Starting phenix.real_space_refine on Mon Aug 25 11:54:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jmf_61600/08_2025/9jmf_61600.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jmf_61600/08_2025/9jmf_61600.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jmf_61600/08_2025/9jmf_61600.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jmf_61600/08_2025/9jmf_61600.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jmf_61600/08_2025/9jmf_61600.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jmf_61600/08_2025/9jmf_61600.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 144 5.16 5 C 17583 2.51 5 N 4533 2.21 5 O 5490 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27750 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 8936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1147, 8936 Classifications: {'peptide': 1147} Link IDs: {'PTRANS': 52, 'TRANS': 1094} Chain breaks: 6 Chain: "B" Number of atoms: 8936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1147, 8936 Classifications: {'peptide': 1147} Link IDs: {'PTRANS': 52, 'TRANS': 1094} Chain breaks: 6 Chain: "C" Number of atoms: 8936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1147, 8936 Classifications: {'peptide': 1147} Link IDs: {'PTRANS': 52, 'TRANS': 1094} Chain breaks: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 174 Unusual residues: {'EIC': 1, 'NAG': 11} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 174 Unusual residues: {'EIC': 1, 'NAG': 11} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 174 Unusual residues: {'EIC': 1, 'NAG': 11} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 6.74, per 1000 atoms: 0.24 Number of scatterers: 27750 At special positions: 0 Unit cell: (133.32, 147.84, 159.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 144 16.00 O 5490 8.00 N 4533 7.00 C 17583 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=47, symmetry=0 Simple disulfide: pdb=" SG CYS A 33 " - pdb=" SG CYS A 198 " distance=2.03 Simple disulfide: pdb=" SG CYS A 188 " - pdb=" SG CYS A 240 " distance=2.07 Simple disulfide: pdb=" SG CYS A 342 " - pdb=" SG CYS A 352 " distance=2.03 Simple disulfide: pdb=" SG CYS A 386 " - pdb=" SG CYS A 410 " distance=2.03 Simple disulfide: pdb=" SG CYS A 428 " - pdb=" SG CYS A 481 " distance=2.03 Simple disulfide: pdb=" SG CYS A 440 " - pdb=" SG CYS A 582 " distance=2.04 Simple disulfide: pdb=" SG CYS A 505 " - pdb=" SG CYS A 526 " distance=2.03 Simple disulfide: pdb=" SG CYS A 601 " - pdb=" SG CYS A 652 " distance=2.03 Simple disulfide: pdb=" SG CYS A 618 " - pdb=" SG CYS A 648 " distance=2.04 Simple disulfide: pdb=" SG CYS A 677 " - pdb=" SG CYS A 710 " distance=2.03 Simple disulfide: pdb=" SG CYS A 724 " - pdb=" SG CYS A 733 " distance=2.03 Simple disulfide: pdb=" SG CYS A 797 " - pdb=" SG CYS A 819 " distance=2.03 Simple disulfide: pdb=" SG CYS A 802 " - pdb=" SG CYS A 808 " distance=2.03 Simple disulfide: pdb=" SG CYS A 903 " - pdb=" SG CYS A 916 " distance=2.03 Simple disulfide: pdb=" SG CYS A1097 " - pdb=" SG CYS A1108 " distance=2.03 Simple disulfide: pdb=" SG CYS A1147 " - pdb=" SG CYS A1155 " distance=2.04 Simple disulfide: pdb=" SG CYS B 33 " - pdb=" SG CYS B 198 " distance=2.03 Simple disulfide: pdb=" SG CYS B 188 " - pdb=" SG CYS B 240 " distance=2.06 Simple disulfide: pdb=" SG CYS B 342 " - pdb=" SG CYS B 352 " distance=2.02 Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 410 " distance=2.03 Simple disulfide: pdb=" SG CYS B 428 " - pdb=" SG CYS B 481 " distance=2.03 Simple disulfide: pdb=" SG CYS B 440 " - pdb=" SG CYS B 582 " distance=2.06 Simple disulfide: pdb=" SG CYS B 505 " - pdb=" SG CYS B 526 " distance=2.03 Simple disulfide: pdb=" SG CYS B 601 " - pdb=" SG CYS B 652 " distance=2.03 Simple disulfide: pdb=" SG CYS B 618 " - pdb=" SG CYS B 648 " distance=2.03 Simple disulfide: pdb=" SG CYS B 677 " - pdb=" SG CYS B 710 " distance=2.03 Simple disulfide: pdb=" SG CYS B 724 " - pdb=" SG CYS B 733 " distance=2.03 Simple disulfide: pdb=" SG CYS B 797 " - pdb=" SG CYS B 819 " distance=2.03 Simple disulfide: pdb=" SG CYS B 802 " - pdb=" SG CYS B 808 " distance=2.04 Simple disulfide: pdb=" SG CYS B 903 " - pdb=" SG CYS B 916 " distance=2.03 Simple disulfide: pdb=" SG CYS B1097 " - pdb=" SG CYS B1108 " distance=2.02 Simple disulfide: pdb=" SG CYS B1147 " - pdb=" SG CYS B1155 " distance=2.06 Simple disulfide: pdb=" SG CYS C 33 " - pdb=" SG CYS C 198 " distance=2.03 Simple disulfide: pdb=" SG CYS C 188 " - pdb=" SG CYS C 240 " distance=2.06 Simple disulfide: pdb=" SG CYS C 342 " - pdb=" SG CYS C 352 " distance=2.03 Simple disulfide: pdb=" SG CYS C 428 " - pdb=" SG CYS C 481 " distance=2.03 Simple disulfide: pdb=" SG CYS C 440 " - pdb=" SG CYS C 582 " distance=2.04 Simple disulfide: pdb=" SG CYS C 505 " - pdb=" SG CYS C 526 " distance=2.03 Simple disulfide: pdb=" SG CYS C 601 " - pdb=" SG CYS C 652 " distance=2.03 Simple disulfide: pdb=" SG CYS C 618 " - pdb=" SG CYS C 648 " distance=2.04 Simple disulfide: pdb=" SG CYS C 677 " - pdb=" SG CYS C 710 " distance=2.03 Simple disulfide: pdb=" SG CYS C 724 " - pdb=" SG CYS C 733 " distance=2.03 Simple disulfide: pdb=" SG CYS C 797 " - pdb=" SG CYS C 819 " distance=2.03 Simple disulfide: pdb=" SG CYS C 802 " - pdb=" SG CYS C 808 " distance=2.03 Simple disulfide: pdb=" SG CYS C 903 " - pdb=" SG CYS C 916 " distance=2.03 Simple disulfide: pdb=" SG CYS C1097 " - pdb=" SG CYS C1108 " distance=2.02 Simple disulfide: pdb=" SG CYS C1147 " - pdb=" SG CYS C1155 " 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=3, symmetry=0 Links applied BETA1-4 " 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 H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A1401 " - " ASN A 70 " " NAG A1402 " - " ASN A 107 " " NAG A1403 " - " ASN A 157 " " NAG A1404 " - " ASN A 247 " " NAG A1405 " - " ASN A 488 " " NAG A1406 " - " ASN A 593 " " NAG A1407 " - " ASN A 619 " " NAG A1408 " - " ASN A 718 " " NAG A1409 " - " ASN A 776 " " NAG A1410 " - " ASN A 861 " " NAG A1411 " - " ASN A 162 " " NAG B1401 " - " ASN B 70 " " NAG B1402 " - " ASN B 107 " " NAG B1403 " - " ASN B 157 " " NAG B1405 " - " ASN B 247 " " NAG B1406 " - " ASN B 488 " " NAG B1407 " - " ASN B 593 " " NAG B1408 " - " ASN B 718 " " NAG B1411 " - " ASN B 619 " " NAG C1401 " - " ASN C 70 " " NAG C1402 " - " ASN C 107 " " NAG C1403 " - " ASN C 157 " " NAG C1404 " - " ASN C 162 " " NAG C1405 " - " ASN C 247 " " NAG C1406 " - " ASN C 488 " " NAG C1407 " - " ASN C 619 " " NAG C1408 " - " ASN C 718 " " NAG C1409 " - " ASN C 776 " " NAG C1411 " - " ASN C 593 " " NAG D 1 " - " ASN A 169 " " NAG E 1 " - " ASN A 239 " " NAG F 1 " - " ASN A 387 " " NAG G 1 " - " ASN A 413 " " NAG H 1 " - " ASN A1204 " " NAG I 1 " - " ASN B 169 " " NAG J 1 " - " ASN B 239 " " NAG K 1 " - " ASN B 387 " " NAG L 1 " - " ASN B 413 " " NAG M 1 " - " ASN B1204 " " NAG N 1 " - " ASN C 169 " " NAG O 1 " - " ASN C 239 " " NAG P 1 " - " ASN C 387 " " NAG Q 1 " - " ASN C 413 " " NAG R 1 " - " ASN C1204 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.55 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6402 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 47 sheets defined 28.0% alpha, 26.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 40 through 43 Processing helix chain 'A' and resid 107 through 111 removed outlier: 3.540A pdb=" N TYR A 111 " --> pdb=" O TYR A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 225 removed outlier: 3.539A pdb=" N ARG A 225 " --> pdb=" O ASP A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 233 Processing helix chain 'A' and resid 345 through 355 removed outlier: 3.572A pdb=" N TYR A 354 " --> pdb=" O LEU A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 393 removed outlier: 3.713A pdb=" N PHE A 392 " --> pdb=" O PHE A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 420 removed outlier: 3.712A pdb=" N LEU A 417 " --> pdb=" O ASN A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 438 removed outlier: 3.654A pdb=" N ALA A 437 " --> pdb=" O PRO A 433 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N THR A 438 " --> pdb=" O GLU A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 460 removed outlier: 4.833A pdb=" N SER A 457 " --> pdb=" O ALA A 454 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA A 460 " --> pdb=" O SER A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 471 Processing helix chain 'A' and resid 523 through 533 Processing helix chain 'A' and resid 594 through 598 removed outlier: 3.749A pdb=" N LEU A 598 " --> pdb=" O THR A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 681 removed outlier: 3.837A pdb=" N ILE A 680 " --> pdb=" O ALA A 676 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N SER A 681 " --> pdb=" O CYS A 677 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 676 through 681' Processing helix chain 'A' and resid 682 through 687 removed outlier: 5.536A pdb=" N ALA A 685 " --> pdb=" O THR A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 697 Processing helix chain 'A' and resid 740 through 744 Processing helix chain 'A' and resid 796 through 802 removed outlier: 3.643A pdb=" N CYS A 802 " --> pdb=" O LYS A 798 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 813 removed outlier: 3.747A pdb=" N GLU A 813 " --> pdb=" O GLU A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 816 No H-bonds generated for 'chain 'A' and resid 814 through 816' Processing helix chain 'A' and resid 817 through 845 Processing helix chain 'A' and resid 867 through 872 Processing helix chain 'A' and resid 879 through 889 Processing helix chain 'A' and resid 899 through 906 Processing helix chain 'A' and resid 912 through 917 Processing helix chain 'A' and resid 917 through 922 Processing helix chain 'A' and resid 931 through 945 Processing helix chain 'A' and resid 962 through 975 Processing helix chain 'A' and resid 977 through 984 Processing helix chain 'A' and resid 984 