Starting phenix.real_space_refine on Wed May 28 01:40:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gtp_34261/05_2025/8gtp_34261.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gtp_34261/05_2025/8gtp_34261.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gtp_34261/05_2025/8gtp_34261.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gtp_34261/05_2025/8gtp_34261.map" model { file = "/net/cci-nas-00/data/ceres_data/8gtp_34261/05_2025/8gtp_34261.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gtp_34261/05_2025/8gtp_34261.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.107 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 132 5.16 5 C 19257 2.51 5 N 4959 2.21 5 O 5901 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.49s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 30249 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 8043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 8043 Classifications: {'peptide': 1025} Link IDs: {'PTRANS': 56, 'TRANS': 968} Chain breaks: 8 Chain: "B" Number of atoms: 8043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 8043 Classifications: {'peptide': 1025} Link IDs: {'PTRANS': 56, 'TRANS': 968} Chain breaks: 8 Chain: "C" Number of atoms: 8043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 8043 Classifications: {'peptide': 1025} Link IDs: {'PTRANS': 56, 'TRANS': 968} Chain breaks: 8 Chain: "H" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 902 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 114} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "L" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 816 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 8, 'TRANS': 102} Chain: "I" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 902 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 114} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "M" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 816 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 8, 'TRANS': 102} Chain: "J" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 902 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 114} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "N" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 816 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 8, 'TRANS': 102} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: "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: "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: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 16.52, per 1000 atoms: 0.55 Number of scatterers: 30249 At special positions: 0 Unit cell: (134.625, 178.782, 224.016, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 132 16.00 O 5901 8.00 N 4959 7.00 C 19257 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.08 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.87 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.02 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.20 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=1.99 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.50 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.26 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=1.97 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.17 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.10 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.08 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.66 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.02 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=1.80 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=1.99 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.51 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.26 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=1.97 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.17 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.10 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.08 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.10 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.02 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=1.89 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=1.98 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.74 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.26 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=1.97 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.17 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.10 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " distance=2.17 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 95 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 89 " distance=2.17 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 95 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 89 " distance=2.17 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A1410 " - " NAG A1411 " " NAG B1410 " - " NAG B1411 " " NAG C1410 " - " NAG C1411 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG K 1 " - " NAG K 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 165 " " NAG A1404 " - " ASN A 234 " " NAG A1405 " - " ASN A 282 " " NAG A1406 " - " ASN A 603 " " NAG A1407 " - " ASN A 616 " " NAG A1408 " - " ASN A 657 " " NAG A1409 " - " ASN A 709 " " NAG A1410 " - " ASN A1074 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 122 " " NAG B1403 " - " ASN B 165 " " NAG B1404 " - " ASN B 234 " " NAG B1405 " - " ASN B 282 " " NAG B1406 " - " ASN B 603 " " NAG B1407 " - " ASN B 616 " " NAG B1408 " - " ASN B 657 " " NAG B1409 " - " ASN B 709 " " NAG B1410 " - " ASN B1074 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 122 " " NAG C1403 " - " ASN C 165 " " NAG C1404 " - " ASN C 234 " " NAG C1405 " - " ASN C 282 " " NAG C1406 " - " ASN C 603 " " NAG C1407 " - " ASN C 616 " " NAG C1408 " - " ASN C 657 " " NAG C1409 " - " ASN C 709 " " NAG C1410 " - " ASN C1074 " " NAG D 1 " - " ASN A 331 " " NAG E 1 " - " ASN A 343 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1098 " " NAG O 1 " - " ASN A1134 " " NAG P 1 " - " ASN B 331 " " NAG Q 1 " - " ASN B 343 " " NAG R 1 " - " ASN B 717 " " NAG S 1 " - " ASN B 801 " " NAG T 1 " - " ASN B1098 " " NAG U 1 " - " ASN B1134 " " NAG V 1 " - " ASN C 331 " " NAG W 1 " - " ASN C 343 " " NAG X 1 " - " ASN C 717 " " NAG Y 1 " - " ASN C 801 " " NAG Z 1 " - " ASN C1098 " " NAG a 1 " - " ASN C1134 " Time building additional restraints: 7.66 Conformation dependent library (CDL) restraints added in 3.4 seconds 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6984 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 61 sheets defined 18.8% alpha, 31.