hydrogen bonds : angle 5.61136 / 3.93 ( 3489) link_BETA1-4 : bond 0.00588 / 0.30 ( 18) link_BETA1-4 : angle 1.93408 / 1.28 ( 54) link_NAG-ASN : bond 0.00385 / 0.28 ( 44) link_NAG-ASN : angle 2.55268 / 1.67 ( 132) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 203 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8217 (mt) REVERT: A 386 LYS cc_start: 0.8884 (mttt) cc_final: 0.8597 (mmmt) REVERT: A 449 TYR cc_start: 0.6839 (m-80) cc_final: 0.6552 (m-80) REVERT: A 902 MET cc_start: 0.9068 (tpp) cc_final: 0.8716 (tpt) REVERT: B 585 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8841 (pp) REVERT: C 266 TYR cc_start: 0.7916 (OUTLIER) cc_final: 0.7392 (m-80) REVERT: C 358 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8221 (pt) REVERT: C 455 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.7941 (tp) REVERT: C 474 GLN cc_start: 0.7704 (mt0) cc_final: 0.7201 (tp40) REVERT: C 977 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8557 (tt) REVERT: H 81 MET cc_start: 0.2208 (tpp) cc_final: 0.1939 (tpp) REVERT: H 153 ASP cc_start: 0.7128 (m-30) cc_final: 0.6874 (m-30) REVERT: H 180 GLN cc_start: -0.0851 (mt0) cc_final: -0.2814 (tp40) REVERT: d 116 PHE cc_start: 0.3775 (m-80) cc_final: 0.2742 (m-80) REVERT: g 87 TYR cc_start: 0.7436 (m-80) cc_final: 0.6807 (m-10) REVERT: g 106 ILE cc_start: 0.5220 (mt) cc_final: 0.4866 (tp) REVERT: h 13 LYS cc_start: 0.8357 (ptpp) cc_final: 0.7662 (mmtm) REVERT: h 32 TYR cc_start: 0.5709 (OUTLIER) cc_final: 0.3161 (t80) REVERT: h 72 ARG cc_start: 0.7935 (pmt-80) cc_final: 0.7226 (ptt90) REVERT: h 108 TYR cc_start: 0.7161 (p90) cc_final: 0.6456 (p90) REVERT: L 42 LYS cc_start: 0.5307 (OUTLIER) cc_final: 0.4776 (ptmm) REVERT: L 94 TYR cc_start: 0.3299 (m-10) cc_final: 0.2547 (m-80) REVERT: L 169 LYS cc_start: 0.7302 (pttm) cc_final: 0.6835 (tptp) REVERT: L 188 LYS cc_start: 0.4672 (pttt) cc_final: 0.3853 (mttt) outliers start: 176 outliers final: 122 residues processed: 362 average time/residue: 0.1813 time to fit residues: 109.7122 Evaluate side-chains 317 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 187 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain d residue 21 ILE Chi-restraints excluded: chain d residue 27 GLN Chi-restraints excluded: chain d residue 94 TYR Chi-restraints excluded: chain d residue 178 THR Chi-restraints excluded: chain e residue 11 VAL Chi-restraints excluded: chain e residue 35 HIS Chi-restraints excluded: chain e residue 50 TRP Chi-restraints excluded: chain e residue 174 THR Chi-restraints excluded: chain e residue 178 VAL Chi-restraints excluded: chain g residue 58 VAL Chi-restraints excluded: chain g residue 75 ILE Chi-restraints excluded: chain g residue 94 TYR Chi-restraints excluded: chain h residue 18 VAL Chi-restraints excluded: chain h residue 32 TYR Chi-restraints excluded: chain h residue 206 ASN Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 42 LYS Chi-restraints excluded: chain L residue 52 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 214 optimal weight: 0.1980 chunk 363 optimal weight: 7.9990 chunk 17 optimal weight: 0.9980 chunk 399 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 184 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 275 optimal weight: 0.9980 chunk 293 optimal weight: 0.7980 chunk 403 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN B 675 GLN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.125084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.095718 restraints weight = 114895.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.089490 restraints weight = 145759.