through 998 Processing helix chain 'A' and resid 1007 through 1030 removed outlier: 3.904A pdb=" N GLN A1011 " --> pdb=" O ASN A1007 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS A1012 " --> pdb=" O GLU A1008 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N VAL A1013 " --> pdb=" O ALA A1009 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN A1014 " --> pdb=" O PHE A1010 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU A1027 " --> pdb=" O ALA A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1041 through 1049 Processing helix chain 'A' and resid 1050 through 1097 removed outlier: 3.770A pdb=" N GLU A1055 " --> pdb=" O VAL A1051 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL A1056 " --> pdb=" O LEU A1052 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG A1060 " --> pdb=" O VAL A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1210 through 1214 Processing helix chain 'B' and resid 40 through 45 removed outlier: 3.796A pdb=" N ILE B 44 " --> pdb=" O PRO B 40 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLN B 45 " --> pdb=" O SER B 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 40 through 45' Processing helix chain 'B' and resid 107 through 111 removed outlier: 3.517A pdb=" N TYR B 111 " --> pdb=" O TYR B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 234 removed outlier: 4.093A pdb=" N PHE B 234 " --> pdb=" O ASP B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 278 removed outlier: 3.657A pdb=" N ASN B 277 " --> pdb=" O ASN B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 353 Processing helix chain 'B' and resid 354 through 356 No H-bonds generated for 'chain 'B' and resid 354 through 356' Processing helix chain 'B' and resid 388 through 393 removed outlier: 3.713A pdb=" N PHE B 392 " --> pdb=" O PHE B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 418 removed outlier: 3.579A pdb=" N LEU B 417 " --> pdb=" O ASN B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 437 Processing helix chain 'B' and resid 452 through 459 removed outlier: 3.811A pdb=" N LYS B 456 " --> pdb=" O TYR B 453 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N SER B 457 " --> pdb=" O ALA B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 471 Processing helix chain 'B' and resid 523 through 533 removed outlier: 3.676A pdb=" N ASN B 532 " --> pdb=" O THR B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 560 removed outlier: 3.881A pdb=" N LEU B 560 " --> pdb=" O THR B 557 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 557 through 560' Processing helix chain 'B' and resid 606 through 609 removed outlier: 3.752A pdb=" N ILE B 609 " --> pdb=" O ILE B 606 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 606 through 609' Processing helix chain 'B' and resid 676 through 684 removed outlier: 3.857A pdb=" N ILE B 680 " --> pdb=" O ALA B 676 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N SER B 681 " --> pdb=" O CYS B 677 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N THR B 682 " --> pdb=" O GLN B 678 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N MET B 683 " --> pdb=" O HIS B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 687 No H-bonds generated for 'chain 'B' and resid 685 through 687' Processing helix chain 'B' and resid 688 through 696 Processing helix chain 'B' and resid 740 through 744 Processing helix chain 'B' and resid 805 through 811 Processing helix chain 'B' and resid 812 through 816 Processing helix chain 'B' and resid 821 through 845 removed outlier: 3.965A pdb=" N SER B 843 " --> pdb=" O ASN B 839 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL B 844 " --> pdb=" O LEU B 840 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 888 Processing helix chain 'B' and resid 898 through 906 Processing helix chain 'B' and resid 912 through 917 Processing helix chain 'B' and resid 917 through 922 Processing helix chain 'B' and resid 931 through 945 removed outlier: 3.557A pdb=" N SER B 945 " --> pdb=" O SER B 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 975 Processing helix chain 'B' and resid 977 through 984 Processing helix chain 'B' and resid 984 through 998 Processing helix chain 'B' and resid 1007 through 1029 removed outlier: 3.870A pdb=" N LYS B1012 " --> pdb=" O GLU B1008 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL B1013 " --> pdb=" O ALA B1009 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN B1014 " --> pdb=" O PHE B1010 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU B1027 " --> pdb=" O ALA B1023 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA B1028 " --> pdb=" O LEU B1024 " (cutoff:3.500A) Processing helix chain 'B' and resid 1041 through 1047 removed outlier: 3.633A pdb=" N ILE B1045 " --> pdb=" O SER B1041 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN B1047 " --> pdb=" O GLY B1043 " (cutoff:3.500A) Processing helix chain 'B' and resid 1050 through 1097 removed outlier: 3.883A pdb=" N GLU B1055 " --> pdb=" O VAL B1051 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL B1056 " --> pdb=" O LEU B1052 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN B1057 " --> pdb=" O GLU B1053 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 43 removed outlier: 4.140A pdb=" N TYR C 42 " --> pdb=" O GLN C 39 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE C 43 " --> pdb=" O PRO C 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 39 through 43' Processing helix chain 'C' and resid 222 through 224 No H-bonds generated for 'chain 'C' and resid 222 through 224' Processing helix chain 'C' and resid 225 through 235 removed outlier: 3.533A pdb=" N LYS C 233 " --> pdb=" O ARG C 229 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N PHE C 234 " --> pdb=" O ASP C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 353 Processing helix chain 'C' and resid 388 through 393 removed outlier: 3.651A pdb=" N PHE C 392 " --> pdb=" O PHE C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 420 removed outlier: 3.653A pdb=" N LEU C 417 " --> pdb=" O ASN C 413 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER C 419 " --> pdb=" O SER C 415 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU C 420 " --> pdb=" O LEU C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 437 Processing helix chain 'C' and resid 452 through 459 removed outlier: 4.996A pdb=" N SER C 457 " --> pdb=" O ALA C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 471 Processing helix chain 'C' and resid 523 through 533 Processing helix chain 'C' and resid 557 through 560 removed outlier: 3.731A pdb=" N LEU C 560 " --> pdb=" O THR C 557 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 557 through 560' Processing helix chain 'C' and resid 594 through 598 Processing helix chain 'C' and resid 676 through 681 removed outlier: 3.868A pdb=" N ILE C 680 " --> pdb=" O ALA C 676 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER C 681 " --> pdb=" O CYS C 677 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 676 through 681' Processing helix chain 'C' and resid 683 through 687 Processing helix chain 'C' and resid 688 through 696 Processing helix chain 'C' and resid 740 through 744 removed outlier: 3.551A pdb=" N SER C 743 " --> pdb=" O ASN C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 796 through 802 Processing helix chain 'C' and resid 805 through 812 Processing helix chain 'C' and resid 813 through 816 Processing helix chain 'C' and resid 817 through 843 Processing helix chain 'C' and resid 879 through 888 Processing helix chain 'C' and resid 898 through 906 Processing helix chain 'C' and resid 912 through 917 Processing helix chain 'C' and resid 917 through 922 Processing helix chain 'C' and resid 931 through 945 Processing helix chain 'C' and resid 962 through 974 removed outlier: 3.542A pdb=" N VAL C 974 " --> pdb=" O ARG C 970 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 984 Processing helix chain 'C' and resid 984 through 998 Processing helix chain 'C' and resid 1007 through 1028 Processing helix chain 'C' and resid 1041 through 1049 removed outlier: 3.507A pdb=" N ILE C1045 " --> pdb=" O SER C1041 " (cutoff:3.500A) Processing helix chain 'C' and resid 1052 through 1097 removed outlier: 3.941A pdb=" N VAL C1056 " --> pdb=" O LEU C1052 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 38 removed outlier: 6.581A pdb=" N ASP A 37 " --> pdb=" O ILE A 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 79 removed outlier: 3.659A pdb=" N GLN A 338 " --> pdb=" O ASN A 329 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 209 through 211 removed outlier: 12.033A pdb=" N ARG A 301 " --> pdb=" O GLN A 88 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N VAL A 90 " --> pdb=" O ARG A 301 " (cutoff:3.500A) removed outlier: 9.726A pdb=" N VAL A 303 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N SER A 92 " --> pdb=" O VAL A 303 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU A 255 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N VAL A 266 " --> pdb=" O THR A 286 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N THR A 286 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU A 268 " --> pdb=" O PHE A 284 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 113 through 114 removed outlier: 6.827A pdb=" N PHE A 183 " --> pdb=" O GLU A 244 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLU A 244 " --> pdb=" O PHE A 183 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL A 185 " --> pdb=" O TYR A 242 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N TYR A 242 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N TYR A 187 " --> pdb=" O CYS A 240 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N CYS A 240 " --> pdb=" O TYR A 187 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL A 238 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 154 through 156 removed outlier: 4.477A