Starting phenix.real_space_refine on Mon Aug 25 19:13:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gto_34259/08_2025/8gto_34259.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gto_34259/08_2025/8gto_34259.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8gto_34259/08_2025/8gto_34259.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gto_34259/08_2025/8gto_34259.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gto_34259/08_2025/8gto_34259.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gto_34259/08_2025/8gto_34259.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.096 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 129 5.16 5 C 19227 2.51 5 N 4959 2.21 5 O 5919 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30234 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 8043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 8043 Classifications: {'peptide': 1025} Link IDs: {'PTRANS': 56, 'TRANS': 968} Chain breaks: 8 Chain: "B" Number of atoms: 8043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 8043 Classifications: {'peptide': 1025} Link IDs: {'PTRANS': 56, 'TRANS': 968} Chain breaks: 8 Chain: "C" Number of atoms: 8043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 8043 Classifications: {'peptide': 1025} Link IDs: {'PTRANS': 56, 'TRANS': 968} Chain breaks: 8 Chain: "H" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 910 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "L" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 803 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 102} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 910 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "M" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 803 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 102} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 910 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "N" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 803 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 102} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: 8.08, per 1000 atoms: 0.27 Number of scatterers: 30234 At special positions: 0 Unit cell: (138.933, 184.167, 202.476, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 129 16.00 O 5919 8.00 N 4959 7.00 C 19227 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.08 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.84 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.07 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=1.96 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.20 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.18 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=1.99 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=1.59 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=1.97 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.17 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.10 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.08 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.61 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=1.75 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=1.97 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.11 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=1.99 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.26 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=1.97 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.17 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.10 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.08 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.76 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.14 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.51 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=1.99 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.26 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=1.97 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.17 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.10 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 89 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A1410 " - " NAG A1411 " " NAG B1410 " - " NAG B1411 " " NAG C1410 " - " NAG C1411 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG K 1 " - " NAG K 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 165 " " NAG A1404 " - " ASN A 234 " " NAG A1405 " - " ASN A 282 " " NAG A1406 " - " ASN A 603 " " NAG A1407 " - " ASN A 616 " " NAG A1408 " - " ASN A 657 " " NAG A1409 " - " ASN A 709 " " NAG A1410 " - " ASN A1074 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 122 " " NAG B1403 " - " ASN B 165 " " NAG B1404 " - " ASN B 234 " " NAG B1405 " - " ASN B 282 " " NAG B1406 " - " ASN B 603 " " NAG B1407 " - " ASN B 616 " " NAG B1408 " - " ASN B 657 " " NAG B1409 " - " ASN B 709 " " NAG B1410 " - " ASN B1074 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 122 " " NAG C1403 " - " ASN C 165 " " NAG C1404 " - " ASN C 234 " " NAG C1405 " - " ASN C 282 " " NAG C1406 " - " ASN C 603 " " NAG C1407 " - " ASN C 616 " " NAG C1408 " - " ASN C 657 " " NAG C1409 " - " ASN C 709 " " NAG C1410 " - " ASN C1074 " " NAG D 1 " - " ASN A 331 " " NAG E 1 " - " ASN A 343 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1098 " " NAG O 1 " - " ASN A1134 " " NAG P 1 " - " ASN B 331 " " NAG Q 1 " - " ASN B 343 " " NAG R 1 " - " ASN B 717 " " NAG S 1 " - " ASN B 801 " " NAG T 1 " - " ASN B1098 " " NAG U 1 " - " ASN B1134 " " NAG V 1 " - " ASN C 331 " " NAG W 1 " - " ASN C 343 " " NAG X 1 " - " ASN C 717 " " NAG Y 1 " - " ASN C 801 " " NAG Z 1 " - " ASN C1098 " " NAG a 1 " - " ASN C1134 " Time building additional restraints: 2.60 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 1.4 microseconds 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6978 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 60 sheets defined 18.1% alpha, 31.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 295 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.629A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 4.057A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 747 through 754 removed outlier: 4.088A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.542A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 771 " --> pdb=" O LEU A 767 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 823 removed outlier: 3.591A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.514A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.577A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.650A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.592A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 removed outlier: 4.078A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.756A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 981 removed outlier: 4.057A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 1033 removed outlier: 4.393A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR A 998 " --> pdb=" O ASP A 994 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 