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.25 Creating SS restraints... Processing helix chain 'A' and resid 295 through 304 Processing helix chain 'A' and resid 337 through 342 removed outlier: 4.352A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.918A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.653A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 747 through 754 removed outlier: 4.087A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.986A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 823 removed outlier: 3.589A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.514A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.577A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.652A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.590A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 removed outlier: 4.080A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.757A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 983 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.324A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.953A pdb=" N GLU B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 342 removed outlier: 3.831A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 3.919A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.654A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 754 removed outlier: 4.089A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.986A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 removed outlier: 3.590A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.514A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.577A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.651A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.591A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 4.078A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.757A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 988 through 1033 removed outlier: 4.288A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.719A pdb=" N GLU C 298 " --> pdb=" O ASP C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 342 removed outlier: 4.351A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.919A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.654A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 747 through 754 removed outlier: 4.088A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.985A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 823 removed outlier: 3.591A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.515A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.577A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.651A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.592A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 4.078A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.757A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 983 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.322A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.682A pdb=" N SER H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N HIS H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.507A pdb=" N ARG H 64 " --> pdb=" O GLN H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.682A pdb=" N SER I 31 " --> pdb=" O THR I 28 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N HIS I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 28 through 32' Processing helix chain 'I' and resid 61 through 64 removed outlier: 3.506A pdb=" N ARG I 64 " --> pdb=" O GLN I 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 61 through 64' Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.683A pdb=" N SER J 31 " --> pdb=" O THR J 28 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N HIS J 32 " --> pdb=" O PHE J 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 28 through 32' Processing helix chain 'J' and resid 61 through 64 removed outlier: 3.506A pdb=" N ARG J 64 " --> pdb=" O GLN J 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 61 through 64' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.701A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.815A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN C 542 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG C 328 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.012A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.503A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN A 164 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.503A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 310 through 318 removed outlier: 4.554A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN A 613 " --> pdb=" O GLY A 594 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER A 596 " --> pdb=" O LEU A 611 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU A 611 " --> pdb=" O SER A 596 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.547A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 391 through 392 removed outlier: 3.576A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.694A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 538 through 543 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.956A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 702 through 704 removed outlier: 3.868A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.151A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.151A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.499A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.666A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.945A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.701A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.011A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.503A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN B 164 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.503A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 310 through 314 removed outlier: 4.079A pdb=" N SER B 596 " --> pdb=" O LEU B 611 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU B 611 " --> pdb=" O SER B 596 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 327 through 328 removed outlier: 5.615A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.546A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.695A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.024A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.748A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.150A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.150A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.499A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.944A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.701A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.011A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.502A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASN C 164 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.502A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.632A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N SER C 596 " --> pdb=" O LEU C 611 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU C 611 " --> pdb=" O SER C 596 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.546A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.694A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.820A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 7.151A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 removed outlier: 7.151A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.498A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.945A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.555A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.360A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 9 through 11 removed outlier: 3.696A pdb=" N VAL L 49 " --> pdb=" O TRP L 36 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 9 through 11 Processing sheet with id=AF6, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AF7, first strand: chain 'I' and resid 3 through 5 removed outlier: 3.555A pdb=" N GLN I 3 " --> pdb=" O SER I 25 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 57 through 59 removed outlier: 6.360A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE I 34 " --> pdb=" O ILE I 50 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'M' and resid 9 through 11 removed outlier: 3.696A pdb=" N VAL M 49 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N GLN M 38 " --> pdb=" O LEU M 47 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LEU M 47 " --> pdb=" O GLN M 38 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'M' and resid 9 through 11 Processing sheet with id=AG2, first strand: chain 'M' and resid 17 through 23 Processing sheet with id=AG3, first strand: chain 'J' and resid 3 through 5 removed outlier: 3.555A pdb=" N GLN J 3 " --> pdb=" O SER J 25 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'J' and resid 57 through 59 removed outlier: 6.360A pdb=" N TRP J 36 " --> pdb=" O MET J 48 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE J 34 " --> pdb=" O ILE J 50 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'N' and resid 9 through 11 removed outlier: 3.696A pdb=" N VAL N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N GLN N 38 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LEU N 47 " --> pdb=" O GLN N 38 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'N' and resid 9 through 11 Processing sheet with id=AG7, first strand: chain 'N' and resid 17 through 23 1103 hydrogen bonds defined for protein. 