Starting phenix.real_space_refine on Thu Jun 26 03:27:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gtp_34261/06_2025/8gtp_34261.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gtp_34261/06_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_34261/06_2025/8gtp_34261.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gtp_34261/06_2025/8gtp_34261.map" model { file = "/net/cci-nas-00/data/ceres_data/8gtp_34261/06_2025/8gtp_34261.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gtp_34261/06_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): 0.52s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 17.47, per 1000 atoms: 0.58 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: 8.71 Conformation dependent library (CDL) restraints added in 3.5 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: 5.25 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: 14.74 Time building geometry restraints manager: 10.01 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: 2.020 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: 0.030 Extract box with map and model: 1.150 Check model and map are aligned: 0.210 Set scattering table: 0.260 Process input model: 73.240 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.220 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.100 ------------------------------------------------------------------------------- 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 : 3.036 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: 0.5094 time to fit residues: 570.1153 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 : 2.985 ------------------------------------------------------------------------------- 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 = 0.141368 restraints weight = 47201.595| |-----------------------------------------------------------------------------| 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: 0.7551 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 : 3.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.6764 (OUTLIER) cc_final: 0.6531 (t0) REVERT: A 365 TYR cc_start: 0.7581 (m-80) cc_final: 0.7198 (m-80) REVERT: A 386 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.7767 (mtpm) REVERT: A 498 ARG cc_start: 0.7897 (mmm-85) cc_final: 0.7383 (mmm-85) REVERT: A 514 SER cc_start: 0.8824 (t) cc_final: 0.8550 (p) REVERT: A 516 GLU cc_start: 0.7061 (tm-30) cc_final: 0.6744 (tm-30) REVERT: A 547 THR cc_start: 0.8713 (OUTLIER) cc_final: 0.8479 (t) REVERT: A 675 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.6793 (mp10) REVERT: A 855 PHE cc_start: 0.7855 (m-80) cc_final: 0.7631 (m-80) REVERT: A 859 THR cc_start: 0.8364 (OUTLIER) cc_final: 0.8131 (p) REVERT: A 995 ARG cc_start: 0.8307 (ttm-80) cc_final: 0.8038 (ttm110) REVERT: B 319 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.8148 (ptm160) REVERT: B 751 ASN cc_start: 0.8707 (t0) cc_final: 0.8366 (m-40) REVERT: B 854 LYS cc_start: 0.6973 (OUTLIER) cc_final: 0.5228 (tptt) REVERT: B 988 GLU cc_start: 0.8529 (tp30) cc_final: 0.8321 (tp30) REVERT: C 52 GLN cc_start: 0.8200 (tm-30) cc_final: 0.7941 (tm-30) REVERT: C 169 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7972 (tm-30) REVERT: C 191 GLU cc_start: 0.7324 (mt-10) cc_final: 0.6709 (mp0) REVERT: C 259 THR cc_start: 0.1418 (OUTLIER) cc_final: 0.1201 (t) REVERT: C 321 GLN cc_start: 0.7772 (OUTLIER) cc_final: 0.7381 (mm-40) REVERT: C 529 LYS cc_start: 0.7471 (OUTLIER) cc_final: 0.7214 (mmmt) REVERT: C 693 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8508 (pp) REVERT: H 22 CYS cc_start: 0.1892 (t) cc_final: 0.1408 (t) REVERT: H 63 PHE cc_start: 0.7339 (m-10) cc_final: 0.7079 (m-10) REVERT: H 80 MET cc_start: 0.4404 (tmm) cc_final: 0.4078 (tmm) REVERT: L 92 TRP cc_start: 0.5982 (t-100) cc_final: 0.5387 (t-100) REVERT: J 48 MET cc_start: 0.1523 (mpp) cc_final: 0.1164 (mpp) outliers start: 109 outliers final: 45 residues processed: 422 average time/residue: 0.4039 time to fit residues: 281.5610 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 : 3.156 ------------------------------------------------------------------------------- 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: 10.0000 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 360 ASN 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.198664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.120533 restraints weight = 46060.167| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 3.66 r_work: 0.3300 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.091 31077 Z= 0.326 Angle : 0.850 14.401 42441 Z= 0.424 Chirality : 0.054 0.706 4914 Planarity : 0.006 0.110 5358 Dihedral : 7.151 64.573 5544 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.46 % Favored : 92.30 % Rotamer: Outliers : 4.20 % Allowed : 14.03 % Favored : 81.77 % 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: 0.43 (0.20), residues: 645 sheet: -0.72 (0.15), residues: 1021 loop : -2.17 (0.12), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP H 36 HIS 0.013 0.002 HIS C1064 PHE 0.032 0.002 PHE A 86 TYR 0.023 0.002 TYR C 265 ARG 0.010 0.001 ARG A 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00736 ( 48) link_NAG-ASN : angle 3.20744 ( 144) link_BETA1-4 : bond 0.00770 ( 21) link_BETA1-4 : angle 2.97383 ( 63) hydrogen bonds : bond 0.05815 ( 1025) hydrogen bonds : angle 5.74271 ( 2958) SS BOND : bond 0.00621 ( 45) SS BOND : angle 2.96051 ( 90) covalent geometry : bond 0.00796 (30963) covalent geometry : angle 0.81281 (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 380 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 244 time to evaluate : 3.