Starting phenix.real_space_refine on Fri Mar 6 09:22:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cyp_30503/03_2026/7cyp_30503.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cyp_30503/03_2026/7cyp_30503.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7cyp_30503/03_2026/7cyp_30503.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cyp_30503/03_2026/7cyp_30503.map" model { file = "/net/cci-nas-00/data/ceres_data/7cyp_30503/03_2026/7cyp_30503.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cyp_30503/03_2026/7cyp_30503.cif" } resolution = 3.5 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= 0.001 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 128 5.16 5 C 19027 2.51 5 N 4943 2.21 5 O 5881 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 95 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29979 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 7988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1023, 7988 Classifications: {'peptide': 1023} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 50, 'TRANS': 972} Chain breaks: 6 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 7988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1023, 7988 Classifications: {'peptide': 1023} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 50, 'TRANS': 972} Chain breaks: 6 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 7987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1023, 7987 Classifications: {'peptide': 1023} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 50, 'TRANS': 972} Chain breaks: 6 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 827 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 102} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 903 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 114} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "F" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 827 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 102} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "G" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 903 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 114} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 827 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 102} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "I" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 903 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 114} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 7.01, per 1000 atoms: 0.23 Number of scatterers: 29979 At special positions: 0 Unit cell: (159.6, 173.25, 222.6, 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 128 16.00 O 5881 8.00 N 4943 7.00 C 19027 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.04 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.04 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.01 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.00 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 91 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 91 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 91 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.02 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=2, symmetry=0 Links applied BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG 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-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 603 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 657 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C1074 " " NAG J 1 " - " ASN A 234 " " NAG K 1 " - " ASN A 717 " " NAG L 1 " - " ASN A 801 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN B 234 " " NAG P 1 " - " ASN B 717 " " NAG Q 1 " - " ASN B 801 " " NAG R 1 " - " ASN B1098 " " NAG S 1 " - " ASN B1134 " " NAG T 1 " - " ASN C 234 " " NAG U 1 " - " ASN C 717 " " NAG V 1 " - " ASN C 801 " " NAG W 1 " - " ASN C1098 " " NAG X 1 " - " ASN C1134 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.75 Conformation dependent library (CDL) restraints added in 1.4 seconds 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6972 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 72 sheets defined 19.7% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 295 through 304 removed outlier: 3.563A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N CYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.749A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.344A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 removed outlier: 3.864A pdb=" N ARG A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 408' Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 749 through 755 removed outlier: 3.795A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.688A pdb=" N ARG A 765 " --> pdb=" O THR A 761 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA A 766 " --> pdb=" O GLN A 762 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.813A pdb=" N LEU A 822 " --> pdb=" O ILE A 818 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 884 removed outlier: 3.646A pdb=" N LEU A 878 " --> pdb=" O THR A 874 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 889 removed outlier: 3.990A pdb=" N PHE A 888 " --> pdb=" O GLY A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 905 removed outlier: 3.956A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 914 No H-bonds generated for 'chain 'A' and resid 912 through 914' Processing helix chain 'A' and resid 915 through 940 removed outlier: 5.153A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.562A pdb=" N THR A 961 " --> pdb=" O GLN A 957 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN A 965 " --> pdb=" O THR A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.105A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR A1027 " --> pdb=" O ASN A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 295 