Starting phenix.real_space_refine on Sun Jul 5 20:19:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8gto_34259/07_2026/8gto_34259.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gto_34259/07_2026/8gto_34259.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8gto_34259/07_2026/8gto_34259.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gto_34259/07_2026/8gto_34259.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gto_34259/07_2026/8gto_34259.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gto_34259/07_2026/8gto_34259.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8gto_34259/07_2026/8gto_34259.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8gto_34259/07_2026/8gto_34259.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.096 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 129 5.16 5 C 19227 2.51 5 N 4959 2.21 5 O 5919 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 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: 30234 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: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 910 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "L" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 803 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 102} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 910 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "M" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 803 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 102} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 910 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "N" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 803 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 102} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 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: 6.10, per 1000 atoms: 0.20 Number of scatterers: 30234 At special positions: 0 Unit cell: (138.933, 184.167, 202.476, 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 129 16.00 O 5919 8.00 N 4959 7.00 C 19227 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, 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=2.84 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.07 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=1.96 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.20 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.18 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=1.99 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=1.59 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=2.61 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=1.75 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=1.97 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.11 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=1.99 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=2.76 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.14 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.51 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=1.99 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 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 89 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG 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: 2.53 Conformation dependent library (CDL) restraints added in 1.2 seconds 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6978 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 60 sheets defined 18.1% alpha, 31.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 295 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.629A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 4.057A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 5.284A 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: 4.088A 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 758 through 783 removed outlier: 3.542A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 771 " --> pdb=" O LEU A 767 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 823 removed outlier: 3.591A 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: 3.650A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.592A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 removed outlier: 4.078A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.346A 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: 3.756A 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 976 through 981 removed outlier: 4.057A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 1033 removed outlier: 4.393A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR A 998 " --> pdb=" O ASP A 994 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.536A 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 295 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.629A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 4.056A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 5.285A 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: 4.088A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.874A 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: 3.513A 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: 3.652A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.590A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 4.079A 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: 3.597A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 981 removed outlier: 3.573A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 6.417A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.535A 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 295 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.628A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 4.056A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 5.285A 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: 3.874A 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: 3.590A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.514A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.576A 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: 3.591A 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: 4.238A 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: 3.597A 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: 4.324A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.700A 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: 5.687A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, 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=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.502A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASN A 164 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.502A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.528A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA7, first strand: chain 'A' and resid 538 through 543 removed outlier: 5.814A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 595 through 598 removed outlier: 4.080A pdb=" N SER A 596 " --> pdb=" O LEU A 611 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU A 611 " --> pdb=" O SER A 596 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA A 609 " --> pdb=" O ILE A 598 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 