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.4865 (ttt) cc_final: 0.4506 (tpp) REVERT: A 323 THR cc_start: 0.8059 (OUTLIER) cc_final: 0.7773 (p) REVERT: A 357 ARG cc_start: 0.7893 (ttm-80) cc_final: 0.7630 (ttm-80) REVERT: A 365 TYR cc_start: 0.7990 (m-80) cc_final: 0.7733 (m-80) REVERT: A 515 PHE cc_start: 0.8860 (OUTLIER) cc_final: 0.7630 (p90) REVERT: A 516 GLU cc_start: 0.7400 (tm-30) cc_final: 0.6936 (tm-30) REVERT: A 675 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7081 (mp10) REVERT: A 762 GLN cc_start: 0.8412 (tt0) cc_final: 0.8129 (mt0) REVERT: A 856 ASN cc_start: 0.9097 (OUTLIER) cc_final: 0.8631 (p0) REVERT: A 957 GLN cc_start: 0.8173 (mt0) cc_final: 0.7831 (mm-40) REVERT: A 1017 GLU cc_start: 0.8630 (tt0) cc_final: 0.8430 (pt0) REVERT: A 1050 MET cc_start: 0.8846 (ptm) cc_final: 0.8540 (ptm) REVERT: B 319 ARG cc_start: 0.8504 (ptm-80) cc_final: 0.8303 (ptp-170) REVERT: B 754 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8650 (mt) REVERT: C 52 GLN cc_start: 0.8309 (tm-30) cc_final: 0.8012 (tm-30) REVERT: C 87 ASN cc_start: 0.7798 (t0) cc_final: 0.7060 (t0) REVERT: C 191 GLU cc_start: 0.7579 (mt-10) cc_final: 0.6880 (mp0) REVERT: C 269 TYR cc_start: 0.7927 (m-80) cc_final: 0.7552 (m-80) REVERT: C 321 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7837 (mm-40) REVERT: C 529 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7776 (mmmt) REVERT: C 1002 GLN cc_start: 0.8433 (tt0) cc_final: 0.8216 (tt0) REVERT: H 63 PHE cc_start: 0.7345 (m-10) cc_final: 0.7094 (m-10) REVERT: H 80 MET cc_start: 0.3863 (tmm) cc_final: 0.3492 (tmm) REVERT: H 93 TYR cc_start: 0.7997 (m-10) cc_final: 0.7731 (m-10) REVERT: L 92 TRP cc_start: 0.6455 (t-100) cc_final: 0.6070 (t-100) REVERT: I 80 MET cc_start: -0.0762 (OUTLIER) cc_final: -0.0968 (mmt) REVERT: J 48 MET cc_start: 0.1795 (mpp) cc_final: 0.1365 (mpp) outliers start: 136 outliers final: 76 residues processed: 358 average time/residue: 0.3623 time to fit residues: 219.4461 Evaluate side-chains 285 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 201 time to evaluate : 3.444 ------------------------------------------------------------------------------- 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 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 131 CYS 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 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 1141 LEU 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: 0.9990 chunk 38 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 286 optimal weight: 0.9990 chunk 256 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 236 optimal weight: 0.0870 chunk 20 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 chunk 75 optimal weight: 0.6980 chunk 177 optimal weight: 0.5980 overall best weight: 0.6760 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** N 32 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.201396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.126939 restraints weight = 46074.068| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 3.67 r_work: 0.3375 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 31077 Z= 0.128 Angle : 0.700 13.692 42441 Z= 0.340 Chirality : 0.048 0.618 4914 Planarity : 0.005 0.068 5358 Dihedral : 6.611 64.562 5532 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.19 % Favored : 93.65 % Rotamer: Outliers : 2.87 % Allowed : 15.42 % Favored : 81.71 % 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: -1.43 (0.13), residues: 3702 helix: 1.00 (0.21), residues: 641 sheet: -0.36 (0.16), residues: 1020 loop : -1.99 (0.13), residues: 2041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP H 36 HIS 0.006 0.001 HIS A 519 PHE 0.017 0.001 PHE A 855 TYR 0.010 0.001 TYR B 269 ARG 0.011 0.000 ARG H 23 Details of bonding type rmsd link_NAG-ASN : bond 0.00533 ( 48) link_NAG-ASN : angle 3.29694 ( 144) link_BETA1-4 : bond 0.00910 ( 21) link_BETA1-4 : angle 2.83601 ( 63) hydrogen bonds : bond 0.04205 ( 1025) hydrogen bonds : angle 5.36858 ( 2958) SS BOND : bond 0.00575 ( 45) SS BOND : angle 2.33955 ( 90) covalent geometry : bond 0.00288 (30963) covalent geometry : angle 0.65728 (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 337 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 244 time to evaluate : 4.337 Fit side-chains revert: symmetry clash REVERT: A 177 MET cc_start: 0.4800 (ttt) cc_final: 0.4565 (tpp) REVERT: A 298 GLU cc_start: 0.7932 (tp30) cc_final: 0.7698 (tp30) REVERT: A 323 THR cc_start: 0.7756 (OUTLIER) cc_final: 0.7499 (p) REVERT: A 365 TYR cc_start: 0.7721 (m-80) cc_final: 0.7342 (m-80) REVERT: A 386 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8037 (mtpm) REVERT: A 514 SER cc_start: 0.8728 (t) cc_final: 0.8396 (p) REVERT: A 515 PHE cc_start: 0.8684 (OUTLIER) cc_final: 0.7527 (p90) REVERT: A 516 GLU cc_start: 0.7121 (tm-30) cc_final: 0.6676 (tm-30) REVERT: A 565 PHE cc_start: 0.8205 (p90) cc_final: 0.7993 (p90) REVERT: A 675 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7092 (mp10) REVERT: A 957 GLN cc_start: 0.8113 (mt0) cc_final: 0.7757 (mm-40) REVERT: A 960 ASN cc_start: 0.8302 (m-40) cc_final: 0.8057 (t0) REVERT: A 1050 MET cc_start: 0.8737 (ptm) cc_final: 0.8412 (ptm) REVERT: B 191 GLU cc_start: 0.8344 (mt-10) cc_final: 0.8054 (mt-10) REVERT: B 979 ASP cc_start: 0.7821 (m-30) cc_final: 0.7574 (m-30) REVERT: B 1113 GLN cc_start: 0.8860 (mp10) cc_final: 0.8051 (mt0) REVERT: C 177 MET cc_start: 0.3856 (tmm) cc_final: 0.3625 (tmm) REVERT: C 191 GLU cc_start: 0.7601 (mt-10) cc_final: 0.6825 (mp0) REVERT: C 208 THR cc_start: 0.9032 (OUTLIER) cc_final: 0.8266 (p) REVERT: C 269 TYR cc_start: 0.7851 (m-80) cc_final: 0.7422 (m-80) REVERT: C 321 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.7681 (mm-40) REVERT: C 324 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.5533 (pp20) REVERT: C 357 ARG cc_start: 0.7859 (mmm160) cc_final: 0.7486 (mmm160) REVERT: C 529 LYS cc_start: 0.8102 (OUTLIER) cc_final: 0.7836 (mmmt) REVERT: C 1002 GLN cc_start: 0.8395 (tt0) cc_final: 0.8172 (tt0) REVERT: H 48 MET cc_start: 0.7114 (mtp) cc_final: 0.6345 (ttt) REVERT: H 80 MET cc_start: 0.3453 (tmm) cc_final: 0.2784 (tmm) REVERT: H 94 TYR cc_start: 0.5062 (OUTLIER) cc_final: 0.4751 (t80) REVERT: H 103 TRP cc_start: 0.7007 (p90) cc_final: 0.6396 (p90) REVERT: J 48 MET cc_start: 0.1889 (mpp) cc_final: 0.1576 (mpp) outliers start: 93 outliers final: 48 residues processed: 318 average time/residue: 0.6425 time to fit residues: 350.5523 Evaluate side-chains 277 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 220 time to evaluate : 6.173 ------------------------------------------------------------------------------- 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 130 VAL Chi-restraints excluded: chain A residue 208 THR 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 610 VAL 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 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 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 C residue 63 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 226 LEU 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 696 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 785 VAL 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: 5.9990 chunk 146 optimal weight: 8.9990 chunk 284 optimal weight: 0.9990 chunk 312 optimal weight: 20.0000 chunk 36 optimal weight: 2.9990 chunk 275 optimal weight: 0.9980 chunk 203 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 222 optimal weight: 10.0000 chunk 226 optimal weight: 0.3980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 B 196 ASN B 856 ASN C 207 HIS ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.201585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.127610 restraints weight = 45860.755| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 3.64 r_work: 0.3387 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.4723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 31077 Z= 0.120 Angle : 0.652 12.951 42441 Z= 0.317 Chirality : 0.046 0.536 4914 Planarity : 0.004 0.059 5358 Dihedral : 5.953 62.394 5522 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.78 % Favored : 93.08 % Rotamer: Outliers : 2.63 % Allowed : 16.22 % Favored : 81.16 % 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: -1.14 (0.13), residues: 3702 helix: 1.21 (0.21), residues: 649 sheet: -0.17 (0.16), residues: 1034 loop : -1.81 (0.13), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP L 36 HIS 0.004 0.001 HIS A 519 PHE 0.021 0.001 PHE A 86 TYR 0.021 0.001 TYR A 453 ARG 0.005 0.000 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00452 ( 48) link_NAG-ASN : angle 2.84119 ( 144) link_BETA1-4 : bond 0.00891 ( 21) link_BETA1-4 : angle 2.75690 ( 63) hydrogen bonds : bond 0.03940 ( 1025) hydrogen bonds : angle 5.08011 ( 2958) SS BOND : bond 0.00573 ( 45) SS BOND : angle 1.98082 ( 90) covalent geometry : bond 0.00272 (30963) covalent geometry : angle 0.61711 (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 321 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 236 time to evaluate : 3.090 Fit side-chains revert: symmetry clash REVERT: A 269 TYR cc_start: 0.8307 (m-80) cc_final: 0.7992 (m-80) REVERT: A 298 GLU cc_start: 0.7963 (tp30) cc_final: 0.7669 (tp30) REVERT: A 462 LYS cc_start: 0.8882 (mtmm) cc_final: 0.8644 (mtmm) REVERT: A 503 VAL cc_start: 0.7577 (OUTLIER) cc_final: 0.7326 (m) REVERT: A 514 SER cc_start: 0.8674 (t) cc_final: 0.8381 (p) REVERT: A 515 PHE cc_start: 0.8655 (OUTLIER) cc_final: 0.7577 (p90) REVERT: A 516 GLU cc_start: 0.7070 (tm-30) cc_final: 0.6351 (tm-30) REVERT: A 675 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7166 (mp10) REVERT: A 957 GLN cc_start: 0.8111 (mt0) cc_final: 0.7723 (mm-40) REVERT: A 960 ASN cc_start: 0.8289 (m-40) cc_final: 0.8015 (t0) REVERT: A 1050 MET cc_start: 0.8746 (ptm) cc_final: 0.8427 (ptm) REVERT: B 1113 GLN cc_start: 0.8816 (mp10) cc_final: 0.8073 (mt0) REVERT: C 177 MET cc_start: 0.3624 (tmm) cc_final: 0.3403 (tmm) REVERT: C 191 GLU cc_start: 0.7618 (mt-10) cc_final: 0.6830 (mp0) REVERT: C 208 THR cc_start: 0.9027 (OUTLIER) cc_final: 0.8261 (p) REVERT: C 226 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7896 (mm) REVERT: C 324 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.5502 (pp20) REVERT: C 529 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7920 (mmmt) REVERT: C 1002 GLN cc_start: 0.8381 (tt0) cc_final: 0.8154 (tt0) REVERT: H 93 TYR cc_start: 0.7994 (m-10) cc_final: 0.7543 (m-10) REVERT: H 103 TRP cc_start: 0.7111 (p90) cc_final: 0.6537 (p90) REVERT: L 101 TRP cc_start: 0.5538 (t-100) cc_final: 0.5166 (t-100) REVERT: J 48 MET cc_start: 0.1918 (mpp) cc_final: 0.1630 (mpp) outliers start: 85 outliers final: 49 residues processed: 310 average time/residue: 0.4030 time to fit residues: 206.9100 Evaluate side-chains 264 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 208 time to evaluate : 3.