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.086390 restraints weight = 109179.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.085256 restraints weight = 120607.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.085638 restraints weight = 102088.920| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.5784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 35231 Z= 0.119 Angle : 0.665 15.808 48057 Z= 0.317 Chirality : 0.046 0.420 5582 Planarity : 0.005 0.101 6080 Dihedral : 5.451 61.618 4634 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.49 % Favored : 95.39 % Rotamer: Outliers : 3.73 % Allowed : 19.93 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.35 % 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: -0.99 (0.13), residues: 4250 helix: 1.41 (0.21), residues: 693 sheet: -0.37 (0.14), residues: 1358 loop : -1.55 (0.12), residues: 2199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG h 103 TYR 0.021 0.001 TYR H 60 PHE 0.027 0.001 PHE C 168 TRP 0.015 0.001 TRP H 50 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (35118) covalent geometry : angle 0.64860 / 0.31 (47769) SS BOND : bond 0.00566 / 0.33 ( 51) SS BOND : angle 1.62641 / 1.08 ( 102) hydrogen bonds : bond 0.03273 / 2.17 ( 1213) hydrogen bonds : angle 5.40056 / 3.78 ( 3489) link_BETA1-4 : bond 0.00625 / 0.32 ( 18) link_BETA1-4 : angle 1.89189 / 1.26 ( 54) link_NAG-ASN : bond 0.00359 / 0.27 ( 44) link_NAG-ASN : angle 2.31301 / 1.51 ( 132) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 211 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8877 (mttt) cc_final: 0.8580 (mmmt) REVERT: A 449 TYR cc_start: 0.6903 (m-80) cc_final: 0.6598 (m-80) REVERT: A 902 MET cc_start: 0.9010 (tpp) cc_final: 0.8704 (tpt) REVERT: B 161 SER cc_start: 0.8241 (OUTLIER) cc_final: 0.7429 (p) REVERT: B 585 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8822 (pp) REVERT: C 423 TYR cc_start: 0.8338 (t80) cc_final: 0.7747 (t80) REVERT: C 440 ASN cc_start: 0.8787 (OUTLIER) cc_final: 0.8245 (p0) REVERT: C 455 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7878 (tp) REVERT: C 474 GLN cc_start: 0.7724 (mt0) cc_final: 0.7162 (tp40) REVERT: C 740 MET cc_start: 0.8052 (tmm) cc_final: 0.7845 (tmm) REVERT: C 869 MET cc_start: 0.8685 (mtm) cc_final: 0.8412 (mtt) REVERT: H 48 MET cc_start: 0.6978 (mtp) cc_final: 0.6763 (ptp) REVERT: H 70 ILE cc_start: 0.0127 (OUTLIER) cc_final: -0.0865 (pt) REVERT: H 153 ASP cc_start: 0.7149 (m-30) cc_final: 0.6800 (m-30) REVERT: H 180 GLN cc_start: -0.0661 (mt0) cc_final: -0.2933 (tp40) REVERT: d 116 PHE cc_start: 0.3787 (m-80) cc_final: 0.2742 (m-80) REVERT: e 180 GLN cc_start: -0.3173 (mt0) cc_final: -0.4381 (tp40) REVERT: g 83 PHE cc_start: 0.7837 (m-10) cc_final: 0.7074 (m-80) REVERT: g 87 TYR cc_start: 0.7443 (m-80) cc_final: 0.6704 (m-10) REVERT: h 13 LYS cc_start: 0.8366 (ptpp) cc_final: 0.7700 (mmtm) REVERT: h 32 TYR cc_start: 0.5635 (OUTLIER) cc_final: 0.3168 (t80) REVERT: h 72 ARG cc_start: 0.7918 (pmt-80) cc_final: 0.7613 (ppt170) REVERT: L 42 LYS cc_start: 0.5319 (OUTLIER) cc_final: 0.4866 (ptmm) REVERT: L 94 TYR cc_start: 0.3295 (m-10) cc_final: 0.2602 (m-80) REVERT: L 169 LYS cc_start: 0.7291 (pttm) cc_final: 0.6898 (tptp) outliers start: 140 outliers final: 96 residues processed: 331 average time/residue: 0.1897 time to fit residues: 105.1467 Evaluate side-chains 292 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 189 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain d residue 21 ILE Chi-restraints excluded: chain d residue 94 TYR Chi-restraints excluded: chain d residue 178 THR Chi-restraints excluded: chain e residue 11 VAL Chi-restraints excluded: chain e residue 