670 through 673 Processing sheet with id=AB1, first strand: chain 'A' and resid 702 through 704 removed outlier: 3.938A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.150A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.169A 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: 7.064A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.994A 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: 6.112A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.150A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.169A 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: 7.064A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.994A 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: 6.112A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, 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=AB5, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.384A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.945A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, 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=AB8, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.012A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.503A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASN B 164 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC1, 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=AC2, first strand: chain 'B' and resid 310 through 313 removed outlier: 3.611A pdb=" N GLY B 593 " --> pdb=" O PHE B 318 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 310 through 313 removed outlier: 5.662A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) removed outlier: 4.080A 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=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.529A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 538 through 543 removed outlier: 5.815A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 655 through 656 removed outlier: 4.014A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.869A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.151A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.167A 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: 7.050A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.956A 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: 7.061A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.151A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.167A 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: 7.050A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.956A 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: 7.061A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.112A 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: 3.975A 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=AD2, 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=AD3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.945A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 28 through 31 removed outlier: 6.133A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.012A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.503A 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=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.503A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 313 removed outlier: 3.562A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY C 593 " --> pdb=" O PHE C 318 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 313 removed outlier: 3.562A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN C 613 " --> pdb=" O GLY C 594 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER C 596 " --> pdb=" O LEU C 611 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU C 611 " --> pdb=" O SER C 596 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 324 through 325 removed outlier: 3.991A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASN C 540 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.528A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 391 through 392 removed outlier: 3.563A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (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 670 through 673 Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 7.150A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.143A 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: 6.956A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.060A 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: 5.739A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 7.150A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.143A 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: 6.956A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.060A 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=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.499A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, 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=AF1, first strand: chain 'H' and resid 4 through 5 Processing sheet with id=AF2, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.375A pdb=" N GLU H 10 " --> pdb=" O ALA H 118 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 9 through 12 removed outlier: 7.152A pdb=" N ALA L 10 " --> pdb=" O THR L 108 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 9 through 12 removed outlier: 7.152A pdb=" N ALA L 10 " --> pdb=" O THR L 108 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 18 through 22 Processing sheet with id=AF6, first strand: chain 'I' and resid 4 through 5 Processing sheet with id=AF7, first strand: chain 'I' and resid 10 through 11 removed outlier: 6.375A pdb=" N GLU I 10 " --> pdb=" O ALA I 118 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'M' and resid 9 through 12 removed outlier: 7.151A pdb=" N ALA M 10 " --> pdb=" O THR M 108 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'M' and resid 9 through 12 removed outlier: 7.151A pdb=" N ALA M 10 " --> pdb=" O THR M 108 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'M' and resid 18 through 22 Processing sheet with id=AG2, first strand: chain 'J' and resid 4 through 5 Processing sheet with id=AG3, first strand: chain 'J' and resid 10 through 11 removed outlier: 6.375A pdb=" N GLU J 10 " --> pdb=" O ALA J 118 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'N' and resid 9 through 12 removed outlier: 7.151A pdb=" N ALA N 10 " --> pdb=" O THR N 108 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'N' and resid 9 through 12 removed outlier: 7.151A pdb=" N ALA N 10 " --> pdb=" O THR N 108 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'N' and resid 18 through 22 1111 hydrogen bonds defined for protein. 