pdb=" N SER A 154 " --> pdb=" O PHE A 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 362 through 365 Processing sheet with id=AA7, first strand: chain 'A' and resid 375 through 378 removed outlier: 6.739A pdb=" N GLY A 375 " --> pdb=" O SER A 603 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N ASP A 605 " --> pdb=" O GLY A 375 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N TYR A 377 " --> pdb=" O ASP A 605 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN A 616 " --> pdb=" O CYS A 648 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N TYR A 646 " --> pdb=" O CYS A 618 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ILE A 637 " --> pdb=" O VAL A 649 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 403 through 407 removed outlier: 3.827A pdb=" N SER A 443 " --> pdb=" O LYS A 573 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LYS A 486 " --> pdb=" O VAL A 423 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N VAL A 423 " --> pdb=" O LYS A 486 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 411 through 412 removed outlier: 3.559A pdb=" N TYR A 412 " --> pdb=" O CYS A 582 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 512 through 513 removed outlier: 3.623A pdb=" N LYS A 512 " --> pdb=" O TYR A 507 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N ILE A 502 " --> pdb=" O LEU A 554 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU A 554 " --> pdb=" O ILE A 502 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN A 504 " --> pdb=" O SER A 552 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TRP A 540 " --> pdb=" O VAL A 551 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 714 through 721 removed outlier: 6.278A pdb=" N PHE A 748 " --> pdb=" O HIS A 715 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N THR A 717 " --> pdb=" O PHE A 748 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N LEU A 750 " --> pdb=" O THR A 717 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N ASP A 719 " --> pdb=" O LEU A 750 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER A 752 " --> pdb=" O ASP A 719 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 759 through 760 removed outlier: 6.238A pdb=" N LEU A 759 " --> pdb=" O THR B 849 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 1112 through 1121 removed outlier: 6.953A pdb=" N VAL A1130 " --> pdb=" O ILE A1114 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N SER A1116 " --> pdb=" O MET A1128 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N MET A1128 " --> pdb=" O SER A1116 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N VAL A1118 " --> pdb=" O TYR A1126 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TYR A1126 " --> pdb=" O VAL A1118 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ASN A1120 " --> pdb=" O GLY A1124 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLY A1124 " --> pdb=" O ASN A1120 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N PHE A1163 " --> pdb=" O ALA A1143 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1112 through 1121 removed outlier: 6.953A pdb=" N VAL A1130 " --> pdb=" O ILE A1114 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N SER A1116 " --> pdb=" O MET A1128 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N MET A1128 " --> pdb=" O SER A1116 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N VAL A1118 " --> pdb=" O TYR A1126 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TYR A1126 " --> pdb=" O VAL A1118 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ASN A1120 " --> pdb=" O GLY A1124 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLY A1124 " --> pdb=" O ASN A1120 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ASN A 776 " --> pdb=" O SER A1135 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N HIS A1137 " --> pdb=" O PRO A 774 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLU A1139 " --> pdb=" O SER A 772 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N SER A 772 " --> pdb=" O GLU A1139 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL A1141 " --> pdb=" O LYS A 770 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LYS A 770 " --> pdb=" O VAL A1141 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE B 958 " --> pdb=" O SER A 772 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 793 through 795 Processing sheet with id=AB7, first strand: chain 'A' and resid 848 through 849 removed outlier: 3.682A pdb=" N THR A 849 " --> pdb=" O LEU C 759 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 958 through 959 removed outlier: 6.734A pdb=" N LYS C 770 " --> pdb=" O VAL C1141 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL C1141 " --> pdb=" O LYS C 770 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N SER C 772 " --> pdb=" O GLU C1139 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLU C1139 " --> pdb=" O SER C 772 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N HIS C1137 " --> pdb=" O PRO C 774 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ASN C 776 " --> pdb=" O SER C1135 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL C1115 " --> pdb=" O VAL C1130 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N TYR C1132 " --> pdb=" O HIS C1113 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N HIS C1113 " --> pdb=" O TYR C1132 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 958 through 959 removed outlier: 6.734A pdb=" N LYS C 770 " --> pdb=" O VAL C1141 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL C1141 " --> pdb=" O LYS C 770 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N SER C 772 " --> pdb=" O GLU C1139 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLU C1139 " --> pdb=" O SER C 772 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N HIS C1137 " --> pdb=" O PRO C 774 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ASN C 776 " --> pdb=" O SER C1135 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N PHE C1163 " --> pdb=" O ALA C1143 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR C1162 " --> pdb=" O THR C1178 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1193 through 1196 removed outlier: 3.922A pdb=" N CYS A1155 " --> pdb=" O VAL A1196 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 72 through 79 removed outlier: 3.756A pdb=" N GLN B 338 " --> pdb=" O ASN B 329 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 87 through 91 removed outlier: 3.606A pdb=" N GLU B 255 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA B 285 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N THR B 270 " --> pdb=" O LEU B 283 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N LEU B 283 " --> pdb=" O THR B 270 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 113 through 114 removed outlier: 4.701A pdb=" N SER B 153 " --> pdb=" O HIS B 170 " (cutoff:3.500A) removed outlier: 9.085A pdb=" N HIS B 170 " --> pdb=" O SER B 153 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N PHE B 155 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N PHE B 168 " --> pdb=" O PHE B 155 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ASN B 157 " --> pdb=" O ALA B 166 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ALA B 166 " --> pdb=" O ASN B 157 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 191 through 192 Processing sheet with id=AC6, first strand: chain 'B' and resid 209 through 211 Processing sheet with id=AC7, first strand: chain 'B' and resid 362 through 366 removed outlier: 4.770A pdb=" N VAL B 657 " --> pdb=" O THR B 366 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 375 through 377 removed outlier: 4.056A pdb=" N GLY B 375 " --> pdb=" O CYS B 601 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ILE B 637 " --> pdb=" O VAL B 649 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 403 through 407 removed outlier: 4.042A pdb=" N SER B 443 " --> pdb=" O LYS B 573 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N SER B 480 " --> pdb=" O CYS B 428 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N CYS B 428 " --> pdb=" O SER B 480 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ARG B 482 " --> pdb=" O PHE B 426 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N PHE B 426 " --> pdb=" O ARG B 482 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N HIS B 484 " --> pdb=" O ASP B 424 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 411 through 412 removed outlier: 3.537A pdb=" N TYR B 412 " --> pdb=" O CYS B 582 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 512 through 513 removed outlier: 5.376A pdb=" N ILE B 502 " --> pdb=" O LEU B 554 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LEU B 554 " --> pdb=" O ILE B 502 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL B 547 " --> pdb=" O PHE B 544 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE B 544 " --> pdb=" O VAL B 547 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 714 through 716 Processing sheet with id=AD4, first strand: chain 'B' and resid 759 through 760 removed outlier: 6.132A pdb=" N LEU B 759 " --> pdb=" O THR C 849 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 1112 through 1121 removed outlier: 6.224A pdb=" N HIS B1113 " --> pdb=" O TYR B1132 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TYR B1132 " --> pdb=" O HIS B1113 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL B1115 " --> pdb=" O VAL B1130 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHE B1163 " --> pdb=" O ALA B1143 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1112 through 1121 removed outlier: 6.224A pdb=" N HIS B1113 " --> pdb=" O TYR B1132 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TYR B1132 " --> pdb=" O HIS B1113 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL B1115 " --> pdb=" O VAL B1130 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ASN B 776 " --> pdb=" O SER B1135 