Starting phenix.real_space_refine on Mon Aug 25 19:21:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gtp_34261/08_2025/8gtp_34261.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gtp_34261/08_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_34261/08_2025/8gtp_34261.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gtp_34261/08_2025/8gtp_34261.map" model { file = "/net/cci-nas-00/data/ceres_data/8gtp_34261/08_2025/8gtp_34261.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gtp_34261/08_2025/8gtp_34261.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.107 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 132 5.16 5 C 19257 2.51 5 N 4959 2.21 5 O 5901 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30249 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 8043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 8043 Classifications: {'peptide': 1025} Link IDs: {'PTRANS': 56, 'TRANS': 968} Chain breaks: 8 Chain: "B" Number of atoms: 8043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 8043 Classifications: {'peptide': 1025} Link IDs: {'PTRANS': 56, 'TRANS': 968} Chain breaks: 8 Chain: "C" Number of atoms: 8043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 8043 Classifications: {'peptide': 1025} Link IDs: {'PTRANS': 56, 'TRANS': 968} Chain breaks: 8 Chain: "H" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 902 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 114} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "L" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 816 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 8, 'TRANS': 102} Chain: "I" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 902 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 114} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "M" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 816 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 8, 'TRANS': 102} Chain: "J" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 902 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 114} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "N" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 816 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 8, 'TRANS': 102} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: 6.96, per 1000 atoms: 0.23 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: 3.01 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 1.4 microseconds 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6984 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 61 sheets defined 18.8% alpha, 31.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 295 through 304 Processing helix chain 'A' and resid 337 through 342 removed outlier: 4.352A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.918A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.653A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 747 through 754 removed outlier: 4.087A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.986A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 823 removed outlier: 3.589A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.514A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.577A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.652A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.590A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 removed outlier: 4.080A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.757A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 983 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.324A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.953A pdb=" N GLU B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 342 removed outlier: 3.831A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 3.919A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.654A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 754 removed outlier: 4.089A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.986A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 removed outlier: 3.590A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.514A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.577A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.651A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.591A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 4.078A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.757A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 988 through 1033 removed outlier: 4.288A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.719A pdb=" N GLU C 298 " --> pdb=" O ASP C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 342 removed outlier: 4.351A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.919A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.654A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 747 through 754 removed outlier: 4.088A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.985A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 823 removed outlier: 3.591A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.515A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.577A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.651A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.592A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 4.078A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.757A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 983 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.322A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.682A pdb=" N SER H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N HIS H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.507A pdb=" N ARG H 64 " --> pdb=" O GLN H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.682A pdb=" N SER I 31 " --> pdb=" O THR I 28 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N HIS I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 28 through 32' Processing helix chain 'I' and resid 61 through 64 removed outlier: 3.506A pdb=" N ARG I 64 " --> pdb=" O GLN I 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 61 through 64' Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.683A pdb=" N SER J 31 " --> pdb=" O THR J 28 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N HIS J 32 " --> pdb=" O PHE J 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 28 through 32' Processing helix chain 'J' and resid 61 through 64 removed outlier: 3.506A pdb=" N ARG J 64 " --> pdb=" O GLN J 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 61 through 64' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.701A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.815A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN C 542 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG C 328 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.012A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.503A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN A 164 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.503A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 