Starting phenix.real_space_refine on Sun Jul 5 20:25:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8gtp_34261/07_2026/8gtp_34261.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gtp_34261/07_2026/8gtp_34261.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8gtp_34261/07_2026/8gtp_34261.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gtp_34261/07_2026/8gtp_34261.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8gtp_34261/07_2026/8gtp_34261.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8gtp_34261/07_2026/8gtp_34261.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gtp_34261/07_2026/8gtp_34261.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gtp_34261/07_2026/8gtp_34261.map" } resolution = 3.1 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= 0.004 sd= 0.107 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 132 5.16 5 C 19257 2.51 5 N 4959 2.21 5 O 5901 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30249 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 8043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 8043 Classifications: {'peptide': 1025} Link IDs: {'PTRANS': 56, 'TRANS': 968} Chain breaks: 8 Chain: "B" Number of atoms: 8043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 8043 Classifications: {'peptide': 1025} Link IDs: {'PTRANS': 56, 'TRANS': 968} Chain breaks: 8 Chain: "C" Number of atoms: 8043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 8043 Classifications: {'peptide': 1025} Link IDs: {'PTRANS': 56, 'TRANS': 968} Chain breaks: 8 Chain: "H" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 902 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 114} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "L" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 816 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 8, 'TRANS': 102} Chain: "I" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 902 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 114} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "M" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 816 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 8, 'TRANS': 102} Chain: "J" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 902 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 114} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "N" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 816 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 8, 'TRANS': 102} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" 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 Chain: "B" 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 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: 6.80, per 1000 atoms: 0.22 Number of scatterers: 30249 At special positions: 0 Unit cell: (134.625, 178.782, 224.016, 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 132 16.00 O 5901 8.00 N 4959 7.00 C 19257 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.08 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.87 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.02 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.20 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=1.99 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.50 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.26 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=1.97 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.17 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.10 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.08 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.66 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.02 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=1.80 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=1.99 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.51 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.26 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=1.97 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.17 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.10 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.08 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.10 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.02 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=1.89 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=1.98 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.74 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.26 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=1.97 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.17 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.10 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " distance=2.17 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 95 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 89 " distance=2.17 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 95 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 89 " distance=2.17 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 A1410 " - " NAG A1411 " " NAG B1410 " - " NAG B1411 " " NAG C1410 " - " NAG C1411 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG K 1 " - " NAG K 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 165 " " NAG A1404 " - " ASN A 234 " " NAG A1405 " - " ASN A 282 " " NAG A1406 " - " ASN A 603 " " NAG A1407 " - " ASN A 616 " " NAG A1408 " - " ASN A 657 " " NAG A1409 " - " ASN A 709 " " NAG A1410 " - " ASN A1074 " " 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 B1410 " - " ASN B1074 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 122 " " NAG C1403 " - " ASN C 165 " " NAG C1404 " - " ASN C 234 " " NAG C1405 " - " ASN C 282 " " NAG C1406 " - " ASN C 603 " " NAG C1407 " - " ASN C 616 " " NAG C1408 " - " ASN C 657 " " NAG C1409 " - " ASN C 709 " " NAG C1410 " - " ASN C1074 " " NAG D 1 " - " ASN A 331 " " NAG E 1 " - " ASN A 343 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1098 " " NAG O 1 " - " ASN A1134 " " NAG P 1 " - " ASN B 331 " " NAG Q 1 " - " ASN B 343 " " NAG R 1 " - " ASN B 717 " " NAG S 1 " - " ASN B 801 " " NAG T 1 " - " ASN B1098 " " NAG U 1 " - " ASN B1134 " " NAG V 1 " - " ASN C 331 " " NAG W 1 " - " ASN C 343 " " NAG X 1 " - " ASN C 717 " " NAG Y 1 " - " ASN C 801 " " NAG Z 1 " - " ASN C1098 " " NAG a 1 " - " ASN C1134 " Time building additional restraints: 2.79 Conformation dependent library (CDL) restraints added in 1.3 seconds 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6984 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 61 sheets defined 18.8% alpha, 31.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 295 through 304 Processing helix chain 'A' and resid 337 through 342 removed outlier: 4.352A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.918A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.653A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 747 through 754 removed outlier: 4.087A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.874A 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: 3.986A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 823 removed outlier: 3.589A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.514A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.577A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.652A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.590A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 removed outlier: 4.080A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.757A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 983 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.324A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.953A pdb=" N GLU B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 342 removed outlier: 3.831A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 