2958 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 16.19 Time building geometry restraints manager: 8.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5136 1.32 - 1.44: 8634 1.44 - 1.57: 17021 1.57 - 1.69: 1 1.69 - 1.81: 171 Bond restraints: 30963 Sorted by residual: bond pdb=" N PRO B 561 " pdb=" CD PRO B 561 " ideal model delta sigma weight residual 1.473 1.539 -0.066 1.40e-02 5.10e+03 2.22e+01 bond pdb=" C PHE C 329 " pdb=" N PRO C 330 " ideal model delta sigma weight residual 1.329 1.388 -0.058 1.25e-02 6.40e+03 2.17e+01 bond pdb=" N PRO C 561 " pdb=" CD PRO C 561 " ideal model delta sigma weight residual 1.473 1.538 -0.065 1.40e-02 5.10e+03 2.17e+01 bond pdb=" C ILE C 664 " pdb=" N PRO C 665 " ideal model delta sigma weight residual 1.331 1.387 -0.055 1.20e-02 6.94e+03 2.14e+01 bond pdb=" C ILE A 664 " pdb=" N PRO A 665 " ideal model delta sigma weight residual 1.331 1.386 -0.055 1.20e-02 6.94e+03 2.11e+01 ... (remaining 30958 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 40987 2.74 - 5.48: 994 5.48 - 8.22: 118 8.22 - 10.96: 29 10.96 - 13.70: 16 Bond angle restraints: 42144 Sorted by residual: angle pdb=" N LYS A 310 " pdb=" CA LYS A 310 " pdb=" C LYS A 310 " ideal model delta sigma weight residual 109.15 120.36 -11.21 1.44e+00 4.82e-01 6.06e+01 angle pdb=" N PHE A 559 " pdb=" CA PHE A 559 " pdb=" C PHE A 559 " ideal model delta sigma weight residual 110.32 98.17 12.15 1.59e+00 3.96e-01 5.84e+01 angle pdb=" N PHE C 338 " pdb=" CA PHE C 338 " pdb=" C PHE C 338 " ideal model delta sigma weight residual 111.40 102.37 9.03 1.22e+00 6.72e-01 5.48e+01 angle pdb=" N PHE A 338 " pdb=" CA PHE A 338 " pdb=" C PHE A 338 " ideal model delta sigma weight residual 111.40 102.46 8.94 1.22e+00 6.72e-01 5.37e+01 angle pdb=" N LEU A 560 " pdb=" CA LEU A 560 " pdb=" C LEU A 560 " ideal model delta sigma weight residual 110.40 100.89 9.51 1.31e+00 5.83e-01 5.28e+01 ... (remaining 42139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 17456 17.92 - 35.84: 1337 35.84 - 53.76: 337 53.76 - 71.68: 75 71.68 - 89.60: 37 Dihedral angle restraints: 19242 sinusoidal: 8349 harmonic: 10893 Sorted by residual: dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual 93.00 14.84 78.16 1 1.00e+01 1.00e-02 7.63e+01 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual 93.00 170.54 -77.54 1 1.00e+01 1.00e-02 7.53e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual 93.00 20.28 72.72 1 1.00e+01 1.00e-02 6.75e+01 ... (remaining 19239 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.296: 4896 0.296 - 0.592: 11 0.592 - 0.888: 4 0.888 - 1.183: 2 1.183 - 1.479: 1 Chirality restraints: 4914 Sorted by residual: chirality pdb=" C1 NAG A1411 " pdb=" O4 NAG A1410 " pdb=" C2 NAG A1411 " pdb=" O5 NAG A1411 " both_signs ideal model delta sigma weight residual False -2.40 -3.09 0.69 2.00e-02 2.50e+03 1.19e+03 chirality pdb=" C1 NAG C1411 " pdb=" O4 NAG C1410 " pdb=" C2 NAG C1411 " pdb=" O5 NAG C1411 " both_signs ideal model delta sigma weight residual False -2.40 -3.09 0.69 2.00e-02 2.50e+03 1.18e+03 chirality pdb=" C1 NAG B1411 " pdb=" O4 NAG B1410 " pdb=" C2 NAG B1411 " pdb=" O5 NAG B1411 " both_signs ideal model delta sigma weight residual False -2.40 -3.09 0.69 2.00e-02 2.50e+03 1.17e+03 ... (remaining 4911 not shown) Planarity restraints: 5406 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " 0.099 2.00e-02 2.50e+03 4.03e-01 2.03e+03 pdb=" CG ASN A 331 " -0.118 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " 0.235 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " -0.703 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " 0.488 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " 0.104 2.00e-02 2.50e+03 1.25e-01 1.94e+02 pdb=" CG ASN C 331 " -0.039 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " -0.213 2.00e-02 2.50e+03 pdb=" C1 NAG V 1 " 0.142 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 331 " 0.051 2.00e-02 2.50e+03 9.28e-02 1.08e+02 pdb=" CG ASN B 331 " -0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN B 331 " 0.037 2.00e-02 2.50e+03 pdb=" ND2 ASN B 331 " -0.167 2.00e-02 2.50e+03 pdb=" C1 NAG P 1 " 0.103 2.00e-02 2.50e+03 ... (remaining 5403 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 250 2.51 - 3.11: 21951 3.11 - 3.70: 42673 3.70 - 4.30: 62688 4.30 - 4.90: 104496 Nonbonded interactions: 232058 Sorted by model distance: nonbonded pdb=" O SER B 530 " pdb=" OG1 THR B 531 " model vdw 1.912 3.040 nonbonded pdb=" O ASN B 603 " pdb=" OG1 THR B 604 " model vdw 1.915 3.040 nonbonded pdb=" O ALA A 522 " pdb=" OG1 THR A 523 " model vdw 1.972 3.040 nonbonded pdb=" O ILE B 332 " pdb=" CG2 THR B 333 " model vdw 1.978 3.460 nonbonded pdb=" O ASN B 856 " pdb=" ND2 ASN B 856 " model vdw 1.986 3.120 ... (remaining 232053 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'K' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.320 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: 1.180 Check model and map are aligned: 0.210 Set scattering table: 0.270 Process input model: 69.060 Find NCS groups from input model: 1.420 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.840 31077 Z= 0.685 Angle : 1.467 48.987 42441 Z= 0.764 Chirality : 0.078 1.479 4914 Planarity : 0.007 0.119 5358 Dihedral : 13.836 89.599 12123 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 19.57 Ramachandran Plot: Outliers : 2.73 % Allowed : 7.81 % Favored : 89.47 % Rotamer: Outliers : 4.36 % Allowed : 9.05 % Favored : 86.59 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.18 (0.12), residues: 3702 helix: -1.30 (0.17), residues: 662 sheet: -1.48 (0.15), residues: 987 loop : -2.80 (0.11), residues: 2053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP J 36 HIS 0.005 0.001 HIS C 505 PHE 0.025 0.002 PHE A 400 TYR 0.024 0.002 TYR B 453 ARG 0.004 0.000 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.02854 ( 48) link_NAG-ASN : angle 9.95953 ( 144) link_BETA1-4 : bond 0.07399 ( 21) link_BETA1-4 : angle 6.06221 ( 63) hydrogen bonds : bond 0.20238 ( 1025) hydrogen bonds : angle 8.04542 ( 2958) SS BOND : bond 0.23536 ( 45) SS BOND : angle 16.60861 ( 90) covalent geometry : bond 0.00913 (30963) covalent geometry : angle 1.08887 (42144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 586 time to evaluate : 2.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7603 (tt0) REVERT: A 382 VAL cc_start: 0.9216 (OUTLIER) cc_final: 0.9005 (m) REVERT: A 580 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.8385 (pt0) REVERT: A 675 GLN cc_start: 0.7419 (OUTLIER) cc_final: 0.6387 (mp10) REVERT: A 856 ASN cc_start: 0.8591 (OUTLIER) cc_final: 0.8383 (p0) REVERT: C 321 GLN cc_start: 0.7781 (OUTLIER) cc_final: 0.7366 (mm110) REVERT: C 324 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6556 (pm20) REVERT: C 529 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7296 (tptp) REVERT: C 690 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.7556 (mm110) REVERT: H 22 CYS cc_start: 0.0196 (t) cc_final: -0.0899 (t) REVERT: H 80 MET cc_start: 0.3888 (tmm) cc_final: 0.2972 (tmm) REVERT: L 92 TRP cc_start: 0.6705 (t-100) cc_final: 0.5953 (t-100) outliers start: 141 outliers final: 54 residues processed: 708 average time/residue: 0.4175 time to fit residues: 462.0943 Evaluate side-chains 358 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 295 time to evaluate : 2.