310 through 318 removed outlier: 4.554A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN A 613 " --> pdb=" O GLY A 594 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER A 596 " --> pdb=" O LEU A 611 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU A 611 " --> pdb=" O SER A 596 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.547A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 391 through 392 removed outlier: 3.576A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.694A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 538 through 543 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.956A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 702 through 704 removed outlier: 3.868A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.151A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.151A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.499A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.666A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.945A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.701A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.011A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.503A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN B 164 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.503A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 310 through 314 removed outlier: 4.079A pdb=" N SER B 596 " --> pdb=" O LEU B 611 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU B 611 " --> pdb=" O SER B 596 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 327 through 328 removed outlier: 5.615A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.546A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.695A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.024A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.748A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.150A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.150A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.499A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.944A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.701A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.011A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.502A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASN C 164 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.502A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.632A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N SER C 596 " --> pdb=" O LEU C 611 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU C 611 " --> pdb=" O SER C 596 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.546A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.694A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.820A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 7.151A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 removed outlier: 7.151A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.498A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.945A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.555A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.360A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 9 through 11 removed outlier: 3.696A pdb=" N VAL L 49 " --> pdb=" O TRP L 36 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 9 through 11 Processing sheet with id=AF6, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AF7, first strand: chain 'I' and resid 3 through 5 removed outlier: 3.555A pdb=" N GLN I 3 " --> pdb=" O SER I 25 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 57 through 59 removed outlier: 6.360A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE I 34 " --> pdb=" O ILE I 50 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'M' and resid 9 through 11 removed outlier: 3.696A pdb=" N VAL M 49 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N GLN M 38 " --> pdb=" O LEU M 47 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LEU M 47 " --> pdb=" O GLN M 38 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'M' and resid 9 through 11 Processing sheet with id=AG2, first strand: chain 'M' and resid 17 through 23 Processing sheet with id=AG3, first strand: chain 'J' and resid 3 through 5 removed outlier: 3.555A pdb=" N GLN J 3 " --> pdb=" O SER J 25 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'J' and resid 57 through 59 removed outlier: 6.360A pdb=" N TRP J 36 " --> pdb=" O MET J 48 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE J 34 " --> pdb=" O ILE J 50 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'N' and resid 9 through 11 removed outlier: 3.696A pdb=" N VAL N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N GLN N 38 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LEU N 47 " --> pdb=" O GLN N 38 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'N' and resid 9 through 11 Processing sheet with id=AG7, first strand: chain 'N' and resid 17 through 23 1103 hydrogen bonds defined for protein. 2958 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.41 Time building geometry restraints manager: 3.79 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: 2.110 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 29.820 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.360 ------------------------------------------------------------------------------- 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 : 19.55 Ramachandran Plot: Outliers : 2.73 % Allowed : 7.81 % Favored : 89.47 % Rotamer: Outliers : 4.36 % Allowed : 9.05 % Favored : 86.59 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.18 (0.12), residues: 3702 helix: -1.30 (0.17), residues: 662 sheet: -1.48 (0.15), residues: 987 loop : -2.80 (0.11), residues: 2053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 102 TYR 0.024 0.002 TYR B 453 PHE 0.025 0.002 PHE A 400 TRP 0.016 0.002 TRP J 36 HIS 0.005 0.001 HIS C 505 Details of bonding type rmsd covalent geometry : bond 0.00913 (30963) covalent geometry : angle 1.08887 (42144) SS BOND : bond 0.23536 ( 45) SS BOND : angle 16.60861 ( 90) hydrogen bonds : bond 0.20238 ( 1025) hydrogen bonds : angle 8.04542 ( 2958) link_BETA1-4 : bond 0.07399 ( 21) link_BETA1-4 : angle 6.06221 ( 63) link_NAG-ASN : bond 0.02854 ( 48) link_NAG-ASN : angle 9.95953 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 586 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7604 (tt0) REVERT: A 382 VAL cc_start: 0.9216 (OUTLIER) cc_final: 0.9005 (m) REVERT: A 580 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.8386 (pt0) REVERT: A 675 GLN cc_start: 0.7419 (OUTLIER) cc_final: 0.6387 (mp10) REVERT: A 856 ASN cc_start: 0.8591 (OUTLIER) cc_final: 0.8383 (p0) REVERT: C 321 GLN cc_start: 0.7781 (OUTLIER) cc_final: 0.7364 (mm110) REVERT: C 529 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7296 (tptp) REVERT: C 690 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.7556 (mm110) REVERT: H 22 CYS cc_start: 0.0196 (t) cc_final: -0.0908 (t) REVERT: H 80 MET cc_start: 0.3888 (tmm) cc_final: 0.2973 (tmm) REVERT: L 92 TRP cc_start: 0.6705 (t-100) cc_final: 0.5950 (t-100) outliers start: 141 outliers final: 54 residues processed: 708 average time/residue: 0.1850 time to fit residues: 205.5947 Evaluate side-chains 355 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 293 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 561 PRO Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 690 GLN Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 690 GLN Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain L residue 16 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 0.0980 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 1.