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 317 ASN 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 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 610 VAL Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 738 CYS 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 368 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 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 523 THR Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 4 optimal weight: 7.9990 chunk 350 optimal weight: 8.9990 chunk 170 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 266 optimal weight: 0.7980 chunk 15 optimal weight: 10.0000 chunk 276 optimal weight: 3.9990 chunk 368 optimal weight: 30.0000 chunk 51 optimal weight: 8.9990 chunk 90 optimal weight: 3.9990 chunk 205 optimal weight: 0.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 87 ASN C 207 HIS C 613 GLN 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 = 0.4531 r_free = 0.4531 target = 0.199826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.122366 restraints weight = 45830.697| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 3.71 r_work: 0.3344 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 31077 Z= 0.183 Angle : 0.683 12.977 42441 Z= 0.332 Chirality : 0.047 0.504 4914 Planarity : 0.004 0.070 5358 Dihedral : 5.809 61.380 5515 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.48 % Favored : 93.38 % Rotamer: Outliers : 2.78 % Allowed : 16.19 % Favored : 81.03 % 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: -1.06 (0.14), residues: 3702 helix: 1.14 (0.21), residues: 648 sheet: -0.06 (0.16), residues: 1031 loop : -1.74 (0.13), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP L 36 HIS 0.006 0.001 HIS A1064 PHE 0.022 0.001 PHE A 86 TYR 0.017 0.001 TYR A 453 ARG 0.013 0.000 ARG C 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00376 ( 48) link_NAG-ASN : angle 2.80740 ( 144) link_BETA1-4 : bond 0.00839 ( 21) link_BETA1-4 : angle 2.69373 ( 63) hydrogen bonds : bond 0.04395 ( 1025) hydrogen bonds : angle 5.13099 ( 2958) SS BOND : bond 0.00621 ( 45) SS BOND : angle 2.28141 ( 90) covalent geometry : bond 0.00447 (30963) covalent geometry : angle 0.64828 (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 304 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 214 time to evaluate : 4.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.4776 (tpp) cc_final: 0.3900 (tpt) REVERT: A 269 TYR cc_start: 0.8424 (m-80) cc_final: 0.8136 (m-80) REVERT: A 298 GLU cc_start: 0.8281 (tp30) cc_final: 0.7976 (tp30) REVERT: A 365 TYR cc_start: 0.7772 (m-80) cc_final: 0.7550 (m-80) REVERT: A 462 LYS cc_start: 0.8875 (mtmm) cc_final: 0.8640 (mtmm) REVERT: A 503 VAL cc_start: 0.7785 (OUTLIER) cc_final: 0.7550 (m) REVERT: A 514 SER cc_start: 0.8818 (t) cc_final: 0.8527 (p) REVERT: A 515 PHE cc_start: 0.8828 (OUTLIER) cc_final: 0.7879 (p90) REVERT: A 516 GLU cc_start: 0.7450 (tm-30) cc_final: 0.6593 (tm-30) REVERT: A 646 ARG cc_start: 0.7498 (ptt-90) cc_final: 0.7041 (tpt170) REVERT: A 675 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.7304 (mp10) REVERT: A 821 LEU cc_start: 0.8495 (mt) cc_final: 0.8250 (tt) REVERT: A 957 GLN cc_start: 0.8391 (mt0) cc_final: 0.7945 (mm-40) REVERT: A 960 ASN cc_start: 0.8460 (m-40) cc_final: 0.8214 (t0) REVERT: B 375 PHE cc_start: 0.3632 (OUTLIER) cc_final: 0.2681 (t80) REVERT: B 854 LYS cc_start: 0.7193 (OUTLIER) cc_final: 0.5126 (tptt) REVERT: B 1113 GLN cc_start: 0.8905 (mp10) cc_final: 0.8151 (mt0) REVERT: C 177 MET cc_start: 0.3730 (tmm) cc_final: 0.3415 (tmm) REVERT: C 191 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7149 (mp0) REVERT: C 208 THR cc_start: 0.9061 (OUTLIER) cc_final: 0.8285 (p) REVERT: C 286 THR cc_start: 0.8732 (p) cc_final: 0.8523 (t) REVERT: C 324 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.5639 (pp20) REVERT: C 529 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7930 (mmmt) REVERT: C 675 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.8025 (tp40) REVERT: C 1002 GLN cc_start: 0.8711 (tt0) cc_final: 0.8470 (tt0) REVERT: H 59 TYR cc_start: 0.6367 (m-80) cc_final: 0.6111 (m-10) REVERT: H 103 TRP cc_start: 0.7190 (p90) cc_final: 0.6564 (p90) REVERT: J 48 MET cc_start: 0.1984 (mpp) cc_final: 0.1654 (mpp) outliers start: 90 outliers final: 60 residues processed: 289 average time/residue: 0.3942 time to fit residues: 191.0793 Evaluate side-chains 273 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 204 time to evaluate : 2.