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N HIS B1137 " --> pdb=" O PRO B 774 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLU B1139 " --> pdb=" O SER B 772 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N SER B 772 " --> pdb=" O GLU B1139 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL B1141 " --> pdb=" O LYS B 770 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LYS B 770 " --> pdb=" O VAL B1141 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 793 through 795 Processing sheet with id=AD8, first strand: chain 'B' and resid 1193 through 1196 removed outlier: 4.015A pdb=" N CYS B1155 " --> pdb=" O VAL B1196 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 72 through 79 removed outlier: 6.363A pdb=" N LEU C 327 " --> pdb=" O ALA C 339 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ALA C 339 " --> pdb=" O LEU C 327 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ASN C 329 " --> pdb=" O THR C 337 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 87 through 89 removed outlier: 6.339A pdb=" N VAL C 266 " --> pdb=" O THR C 286 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N THR C 286 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LEU C 268 " --> pdb=" O PHE C 284 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 113 through 114 removed outlier: 4.588A pdb=" N SER C 153 " --> pdb=" O HIS C 170 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N HIS C 170 " --> pdb=" O SER C 153 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N PHE C 155 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N PHE C 168 " --> pdb=" O PHE C 155 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ASN C 157 " --> pdb=" O ALA C 166 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ALA C 166 " --> pdb=" O ASN C 157 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL C 182 " --> pdb=" O SER C 177 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N TYR C 242 " --> pdb=" O TYR C 187 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 209 through 211 Processing sheet with id=AE4, first strand: chain 'C' and resid 362 through 365 removed outlier: 3.965A pdb=" N GLY C 709 " --> pdb=" O THR C 706 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 376 through 379 removed outlier: 4.083A pdb=" N GLU C 379 " --> pdb=" O ASP C 605 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ILE C 637 " --> pdb=" O VAL C 649 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY C 638 " --> pdb=" O VAL C 629 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 403 through 407 removed outlier: 3.928A pdb=" N SER C 443 " --> pdb=" O LYS C 573 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N SER C 480 " --> pdb=" O CYS C 428 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N CYS C 428 " --> pdb=" O SER C 480 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ARG C 482 " --> pdb=" O PHE C 426 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N PHE C 426 " --> pdb=" O ARG C 482 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N HIS C 484 " --> pdb=" O ASP C 424 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 411 through 412 Processing sheet with id=AE8, first strand: chain 'C' and resid 512 through 513 removed outlier: 6.526A pdb=" N SER C 552 " --> pdb=" O THR C 503 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N CYS C 505 " --> pdb=" O ARG C 550 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARG C 550 " --> pdb=" O CYS C 505 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N TYR C 507 " --> pdb=" O PRO C 548 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 714 through 721 removed outlier: 4.214A pdb=" N THR C 717 " --> pdb=" O LEU C 750 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N SER C 752 " --> pdb=" O THR C 717 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ASP C 719 " --> pdb=" O SER C 752 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LEU C 732 " --> pdb=" O LEU C 728 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 792 through 795 removed outlier: 4.759A pdb=" N LYS C 792 " --> pdb=" O LEU C 926 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1193 through 1196 removed outlier: 4.242A pdb=" N CYS C1155 " --> pdb=" O VAL C1196 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE C1205 " --> pdb=" O CYS C1147 " (cutoff:3.500A) 1041 hydrogen bonds defined for protein. 2832 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.65 Time building geometry restraints manager: 3.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 4783 1.32 - 1.47: 11344 1.47 - 1.61: 12061 1.61 - 1.75: 0 1.75 - 1.90: 189 Bond restraints: 28377 Sorted by residual: bond pdb=" CA TYR C 900 " pdb=" C TYR C 900 " ideal model delta sigma weight residual 1.524 1.426 0.098 1.26e-02 6.30e+03 6.00e+01 bond pdb=" CA TYR B 900 " pdb=" C TYR B 900 " ideal model delta sigma weight residual 1.524 1.445 0.079 1.27e-02 6.20e+03 3.83e+01 bond pdb=" C CYS B 582 " pdb=" O CYS B 582 " ideal model delta sigma weight residual 1.236 1.182 0.054 8.90e-03 1.26e+04 3.70e+01 bond pdb=" CA TYR A 607 " pdb=" C TYR A 607 " ideal model delta sigma weight residual 1.530 1.465 0.065 1.10e-02 8.26e+03 3.48e+01 bond pdb=" CA ASP C1092 " pdb=" C ASP C1092 " ideal model delta sigma weight residual 1.524 1.451 0.073 1.29e-02 6.01e+03 3.20e+01 ... (remaining 28372 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.69: 37954 2.69 - 5.37: 544 5.37 - 8.06: 66 8.06 - 10.74: 21 10.74 - 13.43: 7 Bond angle restraints: 38592 Sorted by residual: angle pdb=" N SER C 694 " pdb=" CA SER C 694 " pdb=" C SER C 694 " ideal model delta sigma weight residual 111.28 122.18 -10.90 1.09e+00 8.42e-01 1.00e+02 angle pdb=" N TYR B 590 " pdb=" CA TYR B 590 " pdb=" C TYR B 590 " ideal model delta sigma weight residual 110.24 123.67 -13.43 1.41e+00 5.03e-01 9.07e+01 angle pdb=" N PRO B 588 " pdb=" CA PRO B 588 " pdb=" C PRO B 588 " ideal model delta sigma weight residual 113.40 123.50 -10.10 1.34e+00 5.57e-01 5.68e+01 angle pdb=" N SER C 789 " pdb=" CA SER C 789 " pdb=" C SER C 789 " ideal model delta sigma weight residual 108.79 119.62 -10.83 1.53e+00 4.27e-01 5.01e+01 angle pdb=" N GLY B 31 " pdb=" CA GLY B 31 " pdb=" C GLY B 31 " ideal model delta sigma weight residual 112.54 121.38 -8.84 1.28e+00 6.10e-01 4.77e+01 ... (remaining 38587 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 15717 17.98 - 35.96: 1482 35.96 - 53.94: 325 53.94 - 71.91: 97 71.91 - 89.89: 46 Dihedral angle restraints: 17667 sinusoidal: 7626 harmonic: 10041 Sorted by residual: dihedral pdb=" CB CYS A 724 " pdb=" SG CYS A 724 " pdb=" SG CYS A 733 " pdb=" CB CYS A 733 " ideal model delta sinusoidal sigma weight residual 93.00 -178.93 -88.07 1 1.00e+01 1.00e-02 9.28e+01 dihedral pdb=" CB CYS B 618 " pdb=" SG CYS B 618 " pdb=" SG CYS B 648 " pdb=" CB CYS B 648 " ideal model delta sinusoidal sigma weight residual -86.00 -167.27 81.27 1 1.00e+01 1.00e-02 8.14e+01 dihedral pdb=" CB CYS A 505 " pdb=" SG CYS A 505 " pdb=" SG CYS A 526 " pdb=" CB CYS A 526 " ideal model delta sinusoidal sigma weight residual 93.00 155.30 -62.30 1 1.00e+01 1.00e-02 5.14e+01 ... (remaining 17664 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 4052 0.090 - 0.181: 372 0.181 - 0.271: 14 0.271 - 0.362: 3 0.362 - 0.452: 4 Chirality restraints: 4445 Sorted by residual: chirality pdb=" C1 NAG B1401 " pdb=" ND2 ASN B 70 " pdb=" C2 NAG B1401 " pdb=" O5 NAG B1401 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.11e+00 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A1204 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 3.92e+00 chirality pdb=" C1 NAG C1404 " pdb=" ND2 ASN C 162 " pdb=" C2 NAG C1404 " pdb=" O5 NAG C1404 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.39e+00 ... (remaining 4442 not shown) Planarity restraints: 4985 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 2 " 0.328 2.00e-02 2.50e+03 2.78e-01 9.68e+02 pdb=" C7 NAG H 2 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG H 2 " 0.182 2.00e-02 2.50e+03 pdb=" N2 NAG H 2 " -0.486 2.00e-02 2.50e+03 pdb=" O7 NAG H 2 " 0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 1 " -0.246 2.00e-02 2.50e+03 2.12e-01 5.62e+02 pdb=" C7 NAG H 1 " 0.052 2.00e-02 2.50e+03 pdb=" C8 NAG H 1 " 0.023 2.00e-02 2.50e+03 pdb=" N2 NAG H 1 " 0.356 2.00e-02 2.50e+03 pdb=" O7 NAG H 1 " -0.185 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A1145 " 0.020 2.00e-02 2.50e+03 4.15e-02 1.72e+01 pdb=" C GLY A1145 " -0.072 2.00e-02 2.50e+03 pdb=" O GLY A1145 " 0.027 2.00e-02 2.50e+03 pdb=" N LEU A1146 " 0.024 2.00e-02 2.50e+03 ... (remaining 4982 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 6053 2.78 - 3.31: 23633 3.31 - 3.84: 45227 3.84 - 4.37: 54248 4.37 - 4.90: 95127 Nonbonded interactions: 224288 Sorted by model distance: nonbonded pdb=" O PRO C 80 " pdb=" OH TYR C 326 " model vdw 2.252 3.040 nonbonded pdb=" OH TYR C 110 " pdb=" O VAL C 205 " model vdw 2.263 3.040 nonbonded pdb=" OH TYR B 815 " pdb=" OD1 ASP B1059 " model vdw 2.293 3.040 nonbonded pdb=" OH TYR B 110 " pdb=" O VAL B 205 " model vdw 2.298 3.040 nonbonded pdb=" OG SER C 361 " pdb=" OD1 ASP C 663 " model vdw 2.310 3.040 ... (remaining 224283 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } 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=0.00 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: 0.920 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: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 28.020 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 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 : 0.007 0.499 28486 Z= 0.525 Angle : 0.838 14.644 38863 Z= 0.457 Chirality : 0.051 0.452 4445 Planarity : 0.008 0.278 4941 Dihedral : 15.226 89.892 11124 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.03 % Favored : 95.94 % Rotamer: Outliers : 0.48 % Allowed : 14.20 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.14), residues: 