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 606 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 Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.207254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.136328 restraints weight = 46790.647| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 3.74 r_work: 0.3490 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 31077 Z= 0.186 Angle : 0.810 16.796 42441 Z= 0.398 Chirality : 0.053 1.090 4914 Planarity : 0.006 0.105 5358 Dihedral : 7.918 85.858 5619 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.89 % Favored : 92.76 % Rotamer: Outliers : 3.58 % Allowed : 13.65 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.15 (0.13), residues: 3702 helix: 0.21 (0.20), residues: 654 sheet: -0.92 (0.16), residues: 958 loop : -2.30 (0.12), residues: 2090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 102 TYR 0.026 0.002 TYR H 93 PHE 0.021 0.002 PHE C 375 TRP 0.019 0.001 TRP H 36 HIS 0.009 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00428 (30963) covalent geometry : angle 0.76540 (42144) SS BOND : bond 0.00568 ( 45) SS BOND : angle 2.66424 ( 90) hydrogen bonds : bond 0.05114 ( 1025) hydrogen bonds : angle 5.76866 ( 2958) link_BETA1-4 : bond 0.00840 ( 21) link_BETA1-4 : angle 3.17707 ( 63) link_NAG-ASN : bond 0.00822 ( 48) link_NAG-ASN : angle 3.59152 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 321 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.6795 (OUTLIER) cc_final: 0.6557 (t0) REVERT: A 323 THR cc_start: 0.8152 (OUTLIER) cc_final: 0.7942 (p) REVERT: A 365 TYR cc_start: 0.7665 (m-80) cc_final: 0.7279 (m-80) REVERT: A 386 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.7810 (mtpm) REVERT: A 441 LEU cc_start: 0.8551 (tp) cc_final: 0.8283 (tp) REVERT: A 490 PHE cc_start: 0.5719 (t80) cc_final: 0.5487 (t80) REVERT: A 498 ARG cc_start: 0.7964 (mmm-85) cc_final: 0.7438 (mmm-85) REVERT: A 514 SER cc_start: 0.8910 (t) cc_final: 0.8667 (p) REVERT: A 516 GLU cc_start: 0.7164 (tm-30) cc_final: 0.6822 (tm-30) REVERT: A 675 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.6839 (mp10) REVERT: A 855 PHE cc_start: 0.7841 (m-80) cc_final: 0.7587 (m-80) REVERT: A 859 THR cc_start: 0.8469 (OUTLIER) cc_final: 0.8192 (p) REVERT: A 904 TYR cc_start: 0.8048 (m-10) cc_final: 0.7620 (m-10) REVERT: A 995 ARG cc_start: 0.8356 (ttm-80) cc_final: 0.8100 (ttm110) REVERT: B 319 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.8202 (ptm160) REVERT: B 731 MET cc_start: 0.9182 (OUTLIER) cc_final: 0.8898 (ptp) REVERT: B 751 ASN cc_start: 0.8761 (t0) cc_final: 0.8512 (m-40) REVERT: B 854 LYS cc_start: 0.7060 (OUTLIER) cc_final: 0.5306 (tptt) REVERT: C 87 ASN cc_start: 0.7816 (m-40) cc_final: 0.7144 (t0) REVERT: C 88 ASP cc_start: 0.6506 (m-30) cc_final: 0.6297 (m-30) REVERT: C 169 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7979 (tm-30) REVERT: C 191 GLU cc_start: 0.7477 (mt-10) cc_final: 0.6766 (mp0) REVERT: C 259 THR cc_start: 0.1427 (OUTLIER) cc_final: 0.1209 (t) REVERT: C 321 GLN cc_start: 0.7754 (OUTLIER) cc_final: 0.7387 (mm-40) REVERT: C 693 ILE cc_start: 0.8848 (OUTLIER) cc_final: 0.8559 (pp) REVERT: H 22 CYS cc_start: 0.1969 (t) cc_final: 0.1643 (t) REVERT: H 63 PHE cc_start: 0.7615 (m-10) cc_final: 0.7320 (m-10) REVERT: L 37 TYR cc_start: 0.5169 (m-80) cc_final: 0.4941 (m-80) REVERT: L 92 TRP cc_start: 0.6082 (t-100) cc_final: 0.5388 (t-100) REVERT: J 48 MET cc_start: 0.1779 (mpp) cc_final: 0.1394 (mpp) outliers start: 116 outliers final: 52 residues processed: 414 average time/residue: 0.1543 time to fit residues: 106.1786 Evaluate side-chains 309 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 246 time to evaluate : 1.035 ------------------------------------------------------------------------------- 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 323 THR 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 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 1126 CYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN 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 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 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 533 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain I residue 2 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 228 optimal weight: 0.9990 chunk 265 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 70 optimal weight: 0.0370 chunk 247 optimal weight: 20.0000 chunk 150 optimal weight: 0.8980 chunk 264 optimal weight: 4.9990 chunk 104 optimal weight: 8.9990 chunk 217 optimal weight: 5.9990 chunk 239 optimal weight: 4.9990 chunk 274 optimal weight: 2.9990 overall best weight: 1.9864 ------------------------------------------------------------------------------- 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 907 ASN A 935 GLN B 121 ASN B 644 GLN B 755 GLN B 935 GLN C 196 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.202577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.128013 restraints weight = 46276.601| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 3.79 r_work: 0.3390 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 31077 Z= 0.184 Angle : 0.731 14.489 42441 Z= 0.360 Chirality : 0.049 0.692 4914 Planarity : 0.005 0.111 5358 Dihedral : 6.698 64.859 5540 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.46 % Favored : 93.30 % Rotamer: Outliers : 3.58 % Allowed : 14.33 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.13), residues: 3702 helix: 0.90 (0.21), residues: 641 sheet: -0.57 (0.16), residues: 1002 loop : -2.05 (0.13), residues: 2059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 983 TYR 0.016 0.001 TYR C 396 PHE 0.025 0.002 PHE A 86 TRP 0.023 0.001 TRP L 36 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00437 (30963) covalent geometry : angle 0.69155 (42144) SS BOND : bond 0.00540 ( 45) SS BOND : angle 2.48518 ( 90) hydrogen bonds : bond 0.04771 ( 1025) hydrogen bonds : angle 5.47121 ( 2958) link_BETA1-4 : bond 0.00860 ( 21) link_BETA1-4 : angle 2.94755 ( 63) link_NAG-ASN : bond 0.00578 ( 48) link_NAG-ASN : angle 3.15044 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 257 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.4905 (ttt) cc_final: 0.4585 (tpp) REVERT: A 323 THR cc_start: 0.8095 (OUTLIER) cc_final: 0.7846 (p) REVERT: A 365 TYR cc_start: 