2934 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: 7.05 Time building geometry restraints manager: 3.22 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: 5481 1.32 - 1.45: 8562 1.45 - 1.57: 16721 1.57 - 1.70: 1 1.70 - 1.83: 165 Bond restraints: 30930 Sorted by residual: bond pdb=" CA TYR B 369 " pdb=" C TYR B 369 " ideal model delta sigma weight residual 1.523 1.437 0.086 1.34e-02 5.57e+03 4.13e+01 bond pdb=" CA TYR A 369 " pdb=" C TYR A 369 " ideal model delta sigma weight residual 1.523 1.437 0.086 1.34e-02 5.57e+03 4.11e+01 bond pdb=" CA TYR C 369 " pdb=" C TYR C 369 " ideal model delta sigma weight residual 1.523 1.438 0.085 1.34e-02 5.57e+03 4.04e+01 bond pdb=" CA TYR B 365 " pdb=" C TYR B 365 " ideal model delta sigma weight residual 1.523 1.442 0.081 1.56e-02 4.11e+03 2.69e+01 bond pdb=" C PRO C 862 " pdb=" N PRO C 863 " ideal model delta sigma weight residual 1.329 1.391 -0.062 1.20e-02 6.94e+03 2.65e+01 ... (remaining 30925 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 40833 2.71 - 5.42: 1062 5.42 - 8.13: 134 8.13 - 10.84: 25 10.84 - 13.56: 15 Bond angle restraints: 42069 Sorted by residual: angle pdb=" N VAL A 367 " pdb=" CA VAL A 367 " pdb=" C VAL A 367 " ideal model delta sigma weight residual 110.21 99.55 10.66 1.13e+00 7.83e-01 8.89e+01 angle pdb=" N VAL B 367 " pdb=" CA VAL B 367 " pdb=" C VAL B 367 " ideal model delta sigma weight residual 110.21 99.57 10.64 1.13e+00 7.83e-01 8.87e+01 angle pdb=" N VAL C 367 " pdb=" CA VAL C 367 " pdb=" C VAL C 367 " ideal model delta sigma weight residual 110.21 99.63 10.58 1.13e+00 7.83e-01 8.77e+01 angle pdb=" N SER B 366 " pdb=" CA SER B 366 " pdb=" C SER B 366 " ideal model delta sigma weight residual 111.07 103.23 7.84 1.07e+00 8.73e-01 5.37e+01 angle pdb=" N SER C 366 " pdb=" CA SER C 366 " pdb=" C SER C 366 " ideal model delta sigma weight residual 111.07 103.27 7.80 1.07e+00 8.73e-01 5.31e+01 ... (remaining 42064 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 16076 17.93 - 35.86: 1258 35.86 - 53.79: 367 53.79 - 71.72: 68 71.72 - 89.65: 42 Dihedral angle restraints: 17811 sinusoidal: 6933 harmonic: 10878 Sorted by residual: 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 -86.00 -174.61 88.61 1 1.00e+01 1.00e-02 9.37e+01 dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 20.60 72.40 1 1.00e+01 1.00e-02 6.70e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual 93.00 163.42 -70.42 1 1.00e+01 1.00e-02 6.38e+01 ... (remaining 17808 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.326: 4890 0.326 - 0.652: 12 0.652 - 0.978: 4 0.978 - 1.304: 1 1.304 - 1.630: 1 Chirality restraints: 4908 Sorted by residual: 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 1.20e+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 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 1.17e+03 ... (remaining 4905 not shown) Planarity restraints: 5406 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " -0.151 2.00e-02 2.50e+03 1.99e-01 4.95e+02 pdb=" CG ASN A 331 " 0.065 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " -0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " 0.341 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " -0.234 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 603 " 0.095 2.00e-02 2.50e+03 1.14e-01 1.62e+02 pdb=" CG ASN A 603 " -0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN A 603 " 0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN A 603 " -0.192 2.00e-02 2.50e+03 pdb=" C1 NAG A1406 " 0.133 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 603 " 0.071 2.00e-02 2.50e+03 9.57e-02 1.14e+02 pdb=" CG ASN B 603 " -0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN B 603 " 0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN B 603 " -0.165 2.00e-02 2.50e+03 pdb=" C1 NAG B1406 " 0.112 2.00e-02 2.50e+03 ... (remaining 5403 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 199 2.47 - 3.08: 20470 3.08 - 3.69: 42611 3.69 - 4.29: 63507 4.29 - 4.90: 104714 Nonbonded interactions: 231501 Sorted by model distance: nonbonded pdb=" N GLU A 309 " pdb=" OE1 GLU A 309 " model vdw 1.865 3.120 nonbonded pdb=" O SER A 530 " pdb=" OG1 THR A 531 " model vdw 1.915 3.040 nonbonded pdb=" OD1 ASN C 317 " pdb=" N PHE C 318 " model vdw 1.930 3.120 nonbonded pdb=" O SER C 530 " pdb=" CG2 THR C 531 " model vdw 1.961 3.460 nonbonded pdb=" O ASN A 603 " pdb=" OG1 THR A 604 " model vdw 1.988 3.040 ... (remaining 231496 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: 0.03 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: 2.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 26.950 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 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 0.805 31041 Z= 0.673 Angle : 1.411 56.720 42360 Z= 0.740 Chirality : 0.079 1.630 4908 Planarity : 0.008 0.104 5358 Dihedral : 14.766 89.654 10707 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 20.24 Ramachandran Plot: Outliers : 2.41 % Allowed : 8.72 % Favored : 88.87 % Rotamer: Outliers : 4.19 % Allowed : 9.27 % Favored : 86.54 % 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: -3.26 (0.12), residues: 3693 helix: -1.01 (0.18), residues: 583 sheet: -1.36 (0.15), residues: 998 loop : -3.05 (0.11), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 102 TYR 0.019 0.002 TYR B 265 PHE 0.025 0.002 PHE A 86 TRP 0.020 0.003 TRP I 47 HIS 0.004 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00880 / 0.51 (30930) covalent geometry : angle 1.08346 / 0.64 (42069) SS BOND : bond 0.23445 / 17.04 ( 42) SS BOND : angle 14.01316 / 9.98 ( 84) hydrogen bonds : bond 0.19303 / 12.72 ( 1032) hydrogen bonds : angle 8.04803 / 5.39 ( 2934) link_BETA1-4 : bond 0.07718 / 5.32 ( 21) link_BETA1-4 : angle 9.86636 / 6.57 ( 63) link_NAG-ASN : bond 0.02602 / 1.98 ( 48) link_NAG-ASN : angle 9.24082 / 5.61 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 579 time to evaluate : 1.054 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 321 GLN cc_start: 0.7034 (OUTLIER) cc_final: 0.6665 (mp10) REVERT: A 388 ASN cc_start: 0.8319 (OUTLIER) cc_final: 0.8088 (m-40) REVERT: A 759 PHE cc_start: 0.8064 (OUTLIER) cc_final: 0.7749 (m-10) REVERT: A 764 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8556 (ttpp) REVERT: A 819 GLU cc_start: 0.7405 (mt-10) cc_final: 0.7054 (mt-10) REVERT: A 1081 ILE cc_start: 0.8075 (mm) cc_final: 0.7828 (mm) REVERT: B 314 GLN cc_start: 0.7804 (OUTLIER) cc_final: 0.7335 (tt0) REVERT: B 529 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.8080 (mtmm) REVERT: B 695 TYR cc_start: 0.9203 (OUTLIER) cc_final: 0.8968 (p90) REVERT: C 864 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8285 (tp) REVERT: H 11 VAL cc_start: 0.5001 (t) cc_final: 0.4782 (p) outliers start: 136 outliers final: 60 residues processed: 695 average time/residue: 0.1809 time to fit residues: 200.3102 Evaluate side-chains 327 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 259 time to evaluate : 1.113 ------------------------------------------------------------------------------- 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 315 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain B residue 969 LYS Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 1074 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 1.