3399 helix: -0.31 (0.18), residues: 795 sheet: 0.28 (0.19), residues: 729 loop : -0.91 (0.14), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 409 TYR 0.019 0.002 TYR C 646 PHE 0.026 0.002 PHE A 639 TRP 0.020 0.001 TRP B 540 HIS 0.008 0.001 HIS B 46 Details of bonding type rmsd covalent geometry : bond 0.00602 (28377) covalent geometry : angle 0.81486 (38592) SS BOND : bond 0.01015 ( 47) SS BOND : angle 1.93453 ( 94) hydrogen bonds : bond 0.20551 ( 1018) hydrogen bonds : angle 7.68113 ( 2832) Misc. bond : bond 0.37498 ( 3) link_BETA1-4 : bond 0.00677 ( 15) link_BETA1-4 : angle 1.56904 ( 45) link_NAG-ASN : bond 0.00675 ( 44) link_NAG-ASN : angle 3.01534 ( 132) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 221 time to evaluate : 1.075 Fit side-chains revert: symmetry clash REVERT: A 639 PHE cc_start: 0.8900 (OUTLIER) cc_final: 0.7898 (p90) REVERT: A 725 HIS cc_start: 0.6926 (m90) cc_final: 0.6720 (m-70) REVERT: A 845 LYS cc_start: 0.8294 (ttpt) cc_final: 0.7936 (tttp) REVERT: B 223 ILE cc_start: 0.8121 (mt) cc_final: 0.7669 (tp) REVERT: B 775 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8690 (mm) REVERT: C 77 ASN cc_start: 0.9055 (OUTLIER) cc_final: 0.8639 (t160) outliers start: 14 outliers final: 6 residues processed: 230 average time/residue: 0.1875 time to fit residues: 69.9256 Evaluate side-chains 215 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 206 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 639 PHE Chi-restraints excluded: chain A residue 645 ASN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain C residue 77 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.0470 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 5.9990 overall best weight: 1.5484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 HIS A1123 ASN B 184 GLN B 349 GLN B 543 ASN B 585 GLN B 898 GLN C 39 GLN C 46 HIS C 77 ASN C 226 ASN C 274 ASN C1057 GLN C1203 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.116437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.093630 restraints weight = 36055.531| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 1.85 r_work: 0.2797 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28486 Z= 0.151 Angle : 0.569 10.978 38863 Z= 0.295 Chirality : 0.043 0.366 4445 Planarity : 0.004 0.048 4941 Dihedral : 7.139 77.131 5140 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.24 % Favored : 96.73 % Rotamer: Outliers : 1.90 % Allowed : 13.83 % Favored : 84.27 % 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 aren not related in a simple way. whole: -0.22 (0.14), residues: 3399 helix: 0.78 (0.20), residues: 786 sheet: 0.38 (0.19), residues: 729 loop : -0.75 (0.14), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 409 TYR 0.019 0.001 TYR A 607 PHE 0.011 0.001 PHE C 748 TRP 0.015 0.001 TRP B 540 HIS 0.004 0.001 HIS A1129 Details of bonding type rmsd covalent geometry : bond 0.00344 (28377) covalent geometry : angle 0.54878 (38592) SS BOND : bond 0.00532 ( 47) SS BOND : angle 1.38600 ( 94) hydrogen bonds : bond 0.05025 ( 1018) hydrogen bonds : angle 5.45483 ( 2832) Misc. bond : bond 0.00426 ( 3) link_BETA1-4 : bond 0.00322 ( 15) link_BETA1-4 : angle 1.22477 ( 45) link_NAG-ASN : bond 0.00447 ( 44) link_NAG-ASN : angle 2.32024 ( 132) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 220 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 GLN cc_start: 0.8018 (mm-40) cc_final: 0.7677 (mt0) REVERT: A 639 PHE cc_start: 0.8697 (OUTLIER) cc_final: 0.7886 (p90) REVERT: A 725 HIS cc_start: 0.7517 (m90) cc_final: 0.7168 (m-70) REVERT: B 223 ILE cc_start: 0.7841 (mt) cc_final: 0.7463 (tp) REVERT: B 326 TYR cc_start: 0.9292 (OUTLIER) cc_final: 0.8805 (m-80) REVERT: B 978 GLN cc_start: 0.7475 (tp-100) cc_final: 0.7213 (mm-40) REVERT: B 999 MET cc_start: 0.8887 (mmm) cc_final: 0.8475 (mmm) REVERT: C 32 TYR cc_start: 0.6237 (OUTLIER) cc_final: 0.5863 (t80) REVERT: C 1044 ASP cc_start: 0.8490 (m-30) cc_final: 0.8192 (m-30) outliers start: 56 outliers final: 27 residues processed: 259 average time/residue: 0.1626 time to fit residues: 69.7624 Evaluate side-chains 224 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 194 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 639 PHE Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 952 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 326 TYR Chi-restraints excluded: chain B residue 359 MET Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 610 THR Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 854 THR Chi-restraints excluded: chain C residue 939 THR Chi-restraints excluded: chain C residue 952 THR Chi-restraints excluded: chain C residue 1189 THR Chi-restraints excluded: chain C residue 1200 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 37 optimal weight: 3.9990 chunk 247 optimal weight: 0.9990 chunk 184 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 205 optimal weight: 3.9990 chunk 257 optimal weight: 0.8980 chunk 240 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 238 optimal weight: 0.9980 chunk 68 optimal weight: 6.9990 chunk 203 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A1123 ASN B 323 GLN B 984 ASN C 203 ASN C 226 ASN C 274 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.114823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.091640 restraints weight = 36398.153| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 1.88 r_work: 0.2790 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28486 Z= 0.133 Angle : 0.532 10.328 38863 Z= 0.276 Chirality : 0.042 0.366 4445 Planarity : 0.004 0.047 4941 Dihedral : 6.368 67.046 5128 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.31 % Allowed : 13.76 % Favored : 83.93 % 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 aren not related in a simple way. whole: -0.03 (0.14), residues: 3399 helix: 1.12 (0.20), residues: 786 sheet: 0.40 (0.18), residues: 729 loop : -0.66 (0.14), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 409 TYR 0.015 0.001 TYR A 607 PHE 0.012 0.001 PHE B 841 TRP 0.014 0.001 TRP A 448 HIS 0.004 0.001 HIS A 46 Details of bonding type rmsd covalent geometry : bond 0.00308 (28377) covalent geometry : angle 0.51275 (38592) SS BOND : bond 0.00419 ( 47) SS BOND : angle 1.41668 ( 94) hydrogen bonds : bond 0.04574 ( 1018) hydrogen bonds : angle 5.13537 ( 2832) Misc. bond : bond 0.00047 ( 3) link_BETA1-4 : bond 0.00316 ( 15) link_BETA1-4 : angle 1.16527 ( 45) link_NAG-ASN : bond 0.00402 ( 44) link_NAG-ASN : angle 2.15320 ( 132) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 212 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 VAL cc_start: 0.8636 (OUTLIER) cc_final: 0.8419 (p) REVERT: A 39 GLN cc_start: 0.8035 (mm-40) cc_final: 0.7670 (mt0) REVERT: A 326 TYR cc_start: 0.9319 (OUTLIER) cc_final: 0.8973 (m-10) REVERT: A 579 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7432 (mm-30) REVERT: A 585 GLN cc_start: 0.7586 (tp-100) cc_final: 0.7378 (tt0) REVERT: A 725 HIS cc_start: 0.7527 (m90) cc_final: 0.7215 (m-70) REVERT: A 1001 THR cc_start: 0.7563 (p) cc_final: 0.7164 (m) REVERT: A 1077 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.7939 (mp) REVERT: B 223 ILE cc_start: 0.7813 (mt) cc_final: 0.7462 (tp) REVERT: B 326 TYR cc_start: 0.9276 (OUTLIER) cc_final: 0.8849 (m-80) REVERT: B 653 VAL cc_start: 0.9272 (m) cc_final: 0.9048 (m) REVERT: C 631 ASP cc_start: 0.7858 (t0) cc_final: 0.7568 (t0) REVERT: C 1044 ASP cc_start: 0.8439 (m-30) cc_final: 0.8110 (m-30) outliers start: 68 outliers final: 35 residues processed: 259 average time/residue: 0.1483 time to fit residues: 64.7670 Evaluate side-chains 244 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 205 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 326 TYR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 700 MET Chi-restraints excluded: chain A residue 952 THR Chi-restraints excluded: chain A residue 1077 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 326 TYR Chi-restraints excluded: chain B residue 359 MET Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 649 VAL Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 930 MET Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain B residue 974 VAL Chi-restraints excluded: chain B residue 1059 ASP Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 610 THR Chi-restraints excluded: chain C residue 694 SER Chi-restraints excluded: chain C residue 854 THR Chi-restraints excluded: chain C residue 952 THR Chi-restraints excluded: chain C residue 1130 VAL Chi-restraints excluded: chain C residue 1200 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 280 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 216 optimal weight: 9.9990 chunk 146 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 31 optimal weight: 0.0970 chunk 163 optimal weight: 4.9990 chunk 194 optimal weight: 8.9990 chunk 243 optimal weight: 8.9990 chunk 325 optimal weight: 6.