0.7735 (m-80) cc_final: 0.7271 (m-80) REVERT: A 441 LEU cc_start: 0.8592 (tp) cc_final: 0.8300 (tp) REVERT: A 490 PHE cc_start: 0.6030 (t80) cc_final: 0.5802 (t80) REVERT: A 514 SER cc_start: 0.8847 (t) cc_final: 0.8479 (p) REVERT: A 515 PHE cc_start: 0.8711 (OUTLIER) cc_final: 0.7417 (p90) REVERT: A 516 GLU cc_start: 0.7163 (tm-30) cc_final: 0.6726 (tm-30) REVERT: A 675 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7226 (mp10) REVERT: A 960 ASN cc_start: 0.8346 (m-40) cc_final: 0.8103 (t0) REVERT: B 731 MET cc_start: 0.9359 (OUTLIER) cc_final: 0.8985 (ptp) REVERT: B 979 ASP cc_start: 0.7827 (m-30) cc_final: 0.7555 (m-30) REVERT: B 1113 GLN cc_start: 0.8871 (mp10) cc_final: 0.8089 (mt0) REVERT: C 87 ASN cc_start: 0.7908 (m-40) cc_final: 0.7656 (t0) REVERT: C 106 PHE cc_start: 0.7588 (m-80) cc_final: 0.7353 (m-80) REVERT: C 191 GLU cc_start: 0.7535 (mt-10) cc_final: 0.6772 (mp0) REVERT: C 259 THR cc_start: 0.1471 (OUTLIER) cc_final: 0.1250 (t) REVERT: C 321 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.7441 (mm-40) REVERT: C 693 ILE cc_start: 0.8887 (OUTLIER) cc_final: 0.8568 (pp) REVERT: C 763 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7756 (mt) REVERT: H 63 PHE cc_start: 0.7487 (m-10) cc_final: 0.7272 (m-10) REVERT: H 93 TYR cc_start: 0.7462 (m-80) cc_final: 0.7238 (m-10) REVERT: L 32 ASN cc_start: 0.5562 (t0) cc_final: 0.5195 (t0) REVERT: L 37 TYR cc_start: 0.5376 (m-80) cc_final: 0.5124 (m-80) REVERT: L 92 TRP cc_start: 0.6482 (t-100) cc_final: 0.6049 (t-100) REVERT: J 48 MET cc_start: 0.1713 (mpp) cc_final: 0.1327 (mpp) outliers start: 116 outliers final: 70 residues processed: 353 average time/residue: 0.1516 time to fit residues: 90.1214 Evaluate side-chains 292 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 214 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 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 350 VAL Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 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 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 33 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 130 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 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 763 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain L residue 22 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 293 optimal weight: 1.9990 chunk 360 optimal weight: 40.0000 chunk 296 optimal weight: 0.6980 chunk 151 optimal weight: 8.9990 chunk 147 optimal weight: 50.0000 chunk 3 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 269 optimal weight: 1.9990 chunk 346 optimal weight: 9.9990 chunk 211 optimal weight: 9.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 ** 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** B 641 ASN B 914 ASN C 207 HIS ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 16 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.201403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.128805 restraints weight = 45968.086| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 3.93 r_work: 0.3352 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.4212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 31077 Z= 0.171 Angle : 0.707 14.262 42441 Z= 0.343 Chirality : 0.048 0.600 4914 Planarity : 0.005 0.070 5358 Dihedral : 6.484 65.138 5524 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.43 % Favored : 93.41 % Rotamer: Outliers : 3.24 % Allowed : 15.32 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.42 (0.13), residues: 3702 helix: 0.99 (0.21), residues: 642 sheet: -0.35 (0.16), residues: 1024 loop : -1.99 (0.13), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1019 TYR 0.015 0.001 TYR C 655 PHE 0.022 0.001 PHE A 86 TRP 0.025 0.001 TRP L 36 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00411 (30963) covalent geometry : angle 0.66532 (42144) SS BOND : bond 0.00498 ( 45) SS BOND : angle 2.27003 ( 90) hydrogen bonds : bond 0.04429 ( 1025) hydrogen bonds : angle 5.33821 ( 2958) link_BETA1-4 : bond 0.00858 ( 21) link_BETA1-4 : angle 2.83643 ( 63) link_NAG-ASN : bond 0.00646 ( 48) link_NAG-ASN : angle 3.29982 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 240 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.4947 (ttt) cc_final: 0.4622 (tpp) REVERT: A 298 GLU cc_start: 0.7994 (tp30) cc_final: 0.7708 (tp30) REVERT: A 323 THR cc_start: 0.8025 (OUTLIER) cc_final: 0.7763 (p) REVERT: A 357 ARG cc_start: 0.7857 (ttm-80) cc_final: 0.7626 (ttm-80) REVERT: A 365 TYR cc_start: 0.7720 (m-80) cc_final: 0.7267 (m-80) REVERT: A 441 LEU cc_start: 0.8590 (tp) cc_final: 0.8277 (tp) REVERT: A 490 PHE cc_start: 0.6085 (t80) cc_final: 0.5849 (t80) REVERT: A 514 SER cc_start: 0.8787 (t) cc_final: 0.8466 (p) REVERT: A 515 PHE cc_start: 0.8735 (OUTLIER) cc_final: 0.7597 (p90) REVERT: A 516 GLU cc_start: 0.7197 (tm-30) cc_final: 0.6526 (tm-30) REVERT: A 675 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.7191 (mp10) REVERT: A 957 GLN cc_start: 0.8146 (mt0) cc_final: 0.7828 (mm-40) REVERT: A 960 ASN cc_start: 0.8347 (m-40) cc_final: 0.8109 (t0) REVERT: A 1050 MET cc_start: 0.8722 (ptm) cc_final: 0.8438 (ptm) REVERT: B 731 MET cc_start: 0.9408 (OUTLIER) cc_final: 0.9077 (ptp) REVERT: B 854 LYS cc_start: 0.7163 (OUTLIER) cc_final: 0.5298 (tptt) REVERT: B 960 ASN cc_start: 0.8154 (m-40) cc_final: 0.7940 (t0) REVERT: B 979 ASP cc_start: 0.7863 (m-30) cc_final: 0.7614 (m-30) REVERT: B 1113 GLN cc_start: 0.8887 (mp10) cc_final: 0.8135 (mt0) REVERT: C 87 ASN cc_start: 0.7912 (m-40) cc_final: 0.7705 (t0) REVERT: C 177 MET cc_start: 0.3829 (tmm) cc_final: 0.3549 (tmm) REVERT: C 191 GLU cc_start: 0.7588 (mt-10) cc_final: 0.6831 (mp0) REVERT: C 259 THR cc_start: 0.1386 (OUTLIER) cc_final: 0.1184 (t) REVERT: C 321 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.7728 (mm-40) REVERT: C 693 ILE cc_start: 0.8903 (OUTLIER) cc_final: 0.8596 (pp) REVERT: C 763 LEU cc_start: 0.8061 (mm) cc_final: 0.7826 (mt) REVERT: H 63 PHE cc_start: 0.7602 (m-10) cc_final: 0.7379 (m-10) REVERT: H 93 TYR cc_start: 0.7550 (m-80) cc_final: 0.7159 (m-10) REVERT: L 37 TYR cc_start: 0.5302 (m-80) cc_final: 0.4997 (m-80) REVERT: J 48 MET cc_start: 0.1769 (mpp) cc_final: 0.1442 (mpp) outliers start: 105 outliers final: 65 residues processed: 325 average time/residue: 0.1458 time to fit residues: 80.2362 Evaluate side-chains 288 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 215 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 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 341 VAL 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 588 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 518 LEU 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 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 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 226 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 518 LEU 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 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 711 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 