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 317 ASN 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 610 VAL Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 738 CYS 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 326 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 362 VAL 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 1141 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL 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 569 ILE 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 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 991 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 94 TYR 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: 0.9990 chunk 261 optimal weight: 6.9990 chunk 374 optimal weight: 50.0000 chunk 88 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 chunk 295 optimal weight: 0.9980 chunk 241 optimal weight: 6.9990 chunk 165 optimal weight: 1.9990 chunk 331 optimal weight: 40.0000 chunk 31 optimal weight: 0.9980 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 87 ASN 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 = 0.4539 r_free = 0.4539 target = 0.200772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.121939 restraints weight = 45802.010| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.81 r_work: 0.3414 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.5176 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= 0.125 Angle : 0.633 12.254 42441 Z= 0.306 Chirality : 0.046 0.475 4914 Planarity : 0.004 0.066 5358 Dihedral : 5.504 59.819 5512 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.56 % Favored : 93.30 % Rotamer: Outliers : 2.50 % Allowed : 16.77 % Favored : 80.72 % 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: -0.88 (0.14), residues: 3702 helix: 1.39 (0.21), residues: 643 sheet: 0.05 (0.16), residues: 1031 loop : -1.65 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP L 36 HIS 0.004 0.001 HIS A1064 PHE 0.018 0.001 PHE C 106 TYR 0.018 0.001 TYR A 453 ARG 0.009 0.000 ARG C 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00336 ( 48) link_NAG-ASN : angle 2.68976 ( 144) link_BETA1-4 : bond 0.00854 ( 21) link_BETA1-4 : angle 2.61657 ( 63) hydrogen bonds : bond 0.03909 ( 1025) hydrogen bonds : angle 4.93769 ( 2958) SS BOND : bond 0.00466 ( 45) SS BOND : angle 1.90442 ( 90) covalent geometry : bond 0.00293 (30963) covalent geometry : angle 0.60052 (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 296 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 215 time to evaluate : 2.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.4789 (tpp) cc_final: 0.3931 (tpt) REVERT: A 269 TYR cc_start: 0.8324 (m-80) cc_final: 0.8066 (m-80) REVERT: A 298 GLU cc_start: 0.8232 (tp30) cc_final: 0.7874 (tp30) REVERT: A 357 ARG cc_start: 0.7718 (ttm-80) cc_final: 0.7428 (ttm-80) REVERT: A 365 TYR cc_start: 0.7743 (m-80) cc_final: 0.7465 (m-80) REVERT: A 514 SER cc_start: 0.8734 (t) cc_final: 0.8458 (p) REVERT: A 515 PHE cc_start: 0.8756 (OUTLIER) cc_final: 0.7953 (p90) REVERT: A 516 GLU cc_start: 0.7391 (tm-30) cc_final: 0.6583 (tm-30) REVERT: A 646 ARG cc_start: 0.7507 (ptt-90) cc_final: 0.7149 (tpt170) REVERT: A 675 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.7192 (mp10) REVERT: A 957 GLN cc_start: 0.8335 (mt0) cc_final: 0.7880 (mm110) REVERT: A 960 ASN cc_start: 0.8409 (m-40) cc_final: 0.8169 (t0) REVERT: B 375 PHE cc_start: 0.3700 (OUTLIER) cc_final: 0.2765 (t80) REVERT: B 854 LYS cc_start: 0.7271 (OUTLIER) cc_final: 0.5197 (tptt) REVERT: B 1113 GLN cc_start: 0.8853 (mp10) cc_final: 0.8277 (mt0) REVERT: C 177 MET cc_start: 0.3492 (tmm) cc_final: 0.3226 (tmm) REVERT: C 191 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7197 (mp0) REVERT: C 208 THR cc_start: 0.9069 (OUTLIER) cc_final: 0.8293 (p) REVERT: C 286 THR cc_start: 0.8805 (p) cc_final: 0.8528 (t) REVERT: C 324 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.5629 (pp20) REVERT: C 529 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7961 (mmmt) REVERT: C 675 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.8136 (tp40) REVERT: C 1002 GLN cc_start: 0.8645 (tt0) cc_final: 0.8421 (tt0) REVERT: H 23 ARG cc_start: 0.7760 (tpp80) cc_final: 0.7379 (ptt90) REVERT: H 59 TYR cc_start: 0.6592 (m-80) cc_final: 0.6329 (m-10) REVERT: H 93 TYR cc_start: 0.7864 (m-10) cc_final: 0.7486 (m-10) REVERT: H 94 TYR cc_start: 0.4635 (OUTLIER) cc_final: 0.4369 (t80) REVERT: H 103 TRP cc_start: 0.7181 (p90) cc_final: 0.6679 (p90) REVERT: J 48 MET cc_start: 0.1999 (mpp) cc_final: 0.1641 (mpp) outliers start: 81 outliers final: 51 residues processed: 287 average time/residue: 0.3828 time to fit residues: 181.5929 Evaluate side-chains 270 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 210 time to evaluate : 2.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 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 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 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 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 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 129 LYS 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 529 LYS Chi-restraints excluded: chain C residue 533 LEU 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 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 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 94 TYR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 17 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 25 optimal weight: 2.9990 chunk 230 optimal weight: 8.9990 chunk 136 optimal weight: 0.0470 chunk 51 optimal weight: 9.9990 chunk 241 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 296 optimal weight: 0.5980 chunk 154 