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1123 ASN B1054 GLN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.109452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.083306 restraints weight = 36447.869| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 2.26 r_work: 0.2761 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 28486 Z= 0.285 Angle : 0.658 9.861 38863 Z= 0.339 Chirality : 0.047 0.378 4445 Planarity : 0.005 0.051 4941 Dihedral : 6.510 59.843 5126 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.13 % Allowed : 13.59 % Favored : 83.28 % 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 aren not related in a simple way. whole: -0.25 (0.14), residues: 3399 helix: 0.81 (0.19), residues: 804 sheet: 0.23 (0.18), residues: 741 loop : -0.75 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 409 TYR 0.022 0.002 TYR A 607 PHE 0.021 0.002 PHE B 841 TRP 0.018 0.002 TRP C 448 HIS 0.006 0.002 HIS C1129 Details of bonding type rmsd covalent geometry : bond 0.00696 (28377) covalent geometry : angle 0.63632 (38592) SS BOND : bond 0.00731 ( 47) SS BOND : angle 1.87309 ( 94) hydrogen bonds : bond 0.05627 ( 1018) hydrogen bonds : angle 5.30396 ( 2832) Misc. bond : bond 0.00060 ( 3) link_BETA1-4 : bond 0.00281 ( 15) link_BETA1-4 : angle 1.44428 ( 45) link_NAG-ASN : bond 0.00469 ( 44) link_NAG-ASN : angle 2.44513 ( 132) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 206 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 579 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7498 (mm-30) REVERT: A 585 GLN cc_start: 0.7568 (tp-100) cc_final: 0.7330 (tt0) REVERT: A 639 PHE cc_start: 0.8719 (OUTLIER) cc_final: 0.7978 (p90) REVERT: A 905 GLN cc_start: 0.7663 (mm-40) cc_final: 0.7458 (mm-40) REVERT: A 1001 THR cc_start: 0.7890 (p) cc_final: 0.7365 (m) REVERT: B 326 TYR cc_start: 0.9382 (OUTLIER) cc_final: 0.8979 (m-80) REVERT: C 429 ASP cc_start: 0.8657 (p0) cc_final: 0.8384 (p0) outliers start: 92 outliers final: 63 residues processed: 278 average time/residue: 0.1629 time to fit residues: 75.3518 Evaluate side-chains 260 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 195 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 639 PHE Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 939 THR Chi-restraints excluded: chain A residue 952 THR Chi-restraints excluded: chain A residue 1034 THR Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1059 ASP Chi-restraints excluded: chain A residue 1098 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 326 TYR Chi-restraints excluded: chain B residue 359 MET Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 649 VAL Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 782 THR Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 930 MET Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain B residue 974 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1112 THR Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 610 THR Chi-restraints excluded: chain C residue 694 SER Chi-restraints excluded: chain C residue 854 THR Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 939 THR Chi-restraints excluded: chain C residue 946 ILE Chi-restraints excluded: chain C residue 952 THR Chi-restraints excluded: chain C residue 1130 VAL Chi-restraints excluded: chain C residue 1189 THR Chi-restraints excluded: chain C residue 1200 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 54 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 191 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 186 optimal weight: 4.9990 chunk 338 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 217 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 HIS A 725 HIS A1123 ASN C 274 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.111980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.089540 restraints weight = 36664.197| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 1.78 r_work: 0.2758 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2618 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28486 Z= 0.148 Angle : 0.560 9.283 38863 Z= 0.290 Chirality : 0.043 0.353 4445 Planarity : 0.004 0.046 4941 Dihedral : 6.121 55.263 5126 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.65 % Allowed : 14.37 % Favored : 82.98 % 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 aren not related in a simple way. whole: -0.14 (0.14), residues: 3399 helix: 1.09 (0.20), residues: 786 sheet: 0.25 (0.18), residues: 729 loop : -0.74 (0.14), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 409 TYR 0.016 0.001 TYR C 646 PHE 0.014 0.001 PHE B 841 TRP 0.017 0.001 TRP C 448 HIS 0.004 0.001 HIS B 715 Details of bonding type rmsd covalent geometry : bond 0.00343 (28377) covalent geometry : angle 0.53771 (38592) SS BOND : bond 0.00612 ( 47) SS BOND : angle 1.80420 ( 94) hydrogen bonds : bond 0.04666 ( 1018) hydrogen bonds : angle 5.08212 ( 2832) Misc. bond : bond 0.00042 ( 3) link_BETA1-4 : bond 0.00267 ( 15) link_BETA1-4 : angle 1.24349 ( 45) link_NAG-ASN : bond 0.00392 ( 44) link_NAG-ASN : angle 2.21564 ( 132) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 215 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 579 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7351 (mm-30) REVERT: A 639 PHE cc_start: 0.8586 (OUTLIER) cc_final: 0.7686 (p90) REVERT: A 905 GLN cc_start: 0.7566 (mm-40) cc_final: 0.7328 (mm-40) REVERT: A 1001 THR cc_start: 0.7720 (p) cc_final: 0.7220 (m) REVERT: B 326 TYR cc_start: 0.9309 (OUTLIER) cc_final: 0.8885 (m-80) REVERT: B 579 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7405 (mm-30) REVERT: B 999 MET cc_start: 0.8814 (mmm) cc_final: 0.8308 (mmm) REVERT: C 429 ASP cc_start: 0.8599 (p0) cc_final: 0.8302 (p0) REVERT: C 631 ASP cc_start: 0.7676 (t0) cc_final: 0.7449 (t0) outliers start: 78 outliers final: 50 residues processed: 264 average time/residue: 0.1577 time to fit residues: 68.7825 Evaluate side-chains 256 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 203 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 639 PHE Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 700 MET Chi-restraints excluded: chain A residue 724 CYS Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 939 THR Chi-restraints excluded: chain A residue 952 THR Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1098 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 326 TYR Chi-restraints excluded: chain B residue 359 MET Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 579 GLU Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 649 VAL Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 782 THR Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 930 MET Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain B residue 974 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 610 THR Chi-restraints excluded: chain C residue 694 SER Chi-restraints excluded: chain C residue 710 CYS Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 848 GLN Chi-restraints excluded: chain C residue 854 THR Chi-restraints excluded: chain C residue 870 VAL Chi-restraints excluded: chain C residue 939 THR Chi-restraints excluded: chain C residue 952 THR Chi-restraints excluded: chain C residue 1130 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 261 optimal weight: 4.9990 chunk 330 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 147 optimal weight: 0.2980 chunk 283 optimal weight: 3.9990 chunk 218 optimal weight: 6.9990 chunk 111 optimal weight: 0.0770 chunk 158 optimal weight: 0.9990 chunk 221 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 231 optimal weight: 3.9990 overall best weight: 1.4744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 GLN A 725 HIS A1123 ASN C 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.112230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.089760 restraints weight = 36637.239| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 1.78 r_work: 0.2769 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28486 Z= 0.140 Angle : 0.537 9.006 38863 Z= 0.278 Chirality : 0.043 0.349 4445 Planarity : 0.004 0.046 4941 Dihedral : 5.790 56.186 5126 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.68 % Allowed : 14.64 % Favored : 82.67 % 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 aren not related in a simple way. whole: -0.03 (0.14), residues: 3399 helix: 1.24 (0.20), residues: 786 sheet: 0.28 (0.18), residues: 741 loop : -0.68 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 409 TYR 0.015 0.001 TYR A 326 PHE 0.013 0.001 PHE B 841 TRP 0.015 0.001 TRP C 448 HIS 0.004 0.001 HIS B 715 Details of bonding type rmsd covalent geometry : bond 0.00329 (28377) covalent geometry : angle 0.51734 (38592) SS BOND : bond 0.00587 ( 47) SS BOND : angle 1.63929 ( 94) hydrogen bonds : bond 0.04382 ( 1018) hydrogen bonds : angle 4.93868 ( 2832) Misc. bond : bond 0.00044 ( 3) link_BETA1-4 : bond 0.00297 ( 15) link_BETA1-4 : angle 1.18664 ( 45) link_NAG-ASN : bond 0.00351 ( 44) link_NAG-ASN : angle 2.08460 ( 132) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 218 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 538 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.6963 (mp-120) REVERT: A 579 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7357 (mm-30) REVERT: A 627 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.6796 (ptpt) REVERT: A 639 PHE cc_start: 0.8572 (OUTLIER) cc_final: 0.7646 (p90) REVERT: A 700 MET cc_start: 0.7355 (OUTLIER) cc_final: 0.6992 (mmm) REVERT: A 905 GLN cc_start: 0.7610 (mm-40) cc_final: 0.7362 (mm-40) REVERT: A 1001 THR cc_start: 0.7726 (p) cc_final: 0.7211 (m) REVERT: B 326 TYR cc_start: 0.9305 (OUTLIER) cc_final: 0.8906 (m-80) REVERT: B 390 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8183 (mm-30) REVERT: B 579 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7382 (mm-30) REVERT: B 999 MET cc_start: 0.8748 (mmm) cc_final: 0.8193 (mmm) REVERT: C 429 ASP cc_start: 0.8553 (p0) cc_final: 0.8250 (p0) REVERT: C 631 ASP cc_start: 0.7617 (t0) cc_final: 0.7341 (t0) outliers start: 79 outliers final: 55 residues processed: 273 average time/residue: 0.1600 time to fit residues: 72.8471 Evaluate side-chains 269 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 208 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 538 GLN Chi-restraints excluded: chain A residue 627 LYS Chi-restraints excluded: chain A residue 639 PHE Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 700 MET Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 724 CYS Chi-restraints excluded: chain A residue 939 THR Chi-restraints excluded: chain A residue 952 THR Chi-restraints excluded: chain A residue 1059 ASP Chi-restraints excluded: chain A residue 1098 VAL Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 326 TYR Chi-restraints excluded: chain B residue 359 MET Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 