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 561 PRO Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 690 GLN Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 690 GLN Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain L residue 16 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 316 optimal weight: 0.9980 chunk 284 optimal weight: 2.9990 chunk 157 optimal weight: 0.9990 chunk 97 optimal weight: 0.6980 chunk 191 optimal weight: 0.6980 chunk 151 optimal weight: 6.9990 chunk 293 optimal weight: 0.7980 chunk 113 optimal weight: 4.9990 chunk 178 optimal weight: 1.9990 chunk 218 optimal weight: 7.9990 chunk 340 optimal weight: 30.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 121 ASN A 164 ASN A 173 GLN A 334 ASN A 360 ASN A 422 ASN A 450 ASN ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN A 907 ASN B 121 ASN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 ASN B 173 GLN B 422 ASN B 450 ASN B 690 GLN B 779 GLN B1058 HIS C 164 ASN C 173 GLN C 207 HIS C 422 ASN C 450 ASN C 607 GLN C 644 GLN C 856 ASN C 955 ASN C1005 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.210601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.141367 restraints weight = 47201.594| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 3.73 r_work: 0.3563 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 31077 Z= 0.157 Angle : 0.790 16.259 42441 Z= 0.387 Chirality : 0.052 1.173 4914 Planarity : 0.006 0.104 5358 Dihedral : 7.883 86.283 5622 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.83 % Favored : 92.81 % Rotamer: Outliers : 3.37 % Allowed : 13.78 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.13), residues: 3702 helix: 0.31 (0.20), residues: 654 sheet: -0.89 (0.16), residues: 956 loop : -2.31 (0.12), residues: 2092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP H 36 HIS 0.011 0.001 HIS A 519 PHE 0.022 0.002 PHE C 375 TYR 0.020 0.001 TYR C 170 ARG 0.008 0.001 ARG C 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00463 ( 48) link_NAG-ASN : angle 3.64302 ( 144) link_BETA1-4 : bond 0.01008 ( 21) link_BETA1-4 : angle 3.18539 ( 63) hydrogen bonds : bond 0.05045 ( 1025) hydrogen bonds : angle 5.79887 ( 2958) SS BOND : bond 0.00557 ( 45) SS BOND : angle 2.68540 ( 90) covalent geometry : bond 0.00345 (30963) covalent geometry : angle 0.74298 (42144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 335 time to evaluate : 3.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.6771 (OUTLIER) cc_final: 0.6540 (t0) REVERT: A 365 TYR cc_start: 0.7582 (m-80) cc_final: 0.7196 (m-80) REVERT: A 386 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.7768 (mtpm) REVERT: A 498 ARG cc_start: 0.7911 (mmm-85) cc_final: 0.7395 (mmm-85) REVERT: A 514 SER cc_start: 0.8821 (t) cc_final: 0.8545 (p) REVERT: A 516 GLU cc_start: 0.7066 (tm-30) cc_final: 0.6748 (tm-30) REVERT: A 547 THR cc_start: 0.8712 (OUTLIER) cc_final: 0.8477 (t) REVERT: A 675 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.6801 (mp10) REVERT: A 855 PHE cc_start: 0.7856 (m-80) cc_final: 0.7632 (m-80) REVERT: A 859 THR cc_start: 0.8367 (OUTLIER) cc_final: 0.8133 (p) REVERT: A 995 ARG cc_start: 0.8301 (ttm-80) cc_final: 0.8031 (ttm110) REVERT: B 319 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.8166 (ptm160) REVERT: B 751 ASN cc_start: 0.8707 (t0) cc_final: 0.8367 (m-40) REVERT: B 854 LYS cc_start: 0.6979 (OUTLIER) cc_final: 0.5234 (tptt) REVERT: B 988 GLU cc_start: 0.8531 (tp30) cc_final: 0.8324 (tp30) REVERT: C 52 GLN cc_start: 0.8204 (tm-30) cc_final: 0.7945 (tm-30) REVERT: C 169 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7972 (tm-30) REVERT: C 191 GLU cc_start: 0.7324 (mt-10) cc_final: 0.6710 (mp0) REVERT: C 259 THR cc_start: 0.1418 (OUTLIER) cc_final: 0.1201 (t) REVERT: C 321 GLN cc_start: 0.7776 (OUTLIER) cc_final: 0.7382 (mm-40) REVERT: C 529 LYS cc_start: 0.7475 (OUTLIER) cc_final: 0.7219 (mmmt) REVERT: C 693 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8507 (pp) REVERT: H 22 CYS cc_start: 0.1885 (t) cc_final: 0.1393 (t) REVERT: H 63 PHE cc_start: 0.7339 (m-10) cc_final: 0.7079 (m-10) REVERT: H 80 MET cc_start: 0.4406 (tmm) cc_final: 0.4075 (tmm) REVERT: L 92 TRP cc_start: 0.6001 (t-100) cc_final: 0.5400 (t-100) REVERT: J 48 MET cc_start: 0.1518 (mpp) cc_final: 0.1158 (mpp) outliers start: 109 outliers final: 45 residues processed: 422 average time/residue: 0.3967 time to fit residues: 275.2021 Evaluate side-chains 313 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 257 time to evaluate : 3.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain L residue 22 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 282 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 133 optimal weight: 20.0000 chunk 25 optimal weight: 5.9990 chunk 186 optimal weight: 3.9990 chunk 255 optimal weight: 10.0000 chunk 288 optimal weight: 3.9990 chunk 247 optimal weight: 30.0000 chunk 82 optimal weight: 4.9990 chunk 212 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 360 ASN ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN A 856 ASN A 907 ASN A 935 GLN B 121 ASN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 ASN B 644 GLN B 755 GLN B 914 ASN C 196 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN C 919 ASN C 955 ASN L 16 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.198799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.122275 restraints weight = 46085.622| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 3.67 r_work: 0.3301 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.092 31077 Z= 0.322 Angle : 0.841 14.248 42441 Z= 0.419 Chirality : 0.054 0.710 4914 Planarity : 0.006 0.100 5358 Dihedral : 7.142 64.515 5544 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.35 % Favored : 92.41 % Rotamer: Outliers : 4.23 % Allowed : 13.90 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.13), residues: 3702 helix: 0.44 (0.20), residues: 641 sheet: -0.70 (0.15), residues: 1018 loop : -2.18 (0.12), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP H 36 HIS 0.013 0.002 HIS A1064 PHE 0.031 0.002 PHE A 86 TYR 0.023 0.002 TYR C 265 ARG 0.008 0.001 ARG C1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00768 ( 48) link_NAG-ASN : angle 3.22007 ( 144) link_BETA1-4 : bond 0.00769 ( 21) link_BETA1-4 : angle 3.02590 ( 63) hydrogen bonds : bond 0.05785 ( 1025) hydrogen bonds : angle 5.74066 ( 2958) SS BOND : bond 0.00649 ( 45) SS BOND : angle 2.97409 ( 90) covalent geometry : bond 0.00783 (30963) covalent geometry : angle 0.80249 (42144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 244 time to evaluate : 3.