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 ASN A 173 GLN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN A 607 GLN A 755 GLN A 762 GLN B 121 ASN B 164 ASN B 207 HIS B 321 GLN B 360 ASN B 422 ASN B 505 HIS B 532 ASN B 564 GLN B 607 GLN B 703 ASN B 755 GLN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN C 121 ASN C 164 ASN C 173 GLN C 360 ASN C 422 ASN C 439 ASN C 532 ASN C 607 GLN ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN H 65 GLN H 100 GLN L 35 ASN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 ASN M 88 HIS N 52 ASN N 88 HIS Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.198281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 115)---------------| | r_work = 0.3789 r_free = 0.3789 target = 0.137100 restraints weight = 45086.648| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 3.95 r_work: 0.3517 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 31041 Z= 0.190 Angle : 0.816 17.591 42360 Z= 0.400 Chirality : 0.050 0.722 4908 Planarity : 0.006 0.072 5358 Dihedral : 8.099 78.789 4180 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.80 % Favored : 91.69 % Rotamer: Outliers : 3.73 % Allowed : 13.31 % Favored : 82.96 % 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: -2.32 (0.13), residues: 3693 helix: 0.57 (0.21), residues: 597 sheet: -1.03 (0.15), residues: 1009 loop : -2.56 (0.12), residues: 2087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 995 TYR 0.020 0.002 TYR A 313 PHE 0.025 0.002 PHE C 86 TRP 0.016 0.001 TRP H 111 HIS 0.019 0.002 HIS I 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.19 (30930) covalent geometry : angle 0.74636 / 0.38 (42069) SS BOND : bond 0.00553 / 0.31 ( 42) SS BOND : angle 2.90835 / 1.95 ( 84) hydrogen bonds : bond 0.05658 / 3.78 ( 1032) hydrogen bonds : angle 5.83493 / 3.90 ( 2934) link_BETA1-4 : bond 0.01297 / 0.89 ( 21) link_BETA1-4 : angle 3.11913 / 1.85 ( 63) link_NAG-ASN : bond 0.00645 / 0.41 ( 48) link_NAG-ASN : angle 4.89465 / 3.11 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 284 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.6929 (OUTLIER) cc_final: 0.6126 (m-40) REVERT: A 129 LYS cc_start: 0.7712 (ptmt) cc_final: 0.7469 (pttt) REVERT: A 153 MET cc_start: 0.5125 (mpp) cc_final: 0.4693 (mpp) REVERT: A 525 CYS cc_start: 0.4701 (OUTLIER) cc_final: 0.4049 (m) REVERT: A 764 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8459 (ttpp) REVERT: A 917 TYR cc_start: 0.7736 (m-80) cc_final: 0.7470 (m-80) REVERT: A 982 SER cc_start: 0.8836 (t) cc_final: 0.8573 (m) REVERT: B 433 VAL cc_start: 0.6647 (OUTLIER) cc_final: 0.6439 (t) REVERT: B 517 LEU cc_start: 0.7033 (OUTLIER) cc_final: 0.6746 (pp) REVERT: B 529 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8403 (mtmm) REVERT: B 731 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8273 (ptm) REVERT: B 869 MET cc_start: 0.8306 (mtp) cc_final: 0.7959 (mtp) REVERT: B 904 TYR cc_start: 0.7864 (m-10) cc_final: 0.7318 (m-10) REVERT: B 1008 VAL cc_start: 0.9288 (OUTLIER) cc_final: 0.9088 (t) REVERT: C 303 LEU cc_start: 0.8509 (mt) cc_final: 0.8285 (mt) REVERT: C 326 ILE cc_start: 0.8009 (OUTLIER) cc_final: 0.7794 (pt) REVERT: C 328 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7719 (mmp80) REVERT: C 329 PHE cc_start: 0.8749 (OUTLIER) cc_final: 0.6858 (t80) REVERT: C 396 TYR cc_start: 0.7106 (m-10) cc_final: 0.6894 (m-10) REVERT: I 111 TRP cc_start: 0.0703 (OUTLIER) cc_final: 0.0448 (t-100) REVERT: J 48 MET cc_start: 0.1541 (ptt) cc_final: 0.0598 (mmt) REVERT: J 107 TYR cc_start: 0.5780 (t80) cc_final: 0.5320 (t80) outliers start: 121 outliers final: 54 residues processed: 385 average time/residue: 0.1571 time to fit residues: 101.4215 Evaluate side-chains 285 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 219 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 969 LYS Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain I residue 106 PHE Chi-restraints excluded: chain I residue 111 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 123 optimal weight: 2.9990 chunk 298 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 163 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 144 optimal weight: 30.0000 chunk 41 optimal weight: 1.9990 chunk 140 optimal weight: 40.0000 chunk 46 optimal weight: 0.5980 chunk 310 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN A 207 HIS ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN B 207 HIS B 505 HIS B 901 GLN B1101 HIS B1119 ASN C 121 ASN C 188 ASN ** H 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 HIS N 35 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.192218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.146689 restraints weight = 44421.853| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 2.49 r_work: 0.3405 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 31041 Z= 0.220 Angle : 0.790 21.094 42360 Z= 0.386 Chirality : 0.050 0.311 4908 Planarity : 0.005 0.068 5358 Dihedral : 6.603 69.379 4098 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.82 % Favored : 92.80 % Rotamer: Outliers : 3.48 % Allowed : 14.63 % Favored : 81.89 % 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: -1.97 (0.13), residues: 3693 helix: 0.70 (0.21), residues: 594 sheet: -0.85 (0.15), residues: 1066 loop : -2.27 (0.12), residues: 2033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 102 TYR 0.022 0.002 TYR J 108 PHE 0.033 0.002 PHE C 86 TRP 0.025 0.002 TRP H 111 HIS 0.010 0.002 HIS A1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.22 (30930) covalent geometry : angle 0.73485 / 0.37 (42069) SS BOND : bond 0.00608 / 0.37 ( 42) SS BOND : angle 2.47833 / 1.55 ( 84) hydrogen bonds : bond 0.04944 / 3.30 ( 1032) hydrogen bonds : angle 5.50080 / 3.69 ( 2934) link_BETA1-4 : bond 0.00781 / 0.52 ( 21) link_BETA1-4 : angle 2.75161 / 1.63 ( 63) link_NAG-ASN : bond 0.01013 / 0.56 ( 48) link_NAG-ASN : angle 4.37295 / 2.71 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 228 time to evaluate : 0.996 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 129 LYS cc_start: 0.7597 (ptmt) cc_final: 0.7346 (pttt) REVERT: A 298 GLU cc_start: 0.7722 (tm-30) cc_final: 0.7452 (tp30) REVERT: A 405 ASN cc_start: 0.8234 (m110) cc_final: 0.7784 (p0) REVERT: A 764 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8609 (ttpp) REVERT: B 207 HIS cc_start: 0.7706 (OUTLIER) cc_final: 0.7409 (m90) REVERT: B 433 VAL cc_start: 0.6786 (OUTLIER) cc_final: 0.6555 (t) REVERT: B 859 THR cc_start: 0.8352 (t) cc_final: 0.8113 (p) REVERT: B 869 MET cc_start: 0.8466 (mtp) cc_final: 0.8071 (mtt) REVERT: C 63 THR cc_start: 0.6756 (OUTLIER) cc_final: 0.6535 (m) REVERT: C 238 PHE cc_start: 0.7028 (p90) cc_final: 0.6201 (p90) REVERT: C 366 SER cc_start: 0.7296 (OUTLIER) cc_final: 0.7088 (p) REVERT: I 81 MET cc_start: 0.0831 (ttp) cc_final: -0.0419 (tmm) REVERT: J 107 TYR cc_start: 0.6240 (t80) cc_final: 0.5820 (t80) outliers start: 113 outliers final: 62 residues processed: 326 average time/residue: 0.1540 time to fit residues: 84.4139 Evaluate side-chains 248 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 181 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain I residue 106 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 367 optimal weight: 30.0000 chunk 146 optimal weight: 20.0000 chunk 144 optimal weight: 9.9990 chunk 296 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 211 optimal weight: 10.0000 chunk 225 optimal weight: 5.9990 chunk 212 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 314 GLN B 505 HIS B 703 ASN B 762 GLN C 907 ASN H 43 GLN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.190552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.145492 restraints weight = 44012.445| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 