optimal weight: 10.0000 chunk 143 optimal weight: 0.0270 chunk 222 optimal weight: 4.9990 chunk 114 optimal weight: 20.0000 overall best weight: 1.7340 ------------------------------------------------------------------------------- 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 87 ASN 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 = 0.4527 r_free = 0.4527 target = 0.199604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.121780 restraints weight = 45789.526| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 3.21 r_work: 0.3363 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.5347 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= 0.155 Angle : 0.651 12.075 42441 Z= 0.316 Chirality : 0.046 0.464 4914 Planarity : 0.004 0.069 5358 Dihedral : 5.441 58.124 5507 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.73 % Favored : 93.14 % Rotamer: Outliers : 2.69 % Allowed : 16.96 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.86 (0.14), residues: 3702 helix: 1.36 (0.21), residues: 645 sheet: 0.10 (0.16), residues: 1030 loop : -1.65 (0.13), residues: 2027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP L 36 HIS 0.005 0.001 HIS A1064 PHE 0.019 0.001 PHE A 86 TYR 0.017 0.001 TYR C 170 ARG 0.007 0.000 ARG C 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00313 ( 48) link_NAG-ASN : angle 2.62952 ( 144) link_BETA1-4 : bond 0.00808 ( 21) link_BETA1-4 : angle 2.57260 ( 63) hydrogen bonds : bond 0.04139 ( 1025) hydrogen bonds : angle 4.93852 ( 2958) SS BOND : bond 0.00461 ( 45) SS BOND : angle 2.08652 ( 90) covalent geometry : bond 0.00374 (30963) covalent geometry : angle 0.61979 (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: 87 poor density : 218 time to evaluate : 2.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.8381 (t60) cc_final: 0.8126 (t60) REVERT: A 177 MET cc_start: 0.4437 (tpp) cc_final: 0.3531 (tpt) REVERT: A 269 TYR cc_start: 0.8383 (m-80) cc_final: 0.8123 (m-80) REVERT: A 298 GLU cc_start: 0.8270 (tp30) cc_final: 0.7919 (tp30) REVERT: A 365 TYR cc_start: 0.7852 (m-80) cc_final: 0.7585 (m-80) REVERT: A 514 SER cc_start: 0.8771 (t) cc_final: 0.8482 (p) REVERT: A 515 PHE cc_start: 0.8736 (OUTLIER) cc_final: 0.7852 (p90) REVERT: A 516 GLU cc_start: 0.7427 (tm-30) cc_final: 0.6572 (tm-30) REVERT: A 646 ARG cc_start: 0.7659 (ptt-90) cc_final: 0.7253 (tpt170) REVERT: A 675 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7194 (mp10) REVERT: A 957 GLN cc_start: 0.8368 (mt0) cc_final: 0.7868 (mm110) REVERT: A 960 ASN cc_start: 0.8434 (m-40) cc_final: 0.8194 (t0) REVERT: B 375 PHE cc_start: 0.3789 (OUTLIER) cc_final: 0.2931 (t80) REVERT: B 854 LYS cc_start: 0.7183 (OUTLIER) cc_final: 0.5098 (tptt) REVERT: B 1113 GLN cc_start: 0.8833 (mp10) cc_final: 0.8323 (mt0) REVERT: C 177 MET cc_start: 0.3540 (tmm) cc_final: 0.3269 (tmm) REVERT: C 191 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7216 (mp0) REVERT: C 208 THR cc_start: 0.9080 (OUTLIER) cc_final: 0.8285 (p) REVERT: C 286 THR cc_start: 0.8820 (p) cc_final: 0.8583 (t) REVERT: C 324 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.5623 (pp20) REVERT: C 529 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7965 (mmmt) REVERT: C 675 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.8117 (tp40) REVERT: C 977 LEU cc_start: 0.8599 (mp) cc_final: 0.8381 (mp) REVERT: H 93 TYR cc_start: 0.7974 (m-10) cc_final: 0.7557 (m-10) REVERT: H 94 TYR cc_start: 0.4792 (OUTLIER) cc_final: 0.4461 (t80) REVERT: H 103 TRP cc_start: 0.7166 (p90) cc_final: 0.6728 (p90) outliers start: 87 outliers final: 60 residues processed: 287 average time/residue: 0.3962 time to fit residues: 189.4048 Evaluate side-chains 281 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 212 time to evaluate : 3.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 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 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 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 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 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 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 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 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 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 991 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 52 ASN Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 94 TYR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 78 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 232 optimal weight: 8.9990 chunk 62 optimal weight: 0.7980 chunk 294 optimal weight: 2.9990 chunk 146 optimal weight: 0.5980 chunk 114 optimal weight: 20.0000 chunk 269 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 236 optimal weight: 10.0000 chunk 111 optimal weight: 0.6980 chunk 302 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 87 ASN C 173 GLN C 196 ASN C 207 HIS ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.200216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.123157 restraints weight = 45599.702| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 3.03 r_work: 0.3377 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.5498 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= 0.135 Angle : 0.634 12.887 42441 Z= 0.307 Chirality : 0.046 0.454 4914 Planarity : 0.004 0.074 5358 