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.4806 (ttt) cc_final: 0.4452 (tpp) REVERT: A 323 THR cc_start: 0.8085 (OUTLIER) cc_final: 0.7793 (p) REVERT: A 357 ARG cc_start: 0.7870 (ttm-80) cc_final: 0.7598 (ttm-80) REVERT: A 515 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.7602 (p90) REVERT: A 516 GLU cc_start: 0.7408 (tm-30) cc_final: 0.6939 (tm-30) REVERT: A 675 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7130 (mp10) REVERT: A 762 GLN cc_start: 0.8410 (tt0) cc_final: 0.8127 (mt0) REVERT: A 856 ASN cc_start: 0.9096 (OUTLIER) cc_final: 0.8643 (p0) REVERT: A 957 GLN cc_start: 0.8179 (mt0) cc_final: 0.7850 (mm-40) REVERT: A 977 LEU cc_start: 0.7886 (mp) cc_final: 0.7680 (mp) REVERT: A 1017 GLU cc_start: 0.8634 (tt0) cc_final: 0.8433 (pt0) REVERT: A 1050 MET cc_start: 0.8819 (ptm) cc_final: 0.8508 (ptm) REVERT: B 319 ARG cc_start: 0.8550 (ptm-80) cc_final: 0.8340 (ptp-170) REVERT: B 754 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8659 (mt) REVERT: C 52 GLN cc_start: 0.8306 (tm-30) cc_final: 0.8016 (tm-30) REVERT: C 87 ASN cc_start: 0.7798 (t0) cc_final: 0.7040 (t0) REVERT: C 88 ASP cc_start: 0.6723 (m-30) cc_final: 0.6519 (m-30) REVERT: C 191 GLU cc_start: 0.7588 (mt-10) cc_final: 0.6861 (mp0) REVERT: C 259 THR cc_start: 0.1122 (OUTLIER) cc_final: 0.0920 (t) REVERT: C 321 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7835 (mm-40) REVERT: C 529 LYS cc_start: 0.8001 (OUTLIER) cc_final: 0.7751 (mmmt) REVERT: C 1002 GLN cc_start: 0.8429 (tt0) cc_final: 0.8225 (tt0) REVERT: H 63 PHE cc_start: 0.7421 (m-10) cc_final: 0.7152 (m-10) REVERT: H 93 TYR cc_start: 0.8034 (m-10) cc_final: 0.7798 (m-10) REVERT: L 92 TRP cc_start: 0.6461 (t-100) cc_final: 0.6074 (t-100) REVERT: I 80 MET cc_start: -0.0921 (OUTLIER) cc_final: -0.1194 (mmm) REVERT: J 48 MET cc_start: 0.1806 (mpp) cc_final: 0.1400 (mpp) outliers start: 137 outliers final: 78 residues processed: 361 average time/residue: 0.3643 time to fit residues: 222.1638 Evaluate side-chains 292 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 205 time to evaluate : 3.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 80 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 106 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 286 optimal weight: 0.9980 chunk 256 optimal weight: 4.9990 chunk 58 optimal weight: 0.0070 chunk 236 optimal weight: 0.0020 chunk 20 optimal weight: 9.9990 chunk 96 optimal weight: 6.9990 chunk 75 optimal weight: 0.6980 chunk 177 optimal weight: 0.8980 overall best weight: 0.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS N 32 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.202137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.129135 restraints weight = 46108.579| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 3.73 r_work: 0.3385 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 31077 Z= 0.121 Angle : 0.697 14.141 42441 Z= 0.337 Chirality : 0.048 0.614 4914 Planarity : 0.005 0.068 5358 Dihedral : 6.554 64.598 5532 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.10 % Favored : 93.73 % Rotamer: Outliers : 2.78 % Allowed : 15.79 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.13), residues: 3702 helix: 1.04 (0.21), residues: 641 sheet: -0.34 (0.16), residues: 1020 loop : -1.98 (0.13), residues: 2041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP L 36 HIS 0.006 0.001 HIS A 519 PHE 0.021 0.001 PHE A 855 TYR 0.011 0.001 TYR A 365 ARG 0.008 0.000 ARG H 23 Details of bonding type rmsd link_NAG-ASN : bond 0.00436 ( 48) link_NAG-ASN : angle 3.36215 ( 144) link_BETA1-4 : bond 0.00905 ( 21) link_BETA1-4 : angle 2.83265 ( 63) hydrogen bonds : bond 0.04077 ( 1025) hydrogen bonds : angle 5.33785 ( 2958) SS BOND : bond 0.00530 ( 45) SS BOND : angle 2.20698 ( 90) covalent geometry : bond 0.00268 (30963) covalent geometry : angle 0.65386 (42144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 246 time to evaluate : 3.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.4806 (ttt) cc_final: 0.4542 (tpp) REVERT: A 298 GLU cc_start: 0.7923 (tp30) cc_final: 0.7678 (tp30) REVERT: A 323 THR cc_start: 0.7750 (OUTLIER) cc_final: 0.7497 (p) REVERT: A 365 TYR cc_start: 0.7540 (m-80) cc_final: 0.7243 (m-80) REVERT: A 386 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8037 (mtpm) REVERT: A 441 LEU cc_start: 0.8577 (tp) cc_final: 0.8243 (tp) REVERT: A 514 SER cc_start: 0.8718 (t) cc_final: 0.8395 (p) REVERT: A 515 PHE cc_start: 0.8643 (OUTLIER) cc_final: 0.7403 (p90) REVERT: A 516 GLU cc_start: 0.7083 (tm-30) cc_final: 0.6650 (tm-30) REVERT: A 675 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.7119 (mp10) REVERT: A 957 GLN cc_start: 0.8117 (mt0) cc_final: 0.7767 (mm-40) REVERT: A 960 ASN cc_start: 0.8295 (m-40) cc_final: 0.8067 (t0) REVERT: A 1050 MET cc_start: 0.8700 (ptm) cc_final: 0.8392 (ptm) REVERT: B 191 GLU cc_start: 0.8299 (mt-10) cc_final: 0.8022 (mt-10) REVERT: B 979 ASP cc_start: 0.7813 (m-30) cc_final: 0.7563 (m-30) REVERT: B 1113 GLN cc_start: 0.8866 (mp10) cc_final: 0.8089 (mt0) REVERT: C 177 MET cc_start: 0.3964 (tmm) cc_final: 0.3652 (tmm) REVERT: C 191 GLU cc_start: 0.7578 (mt-10) cc_final: 0.6818 (mp0) REVERT: C 208 THR cc_start: 0.9040 (OUTLIER) cc_final: 0.8276 (p) REVERT: C 259 THR cc_start: 0.1562 (OUTLIER) cc_final: 0.1359 (t) REVERT: C 321 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7670 (mm-40) REVERT: C 324 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.5479 (pp20) REVERT: C 357 ARG cc_start: 0.7860 (mmm160) cc_final: 0.7490 (mmm160) REVERT: C 529 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7851 (mmmt) REVERT: C 1002 GLN cc_start: 0.8398 (tt0) cc_final: 0.8171 (tt0) REVERT: H 48 MET cc_start: 0.7121 (mtp) cc_final: 0.6265 (ttt) REVERT: H 93 TYR cc_start: 0.8053 (m-10) cc_final: 0.7832 (m-10) REVERT: H 94 TYR cc_start: 0.5652 (OUTLIER) cc_final: 0.5120 (t80) REVERT: J 48 MET cc_start: 0.1815 (mpp) cc_final: 0.1508 (mpp) outliers start: 90 outliers final: 45 residues processed: 317 average time/residue: 0.3774 time to fit residues: 199.6020 Evaluate side-chains 271 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 216 time to evaluate : 2.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 94 TYR Chi-restraints excluded: chain I residue 2 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 321 optimal weight: 20.0000 chunk 146 optimal weight: 6.9990 chunk 284 optimal weight: 1.9990 chunk 312 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 275 optimal weight: 3.9990 chunk 203 optimal weight: 3.9990 chunk 29 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 222 optimal weight: 9.9990 chunk 226 optimal weight: 0.6980 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN C 207 HIS C1010 GLN ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.199501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.121682 restraints weight = 45792.524| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 3.19 r_work: 0.3356 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.4794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 31077 Z= 0.191 Angle : 0.698 12.574 42441 Z= 0.340 Chirality : 0.048 0.538 4914 Planarity : 0.004 0.061 5358 Dihedral : 6.162 62.743 5524 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.16 % Favored : 92.71 % Rotamer: Outliers : 2.90 % Allowed : 15.88 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.13), residues: 3702 helix: 1.01 (0.21), residues: 645 sheet: -0.21 (0.16), residues: 1047 loop : -1.88 (0.13), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP L 36 HIS 0.007 0.001 HIS C1064 PHE 0.023 0.002 PHE A 86 TYR 0.020 0.001 TYR A 453 ARG 0.005 0.000 ARG C1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00462 ( 48) link_NAG-ASN : angle 2.95173 ( 144) link_BETA1-4 : bond 0.00936 ( 21) link_BETA1-4 : angle 2.79338 ( 63) hydrogen bonds : bond 0.04665 ( 1025) hydrogen bonds : angle 5.23655 ( 2958) SS BOND : bond 0.00582 ( 45) SS BOND : angle 2.44208 ( 90) covalent geometry : bond 0.00467 (30963) covalent geometry : angle 0.66082 (42144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 231 time to evaluate : 3.