2.45 r_work: 0.3369 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.4412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 31041 Z= 0.197 Angle : 0.736 19.889 42360 Z= 0.356 Chirality : 0.048 0.256 4908 Planarity : 0.005 0.052 5358 Dihedral : 6.186 66.161 4077 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.28 % Favored : 93.37 % Rotamer: Outliers : 3.30 % Allowed : 15.83 % Favored : 80.87 % 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: -1.73 (0.13), residues: 3693 helix: 0.79 (0.21), residues: 605 sheet: -0.49 (0.16), residues: 1000 loop : -2.18 (0.12), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 983 TYR 0.022 0.001 TYR H 107 PHE 0.030 0.002 PHE C 86 TRP 0.024 0.002 TRP H 111 HIS 0.032 0.002 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.20 (30930) covalent geometry : angle 0.68351 / 0.34 (42069) SS BOND : bond 0.00817 / 0.57 ( 42) SS BOND : angle 2.23302 / 1.39 ( 84) hydrogen bonds : bond 0.04607 / 3.08 ( 1032) hydrogen bonds : angle 5.27073 / 3.54 ( 2934) link_BETA1-4 : bond 0.00891 / 0.58 ( 21) link_BETA1-4 : angle 2.56936 / 1.51 ( 63) link_NAG-ASN : bond 0.00734 / 0.46 ( 48) link_NAG-ASN : angle 4.11948 / 2.60 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 208 time to evaluate : 1.021 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 129 LYS cc_start: 0.7804 (ptmt) cc_final: 0.7516 (pttt) REVERT: A 153 MET cc_start: 0.5059 (mpp) cc_final: 0.4596 (ptt) REVERT: A 176 LEU cc_start: 0.6432 (tp) cc_final: 0.6042 (tt) REVERT: A 298 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7694 (tp30) REVERT: A 405 ASN cc_start: 0.8274 (m110) cc_final: 0.7770 (p0) REVERT: A 574 ASP cc_start: 0.8034 (m-30) cc_final: 0.7351 (t0) REVERT: A 1072 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8263 (pt0) REVERT: B 318 PHE cc_start: 0.9065 (OUTLIER) cc_final: 0.8386 (p90) REVERT: B 433 VAL cc_start: 0.6727 (OUTLIER) cc_final: 0.6396 (t) REVERT: B 613 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.7441 (mp10) REVERT: B 859 THR cc_start: 0.8590 (t) cc_final: 0.8342 (p) REVERT: B 869 MET cc_start: 0.8678 (mtp) cc_final: 0.8436 (mtt) REVERT: C 65 PHE cc_start: 0.7068 (m-80) cc_final: 0.6777 (m-80) REVERT: C 238 PHE cc_start: 0.7190 (p90) cc_final: 0.6344 (p90) REVERT: C 358 ILE cc_start: 0.7756 (mm) cc_final: 0.7517 (mm) REVERT: C 396 TYR cc_start: 0.7494 (m-10) cc_final: 0.7232 (m-10) REVERT: C 904 TYR cc_start: 0.8236 (m-10) cc_final: 0.7857 (m-10) REVERT: H 37 VAL cc_start: 0.4302 (OUTLIER) cc_final: 0.3964 (m) REVERT: H 107 TYR cc_start: 0.5703 (t80) cc_final: 0.5397 (t80) REVERT: I 81 MET cc_start: 0.0702 (ttp) cc_final: -0.0402 (tmm) REVERT: J 107 TYR cc_start: 0.6508 (t80) cc_final: 0.5978 (t80) REVERT: N 71 SER cc_start: 0.6117 (t) cc_final: 0.5722 (p) outliers start: 107 outliers final: 67 residues processed: 297 average time/residue: 0.1629 time to fit residues: 82.4983 Evaluate side-chains 257 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 185 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain I residue 106 PHE Chi-restraints excluded: chain M residue 22 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 240 optimal weight: 10.0000 chunk 294 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 190 optimal weight: 0.6980 chunk 361 optimal weight: 20.0000 chunk 366 optimal weight: 40.0000 chunk 164 optimal weight: 0.5980 chunk 73 optimal weight: 4.9990 chunk 270 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 334 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 388 ASN B 505 HIS C 935 GLN C1010 GLN L 39 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.190862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.138136 restraints weight = 44107.378| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 2.61 r_work: 0.3352 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.4728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 31041 Z= 0.155 Angle : 0.686 20.670 42360 Z= 0.332 Chirality : 0.046 0.233 4908 Planarity : 0.004 0.050 5358 Dihedral : 5.877 65.344 4067 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.44 % Favored : 93.20 % Rotamer: Outliers : 3.30 % Allowed : 16.36 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.13), residues: 3693 helix: 1.09 (0.21), residues: 599 sheet: -0.40 (0.15), residues: 1031 loop : -2.04 (0.13), residues: 2063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 983 TYR 0.025 0.001 TYR L 50 PHE 0.025 0.001 PHE C 86 TRP 0.024 0.002 TRP H 111 HIS 0.009 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 (30930) covalent geometry : angle 0.63739 / 0.32 (42069) SS BOND : bond 0.00556 / 0.32 ( 42) SS BOND : angle 1.95339 / 1.24 ( 84) hydrogen bonds : bond 0.04147 / 2.77 ( 1032) hydrogen bonds : angle 5.11348 / 3.43 ( 2934) link_BETA1-4 : bond 0.00801 / 0.57 ( 21) link_BETA1-4 : angle 2.44792 / 1.42 ( 63) link_NAG-ASN : bond 0.00592 / 0.33 ( 48) link_NAG-ASN : angle 3.86568 / 2.39 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 196 time to evaluate : 1.151 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 126 VAL cc_start: 0.7331 (OUTLIER) cc_final: 0.6979 (m) REVERT: A 129 LYS cc_start: 0.7699 (ptmt) cc_final: 0.7391 (pttt) REVERT: A 153 MET cc_start: 0.5147 (mpp) cc_final: 0.4699 (ptt) REVERT: A 176 LEU cc_start: 0.6372 (tp) cc_final: 0.6027 (tt) REVERT: A 298 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7695 (tp30) REVERT: A 405 ASN cc_start: 0.8229 (m110) cc_final: 0.7722 (p0) REVERT: A 574 ASP cc_start: 0.7900 (m-30) cc_final: 0.7248 (t0) REVERT: B 318 PHE cc_start: 0.9050 (OUTLIER) cc_final: 0.8260 (p90) REVERT: B 433 VAL cc_start: 0.6653 (OUTLIER) cc_final: 0.6344 (t) REVERT: B 613 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.7401 (mp10) REVERT: B 859 THR cc_start: 0.8589 (t) cc_final: 0.8356 (p) REVERT: B 869 MET cc_start: 0.8682 (OUTLIER) cc_final: 0.8423 (mtt) REVERT: B 983 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.7865 (ptm160) REVERT: C 52 GLN cc_start: 0.8201 (tp-100) cc_final: 0.7912 (tp-100) REVERT: C 115 GLN cc_start: 0.7317 (mt0) cc_final: 0.6856 (mm-40) REVERT: C 358 ILE cc_start: 0.7678 (mm) cc_final: 0.7444 (mm) REVERT: C 396 TYR cc_start: 0.7446 (m-10) cc_final: 0.7230 (m-10) REVERT: C 519 HIS cc_start: 0.1323 (OUTLIER) cc_final: 0.0517 (t70) REVERT: H 37 VAL cc_start: 0.4027 (OUTLIER) cc_final: 0.3536 (m) REVERT: J 107 TYR cc_start: 0.6546 (t80) cc_final: 0.6017 (t80) REVERT: N 71 SER cc_start: 0.6164 (t) cc_final: 0.5825 (p) outliers start: 107 outliers final: 63 residues processed: 286 average time/residue: 0.1737 time to fit residues: 84.3545 Evaluate side-chains 243 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 172 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 106 PHE Chi-restraints excluded: chain M residue 22 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 248 optimal weight: 0.6980 chunk 212 optimal weight: 6.9990 chunk 265 optimal weight: 0.9980 chunk 119 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 255 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 42 optimal weight: 0.1980 chunk 76 optimal weight: 0.9980 chunk 133 optimal weight: 7.9990 chunk 217 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 388 ASN B 