Processing helix chain 'B' and resid 295 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.629A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 4.056A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 754 removed outlier: 4.088A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.986A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 removed outlier: 3.590A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.513A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.577A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.652A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.590A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 4.079A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.757A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 981 removed outlier: 3.573A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 6.417A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 295 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.628A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 4.056A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 747 through 754 removed outlier: 4.088A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.985A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 823 removed outlier: 3.590A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.514A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.576A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.651A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.591A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 4.078A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.757A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 983 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.324A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.700A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.012A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.502A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASN A 164 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.502A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.528A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA7, first strand: chain 'A' and resid 538 through 543 removed outlier: 5.814A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 595 through 598 removed outlier: 4.080A pdb=" N SER A 596 " --> pdb=" O LEU A 611 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU A 611 " --> pdb=" O SER A 596 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA A 609 " --> pdb=" O ILE A 598 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 670 through 673 Processing sheet with id=AB1, first strand: chain 'A' and resid 702 through 704 removed outlier: 3.938A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.150A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.150A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.499A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.384A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.945A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.701A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.012A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.503A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASN B 164 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.503A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 310 through 313 removed outlier: 3.611A pdb=" N GLY B 593 " --> pdb=" O PHE B 318 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 310 through 313 removed outlier: 5.662A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N SER B 596 " --> pdb=" O LEU B 611 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU B 611 " --> pdb=" O SER B 596 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.529A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 538 through 543 removed outlier: 5.815A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 655 through 656 removed outlier: 4.014A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.869A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.151A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.151A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.499A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.945A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 28 through 31 removed outlier: 6.133A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.012A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.503A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASN C 164 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.503A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 313 removed outlier: 3.562A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY C 593 " --> pdb=" O PHE C 318 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 313 removed outlier: 3.562A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN C 613 " --> pdb=" O GLY C 594 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER C 596 " --> pdb=" O LEU C 611 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU C 611 " --> pdb=" O SER C 596 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 324 through 325 removed outlier: 3.991A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASN C 540 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.528A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 391 through 392 removed outlier: 3.563A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 670 through 673 Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 7.150A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 7.150A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.499A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.945A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 4 through 5 Processing sheet with id=AF2, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.375A pdb=" N GLU H 10 " --> pdb=" O ALA H 118 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 9 through 12 removed outlier: 7.152A pdb=" N ALA L 10 " --> pdb=" O THR L 108 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 9 through 12 removed outlier: 7.152A pdb=" N ALA L 10 " --> pdb=" O THR L 108 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 18 through 22 Processing sheet with id=AF6, first strand: chain 'I' and resid 4 through 5 Processing sheet with id=AF7, first strand: chain 'I' and resid 10 through 11 removed outlier: 6.375A pdb=" N GLU I 10 " --> pdb=" O ALA I 118 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'M' and resid 9 through 12 removed outlier: 7.151A pdb=" N ALA M 10 " --> pdb=" O THR M 108 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'M' and resid 9 through 12 removed outlier: 7.151A pdb=" N ALA M 10 " --> pdb=" O THR M 108 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'M' and resid 18 through 22 Processing sheet with id=AG2, first strand: chain 'J' and resid 4 through 5 Processing sheet with id=AG3, first strand: chain 'J' and resid 10 through 11 removed outlier: 6.375A pdb=" N GLU J 10 " --> pdb=" O ALA J 118 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'N' and resid 9 through 12 removed outlier: 7.151A pdb=" N ALA N 10 " --> pdb=" O THR N 108 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'N' and resid 9 through 12 removed outlier: 7.151A pdb=" N ALA N 10 " --> pdb=" O THR N 108 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'N' and resid 18 through 22 1111 hydrogen bonds defined for protein. 