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 GLU cc_start: 0.8249 (tp30) cc_final: 0.7962 (tp30) REVERT: A 365 TYR cc_start: 0.7867 (m-80) cc_final: 0.7579 (m-80) REVERT: A 462 LYS cc_start: 0.8946 (mtmm) cc_final: 0.8731 (mtmm) REVERT: A 515 PHE cc_start: 0.8796 (OUTLIER) cc_final: 0.7758 (p90) REVERT: A 516 GLU cc_start: 0.7325 (tm-30) cc_final: 0.6526 (tm-30) REVERT: A 646 ARG cc_start: 0.7318 (ptt-90) cc_final: 0.6970 (tpt170) REVERT: A 675 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.7248 (mp10) REVERT: A 762 GLN cc_start: 0.8520 (tt0) cc_final: 0.8270 (mt0) REVERT: A 957 GLN cc_start: 0.8368 (mt0) cc_final: 0.7943 (mm-40) REVERT: B 619 GLU cc_start: 0.7883 (tp30) cc_final: 0.7618 (tp30) REVERT: B 1113 GLN cc_start: 0.8929 (mp10) cc_final: 0.8140 (mt0) REVERT: C 177 MET cc_start: 0.3683 (tmm) cc_final: 0.3399 (tmm) REVERT: C 191 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7155 (mp0) REVERT: C 208 THR cc_start: 0.9065 (OUTLIER) cc_final: 0.8316 (p) REVERT: C 259 THR cc_start: 0.1894 (OUTLIER) cc_final: 0.1682 (t) REVERT: C 321 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7715 (mm-40) REVERT: C 324 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.5546 (pp20) REVERT: C 529 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7928 (mmmt) REVERT: C 675 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.8010 (tp40) REVERT: C 1002 GLN cc_start: 0.8690 (tt0) cc_final: 0.8442 (tt0) REVERT: H 23 ARG cc_start: 0.8197 (tpt-90) cc_final: 0.7747 (ppt170) REVERT: H 93 TYR cc_start: 0.8027 (m-10) cc_final: 0.7798 (m-10) REVERT: H 94 TYR cc_start: 0.5705 (OUTLIER) cc_final: 0.5395 (t80) REVERT: H 103 TRP cc_start: 0.7249 (p90) cc_final: 0.6598 (p90) REVERT: L 101 TRP cc_start: 0.5595 (t-100) cc_final: 0.4957 (t-100) REVERT: I 48 MET cc_start: 0.2692 (tpt) cc_final: 0.2383 (tpp) REVERT: J 48 MET cc_start: 0.1883 (mpp) cc_final: 0.1593 (mpp) outliers start: 94 outliers final: 57 residues processed: 311 average time/residue: 0.3805 time to fit residues: 196.1182 Evaluate side-chains 271 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 205 time to evaluate : 3.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 94 TYR Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain N residue 25 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 4 optimal weight: 0.0870 chunk 350 optimal weight: 0.5980 chunk 170 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 266 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 276 optimal weight: 2.9990 chunk 368 optimal weight: 30.0000 chunk 51 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 205 optimal weight: 2.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN B 856 ASN C 196 ASN C 207 HIS C 613 GLN C1010 GLN ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 52 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.201799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.124246 restraints weight = 45809.533| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 3.37 r_work: 0.3395 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.4977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 31077 Z= 0.112 Angle : 0.638 12.546 42441 Z= 0.309 Chirality : 0.046 0.504 4914 Planarity : 0.004 0.068 5358 Dihedral : 5.795 61.529 5519 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.16 % Favored : 93.71 % Rotamer: Outliers : 2.16 % Allowed : 17.08 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.14), residues: 3702 helix: 1.29 (0.21), residues: 647 sheet: -0.03 (0.16), residues: 1036 loop : -1.72 (0.13), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP L 36 HIS 0.004 0.000 HIS A 519 PHE 0.017 0.001 PHE A 86 TYR 0.017 0.001 TYR A 453 ARG 0.014 0.000 ARG C 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00354 ( 48) link_NAG-ASN : angle 2.75336 ( 144) link_BETA1-4 : bond 0.00898 ( 21) link_BETA1-4 : angle 2.68211 ( 63) hydrogen bonds : bond 0.03792 ( 1025) hydrogen bonds : angle 5.00779 ( 2958) SS BOND : bond 0.00493 ( 45) SS BOND : angle 2.14447 ( 90) covalent geometry : bond 0.00253 (30963) covalent geometry : angle 0.60244 (42144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 227 time to evaluate : 3.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.4772 (tpp) cc_final: 0.3899 (tpt) REVERT: A 269 TYR cc_start: 0.8380 (m-80) cc_final: 0.8033 (m-80) REVERT: A 298 GLU cc_start: 0.8249 (tp30) cc_final: 0.7937 (tp30) REVERT: A 462 LYS cc_start: 0.8878 (mtmm) cc_final: 0.8639 (mtmm) REVERT: A 514 SER cc_start: 0.8778 (t) cc_final: 0.8492 (p) REVERT: A 515 PHE cc_start: 0.8752 (OUTLIER) cc_final: 0.7859 (p90) REVERT: A 516 GLU cc_start: 0.7342 (tm-30) cc_final: 0.6518 (tm-30) REVERT: A 646 ARG cc_start: 0.7448 (ptt-90) cc_final: 0.7014 (tpt170) REVERT: A 675 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.7180 (mp10) REVERT: A 957 GLN cc_start: 0.8355 (mt0) cc_final: 0.7901 (mm-40) REVERT: A 960 ASN cc_start: 0.8376 (m-40) cc_final: 0.8135 (t0) REVERT: A 1050 MET cc_start: 0.8877 (ptm) cc_final: 0.8610 (ptm) REVERT: B 191 GLU cc_start: 0.8462 (mt-10) cc_final: 0.8197 (mt-10) REVERT: B 375 PHE cc_start: 0.3658 (OUTLIER) cc_final: 0.2744 (t80) REVERT: B 854 LYS cc_start: 0.7251 (OUTLIER) cc_final: 0.5119 (tptt) REVERT: B 1113 GLN cc_start: 0.8922 (mp10) cc_final: 0.8281 (mt0) REVERT: C 169 GLU cc_start: 0.8362 (mm-30) cc_final: 0.7599 (tm-30) REVERT: C 177 MET cc_start: 0.3622 (tmm) cc_final: 0.3317 (tmm) REVERT: C 191 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7145 (mp0) REVERT: C 208 THR cc_start: 0.9049 (OUTLIER) cc_final: 0.8258 (p) REVERT: C 324 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.5564 (pp20) REVERT: C 357 ARG cc_start: 0.7433 (mmm160) cc_final: 0.7081 (mmp-170) REVERT: C 529 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7932 (mmmt) REVERT: C 1002 GLN cc_start: 0.8648 (tt0) cc_final: 0.8432 (tt0) REVERT: H 23 ARG cc_start: 0.8249 (tpt-90) cc_final: 0.7766 (ppt170) REVERT: H 93 TYR cc_start: 0.7998 (m-10) cc_final: 0.7692 (m-10) REVERT: H 94 TYR cc_start: 0.5867 (m-80) cc_final: 0.5622 (t80) REVERT: H 103 TRP cc_start: 0.7166 (p90) cc_final: 0.6525 (p90) REVERT: J 48 MET cc_start: 0.1910 (mpp) cc_final: 0.1619 (mpp) outliers start: 70 outliers final: 44 residues processed: 286 average time/residue: 0.3828 time to fit residues: 180.2491 Evaluate side-chains 255 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 204 time to evaluate : 2.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 78 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 156 optimal weight: 1.9990 chunk 261 optimal weight: 8.9990 chunk 374 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 chunk 295 optimal weight: 1.9990 chunk 241 optimal weight: 4.9990 chunk 165 optimal weight: 2.9990 chunk 331 optimal weight: 30.0000 chunk 31 optimal weight: 0.0670 overall best weight: 1.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN C 196 ASN C 207 HIS C1010 GLN ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 52 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.199858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.122841 restraints weight = 45785.066| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 3.71 r_work: 0.3332 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.5157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 31077 Z= 0.160 Angle : 0.653 11.998 42441 Z= 0.317 Chirality : 0.046 0.481 4914 Planarity : 0.004 0.065 5358 Dihedral : 5.539 59.831 5509 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.78 % Favored : 93.08 % Rotamer: Outliers : 2.63 % Allowed : 16.84 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.14), residues: 3702 helix: 1.30 (0.21), residues: 646 sheet: 0.07 (0.16), residues: 1031 loop : -1.69 (0.13), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP L 36 HIS 0.005 0.001 HIS A1064 PHE 0.020 0.001 PHE A 86 TYR 0.016 0.001 TYR A 453 ARG 0.010 0.000 ARG C 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00344 ( 48) link_NAG-ASN : angle 2.74180 ( 144) link_BETA1-4 : bond 0.00796 ( 21) link_BETA1-4 : angle 2.63763 ( 63) hydrogen bonds : bond 0.04223 ( 1025) hydrogen bonds : angle 4.97944 ( 2958) SS BOND : bond 0.00502 ( 45) SS BOND : angle 2.35301 ( 90) covalent geometry : bond 0.00388 (30963) covalent geometry : angle 0.61785 (42144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 216 time to evaluate : 4.