3.919A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.654A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 754 removed outlier: 4.089A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.986A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 removed outlier: 3.590A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.514A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.577A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.651A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.591A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 4.078A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.757A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 988 through 1033 removed outlier: 4.288A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.719A pdb=" N GLU C 298 " --> pdb=" O ASP C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 342 removed outlier: 4.351A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.919A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.654A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 747 through 754 removed outlier: 4.088A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.985A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 823 removed outlier: 3.591A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.515A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.577A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.651A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.592A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 4.078A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.757A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 983 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.322A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 3.535A 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 28 through 32 removed outlier: 3.682A pdb=" N SER H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N HIS H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.507A pdb=" N ARG H 64 " --> pdb=" O GLN H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.682A pdb=" N SER I 31 " --> pdb=" O THR I 28 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N HIS I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 28 through 32' Processing helix chain 'I' and resid 61 through 64 removed outlier: 3.506A pdb=" N ARG I 64 " --> pdb=" O GLN I 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 61 through 64' Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.683A pdb=" N SER J 31 " --> pdb=" O THR J 28 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N HIS J 32 " --> pdb=" O PHE J 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 28 through 32' Processing helix chain 'J' and resid 61 through 64 removed outlier: 3.506A pdb=" N ARG J 64 " --> pdb=" O GLN J 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 61 through 64' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.701A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.815A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN C 542 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG C 328 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.012A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.503A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN A 164 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.503A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 310 through 318 removed outlier: 4.554A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN A 613 " --> pdb=" O GLY A 594 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER A 596 " --> pdb=" O LEU A 611 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU A 611 " --> pdb=" O SER A 596 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.547A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 391 through 392 removed outlier: 3.576A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.694A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 538 through 543 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.956A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 702 through 704 removed outlier: 3.868A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.151A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.151A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.499A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.666A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.945A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.701A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.011A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.503A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN B 164 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.503A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 310 through 314 removed outlier: 4.079A pdb=" N SER B 596 " --> pdb=" O LEU B 611 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU B 611 " --> pdb=" O SER B 596 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 327 through 328 removed outlier: 5.615A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.546A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.695A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.024A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.748A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.150A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.150A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.499A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.944A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.701A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.011A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.502A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASN C 164 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.502A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.632A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N SER C 596 " --> pdb=" O LEU C 611 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU C 611 " --> pdb=" O SER C 596 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.546A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.694A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.820A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 7.151A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 removed outlier: 7.151A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.498A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.945A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.555A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.360A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 9 through 11 removed outlier: 3.696A pdb=" N VAL L 49 " --> pdb=" O TRP L 36 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 9 through 11 Processing sheet with id=AF6, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AF7, first strand: chain 'I' and resid 3 through 5 removed outlier: 3.555A pdb=" N GLN I 3 " --> pdb=" O SER I 25 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 57 through 59 removed outlier: 6.360A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE I 34 " --> pdb=" O ILE I 50 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'M' and resid 9 through 11 removed outlier: 3.696A pdb=" N VAL M 49 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N GLN M 38 " --> pdb=" O LEU M 47 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LEU M 47 " --> pdb=" O GLN M 38 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'M' and resid 9 through 11 Processing sheet with id=AG2, first strand: chain 'M' and resid 17 through 23 Processing sheet with id=AG3, first strand: chain 'J' and resid 3 through 5 removed outlier: 3.555A pdb=" N GLN J 3 " --> pdb=" O SER J 25 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'J' and resid 57 through 59 removed outlier: 6.360A pdb=" N TRP J 36 " --> pdb=" O MET J 48 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE J 34 " --> pdb=" O ILE J 50 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'N' and resid 9 through 11 removed outlier: 3.696A pdb=" N VAL N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N GLN N 38 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LEU N 47 " --> pdb=" O GLN N 38 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'N' and resid 9 through 11 Processing sheet with id=AG7, first strand: chain 'N' and resid 17 through 23 1103 hydrogen bonds defined for protein. 