through 304 removed outlier: 3.563A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N CYS B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.750A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.343A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 removed outlier: 3.864A pdb=" N ARG B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 408' Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 749 through 755 removed outlier: 3.795A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.688A pdb=" N ARG B 765 " --> pdb=" O THR B 761 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA B 766 " --> pdb=" O GLN B 762 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.813A pdb=" N LEU B 822 " --> pdb=" O ILE B 818 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 868 through 884 removed outlier: 3.646A pdb=" N LEU B 878 " --> pdb=" O THR B 874 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 885 through 889 removed outlier: 3.990A pdb=" N PHE B 888 " --> pdb=" O GLY B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 905 removed outlier: 3.956A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 914 No H-bonds generated for 'chain 'B' and resid 912 through 914' Processing helix chain 'B' and resid 915 through 940 removed outlier: 5.153A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER B 940 " --> pdb=" O ASP B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.561A pdb=" N THR B 961 " --> pdb=" O GLN B 957 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN B 965 " --> pdb=" O THR B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.106A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR B1027 " --> pdb=" O ASN B1023 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 295 through 304 removed outlier: 4.051A pdb=" N CYS C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 342 removed outlier: 3.549A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 748 through 753 removed outlier: 3.556A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.915A pdb=" N ARG C 765 " --> pdb=" O THR C 761 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA C 766 " --> pdb=" O GLN C 762 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.560A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.930A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU C 878 " --> pdb=" O THR C 874 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA C 879 " --> pdb=" O SER C 875 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE C 882 " --> pdb=" O LEU C 878 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 898 through 907 removed outlier: 3.724A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASN C 907 " --> pdb=" O ALA C 903 " (cutoff:3.500A) Processing helix chain 'C' and resid 908 through 910 No H-bonds generated for 'chain 'C' and resid 908 through 910' Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.648A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.581A pdb=" N GLY C 932 " --> pdb=" O ASN C 928 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.530A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 5.228A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'I' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 52 removed outlier: 3.601A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 63 through 65 removed outlier: 3.725A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.556A pdb=" N LEU A 241 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 121 through 122 removed outlier: 3.945A pdb=" N ASN A 122 " --> pdb=" O ASN A 125 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN A 125 " --> pdb=" O ASN A 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 194 through 195 removed outlier: 3.506A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 313 through 314 Processing sheet with id=AA7, first strand: chain 'A' and resid 327 through 328 Processing sheet with id=AA8, first strand: chain 'A' and resid 355 through 357 Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.998A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 656 removed outlier: 5.824A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY A 667 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.144A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1089 through 1090 Processing sheet with id=AB7, first strand: chain 'A' and resid 1095 through 1097 Processing sheet with id=AB8, first strand: chain 'B' and resid 36 through 37 removed outlier: 6.856A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 52 removed outlier: 3.600A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 63 through 65 removed outlier: 3.725A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.556A pdb=" N LEU B 241 " --> pdb=" O GLY B 103 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 121 through 122 removed outlier: 3.945A pdb=" N ASN B 122 " --> pdb=" O ASN B 125 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN B 125 " --> pdb=" O ASN B 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 194 through 195 removed outlier: 3.506A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 313 through 314 Processing sheet with id=AC6, first strand: chain 'B' and resid 327 through 328 Processing sheet with id=AC7, first strand: chain 'B' and resid 355 through 357 Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.998A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 656 removed outlier: 5.824A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY B 667 " --> pdb=" O ILE B 670 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AD4, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.144A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1089 through 1090 Processing sheet with id=AD6, first strand: chain 'B' and resid 1095 through 1097 Processing sheet with id=AD7, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.638A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 