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.4588 (tpp) cc_final: 0.3815 (tpt) REVERT: A 269 TYR cc_start: 0.8262 (m-80) cc_final: 0.7952 (m-80) REVERT: A 298 GLU cc_start: 0.8075 (tp30) cc_final: 0.7679 (tp30) REVERT: A 357 ARG cc_start: 0.7660 (ttm-80) cc_final: 0.7355 (ttm-80) REVERT: A 409 GLN cc_start: 0.8398 (mt0) cc_final: 0.8022 (mt0) REVERT: A 462 LYS cc_start: 0.8894 (mtmm) cc_final: 0.8637 (mtmm) REVERT: A 514 SER cc_start: 0.8706 (t) cc_final: 0.8362 (p) REVERT: A 515 PHE cc_start: 0.8694 (OUTLIER) cc_final: 0.7840 (p90) REVERT: A 516 GLU cc_start: 0.7284 (tm-30) cc_final: 0.6480 (tm-30) REVERT: A 646 ARG cc_start: 0.7395 (ptt-90) cc_final: 0.7162 (tpt170) REVERT: A 675 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7034 (mp10) REVERT: A 762 GLN cc_start: 0.8295 (tt0) cc_final: 0.8087 (mt0) REVERT: A 957 GLN cc_start: 0.8145 (mt0) cc_final: 0.7712 (mm110) REVERT: A 960 ASN cc_start: 0.8286 (m-40) cc_final: 0.8032 (t0) REVERT: A 1050 MET cc_start: 0.8751 (ptm) cc_final: 0.8475 (ptm) REVERT: B 375 PHE cc_start: 0.3654 (OUTLIER) cc_final: 0.2680 (t80) REVERT: B 854 LYS cc_start: 0.7200 (OUTLIER) cc_final: 0.5201 (tptt) REVERT: B 1113 GLN cc_start: 0.8701 (mp10) cc_final: 0.8099 (mt0) REVERT: C 177 MET cc_start: 0.3614 (tmm) cc_final: 0.3352 (tmm) REVERT: C 191 GLU cc_start: 0.7647 (mt-10) cc_final: 0.6953 (mp0) REVERT: C 208 THR cc_start: 0.9053 (OUTLIER) cc_final: 0.8239 (p) REVERT: C 324 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.5538 (pp20) REVERT: C 529 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7933 (mmmt) REVERT: C 1002 GLN cc_start: 0.8466 (tt0) cc_final: 0.8231 (tt0) REVERT: H 23 ARG cc_start: 0.8073 (tpt-90) cc_final: 0.7672 (ppt170) REVERT: H 103 TRP cc_start: 0.7108 (p90) cc_final: 0.6600 (p90) REVERT: J 48 MET cc_start: 0.2011 (mpp) cc_final: 0.1789 (mpp) outliers start: 85 outliers final: 60 residues processed: 289 average time/residue: 0.4086 time to fit residues: 196.6587 Evaluate side-chains 274 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 207 time to evaluate : 3.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain N residue 25 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 25 optimal weight: 0.6980 chunk 230 optimal weight: 7.9990 chunk 136 optimal weight: 0.0040 chunk 51 optimal weight: 8.9990 chunk 241 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 296 optimal weight: 2.9990 chunk 154 optimal weight: 9.9990 chunk 143 optimal weight: 0.8980 chunk 222 optimal weight: 4.9990 chunk 114 optimal weight: 20.0000 overall best weight: 1.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN C 196 ASN C 207 HIS C 450 ASN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.199244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.119977 restraints weight = 45889.440| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.78 r_work: 0.3401 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.5405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 31077 Z= 0.162 Angle : 0.653 11.987 42441 Z= 0.317 Chirality : 0.047 0.465 4914 Planarity : 0.004 0.066 5358 Dihedral : 5.509 58.295 5507 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.73 % Favored : 93.17 % Rotamer: Outliers : 2.66 % Allowed : 16.84 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.14), residues: 3702 helix: 1.27 (0.21), residues: 641 sheet: 0.13 (0.16), residues: 1046 loop : -1.68 (0.13), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP L 36 HIS 0.005 0.001 HIS A1064 PHE 0.019 0.001 PHE A 86 TYR 0.015 0.001 TYR H 93 ARG 0.007 0.000 ARG C 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00333 ( 48) link_NAG-ASN : angle 2.66525 ( 144) link_BETA1-4 : bond 0.00808 ( 21) link_BETA1-4 : angle 2.57836 ( 63) hydrogen bonds : bond 0.04247 ( 1025) hydrogen bonds : angle 4.95176 ( 2958) SS BOND : bond 0.00548 ( 45) SS BOND : angle 2.24366 ( 90) covalent geometry : bond 0.00390 (30963) covalent geometry : angle 0.61962 (42144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 219 time to evaluate : 2.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.8355 (t60) cc_final: 0.8106 (t60) REVERT: A 177 MET cc_start: 0.4667 (tpp) cc_final: 0.3830 (tpt) REVERT: A 269 TYR cc_start: 0.8350 (m-80) cc_final: 0.8114 (m-80) REVERT: A 298 GLU cc_start: 0.8305 (tp30) cc_final: 0.7928 (tp30) REVERT: A 409 GLN cc_start: 0.8486 (mt0) cc_final: 0.8109 (mt0) REVERT: A 503 VAL cc_start: 0.7880 (OUTLIER) cc_final: 0.7660 (m) REVERT: A 514 SER cc_start: 0.8821 (t) cc_final: 0.8540 (p) REVERT: A 515 PHE cc_start: 0.8816 (OUTLIER) cc_final: 0.8032 (p90) REVERT: A 516 GLU cc_start: 0.7510 (tm-30) cc_final: 0.6680 (tm-30) REVERT: A 646 ARG cc_start: 0.7804 (ptt-90) cc_final: 0.7467 (tpt170) REVERT: A 675 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7181 (mp10) REVERT: A 957 GLN cc_start: 0.8361 (mt0) cc_final: 0.7877 (mm110) REVERT: A 1050 MET cc_start: 0.8912 (ptm) cc_final: 0.8610 (ptm) REVERT: B 375 PHE cc_start: 0.3677 (OUTLIER) cc_final: 0.2724 (t80) REVERT: B 854 LYS cc_start: 0.7286 (OUTLIER) cc_final: 0.5259 (tptt) REVERT: B 1113 GLN cc_start: 0.8866 (mp10) cc_final: 0.8345 (mt0) REVERT: C 170 TYR cc_start: 0.6969 (t80) cc_final: 0.6686 (t80) REVERT: C 191 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7272 (mp0) REVERT: C 208 THR cc_start: 0.9068 (OUTLIER) cc_final: 0.8283 (p) REVERT: C 324 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.5743 (pp20) REVERT: C 529 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.7983 (mmmt) REVERT: C 675 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.8184 (tp40) REVERT: H 23 ARG cc_start: 0.8192 (tpt-90) cc_final: 0.7936 (mmm160) REVERT: H 103 TRP cc_start: 0.7219 (p90) cc_final: 0.6806 (p90) REVERT: J 48 MET cc_start: 0.1999 (mpp) cc_final: 0.1647 (mpp) outliers start: 86 outliers final: 66 residues processed: 293 average time/residue: 0.3633 time to fit residues: 177.1430 Evaluate side-chains 282 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 207 time to evaluate : 2.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain M residue 23 SER Chi-restraints excluded: chain N residue 25 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 232 optimal weight: 30.0000 chunk 62 optimal weight: 1.9990 chunk 294 optimal weight: 2.9990 chunk 146 optimal weight: 50.0000 chunk 114 optimal weight: 20.0000 chunk 269 optimal weight: 0.5980 chunk 123 optimal weight: 0.0870 chunk 236 optimal weight: 0.0970 chunk 111 optimal weight: 2.9990 chunk 302 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN C 196 ASN C 207 HIS ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.200177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.121185 restraints weight = 45563.780| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.80 r_work: 0.3404 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.5488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 31077 Z= 0.117 Angle : 0.633 15.522 42441 Z= 0.306 Chirality : 0.046 0.465 4914 Planarity : 0.004 0.065 5358 Dihedral : 5.352 56.415 5507 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.56 % Favored : 93.33 % Rotamer: Outliers : 2.29 % Allowed : 17.15 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.14), residues: 3702 helix: 1.47 (0.21), residues: 643 sheet: 0.17 (0.16), residues: 1035 loop : -1.60 (0.13), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP L 36 HIS 0.003 0.000 HIS A 519 PHE 0.017 0.001 PHE B 86 TYR 0.015 0.001 TYR A 453 ARG 0.014 0.000 ARG A 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00307 ( 48) link_NAG-ASN : angle 2.56420 ( 144) link_BETA1-4 : bond 0.00857 ( 21) link_BETA1-4 : angle 2.53939 ( 63) hydrogen bonds : bond 0.03837 ( 1025) hydrogen bonds : angle 4.81154 ( 2958) SS BOND : bond 0.00496 ( 45) SS BOND : angle 2.03705 ( 90) covalent geometry : bond 0.00271 (30963) covalent geometry : angle 0.60239 (42144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 210 time to evaluate : 3.