32 TYR Chi-restraints excluded: chain e residue 35 HIS Chi-restraints excluded: chain e residue 50 TRP Chi-restraints excluded: chain e residue 174 THR Chi-restraints excluded: chain g residue 75 ILE Chi-restraints excluded: chain g residue 94 TYR Chi-restraints excluded: chain h residue 18 VAL Chi-restraints excluded: chain h residue 32 TYR Chi-restraints excluded: chain h residue 51 ILE Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 42 LYS Chi-restraints excluded: chain L residue 52 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 85 optimal weight: 2.9990 chunk 359 optimal weight: 40.0000 chunk 40 optimal weight: 0.4980 chunk 394 optimal weight: 0.1980 chunk 416 optimal weight: 20.0000 chunk 378 optimal weight: 20.0000 chunk 284 optimal weight: 6.9990 chunk 233 optimal weight: 0.0000 chunk 224 optimal weight: 5.9990 chunk 300 optimal weight: 20.0000 chunk 144 optimal weight: 4.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 37 GLN ** g 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.124595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.096374 restraints weight = 115641.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.088009 restraints weight = 131913.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.085597 restraints weight = 99425.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.084209 restraints weight = 102618.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.084487 restraints weight = 97886.215| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.5951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 35231 Z= 0.140 Angle : 0.667 15.757 48057 Z= 0.317 Chirality : 0.046 0.409 5582 Planarity : 0.005 0.104 6080 Dihedral : 5.313 61.034 4632 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.04 % Favored : 94.85 % Rotamer: Outliers : 4.10 % Allowed : 19.98 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.35 % 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: -0.87 (0.13), residues: 4250 helix: 1.54 (0.21), residues: 693 sheet: -0.31 (0.14), residues: 1331 loop : -1.46 (0.12), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG h 87 TYR 0.022 0.001 TYR A 351 PHE 0.031 0.001 PHE C 456 TRP 0.016 0.001 TRP H 50 HIS 0.007 0.001 HIS g 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (35118) covalent geometry : angle 0.65160 / 0.31 (47769) SS BOND : bond 0.00441 / 0.27 ( 51) SS BOND : angle 1.53722 / 1.03 ( 102) hydrogen bonds : bond 0.03343 / 2.20 ( 1213) hydrogen bonds : angle 5.33563 / 3.73 ( 3489) link_BETA1-4 : bond 0.00578 / 0.30 ( 18) link_BETA1-4 : angle 1.86268 / 1.23 ( 54) link_NAG-ASN : bond 0.00344 / 0.26 ( 44) link_NAG-ASN : angle 2.26869 / 1.49 ( 132) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 204 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8235 (mt) REVERT: A 449 TYR cc_start: 0.6915 (m-80) cc_final: 0.6599 (m-80) REVERT: A 902 MET cc_start: 0.9025 (tpp) cc_final: 0.8815 (tpt) REVERT: B 161 SER cc_start: 0.8178 (OUTLIER) cc_final: 0.7350 (p) REVERT: B 585 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8862 (pp) REVERT: C 423 TYR cc_start: 0.8373 (t80) cc_final: 0.7702 (t80) REVERT: C 440 ASN cc_start: 0.8783 (OUTLIER) cc_final: 0.8270 (p0) REVERT: C 474 GLN cc_start: 0.7756 (mt0) cc_final: 0.7169 (tp40) REVERT: C 977 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8554 (tt) REVERT: H 70 ILE cc_start: 0.0061 (OUTLIER) cc_final: -0.0959 (pt) REVERT: H 81 MET cc_start: 0.2318 (tpp) cc_final: 0.1896 (tpp) REVERT: d 116 PHE cc_start: 0.3648 (m-80) cc_final: 0.2661 (m-80) REVERT: g 83 PHE cc_start: 0.7782 (m-10) cc_final: 0.7026 (m-80) REVERT: g 87 TYR cc_start: 