2934 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.75 Time building geometry restraints manager: 3.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5481 1.32 - 1.45: 8562 1.45 - 1.57: 16721 1.57 - 1.70: 1 1.70 - 1.83: 165 Bond restraints: 30930 Sorted by residual: bond pdb=" CA TYR B 369 " pdb=" C TYR B 369 " ideal model delta sigma weight residual 1.523 1.437 0.086 1.34e-02 5.57e+03 4.13e+01 bond pdb=" CA TYR A 369 " pdb=" C TYR A 369 " ideal model delta sigma weight residual 1.523 1.437 0.086 1.34e-02 5.57e+03 4.11e+01 bond pdb=" CA TYR C 369 " pdb=" C TYR C 369 " ideal model delta sigma weight residual 1.523 1.438 0.085 1.34e-02 5.57e+03 4.04e+01 bond pdb=" CA TYR B 365 " pdb=" C TYR B 365 " ideal model delta sigma weight residual 1.523 1.442 0.081 1.56e-02 4.11e+03 2.69e+01 bond pdb=" C PRO C 862 " pdb=" N PRO C 863 " ideal model delta sigma weight residual 1.329 1.391 -0.062 1.20e-02 6.94e+03 2.65e+01 ... (remaining 30925 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 40833 2.71 - 5.42: 1062 5.42 - 8.13: 134 8.13 - 10.84: 25 10.84 - 13.56: 15 Bond angle restraints: 42069 Sorted by residual: angle pdb=" N VAL A 367 " pdb=" CA VAL A 367 " pdb=" C VAL A 367 " ideal model delta sigma weight residual 110.21 99.55 10.66 1.13e+00 7.83e-01 8.89e+01 angle pdb=" N VAL B 367 " pdb=" CA VAL B 367 " pdb=" C VAL B 367 " ideal model delta sigma weight residual 110.21 99.57 10.64 1.13e+00 7.83e-01 8.87e+01 angle pdb=" N VAL C 367 " pdb=" CA VAL C 367 " pdb=" C VAL C 367 " ideal model delta sigma weight residual 110.21 99.63 10.58 1.13e+00 7.83e-01 8.77e+01 angle pdb=" N SER B 366 " pdb=" CA SER B 366 " pdb=" C SER B 366 " ideal model delta sigma weight residual 111.07 103.23 7.84 1.07e+00 8.73e-01 5.37e+01 angle pdb=" N SER C 366 " pdb=" CA SER C 366 " pdb=" C SER C 366 " ideal model delta sigma weight residual 111.07 103.27 7.80 1.07e+00 8.73e-01 5.31e+01 ... (remaining 42064 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 17452 17.93 - 35.86: 1295 35.86 - 53.79: 391 53.79 - 71.72: 80 71.72 - 89.65: 42 Dihedral angle restraints: 19260 sinusoidal: 8382 harmonic: 10878 Sorted by residual: dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -174.61 88.61 1 1.00e+01 1.00e-02 9.37e+01 dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 20.60 72.40 1 1.00e+01 1.00e-02 6.70e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual 93.00 163.42 -70.42 1 1.00e+01 1.00e-02 6.38e+01 ... (remaining 19257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.326: 4890 0.326 - 0.652: 12 0.652 - 0.978: 4 0.978 - 1.304: 1 1.304 - 1.630: 1 Chirality restraints: 4908 Sorted by residual: chirality pdb=" C1 NAG B1411 " pdb=" O4 NAG B1410 " pdb=" C2 NAG B1411 " pdb=" O5 NAG B1411 " both_signs ideal model delta sigma weight residual False -2.40 -3.09 0.69 2.00e-02 2.50e+03 1.20e+03 chirality pdb=" C1 NAG C1411 " pdb=" O4 NAG C1410 " pdb=" C2 NAG C1411 " pdb=" O5 NAG C1411 " both_signs ideal model delta sigma weight residual False -2.40 -3.09 0.69 2.00e-02 2.50e+03 1.18e+03 chirality pdb=" C1 NAG A1411 " pdb=" O4 NAG A1410 " pdb=" C2 NAG A1411 " pdb=" O5 NAG A1411 " both_signs ideal model delta sigma weight residual False -2.40 -3.09 0.69 2.00e-02 2.50e+03 1.17e+03 ... (remaining 4905 not shown) Planarity restraints: 5406 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " -0.151 2.00e-02 2.50e+03 1.99e-01 4.95e+02 pdb=" CG ASN A 331 " 0.065 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " -0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " 0.341 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " -0.234 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 603 " 0.095 2.00e-02 2.50e+03 1.14e-01 1.62e+02 pdb=" CG ASN A 603 " -0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN A 603 " 0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN A 603 " -0.192 2.00e-02 2.50e+03 pdb=" C1 NAG A1406 " 0.133 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 603 " 0.071 2.00e-02 2.50e+03 9.57e-02 1.14e+02 pdb=" CG ASN B 603 " -0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN B 603 " 0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN B 603 " -0.165 2.00e-02 2.50e+03 pdb=" C1 NAG B1406 " 0.112 2.00e-02 2.50e+03 ... (remaining 5403 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 199 2.47 - 3.08: 20470 3.08 - 3.69: 42611 3.69 - 4.29: 63507 4.29 - 4.90: 104714 Nonbonded interactions: 231501 Sorted by model distance: nonbonded pdb=" N GLU A 309 " pdb=" OE1 GLU A 309 " model vdw 1.865 3.120 nonbonded pdb=" O SER A 530 " pdb=" OG1 THR A 531 " model vdw 1.915 3.040 nonbonded pdb=" OD1 ASN C 317 " pdb=" N PHE C 318 " model vdw 1.930 3.120 nonbonded pdb=" O SER C 530 " pdb=" CG2 THR C 531 " model vdw 1.961 3.460 nonbonded pdb=" O ASN A 603 " pdb=" OG1 THR A 604 " model vdw 1.988 3.040 ... (remaining 231496 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 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: 2.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 28.610 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6623 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.805 31041 Z= 0.673 Angle : 1.411 56.720 42360 Z= 0.740 Chirality : 0.079 1.630 4908 Planarity : 0.008 0.104 5358 Dihedral : 14.253 89.654 12156 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 20.24 Ramachandran Plot: Outliers : 2.41 % Allowed : 8.72 % Favored : 88.87 % Rotamer: Outliers : 4.19 % Allowed : 9.27 % Favored : 86.54 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.26 (0.12), residues: 3693 helix: -1.01 (0.18), residues: 583 sheet: -1.36 (0.15), residues: 998 loop : -3.05 (0.11), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 102 TYR 0.019 0.002 TYR B 265 PHE 0.025 0.002 PHE A 86 TRP 0.020 0.003 TRP I 47 HIS 0.004 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00880 (30930) covalent geometry : angle 1.08346 (42069) SS BOND : bond 0.23445 ( 42) SS BOND : angle 14.01316 ( 84) hydrogen bonds : bond 0.19303 ( 1032) hydrogen bonds : angle 8.04803 ( 2934) link_BETA1-4 : bond 0.07718 ( 21) link_BETA1-4 : angle 9.86636 ( 63) link_NAG-ASN : bond 0.02602 ( 48) link_NAG-ASN : angle 9.24082 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 579 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 GLN cc_start: 0.7034 (OUTLIER) cc_final: 0.6665 (mp10) REVERT: A 388 ASN cc_start: 0.8319 (OUTLIER) cc_final: 0.8088 (m-40) REVERT: A 759 PHE cc_start: 0.8064 (OUTLIER) cc_final: 0.7749 (m-10) REVERT: A 764 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8556 (ttpp) REVERT: A 819 GLU cc_start: 0.7405 (mt-10) cc_final: 0.7054 (mt-10) REVERT: A 1081 ILE cc_start: 0.8075 (mm) cc_final: 0.7828 (mm) REVERT: B 314 GLN cc_start: 0.7804 (OUTLIER) cc_final: 0.7335 (tt0) REVERT: B 529 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.8080 (mtmm) REVERT: B 695 TYR cc_start: 0.9203 (OUTLIER) cc_final: 0.8968 (p90) REVERT: C 864 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8285 (tp) REVERT: H 11 VAL cc_start: 0.5001 (t) cc_final: 0.4782 (p) outliers start: 136 outliers final: 60 residues processed: 695 average time/residue: 0.1652 time to fit residues: 182.4199 Evaluate side-chains 327 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 259 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain B residue 969 LYS Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 1074 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 1.