2958 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.98 Time building geometry restraints manager: 3.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5136 1.32 - 1.44: 8634 1.44 - 1.57: 17021 1.57 - 1.69: 1 1.69 - 1.81: 171 Bond restraints: 30963 Sorted by residual: bond pdb=" N PRO B 561 " pdb=" CD PRO B 561 " ideal model delta sigma weight residual 1.473 1.539 -0.066 1.40e-02 5.10e+03 2.22e+01 bond pdb=" C PHE C 329 " pdb=" N PRO C 330 " ideal model delta sigma weight residual 1.329 1.388 -0.058 1.25e-02 6.40e+03 2.17e+01 bond pdb=" N PRO C 561 " pdb=" CD PRO C 561 " ideal model delta sigma weight residual 1.473 1.538 -0.065 1.40e-02 5.10e+03 2.17e+01 bond pdb=" C ILE C 664 " pdb=" N PRO C 665 " ideal model delta sigma weight residual 1.331 1.387 -0.055 1.20e-02 6.94e+03 2.14e+01 bond pdb=" C ILE A 664 " pdb=" N PRO A 665 " ideal model delta sigma weight residual 1.331 1.386 -0.055 1.20e-02 6.94e+03 2.11e+01 ... (remaining 30958 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 40987 2.74 - 5.48: 994 5.48 - 8.22: 118 8.22 - 10.96: 29 10.96 - 13.70: 16 Bond angle restraints: 42144 Sorted by residual: angle pdb=" N LYS A 310 " pdb=" CA LYS A 310 " pdb=" C LYS A 310 " ideal model delta sigma weight residual 109.15 120.36 -11.21 1.44e+00 4.82e-01 6.06e+01 angle pdb=" N PHE A 559 " pdb=" CA PHE A 559 " pdb=" C PHE A 559 " ideal model delta sigma weight residual 110.32 98.17 12.15 1.59e+00 3.96e-01 5.84e+01 angle pdb=" N PHE C 338 " pdb=" CA PHE C 338 " pdb=" C PHE C 338 " ideal model delta sigma weight residual 111.40 102.37 9.03 1.22e+00 6.72e-01 5.48e+01 angle pdb=" N PHE A 338 " pdb=" CA PHE A 338 " pdb=" C PHE A 338 " ideal model delta sigma weight residual 111.40 102.46 8.94 1.22e+00 6.72e-01 5.37e+01 angle pdb=" N LEU A 560 " pdb=" CA LEU A 560 " pdb=" C LEU A 560 " ideal model delta sigma weight residual 110.40 100.89 9.51 1.31e+00 5.83e-01 5.28e+01 ... (remaining 42139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 16082 17.92 - 35.84: 1292 35.84 - 53.76: 313 53.76 - 71.68: 69 71.68 - 89.60: 37 Dihedral angle restraints: 17793 sinusoidal: 6900 harmonic: 10893 Sorted by residual: dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual 93.00 14.84 78.16 1 1.00e+01 1.00e-02 7.63e+01 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual 93.00 170.54 -77.54 1 1.00e+01 1.00e-02 7.53e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual 93.00 20.28 72.72 1 1.00e+01 1.00e-02 6.75e+01 ... (remaining 17790 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.296: 4896 0.296 - 0.592: 11 0.592 - 0.888: 4 0.888 - 1.183: 2 1.183 - 1.479: 1 Chirality restraints: 4914 Sorted by residual: chirality pdb=" C1 NAG A1411 " pdb=" O4 NAG A1410 " pdb=" C2 NAG A1411 " pdb=" O5 NAG A1411 " both_signs ideal model delta sigma weight residual False -2.40 -3.09 0.69 2.00e-02 2.50e+03 1.19e+03 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 -3.09 0.69 2.00e-02 2.50e+03 1.18e+03 chirality pdb=" C1 NAG B1411 " pdb=" O4 NAG B1410 " pdb=" C2 NAG B1411 " pdb=" O5 NAG B1411 " both_signs ideal model delta sigma weight residual False -2.40 -3.09 0.69 2.00e-02 2.50e+03 1.17e+03 ... (remaining 4911 not shown) Planarity restraints: 5406 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " 0.099 2.00e-02 2.50e+03 4.03e-01 2.03e+03 pdb=" CG ASN A 331 " -0.118 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " 0.235 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " -0.703 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " 0.488 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " 0.104 2.00e-02 2.50e+03 1.25e-01 1.94e+02 pdb=" CG ASN C 331 " -0.039 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " -0.213 2.00e-02 2.50e+03 pdb=" C1 NAG V 1 " 0.142 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 331 " 0.051 2.00e-02 2.50e+03 9.28e-02 1.08e+02 pdb=" CG ASN B 331 " -0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN B 331 " 0.037 2.00e-02 2.50e+03 pdb=" ND2 ASN B 331 " -0.167 2.00e-02 2.50e+03 pdb=" C1 NAG P 1 " 0.103 2.00e-02 2.50e+03 ... (remaining 5403 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 250 2.51 - 3.11: 21951 3.11 - 3.70: 42673 3.70 - 4.30: 62688 4.30 - 4.90: 104496 Nonbonded interactions: 232058 Sorted by model distance: nonbonded pdb=" O SER B 530 " pdb=" OG1 THR B 531 " model vdw 1.912 3.040 nonbonded pdb=" O ASN B 603 " pdb=" OG1 THR B 604 " model vdw 1.915 3.040 nonbonded pdb=" O ALA A 522 " pdb=" OG1 THR A 523 " model vdw 1.972 3.040 nonbonded pdb=" O ILE B 332 " pdb=" CG2 THR B 333 " model vdw 1.978 3.460 nonbonded pdb=" O ASN B 856 " pdb=" ND2 ASN B 856 " model vdw 1.986 3.120 ... (remaining 232053 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'K' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 30.340 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.840 31077 Z= 0.685 Angle : 1.467 48.987 42441 Z= 0.764 Chirality : 0.078 1.479 4914 Planarity : 0.007 0.119 5358 Dihedral : 14.336 89.599 10674 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 2.73 % Allowed : 7.81 % Favored : 89.47 % Rotamer: Outliers : 4.36 % Allowed : 9.05 % Favored : 86.59 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.18 (0.12), residues: 3702 helix: -1.30 (0.17), residues: 662 sheet: -1.48 (0.15), residues: 987 loop : -2.80 (0.11), residues: 2053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 102 TYR 0.024 0.002 TYR B 453 PHE 0.025 0.002 PHE A 400 TRP 0.016 0.002 TRP J 36 HIS 0.005 0.001 HIS C 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00913 / 0.51 (30963) covalent geometry : angle 1.08887 / 0.64 (42144) SS BOND : bond 0.23536 / 16.94 ( 45) SS BOND : angle 16.60861 / 11.59 ( 90) hydrogen bonds : bond 0.20238 / 12.84 ( 1025) hydrogen bonds : angle 8.04542 / 5.40 ( 2958) link_BETA1-4 : bond 0.07399 / 5.04 ( 21) link_BETA1-4 : angle 6.06221 / 4.06 ( 63) link_NAG-ASN : bond 0.02854 / 1.94 ( 48) link_NAG-ASN : angle 9.95953 / 6.05 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 586 time to evaluate : 1.113 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 314 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7604 (tt0) REVERT: A 382 VAL cc_start: 0.9216 (OUTLIER) cc_final: 0.9005 (m) REVERT: A 580 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.8386 (pt0) REVERT: A 675 GLN cc_start: 0.7419 (OUTLIER) cc_final: 0.6387 (mp10) REVERT: A 856 ASN cc_start: 0.8591 (OUTLIER) cc_final: 0.8383 (p0) REVERT: C 321 GLN cc_start: 0.7781 (OUTLIER) cc_final: 0.7364 (mm110) REVERT: C 529 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7296 (tptp) REVERT: C 690 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.7556 (mm110) REVERT: H 22 CYS cc_start: 0.0196 (t) cc_final: -0.0908 (t) REVERT: H 80 MET cc_start: 0.3888 (tmm) cc_final: 0.2973 (tmm) REVERT: L 92 TRP cc_start: 0.6705 (t-100) cc_final: 0.5950 (t-100) outliers start: 141 outliers final: 54 residues processed: 708 average time/residue: 0.2074 time to fit residues: 231.5985 Evaluate side-chains 355 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 293 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 561 PRO Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 690 GLN Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 690 GLN Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain L residue 16 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 0.0980 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 1.