579 GLU Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 649 VAL Chi-restraints excluded: chain B residue 782 THR Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 930 MET Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain B residue 974 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 610 THR Chi-restraints excluded: chain C residue 694 SER Chi-restraints excluded: chain C residue 710 CYS Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 848 GLN Chi-restraints excluded: chain C residue 854 THR Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 870 VAL Chi-restraints excluded: chain C residue 939 THR Chi-restraints excluded: chain C residue 946 ILE Chi-restraints excluded: chain C residue 952 THR Chi-restraints excluded: chain C residue 1130 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 129 optimal weight: 9.9990 chunk 143 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 317 optimal weight: 4.9990 chunk 183 optimal weight: 8.9990 chunk 284 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 244 optimal weight: 4.9990 chunk 157 optimal weight: 3.9990 chunk 192 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 GLN A 725 HIS A1123 ASN ** B1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 978 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.108173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.084559 restraints weight = 36890.976| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 1.93 r_work: 0.2777 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 28486 Z= 0.282 Angle : 0.656 9.395 38863 Z= 0.337 Chirality : 0.047 0.365 4445 Planarity : 0.005 0.050 4941 Dihedral : 6.203 59.898 5126 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.09 % Allowed : 14.44 % Favored : 82.47 % 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 aren not related in a simple way. whole: -0.27 (0.14), residues: 3399 helix: 0.89 (0.19), residues: 804 sheet: 0.16 (0.18), residues: 741 loop : -0.78 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 409 TYR 0.019 0.002 TYR C 646 PHE 0.022 0.002 PHE B 841 TRP 0.017 0.002 TRP C 448 HIS 0.005 0.001 HIS B1113 Details of bonding type rmsd covalent geometry : bond 0.00685 (28377) covalent geometry : angle 0.63097 (38592) SS BOND : bond 0.00851 ( 47) SS BOND : angle 2.32766 ( 94) hydrogen bonds : bond 0.05351 ( 1018) hydrogen bonds : angle 5.20630 ( 2832) Misc. bond : bond 0.00068 ( 3) link_BETA1-4 : bond 0.00248 ( 15) link_BETA1-4 : angle 1.44568 ( 45) link_NAG-ASN : bond 0.00473 ( 44) link_NAG-ASN : angle 2.39723 ( 132) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 201 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.8242 (mm-40) REVERT: A 538 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.7146 (mp-120) REVERT: A 579 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7409 (mm-30) REVERT: A 627 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.6758 (ptpt) REVERT: A 639 PHE cc_start: 0.8710 (OUTLIER) cc_final: 0.7974 (p90) REVERT: A 1001 THR cc_start: 0.7845 (p) cc_final: 0.7260 (m) REVERT: A 1214 LEU cc_start: 0.8585 (mp) cc_final: 0.8371 (mp) REVERT: B 326 TYR cc_start: 0.9355 (OUTLIER) cc_final: 0.8954 (m-80) REVERT: B 390 GLU cc_start: 0.8456 (mm-30) cc_final: 0.8250 (mm-30) REVERT: B 999 MET cc_start: 0.8762 (mmm) cc_final: 0.8055 (mmm) REVERT: C 429 ASP cc_start: 0.8521 (p0) cc_final: 0.8208 (p0) outliers start: 91 outliers final: 70 residues processed: 268 average time/residue: 0.1683 time to fit residues: 75.0975 Evaluate side-chains 272 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 197 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 538 GLN Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 627 LYS Chi-restraints excluded: chain A residue 639 PHE Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 700 MET Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 724 CYS Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 939 THR Chi-restraints excluded: chain A residue 952 THR Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1059 ASP Chi-restraints excluded: chain A residue 1098 VAL Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 326 TYR Chi-restraints excluded: chain B residue 359 MET Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 579 GLU Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 649 VAL Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 782 THR Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 930 MET Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain B residue 974 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1112 THR Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 359 MET Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 610 THR Chi-restraints excluded: chain C residue 694 SER Chi-restraints excluded: chain C residue 710 CYS Chi-restraints excluded: chain C residue 848 GLN Chi-restraints excluded: chain C residue 854 THR Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 870 VAL Chi-restraints excluded: chain C residue 939 THR Chi-restraints excluded: chain C residue 946 ILE Chi-restraints excluded: chain C residue 952 THR Chi-restraints excluded: chain C residue 1130 VAL Chi-restraints excluded: chain C residue 1189 THR Chi-restraints excluded: chain C residue 1200 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 22 optimal weight: 10.0000 chunk 249 optimal weight: 3.9990 chunk 244 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 139 optimal weight: 0.9990 chunk 198 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 219 optimal weight: 3.9990 chunk 307 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 327 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 GLN A 686 GLN A 725 HIS A1123 ASN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 GLN C 274 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.111391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.087976 restraints weight = 36606.787| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 1.93 r_work: 0.2811 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28486 Z= 0.125 Angle : 0.550 9.670 38863 Z= 0.285 Chirality : 0.042 0.335 4445 Planarity : 0.004 0.045 4941 Dihedral : 5.770 58.978 5126 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.34 % Allowed : 15.46 % Favored : 82.20 % 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 aren not related in a simple way. whole: -0.09 (0.14), residues: 3399 helix: 1.26 (0.20), residues: 786 sheet: 0.22 (0.19), residues: 729 loop : -0.73 (0.14), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 409 TYR 0.015 0.001 TYR B 507 PHE 0.013 0.001 PHE B 284 TRP 0.016 0.001 TRP C 448 HIS 0.005 0.001 HIS C 715 Details of bonding type rmsd covalent geometry : bond 0.00289 (28377) covalent geometry : angle 0.52433 (38592) SS BOND : bond 0.00593 ( 47) SS BOND : angle 2.27656 ( 94) hydrogen bonds : bond 0.04253 ( 1018) hydrogen bonds : angle 4.95409 ( 2832) Misc. bond : bond 0.00044 ( 3) link_BETA1-4 : bond 0.00282 ( 15) link_BETA1-4 : angle 1.19255 ( 45) link_NAG-ASN : bond 0.00392 ( 44) link_NAG-ASN : angle 2.08916 ( 132) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 214 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 538 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7018 (mp-120) REVERT: A 579 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7350 (mm-30) REVERT: A 627 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.6838 (ptpt) REVERT: A 639 PHE cc_start: 0.8577 (OUTLIER) cc_final: 0.7779 (p90) REVERT: A 700 MET cc_start: 0.7306 (OUTLIER) cc_final: 0.6940 (mmm) REVERT: A 905 GLN cc_start: 0.7661 (mm-40) cc_final: 0.7447 (mm-40) REVERT: A 1001 THR cc_start: 0.7938 (p) cc_final: 0.7308 (m) REVERT: A 1214 LEU cc_start: 0.8465 (mp) cc_final: 0.8198 (mp) REVERT: B 326 TYR cc_start: 0.9303 (OUTLIER) cc_final: 0.8927 (m-80) REVERT: B 579 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7393 (mm-30) REVERT: B 999 MET cc_start: 0.8698 (mmm) cc_final: 0.7978 (mmm) REVERT: C 429 ASP cc_start: 0.8570 (p0) cc_final: 0.8278 (p0) outliers start: 69 outliers final: 44 residues processed: 264 average time/residue: 0.1557 time to fit residues: 67.5986 Evaluate side-chains 257 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 207 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 538 GLN Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 627 LYS Chi-restraints excluded: chain A residue 639 PHE Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 700 MET Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 724 CYS Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 952 THR Chi-restraints excluded: chain A residue 1059 ASP Chi-restraints excluded: chain A residue 1098 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 326 TYR Chi-restraints excluded: chain B residue 359 MET Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 579 GLU Chi-restraints excluded: chain B residue 649 VAL Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 930 MET Chi-restraints excluded: chain B residue 974 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 694 SER Chi-restraints excluded: chain C residue 710 CYS Chi-restraints excluded: chain C residue 848 GLN Chi-restraints excluded: chain C residue 854 THR Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 952 THR Chi-restraints excluded: chain C residue 1130 VAL Chi-restraints excluded: chain C residue 1200 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 30 optimal weight: 5.9990 chunk 154 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 282 optimal weight: 0.9990 chunk 341 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 31 optimal weight: 0.3980 chunk 87 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 chunk 203 optimal weight: 4.9990 chunk 207 optimal weight: 4.