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 173 GLN A 360 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN A 606 ASN A 607 GLN A 755 GLN A 762 GLN B 121 ASN B 164 ASN B 207 HIS B 321 GLN B 360 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 HIS B 532 ASN B 607 GLN B1119 ASN C 121 ASN C 164 ASN C 173 GLN C 360 ASN C 422 ASN C 532 ASN C 607 GLN H 100 GLN L 35 ASN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 HIS M 52 ASN M 88 HIS N 52 ASN N 88 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.201755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.139972 restraints weight = 44950.048| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 3.64 r_work: 0.3464 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 31041 Z= 0.181 Angle : 0.816 16.002 42360 Z= 0.400 Chirality : 0.050 0.567 4908 Planarity : 0.006 0.072 5358 Dihedral : 8.470 83.203 5629 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.85 % Favored : 92.74 % Rotamer: Outliers : 3.73 % Allowed : 13.43 % Favored : 82.84 % 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: -2.28 (0.13), residues: 3693 helix: 0.43 (0.20), residues: 600 sheet: -0.99 (0.16), residues: 1016 loop : -2.48 (0.12), residues: 2077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 765 TYR 0.025 0.002 TYR H 107 PHE 0.025 0.002 PHE C 86 TRP 0.021 0.001 TRP H 111 HIS 0.016 0.002 HIS I 110 Details of bonding type rmsd covalent geometry : bond 0.00409 (30930) covalent geometry : angle 0.75979 (42069) SS BOND : bond 0.00536 ( 42) SS BOND : angle 2.36659 ( 84) hydrogen bonds : bond 0.04957 ( 1032) hydrogen bonds : angle 5.67563 ( 2934) link_BETA1-4 : bond 0.00937 ( 21) link_BETA1-4 : angle 3.18227 ( 63) link_NAG-ASN : bond 0.00348 ( 48) link_NAG-ASN : angle 4.39950 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 293 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.6887 (OUTLIER) cc_final: 0.6125 (m-40) REVERT: A 129 LYS cc_start: 0.7383 (ptmt) cc_final: 0.7100 (pttt) REVERT: A 501 TYR cc_start: 0.7211 (m-10) cc_final: 0.6973 (m-10) REVERT: A 525 CYS cc_start: 0.4568 (OUTLIER) cc_final: 0.3998 (m) REVERT: A 759 PHE cc_start: 0.8737 (OUTLIER) cc_final: 0.8327 (m-10) REVERT: A 917 TYR cc_start: 0.7977 (m-80) cc_final: 0.7620 (m-80) REVERT: A 982 SER cc_start: 0.8862 (t) cc_final: 0.8545 (m) REVERT: B 517 LEU cc_start: 0.7089 (OUTLIER) cc_final: 0.6811 (pp) REVERT: B 529 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8340 (mtmm) REVERT: B 731 MET cc_start: 0.8864 (OUTLIER) cc_final: 0.8414 (ptm) REVERT: B 748 GLU cc_start: 0.7107 (mp0) cc_final: 0.6871 (mp0) REVERT: B 869 MET cc_start: 0.8372 (mtp) cc_final: 0.7978 (mtt) REVERT: B 904 TYR cc_start: 0.7997 (m-10) cc_final: 0.7431 (m-10) REVERT: C 303 LEU cc_start: 0.8409 (mt) cc_final: 0.8138 (mt) REVERT: C 675 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.7734 (mm-40) REVERT: I 111 TRP cc_start: 0.0790 (OUTLIER) cc_final: 0.0397 (t-100) REVERT: J 48 MET cc_start: 0.1539 (ptt) cc_final: 0.0657 (mmt) REVERT: J 107 TYR cc_start: 0.5619 (t80) cc_final: 0.5103 (t80) outliers start: 121 outliers final: 54 residues processed: 392 average time/residue: 0.1454 time to fit residues: 95.4653 Evaluate side-chains 279 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 217 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 969 LYS Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain I residue 106 PHE Chi-restraints excluded: chain I residue 111 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 123 optimal weight: 2.9990 chunk 298 optimal weight: 0.7980 chunk 4 optimal weight: 6.9990 chunk 163 optimal weight: 0.9990 chunk 16 optimal weight: 0.0170 chunk 144 optimal weight: 30.0000 chunk 41 optimal weight: 20.0000 chunk 140 optimal weight: 40.0000 chunk 46 optimal weight: 0.0030 chunk 310 optimal weight: 20.0000 chunk 20 optimal weight: 2.9990 overall best weight: 0.9632 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 207 HIS ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN A1101 HIS B 207 HIS B 422 ASN B 505 HIS B 762 GLN B1101 HIS B1119 ASN C 121 ASN C 439 ASN C 779 GLN ** H 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 HIS N 35 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.198932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.133676 restraints weight = 44837.290| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 3.27 r_work: 0.3403 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 31041 Z= 0.148 Angle : 0.732 20.627 42360 Z= 0.352 Chirality : 0.048 0.361 4908 Planarity : 0.005 0.076 5358 Dihedral : 6.780 70.818 5533 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.28 % Favored : 93.37 % Rotamer: Outliers : 3.17 % Allowed : 14.70 % Favored : 82.13 % 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: -1.76 (0.13), residues: 3693 helix: 1.04 (0.21), residues: 597 sheet: -0.68 (0.16), residues: 1048 loop : -2.20 (0.12), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 102 TYR 0.019 0.001 TYR J 108 PHE 0.022 0.001 PHE C 86 TRP 0.023 0.001 TRP H 111 HIS 0.005 0.001 HIS B1101 Details of bonding type rmsd covalent geometry : bond 0.00334 (30930) covalent geometry : angle 0.67063 (42069) SS BOND : bond 0.00495 ( 42) SS BOND : angle 2.21314 ( 84) hydrogen bonds : bond 0.04418 ( 1032) hydrogen bonds : angle 5.33383 ( 2934) link_BETA1-4 : bond 0.01016 ( 21) link_BETA1-4 : angle 2.92524 ( 63) link_NAG-ASN : bond 0.00800 ( 48) link_NAG-ASN : angle 4.42354 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 248 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7249 (ptmt) cc_final: 0.6933 (pttt) REVERT: A 200 TYR cc_start: 0.6638 (OUTLIER) cc_final: 0.6193 (t80) REVERT: A 278 LYS cc_start: 0.8464 (tttt) cc_final: 0.8253 (ttpt) REVERT: A 298 GLU cc_start: 0.7558 (tm-30) cc_final: 0.7302 (tm-30) REVERT: A 405 ASN cc_start: 0.8395 (m110) cc_final: 0.7847 (p0) REVERT: A 764 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8708 (ttpp) REVERT: B 859 THR cc_start: 0.8337 (t) cc_final: 0.8102 (p) REVERT: B 869 MET cc_start: 0.8507 (mtp) cc_final: 0.8301 (mtt) REVERT: B 925 ASN cc_start: 0.8032 (t0) cc_final: 0.7666 (m-40) REVERT: C 468 ILE cc_start: 0.4583 (OUTLIER) cc_final: 0.4231 (mp) REVERT: C 1002 GLN cc_start: 0.8327 (tp40) cc_final: 0.8014 (tp40) REVERT: L 22 CYS cc_start: 0.4236 (OUTLIER) cc_final: 0.3987 (m) REVERT: I 81 MET cc_start: -0.0033 (ttp) cc_final: -0.1068 (tmm) REVERT: J 48 MET cc_start: 0.1407 (ptt) cc_final: 0.0676 (mmt) REVERT: J 107 TYR cc_start: 0.5682 (t80) cc_final: 0.5369 (t80) REVERT: N 71 SER cc_start: 0.6205 (t) cc_final: 0.5930 (p) outliers start: 103 outliers final: 60 residues processed: 333 average time/residue: 0.1380 time to fit residues: 78.5215 Evaluate side-chains 264 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 200 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain I residue 106 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 367 optimal weight: 8.9990 chunk 146 optimal weight: 30.0000 chunk 144 optimal weight: 4.9990 chunk 296 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 211 optimal weight: 10.0000 chunk 225 optimal weight: 5.9990 chunk 212 optimal weight: 8.9990 chunk 125 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 25 optimal weight: 0.3980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS B 207 HIS B 314 GLN B 505 HIS B 856 ASN C 188 ASN M 35 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.194549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 101)---------------| | r_work = 0.3641 r_free = 0.3641 target = 0.128181 restraints weight = 44233.940| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 3.09 r_work: 0.3361 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 31041 Z= 0.156 Angle : 0.697 20.177 42360 Z= 0.338 Chirality : 0.047 0.295 4908 Planarity : 0.004 0.057 5358 Dihedral : 6.199 59.843 5516 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.15 % Favored : 93.50 % Rotamer: Outliers : 2.68 % Allowed : 15.90 % Favored : 81.42 % 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: -1.52 (0.13), residues: 3693 helix: 1.21 (0.21), residues: 594 sheet: -0.39 (0.16), residues: 989 loop : -2.07 (0.12), residues: 2110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 102 TYR 0.030 0.001 TYR L 50 PHE 0.024 0.001 PHE C 86 TRP 0.025 0.001 TRP H 111 HIS 0.005 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00367 (30930) covalent geometry : angle 0.64310 (42069) SS BOND : bond 0.00636 ( 42) SS BOND : angle 1.99413 ( 84) hydrogen bonds : bond 0.04159 ( 1032) hydrogen bonds : angle 5.13846 ( 2934) link_BETA1-4 : bond 0.00882 ( 21) link_BETA1-4 : angle 2.73042 ( 63) link_NAG-ASN : bond 0.00710 ( 48) link_NAG-ASN : angle 4.06228 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 203 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 VAL cc_start: 0.7124 (OUTLIER) cc_final: 0.6733 (m) REVERT: A 129 LYS cc_start: 0.7269 (ptmt) cc_final: 0.6926 (pttt) REVERT: A 298 GLU cc_start: 0.7676 (tm-30) cc_final: 0.7286 (tp30) REVERT: A 366 SER cc_start: 0.7294 (OUTLIER) cc_final: 0.6926 (t) REVERT: A 403 ARG cc_start: 0.6730 (ttm110) cc_final: 0.6446 (ttm110) REVERT: A 405 ASN cc_start: 0.8360 (m110) cc_final: 0.7728 (p0) REVERT: A 501 TYR cc_start: 0.7517 (m-80) cc_final: 0.7164 (m-10) REVERT: A 764 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8664 (ttpp) REVERT: B 859 THR cc_start: 0.8408 (t) cc_final: 0.8165 (p) REVERT: B 869 MET cc_start: 0.8571 (mtp) cc_final: 0.8353 (mtt) REVERT: B 925 ASN cc_start: 0.8082 (t0) cc_final: 0.7854 (m-40) REVERT: C 1002 GLN cc_start: 0.8286 (tp40) cc_final: 0.8072 (tp40) REVERT: I 81 MET cc_start: 0.0102 (ttp) cc_final: -0.0933 (tmm) REVERT: J 48 MET cc_start: 0.1226 (ptt) cc_final: 0.0737 (mmt) REVERT: J 107 TYR cc_start: 0.6113 (t80) cc_final: 0.5655 (t80) REVERT: N 71 SER cc_start: 0.6145 (t) cc_final: 0.5837 (p) outliers start: 87 outliers final: 62 residues processed: 276 average time/residue: 0.1441 time to fit residues: 67.9032 Evaluate side-chains 246 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 181 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain I residue 106 PHE Chi-restraints excluded: chain M residue 22 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 240 optimal weight: 0.8980 chunk 294 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 190 optimal weight: 0.9990 chunk 361 optimal weight: 0.0060 chunk 366 optimal weight: 10.0000 chunk 164 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 270 optimal weight: 1.9990 chunk 128 optimal weight: 0.6980 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS B 388 ASN B 505 HIS ** H 100 GLN ** 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 = 0.4431 r_free = 0.4431 target = 0.194793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.127154 restraints weight = 44353.000| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 3.04 r_work: 0.3375 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31041 Z= 0.121 Angle : 0.659 20.612 42360 Z= 0.317 Chirality : 0.046 0.264 4908 Planarity : 0.004 0.050 5358 Dihedral : 5.899 57.196 5510 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.12 % Favored : 93.56 % Rotamer: Outliers : 2.56 % Allowed : 16.42 % Favored : 81.02 % 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: -1.25 (0.13), residues: 3693 helix: 1.49 (0.21), residues: 594 sheet: -0.21 (0.16), residues: 997 loop : -1.94 (0.13), residues: 2102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 102 TYR 0.018 0.001 TYR B 170 PHE 0.023 0.001 PHE A 65 TRP 0.025 0.001 TRP H 111 HIS 0.004 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00268 (30930) covalent geometry : angle 0.60615 (42069) SS BOND : bond 0.00506 ( 42) SS BOND : angle 1.71446 ( 84) hydrogen bonds : bond 0.03772 ( 1032) hydrogen bonds : angle 4.96332 ( 2934) link_BETA1-4 : bond 0.00843 ( 21) link_BETA1-4 : angle 2.62248 ( 63) link_NAG-ASN : bond 0.00736 ( 48) link_NAG-ASN : angle 3.96104 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 191 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 VAL cc_start: 0.7197 (OUTLIER) cc_final: 0.6823 (m) REVERT: A 129 LYS cc_start: 0.7375 (ptmt) cc_final: 0.7033 (pttt) REVERT: A 153 MET cc_start: 0.5889 (mpp) cc_final: 0.4799 (ptm) REVERT: A 176 LEU cc_start: 0.6081 (tp) cc_final: 0.5701 (tt) REVERT: A 298 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7504 (tp30) REVERT: A 403 ARG cc_start: 0.7320 (ttm110) cc_final: 0.7094 (ttm110) REVERT: A 405 ASN cc_start: 0.8402 (m110) cc_final: 0.7462 (p0) REVERT: A 568 ASP cc_start: 0.8056 (p0) cc_final: 0.7533 (m-30) REVERT: A 693 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8609 (pp) REVERT: B 318 PHE cc_start: 0.9005 (OUTLIER) cc_final: 0.8107 (p90) REVERT: B 762 GLN cc_start: 0.7647 (mp10) cc_final: 0.7246 (mp10) REVERT: B 859 THR cc_start: 0.8535 (t) cc_final: 0.8290 (p) REVERT: B 925 ASN cc_start: 0.8275 (t0) cc_final: 0.8038 (m-40) REVERT: C 63 THR cc_start: 0.6894 (OUTLIER) cc_final: 0.6667 (m) REVERT: C 468 ILE cc_start: 0.4583 (OUTLIER) cc_final: 0.4144 (mp) REVERT: C 1002 GLN cc_start: 0.8548 (tp40) cc_final: 0.8279 (tp40) REVERT: H 107 TYR cc_start: 0.5473 (t80) cc_final: 0.5206 (t80) REVERT: I 81 MET cc_start: 0.0123 (ttp) cc_final: -0.0874 (tmm) REVERT: J 48 MET cc_start: 0.1595 (ptt) cc_final: 0.0780 (mmt) REVERT: J 107 TYR cc_start: 0.6046 (t80) cc_final: 0.5512 (t80) REVERT: N 71 SER cc_start: 