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN A 121 ASN A 164 ASN A 173 GLN A 334 ASN A 360 ASN A 422 ASN A 450 ASN ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN A 907 ASN A1119 ASN B 121 ASN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 ASN B 173 GLN B 422 ASN B 450 ASN B 606 ASN B 690 GLN B 703 ASN B 755 GLN B 779 GLN B1058 HIS C 164 ASN C 173 GLN C 207 HIS C 422 ASN C 450 ASN C 607 GLN C 644 GLN C 856 ASN C 955 ASN C1005 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.208070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.137596 restraints weight = 47031.941| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 3.79 r_work: 0.3521 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 31077 Z= 0.186 Angle : 0.815 17.217 42441 Z= 0.401 Chirality : 0.053 1.162 4914 Planarity : 0.006 0.094 5358 Dihedral : 7.399 85.125 4170 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.24 % Favored : 92.41 % Rotamer: Outliers : 3.49 % Allowed : 14.09 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.13), residues: 3702 helix: 0.33 (0.20), residues: 656 sheet: -0.95 (0.16), residues: 967 loop : -2.34 (0.12), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 102 TYR 0.020 0.002 TYR C 170 PHE 0.020 0.002 PHE A 86 TRP 0.025 0.001 TRP H 36 HIS 0.011 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.19 (30963) covalent geometry : angle 0.76234 / 0.39 (42144) SS BOND : bond 0.00547 / 0.38 ( 45) SS BOND : angle 2.85091 / 1.91 ( 90) hydrogen bonds : bond 0.05375 / 3.50 ( 1025) hydrogen bonds : angle 5.90817 / 3.92 ( 2958) link_BETA1-4 : bond 0.00901 / 0.65 ( 21) link_BETA1-4 : angle 3.03226 / 1.72 ( 63) link_NAG-ASN : bond 0.00703 / 0.49 ( 48) link_NAG-ASN : angle 4.05273 / 2.80 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 313 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.6885 (OUTLIER) cc_final: 0.6586 (t0) REVERT: A 319 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.8470 (ptm160) REVERT: A 323 THR cc_start: 0.8206 (OUTLIER) cc_final: 0.7964 (p) REVERT: A 365 TYR cc_start: 0.7778 (m-80) cc_final: 0.7492 (m-80) REVERT: A 386 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.7856 (mtpm) REVERT: A 498 ARG cc_start: 0.7959 (mmm-85) cc_final: 0.7457 (mmm-85) REVERT: A 514 SER cc_start: 0.8938 (t) cc_final: 0.8701 (p) REVERT: A 516 GLU cc_start: 0.7225 (tm-30) cc_final: 0.6931 (tm-30) REVERT: A 547 THR cc_start: 0.8768 (OUTLIER) cc_final: 0.8542 (t) REVERT: A 675 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.6875 (mp10) REVERT: A 856 ASN cc_start: 0.9075 (OUTLIER) cc_final: 0.8859 (p0) REVERT: A 859 THR cc_start: 0.8428 (OUTLIER) cc_final: 0.8191 (p) REVERT: A 995 ARG cc_start: 0.8367 (ttm-80) cc_final: 0.8101 (ttm110) REVERT: B 703 ASN cc_start: 0.7419 (OUTLIER) cc_final: 0.7171 (p0) REVERT: B 751 ASN cc_start: 0.8777 (t0) cc_final: 0.8463 (m-40) REVERT: B 854 LYS cc_start: 0.7133 (OUTLIER) cc_final: 0.5414 (tptt) REVERT: C 169 GLU cc_start: 0.8264 (mm-30) cc_final: 0.8011 (tm-30) REVERT: C 191 GLU cc_start: 0.7465 (mt-10) cc_final: 0.6891 (mp0) REVERT: C 259 THR cc_start: 0.1445 (OUTLIER) cc_final: 0.1228 (t) REVERT: C 321 GLN cc_start: 0.7761 (OUTLIER) cc_final: 0.7338 (mm-40) REVERT: C 529 LYS cc_start: 0.7447 (OUTLIER) cc_final: 0.7161 (mmmt) REVERT: C 693 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8535 (pp) REVERT: H 63 PHE cc_start: 0.7547 (m-10) cc_final: 0.7270 (m-10) REVERT: H 93 TYR cc_start: 0.7840 (m-10) cc_final: 0.7631 (m-10) REVERT: L 92 TRP cc_start: 0.6059 (t-100) cc_final: 0.5402 (t-100) REVERT: L 101 TRP cc_start: 0.6050 (t-100) cc_final: 0.5750 (t-100) REVERT: J 48 MET cc_start: 0.1563 (mpp) cc_final: 0.1196 (mpp) outliers start: 113 outliers final: 54 residues processed: 403 average time/residue: 0.1861 time to fit residues: 123.9425 Evaluate side-chains 315 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 247 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 2 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 228 optimal weight: 0.6980 chunk 265 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 70 optimal weight: 0.0570 chunk 247 optimal weight: 20.0000 chunk 150 optimal weight: 1.9990 chunk 264 optimal weight: 4.9990 chunk 104 optimal weight: 6.9990 chunk 217 optimal weight: 0.9990 chunk 239 optimal weight: 2.9990 chunk 274 optimal weight: 0.0070 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 ASN ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN A 907 ASN A 935 GLN B 121 ASN B 644 GLN B 935 GLN C 196 ASN C 207 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.207143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.134862 restraints weight = 46870.820| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 3.82 r_work: 0.3499 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 31077 Z= 0.127 Angle : 0.697 14.697 42441 Z= 0.341 Chirality : 0.047 0.674 4914 Planarity : 0.005 0.119 5358 Dihedral : 6.142 65.424 4099 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.02 % Favored : 93.76 % Rotamer: Outliers : 3.12 % Allowed : 15.11 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.13), residues: 3702 helix: 1.13 (0.21), residues: 636 sheet: -0.62 (0.16), residues: 985 loop : -2.01 (0.12), residues: 2081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 319 TYR 0.019 0.001 TYR C 796 PHE 0.020 0.001 PHE B 541 TRP 0.021 0.001 TRP L 36 HIS 0.005 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (30963) covalent geometry : angle 0.65950 / 0.33 (42144) SS BOND : bond 0.00647 / 0.36 ( 45) SS BOND : angle 2.19129 / 1.46 ( 90) hydrogen bonds : bond 0.04307 / 2.81 ( 1025) hydrogen bonds : angle 5.42304 / 3.59 ( 2958) link_BETA1-4 : bond 0.00876 / 0.64 ( 21) link_BETA1-4 : angle 2.71002 / 1.48 ( 63) link_NAG-ASN : bond 0.00506 / 0.32 ( 48) link_NAG-ASN : angle 3.10322 / 2.12 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 263 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 GLU cc_start: 0.7595 (tm-30) cc_final: 0.7361 (tp30) REVERT: A 323 THR cc_start: 0.8102 (OUTLIER) cc_final: 0.7859 (p) REVERT: A 365 TYR cc_start: 0.7580 (m-80) cc_final: 0.7048 (m-80) REVERT: A 386 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.7838 (mtpm) REVERT: A 514 SER cc_start: 0.8745 (t) cc_final: 0.8484 (p) REVERT: A 515 PHE cc_start: 0.8676 (OUTLIER) cc_final: 0.7135 (p90) REVERT: A 516 GLU cc_start: 0.7139 (tm-30) cc_final: 0.6754 (tm-30) REVERT: A 675 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7175 (mp10) REVERT: A 762 GLN cc_start: 0.8316 (tt0) cc_final: 0.8095 (mt0) REVERT: A 855 PHE cc_start: 0.7923 (m-80) cc_final: 0.7698 (m-80) REVERT: A 856 ASN cc_start: 0.9086 (OUTLIER) cc_final: 0.8811 (p0) REVERT: B 641 ASN cc_start: 0.7440 (m-40) cc_final: 0.7132 (t0) REVERT: B 731 MET cc_start: 0.9219 (OUTLIER) cc_final: 0.8929 (ptp) REVERT: B 751 ASN cc_start: 0.8779 (t0) cc_final: 0.8550 (m-40) REVERT: B 854 LYS cc_start: 0.7126 (OUTLIER) cc_final: 0.5320 (tptt) REVERT: B 960 ASN cc_start: 0.8083 (m-40) cc_final: 0.7800 (t0) REVERT: B 979 ASP cc_start: 0.7882 (m-30) cc_final: 0.7606 (m-30) REVERT: B 1113 GLN cc_start: 0.8767 (mp10) cc_final: 0.8166 (mt0) REVERT: C 169 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7785 (tm-30) REVERT: C 191 GLU cc_start: 0.7434 (mt-10) cc_final: 0.6590 (mp0) REVERT: C 208 THR cc_start: 0.9001 (OUTLIER) cc_final: 0.8326 (p) REVERT: C 259 THR cc_start: 0.1490 (OUTLIER) cc_final: 0.1280 (t) REVERT: C 321 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.7380 (mm-40) REVERT: C 529 LYS cc_start: 0.7869 (OUTLIER) cc_final: 0.7591 (mmmt) REVERT: C 693 ILE cc_start: 0.8886 (OUTLIER) cc_final: 0.8554 (pp) REVERT: H 63 PHE cc_start: 0.7548 (m-10) cc_final: 0.7276 (m-10) REVERT: H 93 TYR cc_start: 0.7709 (m-10) cc_final: 0.7247 (m-10) REVERT: J 48 MET cc_start: 0.1630 (mpp) cc_final: 0.1269 (mpp) outliers start: 101 outliers final: 51 residues processed: 344 average time/residue: 0.1670 time to fit residues: 96.3756 Evaluate side-chains 286 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 223 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1117 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 293 optimal weight: 3.9990 chunk 360 optimal weight: 40.0000 chunk 296 optimal weight: 0.8980 chunk 151 optimal weight: 9.9990 chunk 147 optimal weight: 50.0000 chunk 3 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 269 optimal weight: 0.0070 chunk 346 optimal weight: 2.9990 chunk 211 optimal weight: 9.9990 overall best weight: 1.