861 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain M residue 71 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 349 optimal weight: 6.9990 chunk 350 optimal weight: 30.0000 chunk 86 optimal weight: 9.9990 chunk 80 optimal weight: 1.9990 chunk 323 optimal weight: 20.0000 chunk 90 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 152 optimal weight: 0.0870 chunk 28 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 131 optimal weight: 0.9990 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 207 HIS C 613 GLN C1010 GLN H 52 ASN ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.200757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.127649 restraints weight = 45949.086| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 3.73 r_work: 0.3361 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.4611 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= 0.151 Angle : 0.673 12.924 42441 Z= 0.326 Chirality : 0.048 0.538 4914 Planarity : 0.004 0.061 5358 Dihedral : 6.098 64.228 5524 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.37 % Favored : 93.49 % Rotamer: Outliers : 3.31 % Allowed : 15.79 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.20 (0.13), residues: 3702 helix: 1.11 (0.21), residues: 648 sheet: -0.20 (0.16), residues: 1041 loop : -1.84 (0.13), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1019 TYR 0.021 0.001 TYR A 453 PHE 0.021 0.001 PHE A 86 TRP 0.031 0.001 TRP L 36 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00358 (30963) covalent geometry : angle 0.63508 (42144) SS BOND : bond 0.00463 ( 45) SS BOND : angle 2.07150 ( 90) hydrogen bonds : bond 0.04202 ( 1025) hydrogen bonds : angle 5.16027 ( 2958) link_BETA1-4 : bond 0.00898 ( 21) link_BETA1-4 : angle 2.74821 ( 63) link_NAG-ASN : bond 0.00634 ( 48) link_NAG-ASN : angle 3.07831 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 236 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 269 TYR cc_start: 0.8330 (m-80) cc_final: 0.7991 (m-80) REVERT: A 298 GLU cc_start: 0.7971 (tp30) cc_final: 0.7673 (tp30) REVERT: A 365 TYR cc_start: 0.7726 (m-80) cc_final: 0.7328 (m-80) REVERT: A 490 PHE cc_start: 0.5901 (t80) cc_final: 0.5625 (t80) REVERT: A 514 SER cc_start: 0.8711 (t) cc_final: 0.8378 (p) REVERT: A 515 PHE cc_start: 0.8690 (OUTLIER) cc_final: 0.7631 (p90) REVERT: A 516 GLU cc_start: 0.7187 (tm-30) cc_final: 0.6430 (tm-30) REVERT: A 675 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7148 (mp10) REVERT: A 957 GLN cc_start: 0.8138 (mt0) cc_final: 0.7757 (mm-40) REVERT: A 960 ASN cc_start: 0.8307 (m-40) cc_final: 0.8074 (t0) REVERT: A 1050 MET cc_start: 0.8718 (ptm) cc_final: 0.8424 (ptm) REVERT: B 619 GLU cc_start: 0.7593 (tp30) cc_final: 0.7387 (tp30) REVERT: B 731 MET cc_start: 0.9428 (OUTLIER) cc_final: 0.8956 (ptp) REVERT: B 854 LYS cc_start: 0.7077 (OUTLIER) cc_final: 0.5139 (tptt) REVERT: B 1113 GLN cc_start: 0.8835 (mp10) cc_final: 0.8068 (mt0) REVERT: C 87 ASN cc_start: 0.7975 (m-40) cc_final: 0.7727 (t0) REVERT: C 177 MET cc_start: 0.3633 (tmm) cc_final: 0.3345 (tmm) REVERT: C 191 GLU cc_start: 0.7622 (mt-10) cc_final: 0.6876 (mp0) REVERT: C 259 THR cc_start: 0.1838 (OUTLIER) cc_final: 0.1638 (t) REVERT: C 321 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.7716 (mm-40) REVERT: C 357 ARG cc_start: 0.7705 (mmm160) cc_final: 0.7366 (mmp-170) REVERT: C 693 ILE cc_start: 0.8904 (OUTLIER) cc_final: 0.8589 (pp) REVERT: H 63 PHE cc_start: 0.7567 (m-10) cc_final: 0.7360 (m-10) REVERT: H 93 TYR cc_start: 0.7673 (m-80) cc_final: 0.7330 (m-10) REVERT: H 94 TYR cc_start: 0.4978 (OUTLIER) cc_final: 0.4588 (t80) REVERT: H 103 TRP cc_start: 0.7145 (p90) cc_final: 0.6531 (p90) REVERT: H 107 PHE cc_start: 0.3726 (OUTLIER) cc_final: 0.2450 (m-10) REVERT: L 37 TYR cc_start: 0.5332 (m-80) cc_final: 0.4924 (m-80) REVERT: J 48 MET cc_start: 0.1898 (mpp) cc_final: 0.1597 (mpp) outliers start: 107 outliers final: 68 residues processed: 325 average time/residue: 0.1534 time to fit residues: 83.7501 Evaluate side-chains 288 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 211 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 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 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 610 VAL Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 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 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 705 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 861 LEU 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 H residue 107 PHE Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain N residue 25 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 22 optimal weight: 0.5980 chunk 174 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 229 optimal weight: 3.9990 chunk 165 optimal weight: 0.9980 chunk 363 optimal weight: 30.0000 chunk 211 optimal weight: 10.0000 chunk 114 optimal weight: 9.9990 chunk 364 optimal weight: 40.0000 chunk 175 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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** ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 317 ASN C 856 ASN C1010 GLN L 28 ASN ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 52 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.198990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.120837 restraints weight = 45638.696| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 3.29 r_work: 0.3338 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.4983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 31077 Z= 0.206 Angle : 0.701 12.250 42441 Z= 0.341 Chirality : 0.048 0.504 4914 Planarity : 0.005 0.075 5358 Dihedral : 6.010 63.279 5513 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.75 % Favored : 93.11 % Rotamer: Outliers : 3.12 % Allowed : 15.94 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.13), residues: 3702 helix: 1.02 (0.21), residues: 647 sheet: -0.09 (0.16), residues: 1031 loop : -1.80 (0.13), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 102 TYR 0.017 0.001 TYR A 453 PHE 0.023 0.002 PHE A 86 TRP 0.031 0.001 TRP L 36 HIS 0.007 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00500 (30963) covalent geometry : angle 0.66564 (42144) SS BOND : bond 0.00523 ( 45) SS BOND : angle 2.24634 ( 90) hydrogen bonds : bond 0.04634 ( 1025) hydrogen bonds : angle 5.24967 ( 2958) link_BETA1-4 : bond 0.00853 ( 21) link_BETA1-4 : angle 2.70216 ( 63) link_NAG-ASN : bond 0.00458 ( 48) link_NAG-ASN : angle 2.95296 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 221 time to evaluate : 0.936 Fit side-chains revert: symmetry clash REVERT: A 85 PRO cc_start: 0.6922 (Cg_endo) cc_final: 0.6650 (Cg_exo) REVERT: A 177 MET cc_start: 0.4842 (tpp) cc_final: 0.3959 (tpt) REVERT: A 269 TYR cc_start: 0.8349 (m-80) cc_final: 0.8144 (m-80) REVERT: A 298 GLU cc_start: 0.8279 (tp30) cc_final: 0.7966 (tp30) REVERT: A 365 TYR cc_start: 0.7935 (m-80) cc_final: 0.7586 (m-80) REVERT: A 490 PHE cc_start: 0.5976 (t80) cc_final: 0.5581 (t80) REVERT: A 515 PHE cc_start: 0.8808 (OUTLIER) cc_final: 0.7864 (p90) REVERT: A 516 GLU cc_start: 0.7411 (tm-30) cc_final: 0.6543 (tm-30) REVERT: A 646 ARG cc_start: 0.7683 (ptt-90) cc_final: 0.7201 (tpt170) REVERT: A 675 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.7255 (mp10) REVERT: A 957 GLN cc_start: 0.8368 (mt0) cc_final: 0.7929 (mm-40) REVERT: A 1050 MET cc_start: 0.8919 (ptm) cc_final: 0.8701 (ptm) REVERT: B 375 PHE cc_start: 0.3759 (OUTLIER) cc_final: 0.2930 (t80) REVERT: B 619 GLU cc_start: 0.7690 (tp30) cc_final: 0.7448 (tp30) REVERT: B 725 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8507 (tt0) REVERT: B 854 LYS cc_start: 0.7140 (OUTLIER) cc_final: 0.5113 (tptt) REVERT: B 1113 GLN cc_start: 0.8895 (mp10) cc_final: 0.8115 (mt0) REVERT: C 87 ASN cc_start: 0.8029 (m-40) cc_final: 0.7511 (m-40) REVERT: C 88 ASP cc_start: 0.6972 (m-30) cc_final: 0.6760 (m-30) REVERT: C 177 MET cc_start: 0.3645 (tmm) cc_final: 0.3321 (tmm) REVERT: C 191 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7161 (mp0) REVERT: C 259 THR cc_start: 0.1928 (OUTLIER) cc_final: 0.1719 (t) REVERT: C 693 ILE cc_start: 0.8961 (OUTLIER) cc_final: 0.8681 (pp) REVERT: H 93 TYR cc_start: 0.7586 (m-80) cc_final: 0.7265 (m-10) REVERT: H 103 TRP cc_start: 0.7133 (p90) cc_final: 0.6751 (p90) REVERT: H 107 PHE cc_start: 0.3607 (m-80) cc_final: 0.2605 (m-10) REVERT: L 37 TYR cc_start: 0.4996 (m-80) cc_final: 0.4761 (m-80) REVERT: J 48 MET cc_start: 0.1918 (mpp) cc_final: 0.1654 (mpp) outliers start: 101 outliers final: 73 residues processed: 306 average time/residue: 0.1543 time to fit residues: 78.8561 Evaluate side-chains 285 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 205 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 763 LEU 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 208 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 861 LEU 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 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 M residue 71 SER Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain N residue 25 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 62 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 170 optimal weight: 0.6980 chunk 237 optimal weight: 30.0000 chunk 277 optimal weight: 0.5980 chunk 119 optimal weight: 3.9990 chunk 232 optimal weight: 0.3980 chunk 371 optimal weight: 50.0000 chunk 217 optimal weight: 0.7980 chunk 300 optimal weight: 0.9990 chunk 280 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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** B 856 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 = 0.4548 r_free = 0.4548 target = 0.201640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.124619 restraints weight = 45862.393| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 3.08 r_work: 0.3405 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.5150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 31077 Z= 0.110 Angle : 0.634 12.856 42441 Z= 0.306 Chirality : 0.045 0.485 4914 Planarity : 0.004 0.066 5358 Dihedral : 5.584 61.698 5510 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.10 % Favored : 93.76 % Rotamer: Outliers : 1.98 % Allowed : 17.21 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.14), residues: 3702 helix: 1.37 (0.21), residues: 642 sheet: 0.05 (0.16), residues: 1032 loop : -1.66 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 983 TYR 0.016 0.001 TYR A 453 PHE 0.018 0.001 PHE B 86 TRP 0.021 0.001 TRP L 36 HIS 0.003 0.000 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00247 (30963) covalent geometry : angle 0.60181 (42144) SS BOND : bond 0.00468 ( 45) SS BOND : angle 1.74438 ( 90) hydrogen bonds : bond 0.03727 ( 1025) hydrogen bonds : angle 4.94262 ( 2958) link_BETA1-4 : bond 0.00879 ( 21) link_BETA1-4 : angle 2.60914 ( 63) link_NAG-ASN : bond 0.00381 ( 48) link_NAG-ASN : angle 2.74970 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 224 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 PRO cc_start: 0.6924 (Cg_endo) cc_final: 0.6583 (Cg_exo) REVERT: A 177 MET cc_start: 0.4715 (tpp) cc_final: 0.3874 (tpt) REVERT: A 269 TYR cc_start: 0.8293 (m-80) cc_final: 0.8078 (m-80) REVERT: A 357 ARG cc_start: 0.7728 (ttm-80) cc_final: 0.7519 (ttm-80) REVERT: A 365 TYR cc_start: 0.7771 (m-80) cc_final: 0.7286 (m-80) REVERT: A 514 SER cc_start: 0.8728 (t) cc_final: 0.8448 (p) REVERT: A 515 PHE cc_start: 0.8769 (OUTLIER) cc_final: 0.7885 (p90) REVERT: A 516 GLU cc_start: 0.7363 (tm-30) cc_final: 0.6519 (tm-30) REVERT: A 646 ARG cc_start: 0.7603 (ptt-90) cc_final: 0.7094 (tpt170) REVERT: A 675 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.7206 (mp10) REVERT: A 957 GLN cc_start: 0.8343 (mt0) cc_final: 0.7836 (mm110) REVERT: A 960 ASN cc_start: 0.8361 (m-40) cc_final: 0.8142 (t0) REVERT: A 1050 MET cc_start: 0.8853 (ptm) cc_final: 0.8623 (ptm) REVERT: B 88 ASP cc_start: 0.6554 (m-30) cc_final: 0.6201 (m-30) REVERT: B 191 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8218 (mt-10) REVERT: B 375 PHE cc_start: 0.3684 (OUTLIER) cc_final: 0.2732 (t80) REVERT: B 854 LYS cc_start: 0.7200 (OUTLIER) cc_final: 0.5166 (tptt) REVERT: B 856 ASN cc_start: 0.8847 (p0) cc_final: 0.8628 (p0) REVERT: B 960 ASN cc_start: 0.8261 (m-40) cc_final: 0.7875 (t0) REVERT: B 1113 GLN cc_start: 0.8819 (mp10) cc_final: 0.8327 (mt0) REVERT: C 47 VAL cc_start: 0.8424 (p) cc_final: 0.8140 (m) REVERT: C 177 MET cc_start: 0.3569 (tmm) cc_final: 0.3342 (tmm) REVERT: C 259 THR cc_start: 0.2191 (OUTLIER) cc_final: 0.1987 (t) REVERT: C 353 TRP cc_start: 0.4478 (p-90) cc_final: 0.4006 (p-90) REVERT: C 693 ILE cc_start: 0.8963 (OUTLIER) cc_final: 0.8654 (pp) REVERT: H 93 TYR cc_start: 0.7583 (m-10) cc_final: 0.7284 (m-10) REVERT: H 103 TRP cc_start: 0.7188 (p90) cc_final: 0.6839 (p90) REVERT: H 107 PHE cc_start: 0.3656 (m-80) cc_final: 0.2639 (m-10) REVERT: L 37 TYR cc_start: 0.4646 (m-80) cc_final: 0.4429 (m-80) REVERT: J 48 MET cc_start: 0.2002 (mpp) cc_final: 0.1672 (mpp) outliers start: 64 outliers final: 42 residues processed: 279 average time/residue: 0.1659 time to fit residues: 76.9970 Evaluate side-chains 257 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 209 time to evaluate : 0.912 ------------------------------------------------------------------------------- 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 130 VAL Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 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 675 GLN Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 763 LEU 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 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 226 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 973 ILE 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 M residue 71 SER Chi-restraints excluded: chain N residue 25 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 78 optimal weight: 0.8980 chunk 316 optimal weight: 1.9990 chunk 352 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 333 optimal weight: 40.0000 chunk 207 optimal weight: 2.9990 chunk 249 optimal weight: 