0.7465 (m-80) cc_final: 0.6981 (m-10) REVERT: h 13 LYS cc_start: 0.8302 (ptpp) cc_final: 0.7618 (mmtm) REVERT: h 72 ARG cc_start: 0.7959 (pmt-80) cc_final: 0.7664 (ppt170) REVERT: h 87 ARG cc_start: 0.8224 (mtm-85) cc_final: 0.7984 (mpt90) REVERT: h 164 ASN cc_start: 0.7144 (m-40) cc_final: 0.6072 (t0) REVERT: L 42 LYS cc_start: 0.5338 (OUTLIER) cc_final: 0.4894 (ptmm) REVERT: L 91 TYR cc_start: 0.2745 (OUTLIER) cc_final: 0.1998 (p90) REVERT: L 94 TYR cc_start: 0.3327 (m-10) cc_final: 0.2678 (m-80) REVERT: L 169 LYS cc_start: 0.7232 (pttm) cc_final: 0.6906 (tptp) outliers start: 154 outliers final: 113 residues processed: 338 average time/residue: 0.1912 time to fit residues: 108.5120 Evaluate side-chains 308 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 187 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain d residue 21 ILE Chi-restraints excluded: chain d residue 94 TYR Chi-restraints excluded: chain d residue 163 VAL Chi-restraints excluded: chain d residue 178 THR Chi-restraints excluded: chain e residue 11 VAL Chi-restraints excluded: chain e residue 50 TRP Chi-restraints excluded: chain e residue 174 THR Chi-restraints excluded: chain e residue 178 VAL Chi-restraints excluded: chain g residue 75 ILE Chi-restraints excluded: chain g residue 94 TYR Chi-restraints excluded: chain h residue 18 VAL Chi-restraints excluded: chain h residue 51 ILE Chi-restraints excluded: chain h residue 170 SER Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 42 LYS Chi-restraints excluded: chain L residue 91 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 343 optimal weight: 10.0000 chunk 303 optimal weight: 40.0000 chunk 290 optimal weight: 0.9990 chunk 378 optimal weight: 30.0000 chunk 136 optimal weight: 20.0000 chunk 241 optimal weight: 20.0000 chunk 19 optimal weight: 7.9990 chunk 186 optimal weight: 2.9990 chunk 411 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 385 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN A 751 ASN B 245 HIS ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN B 675 GLN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 65 GLN ** e 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 6 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.121082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.091994 restraints weight = 117919.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.086218 restraints weight = 131542.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.082670 restraints weight = 105505.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.081914 restraints weight = 114729.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.082060 restraints weight = 101533.585| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.6446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.115 35231 Z= 0.346 Angle : 0.837 17.258 48057 Z= 0.403 Chirality : 0.052 0.497 5582 Planarity : 0.006 0.094 6080 Dihedral : 5.866 61.217 4632 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.25 % Favored : 92.61 % Rotamer: Outliers : 4.64 % Allowed : 20.09 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.35 % 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: -1.23 (0.13), residues: 4250 helix: 0.96 (0.20), residues: 707 sheet: -0.47 (0.14), residues: 1362 loop : -1.67 (0.13), residues: 2181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG d 24 TYR 0.027 0.002 TYR A1067 PHE 0.024 0.002 PHE C 133 TRP 0.031 0.002 TRP h 36 HIS 0.011 0.002 HIS e 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00805 / 0.35 (35118) covalent geometry : angle 0.81864 / 0.40 (47769) SS BOND : bond 0.00517 / 0.33 ( 51) SS