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN C 196 ASN C 207 HIS C 856 ASN C 913 GLN C1010 GLN ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.204516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.131817 restraints weight = 46393.871| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 3.82 r_work: 0.3431 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 31077 Z= 0.135 Angle : 0.662 13.001 42441 Z= 0.324 Chirality : 0.046 0.487 4914 Planarity : 0.004 0.073 5358 Dihedral : 5.719 65.429 4088 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.27 % Favored : 93.57 % Rotamer: Outliers : 3.27 % Allowed : 15.14 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.13), residues: 3702 helix: 1.26 (0.21), residues: 643 sheet: -0.33 (0.16), residues: 1026 loop : -1.84 (0.13), residues: 2033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 995 TYR 0.013 0.001 TYR C 796 PHE 0.022 0.001 PHE A 86 TRP 0.029 0.001 TRP L 36 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 (30963) covalent geometry : angle 0.63044 / 0.32 (42144) SS BOND : bond 0.00430 / 0.25 ( 45) SS BOND : angle 2.07341 / 1.33 ( 90) hydrogen bonds : bond 0.04091 / 2.66 ( 1025) hydrogen bonds : angle 5.20821 / 3.46 ( 2958) link_BETA1-4 : bond 0.00841 / 0.61 ( 21) link_BETA1-4 : angle 2.59527 / 1.40 ( 63) link_NAG-ASN : bond 0.00412 / 0.25 ( 48) link_NAG-ASN : angle 2.71476 / 1.85 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 245 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.4846 (ttt) cc_final: 0.4311 (tpp) REVERT: A 323 THR cc_start: 0.7928 (OUTLIER) cc_final: 0.7681 (p) REVERT: A 365 TYR cc_start: 0.7535 (m-80) cc_final: 0.7131 (m-80) REVERT: A 514 SER cc_start: 0.8724 (t) cc_final: 0.8396 (p) REVERT: A 515 PHE cc_start: 0.8636 (OUTLIER) cc_final: 0.7299 (p90) REVERT: A 516 GLU cc_start: 0.7117 (tm-30) cc_final: 0.6409 (tm-30) REVERT: A 675 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7317 (mp10) REVERT: A 855 PHE cc_start: 0.7946 (m-80) cc_final: 0.7722 (m-80) REVERT: A 856 ASN cc_start: 0.9139 (OUTLIER) cc_final: 0.8786 (p0) REVERT: A 960 ASN cc_start: 0.8331 (m-40) cc_final: 0.8083 (t0) REVERT: B 641 ASN cc_start: 0.7373 (m-40) cc_final: 0.7094 (t0) REVERT: B 955 ASN cc_start: 0.7808 (m-40) cc_final: 0.7536 (m-40) REVERT: B 960 ASN cc_start: 0.8081 (m-40) cc_final: 0.7816 (t0) REVERT: B 979 ASP cc_start: 0.7848 (m-30) cc_final: 0.7580 (m-30) REVERT: B 1113 GLN cc_start: 0.8802 (mp10) cc_final: 0.8156 (mt0) REVERT: C 169 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7712 (tm-30) REVERT: C 177 MET cc_start: 0.4218 (tmm) cc_final: 0.3927 (tmm) REVERT: C 191 GLU cc_start: 0.7388 (mt-10) cc_final: 0.6554 (mp0) REVERT: C 208 THR cc_start: 0.9036 (OUTLIER) cc_final: 0.8355 (p) REVERT: C 259 THR cc_start: 0.1819 (OUTLIER) cc_final: 0.1608 (t) REVERT: C 321 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.7528 (mm-40) REVERT: C 357 ARG cc_start: 0.7632 (mmm160) cc_final: 0.7180 (mmp-170) REVERT: C 529 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7864 (mmmt) REVERT: C 693 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8552 (pp) REVERT: C 856 ASN cc_start: 0.8800 (OUTLIER) cc_final: 0.8414 (p0) REVERT: H 63 PHE cc_start: 0.7611 (m-10) cc_final: 0.7371 (m-10) REVERT: H 107 PHE cc_start: 0.3795 (m-80) cc_final: 0.3136 (m-10) REVERT: J 48 MET cc_start: 0.1870 (mpp) cc_final: 0.1567 (mpp) outliers start: 106 outliers final: 64 residues processed: 332 average time/residue: 0.1620 time to fit residues: 91.6949 Evaluate side-chains 296 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 222 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 94 TYR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain M residue 71 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 349 optimal weight: 20.0000 chunk 350 optimal weight: 0.0370 chunk 86 optimal weight: 8.9990 chunk 80 optimal weight: 2.9990 chunk 323 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 152 optimal weight: 0.0980 chunk 28 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 131 optimal weight: 5.9990 overall best weight: 1.0264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN C 196 ASN C 207 HIS C 613 GLN C 913 GLN H 52 ASN ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.203822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.129249 restraints weight = 46182.351| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 3.69 r_work: 0.3426 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 31077 Z= 0.127 Angle : 0.641 12.435 42441 Z= 0.312 Chirality : 0.046 0.414 4914 Planarity : 0.004 0.068 5358 Dihedral : 5.333 64.862 4073 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.97 % Favored : 93.90 % Rotamer: Outliers : 3.24 % Allowed : 15.51 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.14), residues: 3702 helix: 1.32 (0.21), residues: 649 sheet: -0.17 (0.16), residues: 1025 loop : -1.70 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1019 TYR 0.019 0.001 TYR A 453 PHE 0.022 0.001 PHE A 168 TRP 0.030 0.001 TRP L 36 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (30963) covalent geometry : angle 0.61085 / 0.30 (42144) SS BOND : bond 0.00486 / 0.29 ( 45) SS BOND : angle 2.10618 / 1.49 ( 90) hydrogen bonds : bond 0.03860 / 2.52 ( 1025) hydrogen bonds : angle 5.03259 / 3.36 ( 2958) link_BETA1-4 : bond 0.00953 / 0.67 ( 21) link_BETA1-4 : angle 2.50526 / 1.34 ( 63) link_NAG-ASN : bond 0.00323 / 0.20 ( 48) link_NAG-ASN : angle 2.52727 / 1.70 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 244 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.4679 (ttt) cc_final: 0.4167 (tpp) REVERT: A 269 TYR cc_start: 0.8256 (m-80) cc_final: 0.8054 (m-80) REVERT: A 298 GLU cc_start: 0.7899 (tp30) cc_final: 0.7624 (tp30) REVERT: A 357 ARG cc_start: 0.7736 (ttm-80) cc_final: 0.7534 (ttm-80) REVERT: A 441 LEU cc_start: 0.8569 (tp) cc_final: 0.8259 (tp) REVERT: A 490 PHE cc_start: 0.5504 (t80) cc_final: 0.5259 (t80) REVERT: A 514 SER cc_start: 0.8592 (t) cc_final: 0.8263 (p) REVERT: A 516 GLU cc_start: 0.7045 (tm-30) cc_final: 0.6264 (tm-30) REVERT: A 675 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7405 (mp10) REVERT: A 855 PHE cc_start: 0.7922 (m-80) cc_final: 0.7711 (m-80) REVERT: A 856 ASN cc_start: 0.9087 (OUTLIER) cc_final: 0.8715 (p0) REVERT: A 859 THR cc_start: 0.8450 (OUTLIER) cc_final: 0.8165 (p) REVERT: A 960 ASN cc_start: 0.8306 (m-40) cc_final: 0.8054 (t0) REVERT: B 641 ASN cc_start: 0.7506 (m-40) cc_final: 0.7274 (t0) REVERT: B 955 ASN cc_start: 0.7794 (m-40) cc_final: 0.7527 (m-40) REVERT: B 979 ASP cc_start: 0.7824 (m-30) cc_final: 0.7578 (m-30) REVERT: B 1113 GLN cc_start: 0.8773 (mp10) cc_final: 0.8088 (mt0) REVERT: C 169 GLU cc_start: 0.8319 (mm-30) cc_final: 0.7699 (tm-30) REVERT: C 177 MET cc_start: 0.3881 (tmm) cc_final: 0.3528 (tmm) REVERT: C 191 GLU cc_start: 0.7514 (mt-10) cc_final: 0.6740 (mp0) REVERT: C 208 THR cc_start: 0.9038 (OUTLIER) cc_final: 0.8307 (p) REVERT: C 259 THR cc_start: 0.1773 (OUTLIER) cc_final: 0.1569 (t) REVERT: C 321 GLN cc_start: 0.7811 (OUTLIER) cc_final: 0.7582 (mm-40) REVERT: C 357 ARG cc_start: 0.7442 (mmm160) cc_final: 0.7084 (mmm160) REVERT: C 529 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7830 (mmmt) REVERT: C 569 ILE