10.0000 chunk 154 optimal weight: 10.0000 chunk 323 optimal weight: 8.9990 chunk 218 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN B 755 GLN B 935 GLN C 173 GLN C 196 ASN C 207 HIS L 28 ASN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.197187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.118513 restraints weight = 45571.898| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 3.48 r_work: 0.3301 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.5445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 31077 Z= 0.244 Angle : 0.722 12.798 42441 Z= 0.353 Chirality : 0.049 0.478 4914 Planarity : 0.005 0.055 5358 Dihedral : 5.862 60.673 5506 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.40 % Favored : 92.49 % Rotamer: Outliers : 2.38 % Allowed : 16.99 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.14), residues: 3702 helix: 1.02 (0.21), residues: 647 sheet: -0.05 (0.16), residues: 1046 loop : -1.76 (0.13), residues: 2009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 983 TYR 0.017 0.002 TYR A1067 PHE 0.026 0.002 PHE A 86 TRP 0.018 0.002 TRP L 36 HIS 0.008 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00601 (30963) covalent geometry : angle 0.68975 (42144) SS BOND : bond 0.00547 ( 45) SS BOND : angle 2.27550 ( 90) hydrogen bonds : bond 0.05038 ( 1025) hydrogen bonds : angle 5.20541 ( 2958) link_BETA1-4 : bond 0.00719 ( 21) link_BETA1-4 : angle 2.60178 ( 63) link_NAG-ASN : bond 0.00405 ( 48) link_NAG-ASN : angle 2.85231 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 217 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 PRO cc_start: 0.7074 (Cg_endo) cc_final: 0.6725 (Cg_exo) REVERT: A 177 MET cc_start: 0.4715 (tpp) cc_final: 0.3838 (tpt) REVERT: A 269 TYR cc_start: 0.8359 (m-80) cc_final: 0.8067 (m-80) REVERT: A 357 ARG cc_start: 0.7700 (ttm-80) cc_final: 0.7448 (ttm-80) REVERT: A 515 PHE cc_start: 0.8934 (OUTLIER) cc_final: 0.8267 (p90) REVERT: A 516 GLU cc_start: 0.7513 (tm-30) cc_final: 0.6655 (tm-30) REVERT: A 646 ARG cc_start: 0.8072 (ptt-90) cc_final: 0.7541 (tpt170) REVERT: A 675 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.7295 (mp10) REVERT: A 957 GLN cc_start: 0.8416 (mt0) cc_final: 0.7918 (mm110) REVERT: A 1050 MET cc_start: 0.9017 (ptm) cc_final: 0.8727 (ptm) REVERT: B 375 PHE cc_start: 0.3661 (OUTLIER) cc_final: 0.2710 (t80) REVERT: B 1113 GLN cc_start: 0.8909 (mp10) cc_final: 0.8230 (mt0) REVERT: C 170 TYR cc_start: 0.7113 (t80) cc_final: 0.6347 (t80) REVERT: C 259 THR cc_start: 0.2287 (OUTLIER) cc_final: 0.2077 (t) REVERT: C 353 TRP cc_start: 0.4503 (p-90) cc_final: 0.3944 (p-90) REVERT: C 693 ILE cc_start: 0.8963 (OUTLIER) cc_final: 0.8680 (pp) REVERT: H 93 TYR cc_start: 0.7569 (m-10) cc_final: 0.7245 (m-10) REVERT: H 103 TRP cc_start: 0.7274 (p90) cc_final: 0.7000 (p90) REVERT: H 107 PHE cc_start: 0.3587 (OUTLIER) cc_final: 0.2567 (m-10) REVERT: L 37 TYR cc_start: 0.5118 (m-80) cc_final: 0.4874 (m-80) REVERT: J 48 MET cc_start: 0.1992 (mpp) cc_final: 0.1658 (mpp) outliers start: 77 outliers final: 58 residues processed: 280 average time/residue: 0.1553 time to fit residues: 73.1155 Evaluate side-chains 268 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 204 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 50 SER 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 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 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 94 TYR Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain N residue 25 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 98 optimal weight: 0.8980 chunk 254 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 301 optimal weight: 0.7980 chunk 327 optimal weight: 20.0000 chunk 23 optimal weight: 0.0370 chunk 157 optimal weight: 1.9990 chunk 355 optimal weight: 20.0000 chunk 58 optimal weight: 0.5980 chunk 311 optimal weight: 0.9980 chunk 262 optimal weight: 0.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- 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 ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN C 196 ASN C 207 HIS C1010 GLN ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.200600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.121994 restraints weight = 45551.171| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.76 r_work: 0.3438 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.5546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 31077 Z= 0.111 Angle : 0.638 15.200 42441 Z= 0.307 Chirality : 0.045 0.474 4914 Planarity : 0.004 0.062 5358 Dihedral : 5.498 59.422 5506 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.05 % Favored : 93.84 % Rotamer: Outliers : 1.82 % Allowed : 17.61 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.14), residues: 3702 helix: 1.38 (0.21), residues: 644 sheet: 0.12 (0.16), residues: 1009 loop : -1.59 (0.13), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 102 TYR 0.015 0.001 TYR A 453 PHE 0.015 0.001 PHE C 92 TRP 0.030 0.001 TRP L 36 HIS 0.003 0.000 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00252 (30963) covalent geometry : angle 0.60891 (42144) SS BOND : bond 0.00443 ( 45) SS BOND : angle 1.70724 ( 90) hydrogen bonds : bond 0.03727 ( 1025) hydrogen bonds : angle 4.86216 ( 2958) link_BETA1-4 : bond 0.00868 ( 21) link_BETA1-4 : angle 2.51825 ( 63) link_NAG-ASN : bond 0.00330 ( 48) link_NAG-ASN : angle 2.60825 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 221 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.8366 (t60) cc_final: 0.8125 (t60) REVERT: A 85 PRO cc_start: 0.7138 (Cg_endo) cc_final: 0.6806 (Cg_exo) REVERT: A 177 MET cc_start: 0.4567 (tpp) cc_final: 0.4058 (tpt) REVERT: A 269 TYR cc_start: 0.8285 (m-80) cc_final: 0.8061 (m-80) REVERT: A 514 SER cc_start: 0.8686 (t) cc_final: 0.8422 (p) REVERT: A 515 PHE cc_start: 0.8797 (OUTLIER) cc_final: 0.8021 (p90) REVERT: A 516 GLU cc_start: 0.7287 (tm-30) cc_final: 0.6528 (tm-30) REVERT: A 646 ARG cc_start: 0.7586 (ptt-90) cc_final: 0.7271 (tpt170) REVERT: A 675 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7225 (mp10) REVERT: A 957 GLN cc_start: 0.8237 (mt0) cc_final: 0.7787 (mm110) REVERT: A 1050 MET cc_start: 0.8787 (ptm) cc_final: 0.8538 (ptm) REVERT: B 191 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8237 (mt-10) REVERT: B 375 PHE cc_start: 0.3614 (OUTLIER) cc_final: 0.2667 (t80) REVERT: B 518 LEU cc_start: 0.4480 (OUTLIER) cc_final: 0.3255 (tp) REVERT: B 854 LYS cc_start: 0.7365 (OUTLIER) cc_final: 0.5269 (tptt) REVERT: B 960 ASN cc_start: 0.8240 (m-40) cc_final: 0.7912 (t0) REVERT: B 1113 GLN cc_start: 0.8805 (mp10) cc_final: 0.8443 (mt0) REVERT: C 170 TYR cc_start: 0.7107 (t80) cc_final: 0.6587 (t80) REVERT: C 177 MET cc_start: 0.4283 (tmm) cc_final: 0.4056 (tpt) REVERT: C 353 TRP cc_start: 0.4575 (p-90) cc_final: 0.4026 (p-90) REVERT: C 693 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8661 (pp) REVERT: C 977 LEU cc_start: 0.8515 (mp) cc_final: 0.8107 (tt) REVERT: H 93 TYR cc_start: 0.7547 (m-10) cc_final: 0.7203 (m-10) REVERT: H 103 TRP cc_start: 0.7283 (p90) cc_final: 0.7078 (p90) REVERT: H 107 PHE cc_start: 0.3677 (m-80) cc_final: 0.2893 (m-10) REVERT: L 37 TYR cc_start: 0.4617 (m-80) cc_final: 0.4278 (m-80) REVERT: L 101 TRP cc_start: 0.5780 (t-100) cc_final: 0.5136 (m100) REVERT: J 48 MET cc_start: 0.2016 (mpp) cc_final: 0.1764 (mpp) outliers start: 59 outliers final: 45 residues processed: 273 average time/residue: 0.1644 time to fit residues: 74.6655 Evaluate side-chains 260 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 209 time to evaluate : 0.867 ------------------------------------------------------------------------------- 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 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 711 SER 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 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 153 MET Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 94 TYR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain N residue 25 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 353 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 282 optimal weight: 0.7980 chunk 292 optimal weight: 3.9990 chunk 313 optimal weight: 10.0000 chunk 272 optimal weight: 3.9990 chunk 229 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 142 optimal weight: 8.9990 chunk 51 optimal weight: 0.8980 chunk 361 optimal weight: 20.0000 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN C 196 ASN C 207 HIS ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.198436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.122087 restraints weight = 45310.601| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 3.69 r_work: 0.3317 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.5616 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= 0.133 Angle : 0.641 13.979 42441 Z= 0.309 Chirality : 0.046 0.462 4914 Planarity : 0.004 0.061 5358 Dihedral : 5.413 59.846 5504 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.54 % Favored : 93.35 % Rotamer: Outliers : 1.79 % Allowed : 17.67 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.14), residues: 3702 helix: 1.44 (0.21), residues: 645 sheet: 0.22 (0.16), residues: 994 loop : -1.56 (0.13), residues: 2063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 983 TYR 0.019 0.001 TYR A 453 PHE 0.017 0.001 PHE A 86 TRP 0.030 0.001 TRP L 36 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00318 (30963) covalent geometry : angle 0.61300 (42144) SS BOND : bond 0.00424 ( 45) SS BOND : angle 1.72625 ( 90) hydrogen bonds : bond 0.03923 ( 1025) hydrogen bonds : angle 4.82944 ( 2958) link_BETA1-4 : bond 0.00815 ( 21) link_BETA1-4 : angle 2.50729 ( 63) link_NAG-ASN : bond 0.00301 ( 48) link_NAG-ASN : angle 2.58755 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 217 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.8310 (t60) cc_final: 0.8069 (t60) REVERT: A 177 MET cc_start: 0.4530 (tpp) cc_final: 0.4022 (tpt) REVERT: A 357 ARG cc_start: 0.7659 (ttm-80) cc_final: 0.7439 (ttm-80) REVERT: A 514 SER cc_start: 0.8569 (t) cc_final: 0.8199 (p) REVERT: A 515 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.7870 (p90) REVERT: A 516 GLU cc_start: 0.7267 (tm-30) cc_final: 0.6537 (tm-30) REVERT: A 581 THR cc_start: 0.8633 (m) cc_final: 0.8395 (p) REVERT: A 646 ARG cc_start: 0.7530 (ptt-90) cc_final: 0.7324 (tpt170) REVERT: A 675 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7123 (mp10) REVERT: A 957 GLN cc_start: 0.8037 (mt0) cc_final: 0.7579 (mm110) REVERT: A 1050 MET cc_start: 0.8726 (ptm) cc_final: 0.8421 (ptm) REVERT: B 191 GLU cc_start: 0.8353 (mt-10) cc_final: 0.8050 (mt-10) REVERT: B 375 PHE cc_start: 0.3616 (OUTLIER) cc_final: 0.2648 (t80) REVERT: B 518 LEU cc_start: 0.4484 (OUTLIER) cc_final: 0.3251 (tp) REVERT: B 854 LYS cc_start: 0.7093 (OUTLIER) cc_final: 0.5091 (tptt) REVERT: B 960 ASN cc_start: 0.8102 (m-40) cc_final: 0.7827 (t0) REVERT: B 1113 GLN cc_start: 0.8612 (mp10) cc_final: 0.8244 (mt0) REVERT: C 63 THR cc_start: 0.5841 (OUTLIER) cc_final: 0.5343 (p) REVERT: C 170 TYR cc_start: 0.6962 (t80) cc_final: 0.6486 (t80) REVERT: C 177 MET cc_start: 0.4184 (tmm) cc_final: 0.3896 (tmm) REVERT: C 353 TRP cc_start: 0.4591 (p-90) cc_final: 0.4043 (p-90) REVERT: C 693 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8543 (pp) REVERT: C 977 LEU cc_start: 0.8497 (mp) cc_final: 0.8195 (tt) REVERT: H 93 TYR cc_start: 0.7605 (m-10) cc_final: 0.7257 (m-10) REVERT: H 107 PHE cc_start: 0.3690 (m-80) cc_final: 0.2890 (m-10) REVERT: L 37 TYR cc_start: 0.4715 (m-80) cc_final: 0.4427 (m-80) REVERT: L 101 TRP cc_start: 0.5565 (t-100) cc_final: 0.5000 (m100) REVERT: J 48 MET cc_start: 0.2070 (mpp) cc_final: 0.1838 (mpp) outliers start: 58 outliers final: 50 residues processed: 268 average time/residue: 0.1598 time to fit residues: 72.3327 Evaluate side-chains 266 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 209 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 711 SER 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 705 VAL Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 1072 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 226 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 94 TYR Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain N residue 25 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 243 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 221 optimal weight: 6.9990 chunk 219 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 363 optimal weight: 40.0000 chunk 266 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 209 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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** ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.197551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.119055 restraints weight = 45698.075| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 3.35 r_work: 0.3322 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.5771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 31077 Z= 0.157 Angle : 0.659 13.018 42441 Z= 0.319 Chirality : 0.046 0.472 4914 Planarity : 0.004 0.072 5358 Dihedral : 5.445 55.528 5504 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.54 % Favored : 93.35 % Rotamer: Outliers : 1.95 % Allowed : 17.70 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.14), residues: 3702 helix: 1.41 (0.21), residues: 638 sheet: 0.21 (0.16), residues: 998 loop : -1.53 (0.13), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 102 TYR 0.018 0.001 TYR A 453 PHE 0.018 0.001 PHE A 86 TRP 0.031 0.001 TRP L 36 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00380 (30963) covalent geometry : angle 0.63118 (42144) SS BOND : bond 0.00446 ( 45) SS BOND : angle 1.80083 ( 90) hydrogen bonds : bond 0.04189 ( 1025) hydrogen bonds : angle 4.87957 ( 2958) link_BETA1-4 : bond 0.00774 ( 21) link_BETA1-4 : angle 2.45231 ( 63) link_NAG-ASN : bond 0.00291 ( 48) link_NAG-ASN : angle 2.59661 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9957.41 seconds wall clock time: 169 minutes 59.25 seconds (10199.25 seconds total)