BOND : angle 1.84176 / 1.27 ( 102) hydrogen bonds : bond 0.04585 / 2.99 ( 1213) hydrogen bonds : angle 5.78576 / 4.03 ( 3489) link_BETA1-4 : bond 0.00567 / 0.31 ( 18) link_BETA1-4 : angle 1.92199 / 1.25 ( 54) link_NAG-ASN : bond 0.00564 / 0.38 ( 44) link_NAG-ASN : angle 2.84771 / 1.91 ( 132) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 184 time to evaluate : 0.880 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 229 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8552 (mm) REVERT: A 449 TYR cc_start: 0.6817 (m-80) cc_final: 0.6566 (m-80) REVERT: B 161 SER cc_start: 0.8120 (OUTLIER) cc_final: 0.7303 (p) REVERT: B 515 PHE cc_start: 0.7438 (m-10) cc_final: 0.7015 (m-10) REVERT: B 585 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8827 (pp) REVERT: C 357 ARG cc_start: 0.8058 (tmt170) cc_final: 0.7548 (tpp-160) REVERT: C 440 ASN cc_start: 0.8926 (OUTLIER) cc_final: 0.8407 (p0) REVERT: C 660 TYR cc_start: 0.8632 (OUTLIER) cc_final: 0.8256 (m-10) REVERT: H 70 ILE cc_start: 0.0304 (OUTLIER) cc_final: -0.0682 (pt) REVERT: H 180 GLN cc_start: -0.0937 (mt0) cc_final: -0.2796 (tp40) REVERT: d 91 TYR cc_start: 0.0189 (OUTLIER) cc_final: -0.0470 (p90) REVERT: e 13 LYS cc_start: 0.3393 (mmpt) cc_final: 0.3178 (mmmt) REVERT: g 87 TYR cc_start: 0.7467 (m-80) cc_final: 0.6928 (m-10) REVERT: h 13 LYS cc_start: 0.8301 (ptpp) cc_final: 0.7602 (mmtm) REVERT: h 32 TYR cc_start: 0.6020 (OUTLIER) cc_final: 0.3182 (t80) REVERT: h 72 ARG cc_start: 0.8087 (pmt-80) cc_final: 0.7809 (ppt170) REVERT: h 164 ASN cc_start: 0.7308 (m-40) cc_final: 0.6273 (t0) REVERT: L 42 LYS cc_start: 0.5322 (OUTLIER) cc_final: 0.4814 (ptmm) REVERT: L 91 TYR cc_start: 0.2980 (OUTLIER) cc_final: 0.2195 (p90) REVERT: L 94 TYR cc_start: 0.3282 (OUTLIER) cc_final: 0.2877 (m-80) REVERT: L 169 LYS cc_start: 0.7262 (pttm) cc_final: 0.7023 (tptp) REVERT: L 188 LYS cc_start: 0.4275 (pttt) cc_final: 0.3392 (mttt) outliers start: 174 outliers final: 135 residues processed: 341 average time/residue: 0.1906 time to fit residues: 109.2174 Evaluate side-chains 311 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 165 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain d residue 21 ILE Chi-restraints excluded: chain d residue 91 TYR Chi-restraints excluded: chain d residue 163 VAL Chi-restraints excluded: chain d residue 178 THR Chi-restraints excluded: chain e residue 11 VAL Chi-restraints excluded: chain e residue 50 TRP Chi-restraints excluded: chain e residue 174 THR Chi-restraints excluded: chain e residue 178 VAL Chi-restraints excluded: chain g residue 58 VAL Chi-restraints excluded: chain g residue 75 ILE Chi-restraints excluded: chain h residue 18 VAL Chi-restraints excluded: chain h residue 32 TYR Chi-restraints excluded: chain h residue 51 ILE Chi-restraints excluded: chain h residue 170 SER Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 42 LYS Chi-restraints excluded: chain L residue 91 TYR Chi-restraints excluded: chain L residue 94 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 217 optimal weight: 6.9990 chunk 199 optimal weight: 5.9990 chunk 18 optimal weight: 0.0980 chunk 15 optimal weight: 0.9980 chunk 301 optimal weight: 4.9990 chunk 420 optimal weight: 5.9990 chunk 428 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 321 optimal weight: 0.6980 chunk 355 optimal weight: 2.9990 chunk 303 optimal weight: 30.0000 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 166 GLN ** g 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.123227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.094741 restraints weight = 117349.