0.6171 (t) cc_final: 0.5903 (p) outliers start: 83 outliers final: 54 residues processed: 263 average time/residue: 0.1456 time to fit residues: 66.4951 Evaluate side-chains 229 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 170 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 505 HIS Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain I residue 106 PHE Chi-restraints excluded: chain M residue 22 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 248 optimal weight: 9.9990 chunk 212 optimal weight: 2.9990 chunk 265 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 255 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 42 optimal weight: 0.4980 chunk 76 optimal weight: 2.9990 chunk 133 optimal weight: 7.9990 chunk 217 optimal weight: 0.0980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 388 ASN ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN C1002 GLN H 43 GLN ** H 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.191637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.140141 restraints weight = 43943.137| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 2.49 r_work: 0.3399 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.4657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 31041 Z= 0.161 Angle : 0.666 13.599 42360 Z= 0.325 Chirality : 0.047 0.492 4908 Planarity : 0.004 0.050 5358 Dihedral : 5.723 56.288 5505 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.07 % Favored : 93.58 % Rotamer: Outliers : 2.59 % Allowed : 16.94 % Favored : 80.47 % 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: -1.21 (0.13), residues: 3693 helix: 1.63 (0.21), residues: 575 sheet: -0.24 (0.16), residues: 1033 loop : -1.89 (0.13), residues: 2085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 403 TYR 0.023 0.001 TYR B 421 PHE 0.028 0.001 PHE C 86 TRP 0.026 0.001 TRP H 111 HIS 0.028 0.002 HIS B 505 Details of bonding type rmsd covalent geometry : bond 0.00383 (30930) covalent geometry : angle 0.62581 (42069) SS BOND : bond 0.00480 ( 42) SS BOND : angle 1.75906 ( 84) hydrogen bonds : bond 0.04054 ( 1032) hydrogen bonds : angle 4.96146 ( 2934) link_BETA1-4 : bond 0.00815 ( 21) link_BETA1-4 : angle 2.59614 ( 63) link_NAG-ASN : bond 0.00457 ( 48) link_NAG-ASN : angle 3.37774 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 175 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 VAL cc_start: 0.7246 (OUTLIER) cc_final: 0.6903 (m) REVERT: A 129 LYS cc_start: 0.7597 (ptmt) cc_final: 0.7324 (pttt) REVERT: A 153 MET cc_start: 0.5447 (mpp) cc_final: 0.4474 (ptm) REVERT: A 176 LEU cc_start: 0.6360 (tp) cc_final: 0.5888 (tt) REVERT: A 298 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7610 (tp30) REVERT: A 405 ASN cc_start: 0.8197 (m110) cc_final: 0.7437 (p0) REVERT: A 693 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8747 (pp) REVERT: A 764 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8702 (ttpp) REVERT: B 318 PHE cc_start: 0.9026 (OUTLIER) cc_final: 0.8290 (p90) REVERT: B 762 GLN cc_start: 0.7707 (mp10) cc_final: 0.7498 (mp10) REVERT: B 859 THR cc_start: 0.8522 (t) cc_final: 0.8296 (p) REVERT: B 869 MET cc_start: 0.8547 (mtt) cc_final: 0.8325 (mtt) REVERT: C 52 GLN cc_start: 0.8176 (tp-100) cc_final: 0.7922 (tp-100) REVERT: C 63 THR cc_start: 0.7061 (OUTLIER) cc_final: 0.6845 (m) REVERT: C 238 PHE cc_start: 0.7122 (p90) cc_final: 0.6243 (p90) REVERT: H 37 VAL cc_start: 0.4064 (OUTLIER) cc_final: 0.3662 (m) REVERT: I 81 MET cc_start: 0.0346 (ttp) cc_final: -0.0581 (tmm) REVERT: I 106 PHE cc_start: 0.5964 (OUTLIER) cc_final: 0.4776 (t80) REVERT: J 107 TYR cc_start: 0.6700 (t80) cc_final: 0.6133 (t80) REVERT: N 71 SER cc_start: 0.6281 (t) cc_final: 0.5891 (p) outliers start: 84 outliers final: 60 residues processed: 247 average time/residue: 0.1363 time to fit residues: 58.6822 Evaluate side-chains 225 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 158 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain I residue 106 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 202 optimal weight: 1.9990 chunk 42 optimal weight: 0.0370 chunk 218 optimal weight: 0.7980 chunk 291 optimal weight: 4.9990 chunk 306 optimal weight: 10.0000 chunk 223 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 238 optimal weight: 1.9990 chunk 230 optimal weight: 0.5980 chunk 166 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 overall best weight: 1.0862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN A 965 GLN A1005 GLN B 505 HIS B 965 GLN C1010 GLN ** H 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.191920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.138490 restraints weight = 43745.478| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.56 r_work: 0.3385 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.4886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31041 Z= 0.133 Angle : 0.637 13.104 42360 Z= 0.311 Chirality : 0.046 0.251 4908 Planarity : 0.004 0.051 5358 Dihedral : 5.544 58.150 5505 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.63 % Favored : 94.07 % Rotamer: Outliers : 2.56 % Allowed : 17.38 % Favored : 80.07 % 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: 3693 helix: 1.69 (0.21), residues: 580 sheet: -0.12 (0.16), residues: 1047 loop : -1.86 (0.13), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 403 TYR 0.019 0.001 TYR B 170 PHE 0.023 0.001 PHE C 86 TRP 0.027 0.001 TRP H 111 HIS 0.007 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00308 (30930) covalent geometry : angle 0.60098 (42069) SS BOND : bond 0.00670 ( 42) SS BOND : angle 1.66694 ( 84) hydrogen bonds : bond 0.03776 ( 1032) hydrogen bonds : angle 4.86065 ( 2934) link_BETA1-4 : bond 0.00825 ( 21) link_BETA1-4 : angle 2.46639 ( 63) link_NAG-ASN : bond 0.00440 ( 48) link_NAG-ASN : angle 3.11941 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 173 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 VAL cc_start: 0.7263 (OUTLIER) cc_final: 0.6931 (m) REVERT: A 129 LYS cc_start: 0.7527 (ptmt) cc_final: 0.7226 (pttt) REVERT: A 153 MET cc_start: 0.5697 (mpp) cc_final: 0.4637 (ptm) REVERT: A 176 LEU cc_start: 0.6288 (tp) cc_final: 0.5811 (tt) REVERT: A 298 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7633 (tp30) REVERT: A 405 ASN cc_start: 0.8103 (m110) cc_final: 0.7256 (p0) REVERT: A 501 TYR cc_start: 0.7340 (m-80) cc_final: 0.7038 (m-10) REVERT: A 568 ASP cc_start: 0.7830 (p0) cc_final: 0.7552 (m-30) REVERT: A 693 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8756 (pp) REVERT: A 914 ASN cc_start: 0.8982 (OUTLIER) cc_final: 0.8742 (p0) REVERT: B 318 PHE cc_start: 0.9056 (OUTLIER) cc_final: 0.8324 (p90) REVERT: B 495 TYR cc_start: 0.3809 (OUTLIER) cc_final: 0.2518 (m-10) REVERT: B 762 GLN cc_start: 0.7733 (mp10) cc_final: 0.7528 (mp10) REVERT: B 859 THR cc_start: 0.8516 (t) cc_final: 0.8306 (p) REVERT: B 988 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7018 (mp0) REVERT: C 115 GLN cc_start: 0.7168 (mt0) cc_final: 0.6798 (mm-40) REVERT: C 238 PHE cc_start: 0.7103 (p90) cc_final: 0.6137 (p90) REVERT: C 421 