Dihedral : 5.369 56.592 5507 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.48 % Favored : 93.41 % Rotamer: Outliers : 2.41 % Allowed : 16.99 % Favored : 80.60 % 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: -0.79 (0.14), residues: 3702 helix: 1.45 (0.21), residues: 641 sheet: 0.11 (0.16), residues: 1062 loop : -1.61 (0.13), residues: 1999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP L 36 HIS 0.004 0.001 HIS A1064 PHE 0.020 0.001 PHE B 86 TYR 0.016 0.001 TYR A 453 ARG 0.008 0.000 ARG C 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00305 ( 48) link_NAG-ASN : angle 2.55165 ( 144) link_BETA1-4 : bond 0.00815 ( 21) link_BETA1-4 : angle 2.52805 ( 63) hydrogen bonds : bond 0.03941 ( 1025) hydrogen bonds : angle 4.88237 ( 2958) SS BOND : bond 0.00439 ( 45) SS BOND : angle 1.96942 ( 90) covalent geometry : bond 0.00323 (30963) covalent geometry : angle 0.60339 (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 291 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 213 time to evaluate : 3.014 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.8317 (t60) cc_final: 0.8073 (t60) REVERT: A 177 MET cc_start: 0.4421 (tpp) cc_final: 0.3947 (tpt) REVERT: A 269 TYR cc_start: 0.8336 (m-80) cc_final: 0.8064 (m-80) REVERT: A 365 TYR cc_start: 0.7876 (m-80) cc_final: 0.7583 (m-80) REVERT: A 514 SER cc_start: 0.8736 (t) cc_final: 0.8459 (p) REVERT: A 515 PHE cc_start: 0.8740 (OUTLIER) cc_final: 0.7917 (p90) REVERT: A 516 GLU cc_start: 0.7427 (tm-30) cc_final: 0.6645 (tm-30) REVERT: A 646 ARG cc_start: 0.7753 (ptt-90) cc_final: 0.7394 (tpt170) REVERT: A 675 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7212 (mp10) REVERT: A 957 GLN cc_start: 0.8329 (mt0) cc_final: 0.7808 (mm110) REVERT: A 960 ASN cc_start: 0.8421 (m-40) cc_final: 0.8190 (t0) REVERT: B 188 ASN cc_start: 0.5993 (m-40) cc_final: 0.5655 (p0) REVERT: B 375 PHE cc_start: 0.3749 (OUTLIER) cc_final: 0.2867 (t80) REVERT: B 854 LYS cc_start: 0.7202 (OUTLIER) cc_final: 0.5125 (tptt) REVERT: B 1113 GLN cc_start: 0.8838 (mp10) cc_final: 0.8464 (mt0) REVERT: C 63 THR cc_start: 0.6198 (OUTLIER) cc_final: 0.5661 (p) REVERT: C 177 MET cc_start: 0.3605 (tmm) cc_final: 0.3392 (tmm) REVERT: C 191 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7213 (mp0) REVERT: C 208 THR cc_start: 0.9069 (OUTLIER) cc_final: 0.8261 (p) REVERT: C 286 THR cc_start: 0.8793 (p) cc_final: 0.8590 (t) REVERT: C 324 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.5647 (pp20) REVERT: C 529 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.7979 (mmmt) REVERT: C 675 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.8113 (tp40) REVERT: C 984 LEU cc_start: 0.8151 (tp) cc_final: 0.7935 (tp) REVERT: H 93 TYR cc_start: 0.8052 (m-10) cc_final: 0.7608 (m-10) REVERT: H 94 TYR cc_start: 0.4748 (OUTLIER) cc_final: 0.4364 (t80) REVERT: H 103 TRP cc_start: 0.7155 (p90) cc_final: 0.6708 (p90) REVERT: I 69 MET cc_start: -0.1539 (tpt) cc_final: -0.2023 (mtt) REVERT: I 80 MET cc_start: -0.2557 (mtt) cc_final: -0.3291 (mtt) outliers start: 78 outliers final: 58 residues processed: 276 average time/residue: 0.4067 time to fit residues: 188.7475 Evaluate side-chains 273 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 205 time to evaluate : 3.370 ------------------------------------------------------------------------------- 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 208 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 409 GLN 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 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 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 573 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 675 GLN 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 129 LYS Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 208 THR 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 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 586 ASP 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 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 52 ASN Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 94 TYR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain N residue 25 SER 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: 5.9990 chunk 276 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 325 optimal weight: 50.0000 chunk 324 optimal weight: 6.9990 chunk 96 optimal weight: 0.0570 chunk 46 optimal weight: 1.9990 chunk 260 optimal weight: 0.0980 chunk 197 optimal weight: 2.9990 chunk 220 optimal weight: 4.9990 overall best weight: 1.2304 ------------------------------------------------------------------------------- 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 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 207 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.200090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.122815 restraints weight = 45552.999| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 3.17 r_work: 0.3379 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.5588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31077 Z= 0.129 Angle : 0.636 12.672 42441 Z= 0.309 Chirality : 0.046 0.459 4914 Planarity : 0.004 0.065 5358 Dihedral : 5.292 54.910 5507 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.67 % Favored : 93.19 % Rotamer: Outliers : 2.32 % Allowed : 17.21 % Favored : 80.48 % 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: -0.74 (0.14), residues: 3702 helix: 1.44 (0.21), residues: 649 sheet: 0.16 (0.16), residues: 1021 loop : -1.54 (0.13), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP L 36 HIS 0.004 0.001 HIS A1064 PHE 0.016 0.001 PHE A 86 TYR 0.016 0.001 TYR A 453 ARG 0.013 0.000 ARG C 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00291 ( 48) link_NAG-ASN : angle 2.49636 ( 144) link_BETA1-4 : bond 0.00820 ( 21) link_BETA1-4 : angle 2.49646 ( 63) hydrogen bonds : bond 0.03879 ( 1025) hydrogen bonds : angle 4.84985 ( 2958) SS BOND : bond 0.00435 ( 45) SS BOND : angle 1.89810 ( 90) covalent geometry : bond 0.00306 (30963) covalent geometry : angle 0.60755 (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 291 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 216 time to evaluate : 2.990 Fit side-chains revert: symmetry clash REVERT: A 64 TRP cc_start: 0.8343 (t60) cc_final: 0.8114 (t60) REVERT: A 177 MET cc_start: 0.4521 (tpp) cc_final: 0.3996 (tpt) REVERT: A 269 TYR cc_start: 0.8363 (m-80) cc_final: 0.8075 (m-80) REVERT: A 365 TYR cc_start: 0.7886 (m-80) cc_final: 0.7583 (m-80) REVERT: A 514 SER cc_start: 0.8681 (t) cc_final: 0.8413 (p) REVERT: A 515 PHE cc_start: 0.8723 (OUTLIER) cc_final: 0.7988 (p90) REVERT: A 516 GLU cc_start: 0.7437 (tm-30) cc_final: 0.6681 (tm-30) REVERT: A 646 ARG cc_start: 0.7777 (ptt-90) cc_final: 0.7431 (tpt170) REVERT: A 675 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.7268 (mp10) REVERT: A 957 GLN cc_start: 0.8276 (mt0) cc_final: 0.7804 (mm110) REVERT: A 960 ASN cc_start: 0.8409 (m-40) cc_final: 0.8177 (t0) REVERT: B 188 ASN cc_start: 0.5982 (m-40) cc_final: 0.5585 (p0) REVERT: B 375 PHE cc_start: 0.3664 (OUTLIER) cc_final: 0.2762 (t80) REVERT: B 854 LYS cc_start: 0.7241 (OUTLIER) cc_final: 0.5142 (tptt) REVERT: B 1113 GLN cc_start: 0.8809 (mp10) cc_final: 0.8494 (mt0) REVERT: C 63 THR cc_start: 0.6195 (OUTLIER) cc_final: 0.5677 (p) REVERT: C 208 THR cc_start: 0.9067 (OUTLIER) cc_final: 0.8742 (p) REVERT: C 324 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.5633 (pp20) REVERT: C 529 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7978 (mmmt) REVERT: C 675 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.8114 (tp40) REVERT: C 984 LEU cc_start: 0.8186 (tp) cc_final: 0.7765 (tp) REVERT: H 93 TYR cc_start: 0.8037 (m-10) cc_final: 0.7576 (m-10) REVERT: H 94 TYR cc_start: 0.5044 (OUTLIER) cc_final: 0.4604 (t80) REVERT: H 103 TRP cc_start: 0.7182 (p90) cc_final: 0.6788 (p90) REVERT: L 101 TRP cc_start: 0.5494 (t-100) cc_final: 0.5252 (t-100) outliers start: 75 outliers final: 61 residues processed: 276 average time/residue: 0.3961 time to fit residues: 183.6286 Evaluate side-chains 280 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 209 time to evaluate : 3.305 ------------------------------------------------------------------------------- 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 350 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 409 GLN 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 277 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 675 GLN 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 320 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 470 THR 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 586 ASP 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 991 VAL Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 52 ASN Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 94 TYR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain N residue 25 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 45 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 282 optimal weight: 0.6980 chunk 177 optimal weight: 2.9990 chunk 285 optimal weight: 0.7980 chunk 199 optimal weight: 0.9980 chunk 152 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 249 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 232 optimal weight: 7.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.196900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.119849 restraints weight = 44577.824| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.57 r_work: 0.3378 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.5733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 31077 Z= 0.152 Angle : 0.650 14.546 42441 Z= 0.315 Chirality : 0.046 0.464 4914 Planarity : 0.004 0.071 5358 Dihedral : 5.320 53.249 5507 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.75 % Favored : 93.08 % Rotamer: Outliers : 2.32 % Allowed : 17.05 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.41 (0.21), residues: 641 sheet: 0.11 (0.16), residues: 1020 loop : -1.52 (0.13), residues: 2041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 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 0.018 0.000 ARG C 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00285 ( 48) link_NAG-ASN : angle 2.50776 ( 144) link_BETA1-4 : bond 0.00775 ( 21) link_BETA1-4 : angle 2.45766 ( 63) hydrogen bonds : bond 0.04102 ( 1025) hydrogen bonds : angle 4.89133 ( 2958) SS BOND : bond 0.00433 ( 45) SS BOND : angle 1.97745 ( 90) covalent geometry : bond 0.00369 (30963) covalent geometry : angle 0.62206 (42144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28913.44 seconds wall clock time: 506 minutes 14.29 seconds (30374.29 seconds total)