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.8349 (t60) cc_final: 0.8108 (t60) REVERT: A 269 TYR cc_start: 0.8313 (m-80) cc_final: 0.8070 (m-80) REVERT: A 409 GLN cc_start: 0.8559 (mt0) cc_final: 0.8131 (mt0) REVERT: A 514 SER cc_start: 0.8701 (t) cc_final: 0.8432 (p) REVERT: A 515 PHE cc_start: 0.8794 (OUTLIER) cc_final: 0.8000 (p90) REVERT: A 516 GLU cc_start: 0.7439 (tm-30) cc_final: 0.6633 (tm-30) REVERT: A 646 ARG cc_start: 0.7726 (ptt-90) cc_final: 0.7400 (tpt170) REVERT: A 675 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.7214 (mp10) REVERT: A 957 GLN cc_start: 0.8313 (mt0) cc_final: 0.7799 (mm110) REVERT: A 960 ASN cc_start: 0.8379 (m-40) cc_final: 0.8158 (t0) REVERT: A 1050 MET cc_start: 0.8853 (ptm) cc_final: 0.8611 (ptm) REVERT: B 88 ASP cc_start: 0.6611 (m-30) cc_final: 0.6312 (m-30) REVERT: B 191 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8169 (mt-10) REVERT: B 375 PHE cc_start: 0.3657 (OUTLIER) cc_final: 0.2709 (t80) REVERT: B 854 LYS cc_start: 0.7265 (OUTLIER) cc_final: 0.5201 (tptt) REVERT: B 1113 GLN cc_start: 0.8796 (mp10) cc_final: 0.8431 (mt0) REVERT: C 170 TYR cc_start: 0.6895 (t80) cc_final: 0.6640 (t80) REVERT: C 177 MET cc_start: 0.4299 (tmm) cc_final: 0.4012 (tpt) REVERT: C 208 THR cc_start: 0.9066 (OUTLIER) cc_final: 0.8750 (p) REVERT: C 324 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.5670 (pp20) REVERT: C 529 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7984 (mmmt) REVERT: C 675 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.8122 (tp40) REVERT: H 23 ARG cc_start: 0.8160 (tpt-90) cc_final: 0.7899 (mmm160) REVERT: H 103 TRP cc_start: 0.7209 (p90) cc_final: 0.6820 (p90) REVERT: J 48 MET cc_start: 0.2080 (mpp) cc_final: 0.1847 (mpp) outliers start: 74 outliers final: 55 residues processed: 272 average time/residue: 0.3938 time to fit residues: 178.3654 Evaluate side-chains 266 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 203 time to evaluate : 2.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 78 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 29 optimal weight: 9.9990 chunk 217 optimal weight: 9.9990 chunk 276 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 325 optimal weight: 50.0000 chunk 324 optimal weight: 3.9990 chunk 96 optimal weight: 0.0020 chunk 46 optimal weight: 3.9990 chunk 260 optimal weight: 8.9990 chunk 197 optimal weight: 0.3980 chunk 220 optimal weight: 2.9990 overall best weight: 1.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.198023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.119652 restraints weight = 45489.031| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 3.33 r_work: 0.3321 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.5619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 31077 Z= 0.150 Angle : 0.650 13.736 42441 Z= 0.315 Chirality : 0.046 0.468 4914 Planarity : 0.004 0.066 5358 Dihedral : 5.354 54.753 5507 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.94 % Favored : 92.95 % Rotamer: Outliers : 2.26 % Allowed : 17.05 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.14), residues: 3702 helix: 1.43 (0.21), residues: 642 sheet: 0.16 (0.16), residues: 1045 loop : -1.60 (0.13), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP L 36 HIS 0.005 0.001 HIS A1064 PHE 0.018 0.001 PHE A 86 TYR 0.015 0.001 TYR A 453 ARG 0.014 0.000 ARG C 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00298 ( 48) link_NAG-ASN : angle 2.56569 ( 144) link_BETA1-4 : bond 0.00792 ( 21) link_BETA1-4 : angle 2.49389 ( 63) hydrogen bonds : bond 0.04103 ( 1025) hydrogen bonds : angle 4.83359 ( 2958) SS BOND : bond 0.00460 ( 45) SS BOND : angle 2.11574 ( 90) covalent geometry : bond 0.00361 (30963) covalent geometry : angle 0.62015 (42144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 206 time to evaluate : 3.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.8325 (t60) cc_final: 0.8087 (t60) REVERT: A 177 MET cc_start: 0.4157 (tpp) cc_final: 0.3576 (tpt) REVERT: A 269 TYR cc_start: 0.8337 (m-80) cc_final: 0.8005 (m-80) REVERT: A 409 GLN cc_start: 0.8526 (mt0) cc_final: 0.8088 (mt0) REVERT: A 503 VAL cc_start: 0.7801 (OUTLIER) cc_final: 0.7570 (m) REVERT: A 514 SER cc_start: 0.8723 (t) cc_final: 0.8433 (p) REVERT: A 515 PHE cc_start: 0.8835 (OUTLIER) cc_final: 0.8090 (p90) REVERT: A 516 GLU cc_start: 0.7464 (tm-30) cc_final: 0.6743 (tm-30) REVERT: A 646 ARG cc_start: 0.7956 (ptt-90) cc_final: 0.7515 (tpt170) REVERT: A 675 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.7224 (mp10) REVERT: A 957 GLN cc_start: 0.8300 (mt0) cc_final: 0.7821 (mm110) REVERT: A 1050 MET cc_start: 0.8907 (ptm) cc_final: 0.8607 (ptm) REVERT: B 375 PHE cc_start: 0.3662 (OUTLIER) cc_final: 0.2742 (t80) REVERT: B 854 LYS cc_start: 0.7193 (OUTLIER) cc_final: 0.5100 (tptt) REVERT: B 1113 GLN cc_start: 0.8827 (mp10) cc_final: 0.8455 (mt0) REVERT: C 169 GLU cc_start: 0.8346 (mm-30) cc_final: 0.7539 (tm-30) REVERT: C 177 MET cc_start: 0.4305 (tmm) cc_final: 0.3944 (tmm) REVERT: C 208 THR cc_start: 0.9039 (OUTLIER) cc_final: 0.8763 (p) REVERT: C 324 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.5634 (pp20) REVERT: C 529 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7997 (mmmt) REVERT: C 675 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.8112 (tp40) REVERT: H 23 ARG cc_start: 0.8143 (tpt-90) cc_final: 0.7783 (mmm160) REVERT: H 103 TRP cc_start: 0.7201 (p90) cc_final: 0.6805 (p90) REVERT: I 69 MET cc_start: -0.1529 (tpt) cc_final: -0.2403 (mtt) REVERT: J 48 MET cc_start: 0.2088 (mpp) cc_final: 0.1765 (mpp) outliers start: 73 outliers final: 58 residues processed: 267 average time/residue: 0.3849 time to fit residues: 173.4589 Evaluate side-chains 268 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 201 time to evaluate : 3.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 78 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 45 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 chunk 282 optimal weight: 0.9990 chunk 177 optimal weight: 1.9990 chunk 285 optimal weight: 1.9990 chunk 199 optimal weight: 2.9990 chunk 152 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 249 optimal weight: 7.9990 chunk 194 optimal weight: 2.9990 chunk 232 optimal weight: 9.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.196395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.117872 restraints weight = 45419.290| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 3.38 r_work: 0.3296 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.5807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 31077 Z= 0.181 Angle : 0.668 12.819 42441 Z= 0.324 Chirality : 0.047 0.469 4914 Planarity : 0.004 0.077 5358 Dihedral : 5.498 53.789 5507 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.16 % Favored : 92.71 % Rotamer: Outliers : 2.29 % Allowed : 16.96 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.14), residues: 3702 helix: 1.28 (0.21), residues: 641 sheet: 0.10 (0.16), residues: 1062 loop : -1.62 (0.13), residues: 1999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP L 36 HIS 0.006 0.001 HIS A1064 PHE 0.021 0.001 PHE A 86 TYR 0.015 0.001 TYR A1067 ARG 0.015 0.001 ARG C 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00293 ( 48) link_NAG-ASN : angle 2.60647 ( 144) link_BETA1-4 : bond 0.00770 ( 21) link_BETA1-4 : angle 2.48024 ( 63) hydrogen bonds : bond 0.04421 ( 1025) hydrogen bonds : angle 4.91492 ( 2958) SS BOND : bond 0.00532 ( 45) SS BOND : angle 2.19945 ( 90) covalent geometry : bond 0.00441 (30963) covalent geometry : angle 0.63778 (42144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23416.93 seconds wall clock time: 404 minutes 19.42 seconds (24259.42 seconds total)