TYR cc_start: 0.6433 (OUTLIER) cc_final: 0.5958 (p90) REVERT: C 519 HIS cc_start: 0.1628 (OUTLIER) cc_final: 0.0769 (t70) REVERT: H 29 PHE cc_start: 0.6588 (t80) cc_final: 0.6380 (t80) REVERT: H 37 VAL cc_start: 0.3886 (OUTLIER) cc_final: 0.3442 (m) REVERT: H 111 TRP cc_start: 0.5149 (t-100) cc_final: 0.4825 (t60) REVERT: I 81 MET cc_start: 0.0349 (ttp) cc_final: -0.0665 (tmm) REVERT: I 106 PHE cc_start: 0.6168 (OUTLIER) cc_final: 0.5125 (t80) REVERT: J 48 MET cc_start: 0.2592 (mmt) cc_final: 0.2258 (mmt) REVERT: J 107 TYR cc_start: 0.6847 (t80) cc_final: 0.6140 (t80) REVERT: N 71 SER cc_start: 0.6295 (t) cc_final: 0.5923 (p) outliers start: 83 outliers final: 58 residues processed: 245 average time/residue: 0.1719 time to fit residues: 73.0719 Evaluate side-chains 232 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 164 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 106 PHE Chi-restraints excluded: chain M residue 25 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 283 optimal weight: 2.9990 chunk 240 optimal weight: 9.9990 chunk 224 optimal weight: 5.9990 chunk 371 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 141 optimal weight: 9.9990 chunk 215 optimal weight: 1.9990 chunk 270 optimal weight: 6.9990 chunk 293 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 ASN A 762 GLN A 965 GLN B 388 ASN B 460 ASN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN C1010 GLN I 100 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.187009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.136994 restraints weight = 43940.364| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.60 r_work: 0.3288 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.5350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 31041 Z= 0.274 Angle : 0.764 13.048 42360 Z= 0.376 Chirality : 0.051 0.306 4908 Planarity : 0.005 0.057 5358 Dihedral : 5.915 58.279 5501 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.04 % Favored : 92.69 % Rotamer: Outliers : 3.11 % Allowed : 16.88 % Favored : 80.01 % 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: -1.44 (0.13), residues: 3693 helix: 1.13 (0.21), residues: 579 sheet: -0.32 (0.15), residues: 1060 loop : -2.02 (0.13), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 403 TYR 0.058 0.002 TYR H 107 PHE 0.043 0.002 PHE C 86 TRP 0.043 0.002 TRP L 92 HIS 0.011 0.002 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00672 (30930) covalent geometry : angle 0.72629 (42069) SS BOND : bond 0.00660 ( 42) SS BOND : angle 2.26721 ( 84) hydrogen bonds : bond 0.05026 ( 1032) hydrogen bonds : angle 5.20777 ( 2934) link_BETA1-4 : bond 0.00728 ( 21) link_BETA1-4 : angle 2.56120 ( 63) link_NAG-ASN : bond 0.00498 ( 48) link_NAG-ASN : angle 3.44435 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 176 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7789 (ptmt) cc_final: 0.7475 (pttt) REVERT: A 153 MET cc_start: 0.5507 (mpp) cc_final: 0.4550 (ptm) REVERT: A 176 LEU cc_start: 0.6593 (tp) cc_final: 0.6147 (tt) REVERT: A 298 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7778 (tp30) REVERT: A 405 ASN cc_start: 0.8125 (m110) cc_final: 0.7298 (p0) REVERT: A 501 TYR cc_start: 0.7482 (m-80) cc_final: 0.7138 (m-10) REVERT: A 574 ASP cc_start: 0.7962 (m-30) cc_final: 0.7345 (t0) REVERT: B 318 PHE cc_start: 0.9107 (OUTLIER) cc_final: 0.8402 (p90) REVERT: B 495 TYR cc_start: 0.4032 (OUTLIER) cc_final: 0.2623 (m-10) REVERT: B 613 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.7673 (mp10) REVERT: B 859 THR cc_start: 0.8677 (t) cc_final: 0.8432 (p) REVERT: B 988 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7209 (mp0) REVERT: C 63 THR cc_start: 0.7251 (OUTLIER) cc_final: 0.6998 (m) REVERT: C 115 GLN cc_start: 0.7403 (mt0) cc_final: 0.6959 (mm-40) REVERT: C 371 PHE cc_start: 0.6883 (m-80) cc_final: 0.6645 (t80) REVERT: C 421 TYR cc_start: 0.6481 (OUTLIER) cc_final: 0.6203 (p90) REVERT: C 917 TYR cc_start: 0.8445 (m-80) cc_final: 0.8117 (m-10) REVERT: H 37 VAL cc_start: 0.3629 (OUTLIER) cc_final: 0.3178 (m) REVERT: H 111 TRP cc_start: 0.5423 (t-100) cc_final: 0.4995 (t60) REVERT: I 106 PHE cc_start: 0.6282 (OUTLIER) cc_final: 0.5149 (t80) REVERT: J 107 TYR cc_start: 0.6973 (t80) cc_final: 0.6205 (t80) REVERT: N 71 SER cc_start: 0.6174 (t) cc_final: 0.5808 (m) outliers start: 101 outliers final: 74 residues processed: 261 average time/residue: 0.1740 time to fit residues: 78.5497 Evaluate side-chains 234 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 152 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 969 LYS Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 106 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 170 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 125 optimal weight: 0.8980 chunk 253 optimal weight: 10.0000 chunk 103 optimal weight: 0.6980 chunk 294 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 287 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 282 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN B 755 GLN I 100 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.190003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.121549 restraints weight = 44309.577| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 3.16 r_work: 0.3304 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.5442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 31041 Z= 0.121 Angle : 0.651 13.105 42360 Z= 0.318 Chirality : 0.046 0.220 4908 Planarity : 0.004 0.051 5358 Dihedral : 5.654 59.540 5501 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.33 % Favored : 94.39 % Rotamer: Outliers : 2.03 % Allowed : 17.96 % Favored : 80.01 % 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: -1.17 (0.13), residues: 3693 helix: 1.47 (0.21), residues: 585 sheet: -0.16 (0.15), residues: 1057 loop : -1.87 (0.13), residues: 2051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 403 TYR 0.047 0.001 TYR H 107 PHE 0.032 0.001 PHE C 565 TRP 0.031 0.002 TRP L 92 HIS 0.011 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00274 (30930) covalent geometry : angle 0.61605 (42069) SS BOND : bond 0.00547 ( 42) SS BOND : angle 1.91209 ( 84) hydrogen bonds : bond 0.03830 ( 1032) hydrogen bonds : angle 4.91374 ( 2934) link_BETA1-4 : bond 0.00839 ( 21) link_BETA1-4 : angle 2.36648 ( 63) link_NAG-ASN : bond 0.00478 ( 48) link_NAG-ASN : angle 3.01335 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 157 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.7184 (OUTLIER) cc_final: 0.6930 (m-40) REVERT: A 126 VAL cc_start: 0.6820 (OUTLIER) cc_final: 0.6213 (m) REVERT: A 129 LYS cc_start: 0.7097 (ptmt) cc_final: 0.6717 (pttt) REVERT: A 153 MET cc_start: 0.5823 (mpp) cc_final: 0.4799 (ptm) REVERT: A 176 LEU cc_start: 0.6183 (tp) cc_final: 0.5090 (pp) REVERT: A 298 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7378 (tp30) REVERT: A 405 ASN cc_start: 0.8159 (m110) cc_final: 0.7208 (p0) REVERT: A 501 TYR cc_start: 0.7687 (m-80) cc_final: 0.7215 (m-10) REVERT: A 574 ASP cc_start: 0.7658 (m-30) cc_final: 0.7005 (t0) REVERT: A 1072 