cc_start: 0.8506 (mp) cc_final: 0.8303 (mp) REVERT: C 693 ILE cc_start: 0.8895 (OUTLIER) cc_final: 0.8557 (pp) REVERT: C 985 ASP cc_start: 0.7048 (p0) cc_final: 0.6694 (p0) REVERT: H 63 PHE cc_start: 0.7528 (m-10) cc_final: 0.7317 (m-10) REVERT: H 93 TYR cc_start: 0.7885 (m-10) cc_final: 0.7618 (m-10) REVERT: H 107 PHE cc_start: 0.3734 (m-80) cc_final: 0.3005 (m-10) REVERT: J 48 MET cc_start: 0.1946 (mpp) cc_final: 0.1653 (mpp) outliers start: 105 outliers final: 66 residues processed: 329 average time/residue: 0.1590 time to fit residues: 89.0364 Evaluate side-chains 288 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 214 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 94 TYR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 78 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 22 optimal weight: 7.9990 chunk 174 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 229 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 363 optimal weight: 30.0000 chunk 211 optimal weight: 9.9990 chunk 114 optimal weight: 9.9990 chunk 364 optimal weight: 30.0000 chunk 175 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 ASN ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A 935 GLN B 196 ASN B 914 ASN C 87 ASN C 173 GLN C 207 HIS C 317 ASN C 856 ASN ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.199022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.119438 restraints weight = 45747.552| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.78 r_work: 0.3384 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.4805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 31077 Z= 0.237 Angle : 0.762 13.996 42441 Z= 0.370 Chirality : 0.050 0.528 4914 Planarity : 0.005 0.061 5358 Dihedral : 5.396 64.483 4066 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.19 % Favored : 92.68 % Rotamer: Outliers : 3.65 % Allowed : 15.45 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.13), residues: 3702 helix: 0.98 (0.21), residues: 650 sheet: -0.11 (0.16), residues: 1030 loop : -1.78 (0.13), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C1019 TYR 0.019 0.002 TYR B 269 PHE 0.025 0.002 PHE A 86 TRP 0.041 0.002 TRP L 36 HIS 0.009 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.24 (30963) covalent geometry : angle 0.72554 / 0.36 (42144) SS BOND : bond 0.00563 / 0.36 ( 45) SS BOND : angle 2.30936 / 1.48 ( 90) hydrogen bonds : bond 0.05073 / 3.29 ( 1025) hydrogen bonds : angle 5.32172 / 3.54 ( 2958) link_BETA1-4 : bond 0.00916 / 0.70 ( 21) link_BETA1-4 : angle 2.50473 / 1.36 ( 63) link_NAG-ASN : bond 0.00619 / 0.44 ( 48) link_NAG-ASN : angle 3.33519 / 2.30 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 217 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.5027 (ttt) cc_final: 0.4720 (tpp) REVERT: A 298 GLU cc_start: 0.8245 (tp30) cc_final: 0.7971 (tp30) REVERT: A 394 ASN cc_start: 0.7268 (OUTLIER) cc_final: 0.6484 (p0) REVERT: A 490 PHE cc_start: 0.5997 (t80) cc_final: 0.5750 (t80) REVERT: A 515 PHE cc_start: 0.8881 (OUTLIER) cc_final: 0.8003 (p90) REVERT: A 646 ARG cc_start: 0.7136 (ptt-90) cc_final: 0.6836 (tpt170) REVERT: A 675 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7159 (mp10) REVERT: A 856 ASN cc_start: 0.9143 (OUTLIER) cc_final: 0.8667 (p0) REVERT: A 957 GLN cc_start: 0.8376 (mt0) cc_final: 0.7986 (mm-40) REVERT: A 977 LEU cc_start: 0.8032 (mp) cc_final: 0.7799 (mp) REVERT: A 1050 MET cc_start: 0.8928 (ptm) cc_final: 0.8643 (ptm) REVERT: B 375 PHE cc_start: 0.3749 (OUTLIER) cc_final: 0.2887 (t80) REVERT: B 725 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8314 (tt0) REVERT: B 854 LYS cc_start: 0.7242 (OUTLIER) cc_final: 0.5255 (tptt) REVERT: B 1113 GLN cc_start: 0.8947 (mp10) cc_final: 0.8147 (mt0) REVERT: B 1117 THR cc_start: 0.9319 (OUTLIER) cc_final: 0.9117 (t) REVERT: C 177 MET cc_start: 0.3877 (tmm) cc_final: 0.3412 (tmm) REVERT: C 191 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7143 (mp0) REVERT: C 321 GLN cc_start: 0.7886 (OUTLIER) cc_final: 0.7673 (mm-40) REVERT: C 529 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7930 (mmmt) REVERT: C 693 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8680 (pp) REVERT: C 856 ASN cc_start: 0.9138 (OUTLIER) cc_final: 0.8881 (p0) REVERT: C 985 ASP cc_start: 0.7189 (p0) cc_final: 0.6835 (p0) REVERT: C 1002 GLN cc_start: 0.8619 (tt0) cc_final: 0.8416 (tt0) REVERT: H 63 PHE cc_start: 0.7603 (m-10) cc_final: 0.7398 (m-10) REVERT: H 103 TRP cc_start: 0.7313 (p90) cc_final: 0.6814 (p90) REVERT: L 101 TRP cc_start: 0.5857 (t-100) cc_final: 0.5368 (m100) REVERT: J 48 MET cc_start: 0.1904 (mpp) cc_final: 0.1566 (mpp) outliers start: 118 outliers final: 76 residues processed: 314 average time/residue: 0.1723 time to fit residues: 90.4497 Evaluate side-chains 284 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 196 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 94 TYR Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain J residue 118 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 62 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 170 optimal weight: 0.9980 chunk 237 optimal weight: 20.0000 chunk 277 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 232 optimal weight: 20.0000 chunk 371 optimal weight: 30.0000 chunk 217 optimal weight: 7.9990 chunk 300 optimal weight: 0.5980 chunk 280 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN B 641 ASN C 87 ASN C 173 GLN C 207 HIS C 856 ASN C1010 GLN ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 52 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.200581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.126908 restraints weight = 45960.387| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 3.82 r_work: 0.3348 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.4962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 31077 Z= 0.124 Angle : 0.650 12.592 42441 Z= 0.315 Chirality : 0.046 0.326 4914 Planarity : 0.004 0.070 5358 Dihedral : 5.143 63.898 4064 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.05 % Favored : 93.81 % Rotamer: Outliers : 2.47 % Allowed : 16.65 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.14), residues: 3702 helix: 1.28 (0.21), residues: 645 sheet: 0.06 (0.16), residues: 1019 loop : -1.67 (0.13), residues: 2038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 102 TYR 0.017 0.001 TYR J 79 PHE 0.019 0.001 PHE C 106 TRP 0.035 0.001 TRP L 36 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (30963) covalent geometry : angle 0.62159 / 0.31 (42144) SS BOND : bond 0.00453 / 0.27 ( 45) SS BOND : angle 1.97788 / 1.25 ( 90) hydrogen bonds : bond 0.04060 / 2.65 ( 1025) hydrogen bonds : angle 5.06855 / 3.37 ( 2958) link_BETA1-4 : bond 0.00826 / 0.60 ( 21) link_BETA1-4 : angle 2.38660 / 1.28 ( 63) link_NAG-ASN : bond 0.00341 / 0.23 ( 48) link_NAG-ASN : angle 2.57725 / 1.73 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 217 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.5045 (ttt) cc_final: 0.4844 (tpp) REVERT: A 269 TYR cc_start: 0.8344 (m-80) cc_final: 0.7983 (m-80) REVERT: A 298 GLU cc_start: 0.8031 (tp30) cc_final: 0.7746 (tp30) REVERT: A 514 SER cc_start: 0.8623 (t) cc_final: 0.8302 (p) REVERT: A 515 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.7640 (p90) REVERT: A 646 ARG cc_start: 0.7140 (ptt-90) cc_final: 0.6915 (tpt170) REVERT: A 675 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7192 (mp10) REVERT: A 823 PHE cc_start: 0.7876 (m-80) cc_final: 0.7669 (m-80) REVERT: A 856 ASN cc_start: 0.9093 (OUTLIER) cc_final: 0.8663 (p0) REVERT: A 957 GLN cc_start: 0.8165 (mt0) cc_final: 0.7762 (mm-40) REVERT: A 960 ASN cc_start: 0.8277 (m-40) cc_final: 0.8038 (t0) REVERT: A 1050 MET cc_start: 0.8715 (ptm) cc_final: 0.8433 (ptm) REVERT: B 375 PHE cc_start: 0.3847 (OUTLIER) cc_final: 0.2977 (t80) REVERT: B 725 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8198 (tt0) REVERT: B 854 LYS cc_start: 0.7147 (OUTLIER) cc_final: 0.5169 (tptt) REVERT: B 1113 GLN cc_start: 0.8746 (mp10) cc_final: 0.8000 (mt0) REVERT: C 177 MET cc_start: 0.3679 (tmm) cc_final: 0.3241 (tmm) REVERT: C 191 GLU cc_start: 0.7655 (mt-10) cc_final: 0.6928 (mp0) REVERT: C 208 THR cc_start: 0.9066 (OUTLIER) cc_final: 0.8297 (p) REVERT: C 529 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7932 (mmmt) REVERT: C 693 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8564 (pp) REVERT: C 1002 GLN cc_start: 0.8384 (tt0) cc_final: 0.8160 (tt0) REVERT: H 93 TYR cc_start: 0.7928 (m-10) cc_final: 0.7601 (m-10) REVERT: H 103 TRP cc_start: 0.7123 (p90) cc_final: 0.6672 (p90) REVERT: H 107 PHE cc_start: 0.3740 (m-80) cc_final: 0.3054 (m-10) REVERT: L 101 TRP cc_start: 0.5671 (t-100) cc_final: 0.5211 (m100) REVERT: J 48 MET cc_start: 0.2026 (mpp) cc_final: 0.1699 (mpp) outliers start: 80 outliers final: 56 residues processed: 284 average time/residue: 0.1689 time to fit residues: 79.7826 Evaluate side-chains 270 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 205 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 94 TYR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 78 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 78 optimal weight: 0.4980 chunk 316 optimal weight: 20.0000 chunk 352 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 333 optimal weight: 20.0000 chunk 207 optimal weight: 4.9990 chunk 249 optimal weight: 40.0000 chunk 154 optimal weight: 8.9990 chunk 323 optimal weight: 7.9990 chunk 218 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 overall best weight: 4.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN B 81 ASN B 239 GLN B 544 ASN B 755 GLN C 207 HIS ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN L 16 GLN ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 52 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.193599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.113004 restraints weight = 45634.060| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 3.19 r_work: 0.3276 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.5494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.107 31077 Z= 0.361 Angle : 0.833 12.148 42441 Z= 0.411 Chirality : 0.053 0.277 4914 Planarity : 0.005 0.067 5358 Dihedral : 5.599 63.122 4061 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.10 % Favored : 91.76 % Rotamer: Outliers : 3.31 % Allowed : 16.06 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.13), residues: 3702 helix: 0.56 (0.21), residues: 644 sheet: -0.26 (0.16), residues: 1011 loop : -1.83 (0.13), residues: 2047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 983 TYR 0.024 0.002 TYR B 269 PHE 0.031 0.003 PHE A 86 TRP 0.029 0.002 TRP L 36 HIS 0.011 0.002 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00884 / 0.36 (30963) covalent geometry : angle 0.80358 / 0.40 (42144) SS BOND : bond 0.00840 / 0.60 ( 45) SS BOND : angle 2.71520 / 1.65 ( 90) hydrogen bonds : bond 0.06062 / 3.92 ( 1025) hydrogen bonds : angle 5.55571 / 3.71 ( 2958) link_BETA1-4 : bond 0.00708 / 0.51 ( 21) link_BETA1-4 : angle 2.47283 / 1.35 ( 63) link_NAG-ASN : bond 0.00579 / 0.37 ( 48) link_NAG-ASN : angle 2.85571 / 1.92 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 216 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.5167 (ttt) cc_final: 0.4295 (tpt) REVERT: A 269 TYR cc_start: 0.8388 (m-80) cc_final: 0.8104 (m-80) REVERT: A 298 GLU cc_start: 0.8284 (tp30) cc_final: 0.7981 (tp30) REVERT: A 357 ARG cc_start: 0.7995 (ttm-80) cc_final: 0.7787 (ttm-80) REVERT: A 515 PHE cc_start: 0.9048 (OUTLIER) cc_final: 0.7839 (p90) REVERT: A 646 ARG cc_start: 0.8198 (ptt-90) cc_final: 0.7698 (tpt170) REVERT: A 675 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.7183 (mp10) REVERT: A 856 ASN cc_start: 0.9162 (OUTLIER) cc_final: 0.8525 (p0) REVERT: A 957 GLN cc_start: 0.8398 (mt0) cc_final: 0.7946 (mm110) REVERT: A 1050 MET cc_start: 0.9049 (ptm) cc_final: 0.8723 (ptm) REVERT: B 226 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7759 (mp) REVERT: B 375 PHE cc_start: 0.3812 (OUTLIER) cc_final: 0.3001 (t80) REVERT: B 613 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.8530 (mt0) REVERT: B 725 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8408 (tt0) REVERT: C 170 TYR cc_start: 0.7080 (t80) cc_final: 0.6644 (t80) REVERT: C 177 MET cc_start: 0.3740 (tmm) cc_final: 0.3317 (tmm) REVERT: C 191 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7264 (mp0) REVERT: C 208 THR cc_start: 0.9083 (OUTLIER) cc_final: 0.8313 (p) REVERT: C 353 TRP cc_start: 0.4314 (p-90) cc_final: 0.3750 (p-90) REVERT: C 529 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7907 (mmmt) REVERT: C 693 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8681 (pp) REVERT: C 1002 GLN cc_start: 0.8717 (tt0) cc_final: 0.8489 (tt0) REVERT: H 33 PHE cc_start: 0.6578 (m-80) cc_final: 0.6356 (m-10) REVERT: H 93 TYR cc_start: 0.7971 (m-10) cc_final: 0.7645 (m-10) REVERT: L 101 TRP cc_start: 0.5536 (t-100) cc_final: 0.5057 (m100) REVERT: J 48 MET cc_start: 0.2033 (mpp) cc_final: 0.1733 (mpp) outliers start: 107 outliers final: 73 residues processed: 307 average time/residue: 0.1712 time to fit residues: 88.1727 Evaluate side-chains 280 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 197 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 94 TYR Chi-restraints excluded: chain L residue 62 ARG Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 17 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 98 optimal weight: 0.8980 chunk 254 optimal weight: 0.7980 chunk 6 optimal weight: 9.9990 chunk 301 optimal weight: 1.9990 chunk 327 optimal weight: 20.0000 chunk 23 optimal weight: 8.9990 chunk 157 optimal weight: 1.9990 chunk 355 optimal weight: 20.0000 chunk 58 optimal weight: 0.8980 chunk 311 optimal weight: 6.9990 chunk 262 optimal weight: 0.1980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 450 ASN C1010 GLN ** L 32 ASN ** 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 = 0.4524 r_free = 0.4524 target = 0.199195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.121975 restraints weight = 45602.591| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 3.11 r_work: 0.3364 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.5567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 31077 Z= 0.127 Angle : 0.659 10.971 42441 Z= 0.321 Chirality : 0.046 0.290 4914 Planarity : 0.004 0.063 5358 Dihedral : 5.173 63.036 4059 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.29 % Favored : 93.60 % Rotamer: Outliers : 1.95 % Allowed : 17.42 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.14), residues: 3702 helix: 1.09 (0.21), residues: 639 sheet: -0.02 (0.16), residues: 978 loop : -1.65 (0.13), residues: 2085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 102 TYR 0.015 0.001 TYR A 453 PHE 0.020 0.001 PHE C 106 TRP 0.027 0.001 TRP L 36 HIS 0.003 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (30963) covalent geometry : angle 0.63475 / 0.31 (42144) SS BOND : bond 0.00473 / 0.29 ( 45) SS BOND : angle 1.91756 / 1.19 ( 90) hydrogen bonds : bond 0.04245 / 2.76 ( 1025) hydrogen bonds : angle 5.10487 / 3.40 ( 2958) link_BETA1-4 : bond 0.00809 / 0.58 ( 21) link_BETA1-4 : angle 2.32855 / 1.24 ( 63) link_NAG-ASN : bond 0.00332 / 0.22 ( 48) link_NAG-ASN : angle 2.36301 / 1.58 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 207 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.4971 (ttt) cc_final: 0.4229 (tpt) REVERT: A 269 TYR cc_start: 0.8317 (m-80) cc_final: 0.8042 (m-80) REVERT: A 298 GLU cc_start: 0.8189 (tp30) cc_final: 0.7842 (tp30) REVERT: A 646 ARG cc_start: 0.7888 (ptt-90) cc_final: 0.7429 (tpt170) REVERT: A 675 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7032 (mp10) REVERT: A 856 ASN cc_start: 0.9113 (OUTLIER) cc_final: 