505 HIS C1010 GLN L 32 ASN L 35 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.192152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.139429 restraints weight = 43879.438| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.45 r_work: 0.3394 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.4929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31041 Z= 0.119 Angle : 0.657 20.517 42360 Z= 0.316 Chirality : 0.045 0.290 4908 Planarity : 0.004 0.051 5358 Dihedral : 5.677 64.820 4067 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.66 % Favored : 93.99 % Rotamer: Outliers : 2.77 % Allowed : 16.97 % Favored : 80.25 % 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: -1.26 (0.13), residues: 3693 helix: 1.47 (0.21), residues: 580 sheet: -0.25 (0.16), residues: 1019 loop : -1.90 (0.13), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 102 TYR 0.042 0.001 TYR H 107 PHE 0.033 0.001 PHE H 29 TRP 0.025 0.001 TRP H 111 HIS 0.009 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (30930) covalent geometry : angle 0.61171 / 0.30 (42069) SS BOND : bond 0.00540 / 0.30 ( 42) SS BOND : angle 1.75659 / 1.06 ( 84) hydrogen bonds : bond 0.03712 / 2.48 ( 1032) hydrogen bonds : angle 4.89377 / 3.29 ( 2934) link_BETA1-4 : bond 0.00804 / 0.56 ( 21) link_BETA1-4 : angle 2.34691 / 1.36 ( 63) link_NAG-ASN : bond 0.00669 / 0.41 ( 48) link_NAG-ASN : angle 3.67524 / 2.27 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 188 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 VAL cc_start: 0.7132 (OUTLIER) cc_final: 0.6836 (m) REVERT: A 129 LYS cc_start: 0.7580 (ptmt) cc_final: 0.7293 (pttt) REVERT: A 153 MET cc_start: 0.5509 (mpp) cc_final: 0.4749 (ptm) REVERT: A 176 LEU cc_start: 0.6366 (tp) cc_final: 0.5842 (tt) REVERT: A 298 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7616 (tp30) REVERT: A 405 ASN cc_start: 0.8042 (m110) cc_final: 0.7626 (p0) REVERT: A 448 ASN cc_start: 0.7245 (t0) cc_final: 0.6947 (m110) REVERT: A 501 TYR cc_start: 0.7485 (m-80) cc_final: 0.7219 (m-10) REVERT: A 574 ASP cc_start: 0.7780 (m-30) cc_final: 0.7185 (t0) REVERT: B 318 PHE cc_start: 0.9045 (OUTLIER) cc_final: 0.8234 (p90) REVERT: B 495 TYR cc_start: 0.3774 (OUTLIER) cc_final: 0.2476 (m-10) REVERT: B 859 THR cc_start: 0.8542 (t) cc_final: 0.8317 (p) REVERT: B 869 MET cc_start: 0.8628 (mtp) cc_final: 0.8390 (mtt) REVERT: B 988 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7201 (mp0) REVERT: C 52 GLN cc_start: 0.8155 (tp-100) cc_final: 0.7895 (tp-100) REVERT: C 63 THR cc_start: 0.7001 (OUTLIER) cc_final: 0.6769 (m) REVERT: C 115 GLN cc_start: 0.7236 (mt0) cc_final: 0.6849 (mm-40) REVERT: C 238 PHE cc_start: 0.7095 (p90) cc_final: 0.6201 (p90) REVERT: C 333 THR cc_start: 0.6303 (OUTLIER) cc_final: 0.6094 (m) REVERT: C 396 TYR cc_start: 0.7497 (m-10) cc_final: 0.7286 (m-10) REVERT: C 762 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.8240 (mt0) REVERT: H 37 VAL cc_start: 0.3764 (OUTLIER) cc_final: 0.3087 (m) REVERT: I 106 PHE cc_start: 0.6041 (OUTLIER) cc_final: 0.4969 (t80) REVERT: J 107 TYR cc_start: 0.6644 (t80) cc_final: 0.6127 (t80) REVERT: N 71 SER cc_start: 0.6146 (t) cc_final: 0.5787 (p) outliers start: 90 outliers final: 57 residues processed: 264 average time/residue: 0.1677 time to fit residues: 76.9782 Evaluate side-chains 236 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 170 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 106 PHE Chi-restraints excluded: chain M residue 22 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 202 optimal weight: 1.9990 chunk 42 optimal weight: 0.0060 chunk 218 optimal weight: 4.9990 chunk 291 optimal weight: 3.9990 chunk 306 optimal weight: 8.9990 chunk 223 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 238 optimal weight: 7.9990 chunk 230 optimal weight: 1.9990 chunk 166 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 overall best weight: 2.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 ASN A 914 ASN B 388 ASN B 505 HIS C 188 ASN C 207 HIS C 907 ASN C 935 GLN I 100 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.187848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.141093 restraints weight = 43831.816| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 2.45 r_work: 0.3316 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.5269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 31041 Z= 0.241 Angle : 0.737 20.926 42360 Z= 0.358 Chirality : 0.049 0.302 4908 Planarity : 0.004 0.051 5358 Dihedral : 5.793 61.633 4063 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.69 % Favored : 93.01 % Rotamer: Outliers : 3.36 % Allowed : 16.88 % Favored : 79.76 % 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: -1.41 (0.13), residues: 3693 helix: 1.14 (0.21), residues: 590 sheet: -0.31 (0.16), residues: 1020 loop : -1.97 (0.13), residues: 2083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 403 TYR 0.027 0.002 TYR L 50 PHE 0.036 0.002 PHE C 86 TRP 0.027 0.002 TRP H 111 HIS 0.009 0.002 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00589 / 0.24 (30930) covalent geometry : angle 0.69109 / 0.35 (42069) SS BOND : bond 0.00639 / 0.36 ( 42) SS BOND : angle 2.21074 / 1.36 ( 84) hydrogen bonds : bond 0.04688 / 3.14 ( 1032) hydrogen bonds : angle 5.10706 / 3.43 ( 2934) link_BETA1-4 : bond 0.00769 / 0.54 ( 21) link_BETA1-4 : angle 2.39679 / 1.39 ( 63) link_NAG-ASN : bond 0.00587 / 0.34 ( 48) link_NAG-ASN : angle 3.84841 / 2.39 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 175 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 VAL cc_start: 0.7196 (OUTLIER) cc_final: 0.6836 (m) REVERT: A 129 LYS cc_start: 0.7678 (ptmt) cc_final: 0.7324 (pttt) REVERT: A 176 LEU cc_start: 0.6557 (tp) cc_final: 0.6101 (tt) REVERT: A 298 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7462 (tp30) REVERT: A 405 ASN cc_start: 0.8036 (m110) cc_final: 0.7349 (p0) REVERT: A 501 TYR cc_start: 0.7559 (m-80) cc_final: 0.7162 (m-10) REVERT: A 574 ASP cc_start: 0.7667 (m-30) cc_final: 0.7126 (t0) REVERT: A 914 ASN cc_start: 0.9041 (OUTLIER) cc_final: 0.8740 (p0) REVERT: A 1072 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8103 (pt0) REVERT: B 318 PHE cc_start: 0.8998 (OUTLIER) cc_final: 0.8297 (p90) REVERT: B 388 ASN cc_start: 0.5070 (OUTLIER) cc_final: 0.4054 (t160) REVERT: B 433 VAL cc_start: 0.6677 (OUTLIER) cc_final: 0.6351 (t) REVERT: B 495 TYR cc_start: 0.4014 (OUTLIER) cc_final: 0.2617 (m-10) REVERT: B 613 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.7382 (mp10) REVERT: B 762 GLN cc_start: 0.7586 (OUTLIER) cc_final: 0.7164 (mp10) REVERT: B 869 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8188 (mtt) REVERT: B 988 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6995 (mp0) REVERT: C 52 GLN cc_start: 0.8058 (tp-100) cc_final: 0.7737 (tp-100) REVERT: C 63 THR cc_start: 0.6891 (OUTLIER) cc_final: 0.6682 (m) REVERT: C 115 GLN cc_start: 0.7357 (mt0) cc_final: 0.6941 (mm110) REVERT: C 238 PHE cc_start: 0.7007 (p90) cc_final: 0.6223 (p90) REVERT: H 37 VAL cc_start: 0.3982 (OUTLIER) cc_final: 0.3556 (m) REVERT: L 92 TRP cc_start: 0.5977 (t-100) cc_final: 0.5572 (t-100) REVERT: I 106 PHE cc_start: 0.6054 (OUTLIER) cc_final: 0.4940 (t80) REVERT: J 107 TYR cc_start: 