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8515 (pt0) REVERT: B 318 PHE cc_start: 0.8998 (OUTLIER) cc_final: 0.8231 (p90) REVERT: B 388 ASN cc_start: 0.5125 (OUTLIER) cc_final: 0.4002 (t0) REVERT: B 495 TYR cc_start: 0.3709 (OUTLIER) cc_final: 0.2351 (m-10) REVERT: B 613 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.7530 (mp10) REVERT: B 762 GLN cc_start: 0.7795 (mp10) cc_final: 0.7398 (mp10) REVERT: B 773 GLU cc_start: 0.8527 (tp30) cc_final: 0.8313 (tp30) REVERT: B 859 THR cc_start: 0.8732 (t) cc_final: 0.8427 (p) REVERT: B 869 MET cc_start: 0.8771 (mtt) cc_final: 0.8496 (mtt) REVERT: B 988 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7057 (mp0) REVERT: C 115 GLN cc_start: 0.7220 (mt0) cc_final: 0.6724 (mm-40) REVERT: H 37 VAL cc_start: 0.3311 (OUTLIER) cc_final: 0.3031 (m) REVERT: I 106 PHE cc_start: 0.6280 (OUTLIER) cc_final: 0.5530 (t80) REVERT: J 107 TYR cc_start: 0.6837 (t80) cc_final: 0.6228 (t80) REVERT: N 71 SER cc_start: 0.6194 (t) cc_final: 0.5867 (p) outliers start: 66 outliers final: 49 residues processed: 213 average time/residue: 0.1726 time to fit residues: 63.9863 Evaluate side-chains 210 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 151 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 969 LYS Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 106 PHE Chi-restraints excluded: chain M residue 22 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 76 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 chunk 282 optimal weight: 0.4980 chunk 180 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 208 optimal weight: 5.9990 chunk 154 optimal weight: 3.9990 chunk 229 optimal weight: 2.9990 chunk 181 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN B 505 HIS ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.188855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.120818 restraints weight = 43830.540| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.97 r_work: 0.3294 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.5522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 31041 Z= 0.141 Angle : 0.652 12.864 42360 Z= 0.318 Chirality : 0.046 0.235 4908 Planarity : 0.004 0.054 5358 Dihedral : 5.572 58.649 5499 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.98 % Favored : 93.74 % Rotamer: Outliers : 2.03 % Allowed : 18.05 % Favored : 79.91 % 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: -1.09 (0.13), residues: 3693 helix: 1.59 (0.22), residues: 579 sheet: -0.16 (0.15), residues: 1074 loop : -1.82 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 403 TYR 0.014 0.001 TYR H 107 PHE 0.034 0.001 PHE C 565 TRP 0.026 0.001 TRP L 92 HIS 0.010 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00331 (30930) covalent geometry : angle 0.61693 (42069) SS BOND : bond 0.00546 ( 42) SS BOND : angle 1.80514 ( 84) hydrogen bonds : bond 0.03870 ( 1032) hydrogen bonds : angle 4.87413 ( 2934) link_BETA1-4 : bond 0.00842 ( 21) link_BETA1-4 : angle 2.34369 ( 63) link_NAG-ASN : bond 0.00431 ( 48) link_NAG-ASN : angle 3.09280 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 156 time to evaluate : 1.134 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: A 129 LYS cc_start: 0.7211 (ptmt) cc_final: 0.6849 (pttt) REVERT: A 153 MET cc_start: 0.5711 (mpp) cc_final: 0.4747 (ptm) REVERT: A 176 LEU cc_start: 0.6281 (tp) cc_final: 0.5839 (tt) REVERT: A 298 GLU cc_start: 0.7939 (tm-30) cc_final: 0.7473 (tp30) REVERT: A 405 ASN cc_start: 0.8163 (m110) cc_final: 0.7240 (p0) REVERT: A 574 ASP cc_start: 0.7712 (m-30) cc_final: 0.7058 (t0) REVERT: A 1072 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8510 (pt0) REVERT: B 318 PHE cc_start: 0.9023 (OUTLIER) cc_final: 0.8256 (p90) REVERT: B 495 TYR cc_start: 0.3751 (OUTLIER) cc_final: 0.2139 (m-10) REVERT: B 613 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.7559 (mp10) REVERT: B 762 GLN cc_start: 0.7838 (mp10) cc_final: 0.7424 (mp10) REVERT: B 859 THR cc_start: 0.8709 (t) cc_final: 0.8413 (p) REVERT: B 988 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7059 (mp0) REVERT: C 115 GLN cc_start: 0.7264 (mt0) cc_final: 0.6782 (mm-40) REVERT: C 238 PHE cc_start: 0.6884 (p90) cc_final: 0.5910 (p90) REVERT: C 421 TYR cc_start: 0.6392 (OUTLIER) cc_final: 0.6166 (p90) REVERT: J 107 TYR cc_start: 0.6782 (t80) cc_final: 0.6274 (t80) REVERT: N 71 SER cc_start: 0.6199 (t) cc_final: 0.5890 (p) outliers start: 66 outliers final: 56 residues processed: 213 average time/residue: 0.1485 time to fit residues: 55.1914 Evaluate side-chains 212 residues out of total 3249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 150 time to evaluate : 0.714 ------------------------------------------------------------------------------- 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 126 VAL Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1111 GLU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 505 HIS Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 969 LYS Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 106 PHE Chi-restraints excluded: chain M residue 22 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 140 optimal weight: 7.9990 chunk 369 optimal weight: 40.0000 chunk 209 optimal weight: 0.7980 chunk 338 optimal weight: 20.0000 chunk 244 optimal weight: 20.0000 chunk 105 optimal weight: 0.0000 chunk 364 optimal weight: 0.8980 chunk 313 optimal weight: 30.0000 chunk 99 optimal weight: 1.9990 chunk 363 optimal weight: 40.0000 chunk 75 optimal weight: 1.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN B 505 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.188988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.121582 restraints weight = 44249.297| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 3.37 r_work: 0.3275 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.5600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31041 Z= 0.138 Angle : 0.646 12.852 42360 Z= 0.315 Chirality : 0.046 0.228 4908 Planarity : 0.004 0.051 5358 Dihedral : 5.545 57.593 5499 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.77 % Favored : 93.96 % Rotamer: Outliers : 1.91 % Allowed : 18.24 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z 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: -1.04 (0.14), residues: 3693 helix: 1.64 (0.21), residues: 580 sheet: -0.12 (0.15), residues: 1074 loop : -1.79 (0.13), residues: 2039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 403 TYR 0.021 0.001 TYR B 170 PHE 0.032 0.001 PHE C 565 TRP 0.026 0.001 TRP L 92 HIS 0.010 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00324 (30930) covalent geometry : angle 0.61223 (42069) SS BOND : bond 0.00539 ( 42) SS BOND : angle 1.72466 ( 84) hydrogen bonds : bond 0.03798 ( 1032) hydrogen bonds : angle 4.83967 ( 2934) link_BETA1-4 : bond 0.00778 ( 21) link_BETA1-4 : angle 2.30825 ( 63) link_NAG-ASN : bond 0.00438 ( 48) link_NAG-ASN : angle 3.04948 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9498.41 seconds wall clock time: 162 minutes 34.84 seconds (9754.84 seconds total)