0.8501 (p0) REVERT: A 957 GLN cc_start: 0.8287 (mt0) cc_final: 0.7790 (mm110) REVERT: A 1050 MET cc_start: 0.8921 (ptm) cc_final: 0.8663 (ptm) REVERT: B 191 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8165 (mt-10) REVERT: B 375 PHE cc_start: 0.3666 (OUTLIER) cc_final: 0.2738 (t80) REVERT: B 725 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8427 (tt0) REVERT: B 854 LYS cc_start: 0.7294 (OUTLIER) cc_final: 0.5215 (tptt) REVERT: B 1113 GLN cc_start: 0.8886 (mp10) cc_final: 0.8216 (mt0) REVERT: C 63 THR cc_start: 0.6147 (OUTLIER) cc_final: 0.5619 (p) REVERT: C 177 MET cc_start: 0.3624 (tmm) cc_final: 0.3300 (tmm) REVERT: C 191 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7172 (mp0) REVERT: C 208 THR cc_start: 0.9062 (OUTLIER) cc_final: 0.8228 (p) REVERT: C 353 TRP cc_start: 0.4507 (p-90) cc_final: 0.3938 (p-90) REVERT: C 529 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.7956 (mmmt) REVERT: C 693 ILE cc_start: 0.8938 (OUTLIER) cc_final: 0.8650 (pp) REVERT: H 33 PHE cc_start: 0.6480 (m-80) cc_final: 0.6242 (m-10) REVERT: H 93 TYR cc_start: 0.7926 (m-10) cc_final: 0.7562 (m-10) REVERT: L 101 TRP cc_start: 0.5602 (t-100) cc_final: 0.5372 (m100) REVERT: I 48 MET cc_start: 0.1369 (tpt) cc_final: 0.1106 (tpp) REVERT: J 48 MET cc_start: 0.2046 (mpp) cc_final: 0.1701 (mpp) outliers start: 63 outliers final: 47 residues processed: 260 average time/residue: 0.1822 time to fit residues: 78.7239 Evaluate side-chains 252 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 196 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 94 TYR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 78 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 353 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 282 optimal weight: 0.5980 chunk 292 optimal weight: 3.9990 chunk 313 optimal weight: 20.0000 chunk 272 optimal weight: 0.5980 chunk 229 optimal weight: 0.0670 chunk 3 optimal weight: 7.9990 chunk 142 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 361 optimal weight: 50.0000 overall best weight: 1.2320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 317 ASN ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 ASN ** 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 = 0.4510 r_free = 0.4510 target = 0.198177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.120078 restraints weight = 45326.030| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 3.43 r_work: 0.3318 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.5699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 31077 Z= 0.134 Angle : 0.644 10.429 42441 Z= 0.312 Chirality : 0.046 0.287 4914 Planarity : 0.004 0.058 5358 Dihedral : 4.927 59.108 4057 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.08 % Favored : 92.81 % Rotamer: Outliers : 1.82 % Allowed : 17.52 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.14), residues: 3702 helix: 1.41 (0.21), residues: 636 sheet: 0.10 (0.16), residues: 982 loop : -1.58 (0.13), residues: 2084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 983 TYR 0.015 0.001 TYR A 453 PHE 0.018 0.001 PHE C 106 TRP 0.029 0.001 TRP L 36 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.13 (30963) covalent geometry : angle 0.61844 / 0.31 (42144) SS BOND : bond 0.00422 / 0.25 ( 45) SS BOND : angle 1.71905 / 1.07 ( 90) hydrogen bonds : bond 0.03996 / 2.60 ( 1025) hydrogen bonds : angle 4.92297 / 3.28 ( 2958) link_BETA1-4 : bond 0.00793 / 0.57 ( 21) link_BETA1-4 : angle 2.25525 / 1.21 ( 63) link_NAG-ASN : bond 0.00310 / 0.21 ( 48) link_NAG-ASN : angle 2.46313 / 1.62 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 212 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.4927 (ttt) cc_final: 0.4154 (tpt) REVERT: A 269 TYR cc_start: 0.8224 (m-80) cc_final: 0.7929 (m-80) REVERT: A 298 GLU cc_start: 0.8025 (tp30) cc_final: 0.7654 (tp30) REVERT: A 403 ARG cc_start: 0.7863 (ttp-170) cc_final: 0.7612 (ttt180) REVERT: A 514 SER cc_start: 0.8513 (t) cc_final: 0.8088 (p) REVERT: A 646 ARG cc_start: 0.7569 (ptt-90) cc_final: 0.7331 (tpt170) REVERT: A 675 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7079 (mp10) REVERT: A 856 ASN cc_start: 0.9089 (OUTLIER) cc_final: 0.8489 (p0) REVERT: A 957 GLN cc_start: 0.8014 (mt0) cc_final: 0.7557 (mm110) REVERT: A 976 VAL cc_start: 0.8105 (t) cc_final: 0.7771 (m) REVERT: A 1050 MET cc_start: 0.8679 (ptm) cc_final: 0.8454 (ptm) REVERT: B 88 ASP cc_start: 0.6608 (m-30) cc_final: 0.6229 (m-30) REVERT: B 191 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8037 (mt-10) REVERT: B 375 PHE cc_start: 0.3842 (OUTLIER) cc_final: 0.3060 (t80) REVERT: B 725 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8233 (tt0) REVERT: B 854 LYS cc_start: 0.7210 (OUTLIER) cc_final: 0.5137 (tptt) REVERT: B 1113 GLN cc_start: 0.8672 (mp10) cc_final: 0.8226 (mt0) REVERT: C 63 THR cc_start: 0.5863 (OUTLIER) cc_final: 0.5393 (p) REVERT: C 170 TYR cc_start: 0.7029 (t80) cc_final: 0.6793 (t80) REVERT: C 191 GLU cc_start: 0.7671 (mt-10) cc_final: 0.6956 (mp0) REVERT: C 208 THR cc_start: 0.9053 (OUTLIER) cc_final: 0.8159 (p) REVERT: C 353 TRP cc_start: 0.4428 (p-90) cc_final: 0.3857 (p-90) REVERT: C 529 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7948 (mmmt) REVERT: C 693 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8547 (pp) REVERT: C 984 LEU cc_start: 0.7918 (tp) cc_final: 0.7542 (tp) REVERT: H 23 ARG cc_start: 0.7816 (tpt90) cc_final: 0.7570 (ppt170) REVERT: H 33 PHE cc_start: 0.6383 (m-80) cc_final: 0.6174 (m-10) REVERT: H 93 TYR cc_start: 0.7856 (m-10) cc_final: 0.7484 (m-10) REVERT: I 69 MET cc_start: -0.1482 (tpt) cc_final: -0.2073 (mtt) REVERT: J 48 MET cc_start: 0.2114 (mpp) cc_final: 0.1832 (mpp) outliers start: 59 outliers final: 44 residues processed: 261 average time/residue: 0.1777 time to fit residues: 77.0647 Evaluate side-chains 251 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 198 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 94 TYR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 17 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 243 optimal weight: 30.0000 chunk 25 optimal weight: 4.9990 chunk 160 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 221 optimal weight: 5.9990 chunk 219 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 363 optimal weight: 40.0000 chunk 266 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 209 optimal weight: 7.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.193912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.115678 restraints weight = 45783.146| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 3.94 r_work: 0.3249 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.5889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 31077 Z= 0.282 Angle : 0.760 15.174 42441 Z= 0.372 Chirality : 0.050 0.267 4914 Planarity : 0.005 0.065 5358 Dihedral : 5.268 58.113 4057 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.35 % Favored : 92.54 % Rotamer: Outliers : 2.26 % Allowed : 17.18 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.13), residues: 3702 helix: 0.90 (0.21), residues: 636 sheet: -0.12 (0.16), residues: 994 loop : -1.70 (0.13), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 983 TYR 0.018 0.002 TYR A 453 PHE 0.030 0.002 PHE A 86 TRP 0.034 0.002 TRP L 36 HIS 0.010 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00693 / 0.28 (30963) covalent geometry : angle 0.73340 / 0.37 (42144) SS BOND : bond 0.00546 / 0.32 ( 45) SS BOND : angle 2.45724 / 1.57 ( 90) hydrogen bonds : bond 0.05344 / 3.46 ( 1025) hydrogen bonds : angle 5.26806 / 3.52 ( 2958) link_BETA1-4 : bond 0.00706 / 0.50 ( 21) link_BETA1-4 : angle 2.30920 / 1.25 ( 63) link_NAG-ASN : bond 0.00456 / 0.29 ( 48) link_NAG-ASN : angle 2.62339 / 1.73 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10154.80 seconds wall clock time: 173 minutes 38.57 seconds (10418.57 seconds total)