0.7019 (t80) cc_final: 0.6385 (t80) REVERT: N 71 SER cc_start: 0.6335 (t) cc_final: 0.5913 (p) outliers start: 109 outliers final: 77 residues processed: 269 average time/residue: 0.1644 time to fit residues: 77.1494 Evaluate side-chains 253 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 162 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 106 PHE Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 25 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 283 optimal weight: 0.5980 chunk 240 optimal weight: 10.0000 chunk 224 optimal weight: 3.9990 chunk 371 optimal weight: 30.0000 chunk 76 optimal weight: 0.8980 chunk 39 optimal weight: 9.9990 chunk 141 optimal weight: 20.0000 chunk 215 optimal weight: 10.0000 chunk 270 optimal weight: 0.9990 chunk 293 optimal weight: 0.8980 chunk 181 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN B 460 ASN B 505 HIS C 907 ASN I 100 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.190207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.142202 restraints weight = 43949.842| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 2.52 r_work: 0.3374 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.5380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 31041 Z= 0.125 Angle : 0.661 20.496 42360 Z= 0.319 Chirality : 0.046 0.322 4908 Planarity : 0.004 0.052 5358 Dihedral : 5.624 61.690 4063 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.50 % Favored : 94.23 % Rotamer: Outliers : 2.56 % Allowed : 17.68 % Favored : 79.76 % 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: -1.20 (0.13), residues: 3693 helix: 1.47 (0.22), residues: 583 sheet: -0.18 (0.16), residues: 1038 loop : -1.88 (0.13), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 102 TYR 0.034 0.001 TYR L 50 PHE 0.018 0.001 PHE C 65 TRP 0.027 0.001 TRP H 111 HIS 0.025 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (30930) covalent geometry : angle 0.61743 / 0.31 (42069) SS BOND : bond 0.00560 / 0.31 ( 42) SS BOND : angle 1.92608 / 1.24 ( 84) hydrogen bonds : bond 0.03835 / 2.57 ( 1032) hydrogen bonds : angle 4.89850 / 3.28 ( 2934) link_BETA1-4 : bond 0.00774 / 0.56 ( 21) link_BETA1-4 : angle 2.25972 / 1.31 ( 63) link_NAG-ASN : bond 0.00565 / 0.31 ( 48) link_NAG-ASN : angle 3.55845 / 2.20 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 167 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 VAL cc_start: 0.7179 (OUTLIER) cc_final: 0.6893 (m) REVERT: A 129 LYS cc_start: 0.7670 (ptmt) cc_final: 0.7385 (pttt) REVERT: A 153 MET cc_start: 0.5508 (mpp) cc_final: 0.4388 (ptm) REVERT: A 176 LEU cc_start: 0.6457 (tp) cc_final: 0.5994 (tt) REVERT: A 298 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7624 (tp30) REVERT: A 369 TYR cc_start: 0.8434 (OUTLIER) cc_final: 0.8089 (m-80) REVERT: A 405 ASN cc_start: 0.8125 (m110) cc_final: 0.7352 (p0) REVERT: A 448 ASN cc_start: 0.7340 (t0) cc_final: 0.7062 (m110) REVERT: A 501 TYR cc_start: 0.7569 (m-80) cc_final: 0.7176 (m-10) REVERT: A 574 ASP cc_start: 0.7960 (m-30) cc_final: 0.7411 (t0) REVERT: B 164 ASN cc_start: 0.3796 (OUTLIER) cc_final: 0.3187 (m110) REVERT: B 318 PHE cc_start: 0.9094 (OUTLIER) cc_final: 0.8398 (p90) REVERT: B 388 ASN cc_start: 0.4933 (OUTLIER) cc_final: 0.3806 (t160) REVERT: B 433 VAL cc_start: 0.6654 (OUTLIER) cc_final: 0.6309 (t) REVERT: B 495 TYR cc_start: 0.4128 (OUTLIER) cc_final: 0.2288 (m-10) REVERT: B 613 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.7510 (mp10) REVERT: B 869 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.8412 (mtt) REVERT: B 988 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7191 (mp0) REVERT: C 52 GLN cc_start: 0.8210 (tp-100) cc_final: 0.7948 (tp-100) REVERT: C 63 THR cc_start: 0.7172 (OUTLIER) cc_final: 0.6939 (m) REVERT: C 115 GLN cc_start: 0.7344 (mt0) cc_final: 0.6972 (mm110) REVERT: C 396 TYR cc_start: 0.7449 (m-10) cc_final: 0.7153 (m-80) REVERT: H 37 VAL cc_start: 0.3819 (OUTLIER) cc_final: 0.3436 (m) REVERT: L 92 TRP cc_start: 0.5664 (t-100) cc_final: 0.5216 (t-100) REVERT: I 106 PHE cc_start: 0.6079 (OUTLIER) cc_final: 0.5254 (t80) REVERT: J 107 TYR cc_start: 0.7080 (t80) cc_final: 0.6413 (t80) REVERT: N 71 SER cc_start: 0.6321 (t) cc_final: 0.5912 (p) outliers start: 83 outliers final: 61 residues processed: 238 average time/residue: 0.1647 time to fit residues: 67.7034 Evaluate side-chains 237 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 163 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 106 PHE Chi-restraints excluded: chain M residue 22 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 170 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 chunk 253 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 294 optimal weight: 2.9990 chunk 107 optimal weight: 0.3980 chunk 287 optimal weight: 4.9990 chunk 10 optimal weight: 0.0370 chunk 111 optimal weight: 7.9990 chunk 282 optimal weight: 0.6980 overall best weight: 1.0262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 334 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN B 505 HIS C 207 HIS C 907 ASN M 35 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.189137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.120848 restraints weight = 44252.252| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.97 r_work: 0.3301 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.5499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31041 Z= 0.133 Angle : 0.650 20.310 42360 Z= 0.314 Chirality : 0.046 0.330 4908 Planarity : 0.004 0.051 5358 Dihedral : 5.464 60.948 4061 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.93 % Favored : 93.80 % Rotamer: Outliers : 2.62 % Allowed : 17.59 % Favored : 79.79 % 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: -1.08 (0.14), residues: 3693 helix: 1.63 (0.22), residues: 579 sheet: -0.08 (0.16), residues: 1030 loop : -1.83 (0.13), residues: 2084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 403 TYR 0.036 0.001 TYR L 50 PHE 0.025 0.001 PHE C 238 TRP 0.023 0.001 TRP I 111 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (30930) covalent geometry : angle 0.60868 / 0.30 (42069) SS BOND : bond 0.00540 / 0.30 ( 42) SS BOND : angle 1.78409 / 1.14 ( 84) hydrogen bonds : bond 0.03764 / 2.52 ( 1032) hydrogen bonds : angle 4.81520 / 3.23 ( 2934) link_BETA1-4 : bond 0.00761 / 0.56 ( 21) link_BETA1-4 : angle 2.21853 / 1.28 ( 63) link_NAG-ASN : bond 0.00543 / 0.29 ( 48) link_NAG-ASN : angle 3.44618 / 2.12 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 168 time to evaluate : 1.213 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 126 VAL cc_start: 0.7042 (OUTLIER) cc_final: 0.6725 (m) REVERT: A 129 LYS cc_start: 0.7326 (ptmt) cc_final: 0.6923 (pttt) REVERT: A 153 MET cc_start: 0.5907 (mpp) cc_final: 0.4696 (ptm) REVERT: A 176 LEU cc_start: 0.6168 (tp) cc_final: 0.5718 (tt) REVERT: A 298 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7444 (tp30) REVERT: A 369 TYR cc_start: 0.8601 (OUTLIER) cc_final: 0.8139 (m-80) REVERT: A 405 ASN cc_start: 0.8190 (m110) cc_final: 0.7321 (p0) REVERT: A 448 ASN cc_start: 0.7534 (t0) cc_final: 0.6977 (m110) REVERT: A 574 ASP cc_start: 0.7592 (m-30) cc_final: 0.7042 (t0) REVERT: B 164 ASN cc_start: 0.3381 (OUTLIER) cc_final: 0.2866 (m110) REVERT: B 318 PHE cc_start: 0.9017 (OUTLIER) cc_final: 0.8256 (p90) REVERT: B 433 VAL cc_start: 0.6466 (OUTLIER) cc_final: 0.6203 (t) REVERT: B 495 TYR cc_start: 0.3787 (OUTLIER) cc_final: 0.2053 (m-10) REVERT: B 613 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.7534 (mp10) REVERT: B 869 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8531 (mtt) REVERT: B 988 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7214 (mp0) REVERT: C 52 GLN cc_start: 0.8295 (tp-100) cc_final: 0.8022 (tp-100) REVERT: C 63 THR cc_start: 0.6795 (OUTLIER) cc_final: 0.6572 (m) REVERT: C 115 GLN cc_start: 0.7286 (mt0) cc_final: 0.6798 (mm110) REVERT: C 238 PHE cc_start: 0.6789 (p90) cc_final: 0.5845 (p90) REVERT: C 396 TYR cc_start: 0.7283 (m-10) cc_final: 0.7072 (m-10) REVERT: H 37 VAL cc_start: 0.3268 (OUTLIER) cc_final: 0.3048 (m) REVERT: L 92 TRP cc_start: 0.5592 (t-100) cc_final: 0.5152 (t-100) REVERT: J 107 TYR cc_start: 0.6787 (t80) cc_final: 0.6185 (t80) REVERT: N 71 SER cc_start: 0.6362 (t) cc_final: 0.6068 (p) outliers start: 85 outliers final: 67 residues processed: 240 average time/residue: 0.1683 time to fit residues: 70.6139 Evaluate side-chains 237 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 159 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 106 PHE Chi-restraints excluded: chain M residue 22 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 76 optimal weight: 3.9990 chunk 189 optimal weight: 1.9990 chunk 282 optimal weight: 0.6980 chunk 180 optimal weight: 0.5980 chunk 144 optimal weight: 0.8980 chunk 86 optimal weight: 0.1980 chunk 208 optimal weight: 7.9990 chunk 154 optimal weight: 0.7980 chunk 229 optimal weight: 2.9990 chunk 181 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.189274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.122464 restraints weight = 43861.966| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 3.01 r_work: 0.3291 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.5517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.209 31041 Z= 0.173 Angle : 0.795 59.178 42360 Z= 0.428 Chirality : 0.052 1.722 4908 Planarity : 0.005 0.193 5358 Dihedral : 5.469 60.929 4061 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.77 % Favored : 93.96 % Rotamer: Outliers : 2.43 % Allowed : 17.99 % Favored : 79.57 % Cbeta Deviations : 0.09 % 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: -1.06 (0.14), residues: 3693 helix: 1.66 (0.22), residues: 578 sheet: -0.06 (0.16), residues: 1030 loop : -1.82 (0.13), residues: 2085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 498 TYR 0.028 0.001 TYR L 50 PHE 0.021 0.001 PHE C 238 TRP 0.021 0.001 TRP I 111 HIS 0.294 0.005 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (30930) covalent geometry : angle 0.74655 / 0.42 (42069) SS BOND : bond 0.01173 / 0.74 ( 42) SS BOND : angle 3.80426 / 2.32 ( 84) hydrogen bonds : bond 0.03748 / 2.51 ( 1032) hydrogen bonds : angle 4.82625 / 3.24 ( 2934) link_BETA1-4 : bond 0.00579 / 0.43 ( 21) link_BETA1-4 : angle 2.42006 / 1.40 ( 63) link_NAG-ASN : bond 0.00540 / 0.29 ( 48) link_NAG-ASN : angle 3.44459 / 2.12 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 160 time to evaluate : 1.132 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 126 VAL cc_start: 0.7057 (OUTLIER) cc_final: 0.6738 (m) REVERT: A 129 LYS cc_start: 0.7323 (ptmt) cc_final: 0.6922 (pttt) REVERT: A 153 MET cc_start: 0.5785 (mpp) cc_final: 0.4640 (ptm) REVERT: A 176 LEU cc_start: 0.6190 (tp) cc_final: 0.5749 (tt) REVERT: A 298 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7438 (tp30) REVERT: A 369 TYR cc_start: 0.8593 (OUTLIER) cc_final: 0.8134 (m-80) REVERT: A 405 ASN cc_start: 0.8202 (m110) cc_final: 0.7321 (p0) REVERT: A 448 ASN cc_start: 0.7536 (t0) cc_final: 0.6942 (m110) REVERT: A 501 TYR cc_start: 0.7830 (m-80) cc_final: 0.7021 (m-10) REVERT: A 574 ASP cc_start: 0.7653 (m-30) cc_final: 0.7069 (t0) REVERT: B 164 ASN cc_start: 0.3505 (OUTLIER) cc_final: 0.2948 (m110) REVERT: B 318 PHE cc_start: 0.9019 (OUTLIER) cc_final: 0.8250 (p90) REVERT: B 433 VAL cc_start: 0.6464 (OUTLIER) cc_final: 0.6198 (t) REVERT: B 495 TYR cc_start: 0.3763 (OUTLIER) cc_final: 0.2048 (m-10) REVERT: B 613 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.7560 (mp10) REVERT: B 869 MET cc_start: 0.8833 (OUTLIER) cc_final: 0.8540 (mtt) REVERT: B 988 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7191 (mp0) REVERT: C 52 GLN cc_start: 0.8292 (tp-100) cc_final: 0.8018 (tp-100) REVERT: C 63 THR cc_start: 0.6830 (OUTLIER) cc_final: 0.6607 (m) REVERT: C 115 GLN cc_start: 0.7299 (mt0) cc_final: 0.6812 (mm110) REVERT: C 238 PHE cc_start: 0.6788 (p90) cc_final: 0.5827 (p90) REVERT: C 396 TYR cc_start: 0.7233 (m-10) cc_final: 0.6952 (m-80) REVERT: L 92 TRP cc_start: 0.5577 (t-100) cc_final: 0.5162 (t-100) REVERT: J 107 TYR cc_start: 0.6762 (t80) cc_final: 0.6172 (t80) REVERT: N 71 SER cc_start: 0.6369 (t) cc_final: 0.6073 (p) outliers start: 79 outliers final: 64 residues processed: 229 average time/residue: 0.1664 time to fit residues: 66.2989 Evaluate side-chains 232 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 158 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 106 PHE Chi-restraints excluded: chain M residue 22 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 140 optimal weight: 10.0000 chunk 369 optimal weight: 20.0000 chunk 209 optimal weight: 0.7980 chunk 338 optimal weight: 5.9990 chunk 244 optimal weight: 9.9990 chunk 105 optimal weight: 4.9990 chunk 364 optimal weight: 7.9990 chunk 313 optimal weight: 40.0000 chunk 99 optimal weight: 0.8980 chunk 363 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN B 505 HIS ** H 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.189307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.122869 restraints weight = 44292.328| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 3.53 r_work: 0.3265 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.5518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.209 31041 Z= 0.173 Angle : 0.795 59.178 42360 Z= 0.428 Chirality : 0.052 1.722 4908 Planarity : 0.005 0.193 5358 Dihedral : 5.469 60.929 4061 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.77 % Favored : 93.96 % Rotamer: Outliers : 2.31 % Allowed : 18.08 % Favored : 79.61 % Cbeta Deviations : 0.09 % 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: -1.06 (0.14), residues: 3693 helix: 1.66 (0.22), residues: 578 sheet: -0.06 (0.16), residues: 1030 loop : -1.82 (0.13), residues: 2085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 498 TYR 0.028 0.001 TYR L 50 PHE 0.021 0.001 PHE C 238 TRP 0.021 0.001 TRP I 111 HIS 0.294 0.005 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (30930) covalent geometry : angle 0.74655 / 0.42 (42069) SS BOND : bond 0.01173 / 0.74 ( 42) SS BOND : angle 3.80426 / 2.32 ( 84) hydrogen bonds : bond 0.03748 / 2.51 ( 1032) hydrogen bonds : angle 4.82625 / 3.24 ( 2934) link_BETA1-4 : bond 0.00579 / 0.43 ( 21) link_BETA1-4 : angle 2.42006 / 1.40 ( 63) link_NAG-ASN : bond 0.00540 / 0.29 ( 48) link_NAG-ASN : angle 3.44459 / 2.12 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9206.25 seconds wall clock time: 158 minutes 1.34 seconds (9481.34 seconds total)