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.088266 restraints weight = 128083.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.085016 restraints weight = 100784.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.083810 restraints weight = 100355.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.084134 restraints weight = 89946.606| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.6506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 35231 Z= 0.146 Angle : 0.703 16.696 48057 Z= 0.334 Chirality : 0.047 0.452 5582 Planarity : 0.005 0.094 6080 Dihedral : 5.521 65.049 4632 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.56 % Favored : 95.32 % Rotamer: Outliers : 3.73 % Allowed : 21.16 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.35 % Twisted General : 0.02 % 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: -1.00 (0.13), residues: 4250 helix: 1.31 (0.20), residues: 707 sheet: -0.36 (0.14), residues: 1352 loop : -1.55 (0.13), residues: 2191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG g 142 TYR 0.038 0.002 TYR d 94 PHE 0.020 0.001 PHE C 168 TRP 0.024 0.002 TRP h 36 HIS 0.007 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (35118) covalent geometry : angle 0.68760 / 0.33 (47769) SS BOND : bond 0.00472 / 0.31 ( 51) SS BOND : angle 1.58004 / 1.13 ( 102) hydrogen bonds : bond 0.03606 / 2.37 ( 1213) hydrogen bonds : angle 5.43596 / 3.80 ( 3489) link_BETA1-4 : bond 0.00570 / 0.29 ( 18) link_BETA1-4 : angle 1.78076 / 1.19 ( 54) link_NAG-ASN : bond 0.00367 / 0.28 ( 44) link_NAG-ASN : angle 2.38848 / 1.58 ( 132) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 183 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8151 (mt) REVERT: A 449 TYR cc_start: 0.6894 (m-80) cc_final: 0.6599 (m-80) REVERT: B 161 SER cc_start: 0.8125 (OUTLIER) cc_final: 0.7312 (p) REVERT: B 585 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8854 (pp) REVERT: C 440 ASN cc_start: 0.8852 (OUTLIER) cc_final: 0.8359 (p0) REVERT: H 70 ILE cc_start: 0.0061 (OUTLIER) cc_final: -0.1023 (pt) REVERT: H 180 GLN cc_start: -0.0823 (mt0) cc_final: -0.2728 (tp40) REVERT: d 91 TYR cc_start: 0.0203 (OUTLIER) cc_final: -0.0475 (p90) REVERT: d 116 PHE cc_start: 0.3574 (m-80) cc_final: 0.2672 (m-80) REVERT: e 13 LYS cc_start: 0.3423 (mmpt) cc_final: 0.3217 (mmmt) REVERT: g 87 TYR cc_start: 0.7522 (m-80) cc_final: 0.6923 (m-10) REVERT: h 13 LYS cc_start: 0.8343 (ptpp) cc_final: 0.7621 (mmtm) REVERT: h 32 TYR cc_start: 0.5908 (OUTLIER) cc_final: 0.3116 (t80) REVERT: h 72 ARG cc_start: 0.8056 (pmt-80) cc_final: 0.7800 (ppt170) REVERT: h 87 ARG cc_start: 0.8308 (mtm-85) cc_final: 0.7906 (mpt90) REVERT: h 164 ASN cc_start: 0.7312 (m-40) cc_final: 0.6807 (m-40) REVERT: L 42 LYS cc_start: 0.5437 (OUTLIER) cc_final: 0.4922 (ptmm) REVERT: L 94 TYR cc_start: 0.3478 (OUTLIER) cc_final: 0.3086 (m-80) REVERT: L 188 LYS cc_start: 0.4139 (pttt) cc_final: 0.3257 (mttt) outliers start: 140 outliers final: 113 residues processed: 309 average time/residue: 0.1934 time to fit residues: 100.9391 Evaluate side-chains 292 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 170 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain d residue 21 ILE Chi-restraints excluded: chain d residue 91 TYR Chi-restraints excluded: chain d residue 163 VAL Chi-restraints excluded: chain d residue 178 THR Chi-restraints excluded: chain e residue 11 VAL Chi-restraints excluded: chain e residue 32 TYR Chi-restraints excluded: chain e residue 50 TRP Chi-restraints excluded: chain e residue 174 THR Chi-restraints excluded: chain g residue 58 VAL Chi-restraints excluded: chain g residue 75 ILE Chi-restraints excluded: chain h residue 