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 GLN A1123 ASN ** C 39 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 = 0.3210 r_free = 0.3210 target = 0.109683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.086212 restraints weight = 36707.541| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 1.92 r_work: 0.2806 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 28486 Z= 0.204 Angle : 0.597 9.786 38863 Z= 0.308 Chirality : 0.044 0.349 4445 Planarity : 0.004 0.048 4941 Dihedral : 5.833 57.882 5126 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.45 % Allowed : 15.22 % Favored : 82.33 % 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 aren not related in a simple way. whole: -0.14 (0.14), residues: 3399 helix: 1.18 (0.20), residues: 786 sheet: 0.18 (0.18), residues: 741 loop : -0.75 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 409 TYR 0.016 0.002 TYR A 607 PHE 0.017 0.001 PHE B 841 TRP 0.016 0.001 TRP C 448 HIS 0.004 0.001 HIS B1113 Details of bonding type rmsd covalent geometry : bond 0.00490 (28377) covalent geometry : angle 0.57165 (38592) SS BOND : bond 0.00751 ( 47) SS BOND : angle 2.34741 ( 94) hydrogen bonds : bond 0.04797 ( 1018) hydrogen bonds : angle 5.04277 ( 2832) Misc. bond : bond 0.00056 ( 3) link_BETA1-4 : bond 0.00241 ( 15) link_BETA1-4 : angle 1.30142 ( 45) link_NAG-ASN : bond 0.00417 ( 44) link_NAG-ASN : angle 2.21963 ( 132) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 199 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 538 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.7145 (mp-120) REVERT: A 579 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7390 (mm-30) REVERT: A 627 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.6821 (ptpt) REVERT: A 639 PHE cc_start: 0.8623 (OUTLIER) cc_final: 0.7900 (p90) REVERT: A 700 MET cc_start: 0.7323 (OUTLIER) cc_final: 0.6960 (mmm) REVERT: A 905 GLN cc_start: 0.7686 (mm-40) cc_final: 0.7470 (mm-40) REVERT: A 1001 THR cc_start: 0.7844 (p) cc_final: 0.7249 (m) REVERT: A 1214 LEU cc_start: 0.8494 (mp) cc_final: 0.8222 (mp) REVERT: B 326 TYR cc_start: 0.9337 (OUTLIER) cc_final: 0.8974 (m-80) REVERT: C 429 ASP cc_start: 0.8561 (p0) cc_final: 0.8268 (p0) outliers start: 72 outliers final: 58 residues processed: 253 average time/residue: 0.1571 time to fit residues: 65.6418 Evaluate side-chains 261 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 198 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 538 GLN Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 627 LYS Chi-restraints excluded: chain A residue 639 PHE Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 700 MET Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 724 CYS Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 952 THR Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1059 ASP Chi-restraints excluded: chain A residue 1098 VAL Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 326 TYR Chi-restraints excluded: chain B residue 359 MET Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 579 GLU Chi-restraints excluded: chain B residue 649 VAL Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 930 MET Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain B residue 974 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 359 MET Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 694 SER Chi-restraints excluded: chain C residue 710 CYS Chi-restraints excluded: chain C residue 848 GLN Chi-restraints excluded: chain C residue 854 THR Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 870 VAL Chi-restraints excluded: chain C residue 946 ILE Chi-restraints excluded: chain C residue 952 THR Chi-restraints excluded: chain C residue 1130 VAL Chi-restraints excluded: chain C residue 1200 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 311 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 chunk 299 optimal weight: 0.7980 chunk 111 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 261 optimal weight: 1.9990 chunk 331 optimal weight: 0.7980 chunk 340 optimal weight: 0.6980 chunk 202 optimal weight: 8.9990 chunk 119 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 GLN A1123 ASN B 686 GLN C 39 GLN C 274 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.111660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.088248 restraints weight = 36585.195| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 1.93 r_work: 0.2812 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 28486 Z= 0.122 Angle : 0.547 12.850 38863 Z= 0.283 Chirality : 0.042 0.332 4445 Planarity : 0.004 0.045 4941 Dihedral : 5.503 58.859 5126 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.14 % Allowed : 15.53 % Favored : 82.33 % 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 aren not related in a simple way. whole: 0.05 (0.14), residues: 3399 helix: 1.48 (0.20), residues: 771 sheet: 0.29 (0.19), residues: 741 loop : -0.68 (0.14), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 409 TYR 0.015 0.001 TYR B1132 PHE 0.011 0.001 PHE B 284 TRP 0.015 0.001 TRP A 448 HIS 0.005 0.001 HIS C 715 Details of bonding type rmsd covalent geometry : bond 0.00282 (28377) covalent geometry : angle 0.52331 (38592) SS BOND : bond 0.00597 ( 47) SS BOND : angle 2.19495 ( 94) hydrogen bonds : bond 0.04125 ( 1018) hydrogen bonds : angle 4.91031 ( 2832) Misc. bond : bond 0.00045 ( 3) link_BETA1-4 : bond 0.00341 ( 15) link_BETA1-4 : angle 1.18736 ( 45) link_NAG-ASN : bond 0.00371 ( 44) link_NAG-ASN : angle 2.03142 ( 132) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 218 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 GLU cc_start: 0.6924 (mm-30) cc_final: 0.6408 (mt-10) REVERT: A 538 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.6949 (mp-120) REVERT: A 579 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7401 (mm-30) REVERT: A 627 LYS cc_start: 0.8071 (OUTLIER) cc_final: 0.6833 (ptpt) REVERT: A 639 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.7613 (p90) REVERT: A 700 MET cc_start: 0.7159 (OUTLIER) cc_final: 0.6772 (mmm) REVERT: A 905 GLN cc_start: 0.7658 (mm-40) cc_final: 0.7450 (mm-40) REVERT: A 1001 THR cc_start: 0.7785 (p) cc_final: 0.7207 (m) REVERT: A 1214 LEU cc_start: 0.8433 (mp) cc_final: 0.8147 (mp) REVERT: B 223 ILE cc_start: 0.7885 (mt) cc_final: 0.7608 (tp) REVERT: B 326 TYR cc_start: 0.9285 (OUTLIER) cc_final: 0.8911 (m-80) REVERT: B 579 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7424 (mm-30) REVERT: C 429 ASP cc_start: 0.8587 (p0) cc_final: 0.8273 (p0) REVERT: C 1044 ASP cc_start: 0.8448 (m-30) cc_final: 0.8121 (m-30) outliers start: 63 outliers final: 53 residues processed: 262 average time/residue: 0.1434 time to fit residues: 61.9556 Evaluate side-chains 266 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 207 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 538 GLN Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 627 LYS Chi-restraints excluded: chain A residue 639 PHE Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 700 MET Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 724 CYS Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 939 THR Chi-restraints excluded: chain A residue 952 THR Chi-restraints excluded: chain A residue 1059 ASP Chi-restraints excluded: chain A residue 1098 VAL Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 326 TYR Chi-restraints excluded: chain B residue 359 MET Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 579 GLU Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 649 VAL Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 930 MET Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain B residue 974 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 694 SER Chi-restraints excluded: chain C residue 710 CYS Chi-restraints excluded: chain C residue 848 GLN Chi-restraints excluded: chain C residue 854 THR Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 870 VAL Chi-restraints excluded: chain C residue 946 ILE Chi-restraints excluded: chain C residue 952 THR Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1130 VAL Chi-restraints excluded: chain C residue 1200 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 187 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 243 optimal weight: 0.6980 chunk 93 optimal weight: 0.0070 chunk 301 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 162 optimal weight: 5.9990 chunk 306 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 282 optimal weight: 2.9990 overall best weight: 1.3404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 GLN A1123 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.110826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.087260 restraints weight = 36581.615| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 1.94 r_work: 0.2826 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 28486 Z= 0.135 Angle : 0.552 12.689 38863 Z= 0.285 Chirality : 0.043 0.337 4445 Planarity : 0.004 0.045 4941 Dihedral : 5.387 58.597 5126 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.34 % Allowed : 15.32 % Favored : 82.33 % 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 aren not related in a simple way. whole: 0.05 (0.14), residues: 3399 helix: 1.41 (0.20), residues: 786 sheet: 0.30 (0.19), residues: 741 loop : -0.66 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 409 TYR 0.014 0.001 TYR B 507 PHE 0.013 0.001 PHE B 284 TRP 0.015 0.001 TRP C 448 HIS 0.004 0.001 HIS C 715 Details of bonding type rmsd covalent geometry : bond 0.00316 (28377) covalent geometry : angle 0.52742 (38592) SS BOND : bond 0.00589 ( 47) SS BOND : angle 2.24462 ( 94) hydrogen bonds : bond 0.04212 ( 1018) hydrogen bonds : angle 4.89110 ( 2832) Misc. bond : bond 0.00044 ( 3) link_BETA1-4 : bond 0.00280 ( 15) link_BETA1-4 : angle 1.20275 ( 45) link_NAG-ASN : bond 0.00377 ( 44) link_NAG-ASN : angle 2.04516 ( 132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5879.57 seconds wall clock time: 101 minutes 48.08 seconds (6108.08 seconds total)