18 VAL Chi-restraints excluded: chain h residue 32 TYR Chi-restraints excluded: chain h residue 51 ILE Chi-restraints excluded: chain h residue 206 ASN Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 42 LYS Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 91 TYR Chi-restraints excluded: chain L residue 94 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 167 optimal weight: 2.9990 chunk 304 optimal weight: 9.9990 chunk 428 optimal weight: 7.9990 chunk 67 optimal weight: 0.5980 chunk 320 optimal weight: 20.0000 chunk 256 optimal weight: 2.9990 chunk 423 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 299 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 chunk 351 optimal weight: 20.0000 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.122497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.093822 restraints weight = 118178.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.086151 restraints weight = 131720.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.083403 restraints weight = 108929.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.082447 restraints weight = 107991.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.082756 restraints weight = 93390.216| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.6656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 35231 Z= 0.197 Angle : 0.715 16.679 48057 Z= 0.340 Chirality : 0.048 0.442 5582 Planarity : 0.005 0.110 6080 Dihedral : 5.466 62.025 4632 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.09 % Favored : 93.79 % Rotamer: Outliers : 3.70 % Allowed : 21.50 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.35 % Twisted General : 0.02 % 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: -1.01 (0.13), residues: 4250 helix: 1.37 (0.20), residues: 709 sheet: -0.38 (0.14), residues: 1352 loop : -1.58 (0.13), residues: 2189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG h 103 TYR 0.023 0.002 TYR A1067 PHE 0.031 0.002 PHE B 392 TRP 0.019 0.002 TRP h 36 HIS 0.014 0.001 HIS g 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.20 (35118) covalent geometry : angle 0.69976 / 0.34 (47769) SS BOND : bond 0.00444 / 0.29 ( 51) SS BOND : angle 1.61838 / 1.15 ( 102) hydrogen bonds : bond 0.03706 / 2.43 ( 1213) hydrogen bonds : angle 5.40580 / 3.77 ( 3489) link_BETA1-4 : bond 0.00555 / 0.29 ( 18) link_BETA1-4 : angle 1.77889 / 1.17 ( 54) link_NAG-ASN : bond 0.00372 / 0.28 ( 44) link_NAG-ASN : angle 2.39936 / 1.59 ( 132) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 170 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8289 (mt) REVERT: A 386 LYS cc_start: 0.8879 (mttt) cc_final: 0.8514 (mmmt) REVERT: A 449 TYR cc_start: 0.6957 (m-80) cc_final: 0.6641 (m-80) REVERT: B 161 SER cc_start: 0.8186 (OUTLIER) cc_final: 0.7402 (p) REVERT: B 585 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8847 (pp) REVERT: C 440 ASN cc_start: 0.8867 (OUTLIER) cc_final: 0.8356 (p0) REVERT: H 70 ILE cc_start: 0.0132 (OUTLIER) cc_final: -0.0818 (pt) REVERT: d 91 TYR cc_start: -0.0003 (OUTLIER) cc_final: -0.0690 (p90) REVERT: d 116 PHE cc_start: 0.3620 (m-80) cc_final: 0.2697 (m-80) REVERT: g 87 TYR cc_start: 0.7506 (m-80) cc_final: 0.6760 (m-10) REVERT: h 13 LYS cc_start: 0.8342 (ptpp) cc_final: 0.7613 (mmtm) REVERT: h 32 TYR cc_start: 0.5797 (OUTLIER) cc_final: 0.3337 (t80) REVERT: h 72 ARG cc_start: 0.8093 (pmt-80) cc_final: 0.7867 (ppt170) REVERT: h 164 ASN cc_start: 0.7367 (m-40) cc_final: 0.6948 (m-40) REVERT: L 42 LYS cc_start: 0.5503 (OUTLIER) cc_final: 0.5024 (ptmm) REVERT: L 94 TYR cc_start: 0.3774 (OUTLIER) cc_final: 0.3449 (m-80) REVERT: L 188 LYS cc_start: 0.3983 (pttt) cc_final: 0.3130 (mttt) outliers start: 139 outliers final: 118 residues processed: 295 average time/residue: 0.1957 time to fit residues: 98.3702 Evaluate side-chains 290 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 163 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain d residue 21 ILE Chi-restraints excluded: chain d residue 91 TYR Chi-restraints excluded: chain d residue 163 VAL Chi-restraints excluded: chain d residue 178 THR Chi-restraints excluded: chain e residue 11 VAL Chi-restraints excluded: chain e residue 32 TYR Chi-restraints excluded: chain e residue 50 TRP Chi-restraints excluded: chain e residue 174 THR Chi-restraints excluded: chain e residue 178 VAL Chi-restraints excluded: chain g residue 58 VAL Chi-restraints excluded: chain g residue 75 ILE Chi-restraints excluded: chain h residue 18 VAL Chi-restraints excluded: chain h residue 32 TYR Chi-restraints excluded: chain h residue 51 ILE Chi-restraints excluded: chain h residue 109 PHE Chi-restraints excluded: chain h residue 206 ASN Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 42 LYS Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 91 TYR Chi-restraints excluded: chain L residue 94 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 322 optimal weight: 9.9990 chunk 135 optimal weight: 30.0000 chunk 77 optimal weight: 0.1980 chunk 379 optimal weight: 0.7980 chunk 229 optimal weight: 6.9990 chunk 302 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 397 optimal weight: 7.9990 chunk 36 optimal weight: 0.0270 chunk 305 optimal weight: 6.9990 chunk 133 optimal weight: 30.0000 overall best weight: 1.2042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN B 207 HIS ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 27 GLN ** e 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.123890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.096245 restraints weight = 117249.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.088719 restraints weight = 129700.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.085337 restraints weight = 106288.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.083756 restraints weight = 116970.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.084245 restraints weight = 100210.599| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.6723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 35231 Z= 0.123 Angle : 0.667 16.581 48057 Z= 0.316 Chirality : 0.046 0.390 5582 Planarity : 0.005 0.110 6080 Dihedral : 5.191 61.361 4632 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.54 % Favored : 95.34 % Rotamer: Outliers : 3.25 % Allowed : 21.90 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.35 % Twisted General : 0.02 % 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 (0.13), residues: 4250 helix: 1.51 (0.20), residues: 712 sheet: -0.21 (0.14), residues: 1317 loop : -1.45 (0.13), residues: 2221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG h 103 TYR 0.027 0.001 TYR B 396 PHE 0.023 0.001 PHE B 515 TRP 0.021 0.002 TRP h 36 HIS 0.008 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (35118) covalent geometry : angle 0.65331 / 0.31 (47769) SS BOND : bond 0.00411 / 0.27 ( 51) SS BOND : angle 1.39543 / 0.97 ( 102) hydrogen bonds : bond 0.03225 / 2.13 ( 1213) hydrogen bonds : angle 5.19769 / 3.64 ( 3489) link_BETA1-4 : bond 0.00568 / 0.30 ( 18) link_BETA1-4 : angle 1.73803 / 1.16 ( 54) link_NAG-ASN : bond 0.00341 / 0.26 ( 44) link_NAG-ASN : angle 2.14498 / 1.41 ( 132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6499.46 seconds wall clock time: 112 minutes 50.31 seconds (6770.31 seconds total)