48 through 51 removed outlier: 3.826A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.650A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU C 241 " --> pdb=" O GLY C 103 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 93 through 95 removed outlier: 4.238A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TYR C 266 " --> pdb=" O ALA C 93 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 127 through 128 removed outlier: 3.853A pdb=" N TYR C 170 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 141 through 142 removed outlier: 7.004A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'C' and resid 313 through 317 removed outlier: 5.769A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 327 through 328 removed outlier: 3.574A pdb=" N PHE C 541 " --> pdb=" O GLY C 548 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 355 through 357 removed outlier: 3.735A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE9, first strand: chain 'C' and resid 401 through 403 removed outlier: 4.091A pdb=" N VAL C 511 " --> pdb=" O ILE C 434 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF2, first strand: chain 'C' and resid 664 through 667 removed outlier: 6.189A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AF4, first strand: chain 'C' and resid 721 through 728 removed outlier: 7.076A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF6, first strand: chain 'C' and resid 1089 through 1090 Processing sheet with id=AF7, first strand: chain 'D' and resid 3 through 6 removed outlier: 4.078A pdb=" N VAL D 3 " --> pdb=" O SER D 25 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 9 through 12 removed outlier: 5.944A pdb=" N LEU D 10 " --> pdb=" O GLU D 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'D' and resid 47 through 52 removed outlier: 6.119A pdb=" N TRP D 38 " --> pdb=" O LEU D 50 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AG2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.071A pdb=" N GLY E 10 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 17 through 18 Processing sheet with id=AG4, first strand: chain 'E' and resid 97 through 99 removed outlier: 7.027A pdb=" N ARG E 98 " --> pdb=" O ASP E 108 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 3 through 6 removed outlier: 4.079A pdb=" N VAL F 3 " --> pdb=" O SER F 25 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 9 through 12 removed outlier: 5.944A pdb=" N LEU F 10 " --> pdb=" O GLU F 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'F' and resid 47 through 52 removed outlier: 6.120A pdb=" N TRP F 38 " --> pdb=" O LEU F 50 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AG9, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.071A pdb=" N GLY G 10 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'G' and resid 17 through 18 Processing sheet with id=AH2, first strand: chain 'G' and resid 97 through 99 removed outlier: 7.026A pdb=" N ARG G 98 " --> pdb=" O ASP G 108 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'H' and resid 3 through 6 removed outlier: 4.078A pdb=" N VAL H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'H' and resid 9 through 12 removed outlier: 5.944A pdb=" N LEU H 10 " --> pdb=" O GLU H 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH4 Processing sheet with id=AH5, first strand: chain 'H' and resid 47 through 52 removed outlier: 6.119A pdb=" N TRP H 38 " --> pdb=" O LEU H 50 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AH7, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.071A pdb=" N GLY I 10 " --> pdb=" O THR I 117 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'I' and resid 17 through 18 Processing sheet with id=AH9, first strand: chain 'I' and resid 97 through 99 removed outlier: 7.027A pdb=" N ARG I 98 " --> pdb=" O ASP I 108 " (cutoff:3.500A) 785 hydrogen bonds defined for protein. 2079 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.06 Time building geometry restraints manager: 3.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 8545 1.33 - 1.45: 7801 1.45 - 1.58: 14134 1.58 - 1.71: 1 1.71 - 1.83: 164 Bond restraints: 30645 Sorted by residual: bond pdb=" C GLN B 271 " pdb=" N PRO B 272 " ideal model delta sigma weight residual 1.334 1.231 0.103 2.34e-02 1.83e+03 1.95e+01 bond pdb=" C GLN A 271 " pdb=" N PRO A 272 " ideal model delta sigma weight residual 1.334 1.231 0.103 2.34e-02 1.83e+03 1.92e+01 bond pdb=" N PRO A 230 " pdb=" CD PRO A 230 " ideal model delta sigma weight residual 1.473 1.534 -0.061 1.40e-02 5.10e+03 1.92e+01 bond pdb=" N PRO B 230 " pdb=" CD PRO B 230 " ideal model delta sigma weight residual 1.473 1.534 -0.061 1.40e-02 5.10e+03 1.91e+01 bond pdb=" N PRO C 527 " pdb=" CD PRO C 527 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.66e+01 ... (remaining 30640 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.31: 40652 3.31 - 6.61: 890 6.61 - 9.92: 107 9.92 - 13.22: 22 13.22 - 16.53: 6 Bond angle restraints: 41677 Sorted by residual: angle pdb=" CA ARG B 102 " pdb=" CB ARG B 102 " pdb=" CG ARG B 102 " ideal model delta sigma weight residual 114.10 101.53 12.57 2.00e+00 2.50e-01 3.95e+01 angle pdb=" CA ARG A 102 " pdb=" CB ARG A 102 " pdb=" CG ARG A 102 " ideal model delta sigma weight residual 114.10 101.55 12.55 2.00e+00 2.50e-01 3.94e+01 angle pdb=" C HIS C 207 " pdb=" N THR C 208 " pdb=" CA THR C 208 " ideal model delta sigma weight residual 122.36 108.76 13.60 2.42e+00 1.71e-01 3.16e+01 angle pdb=" C CYS C1082 " pdb=" N HIS C1083 " pdb=" CA HIS C1083 " ideal model delta sigma weight residual 121.54 111.00 10.54 1.91e+00 2.74e-01 3.04e+01 angle pdb=" C ILE C 105 " pdb=" N PHE C 106 " pdb=" CA PHE C 106 " ideal model delta sigma weight residual 123.27 113.28 9.99 1.85e+00 2.92e-01 2.92e+01 ... (remaining 41672 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.43: 17850 16.43 - 32.86: 849 32.86 - 49.29: 165 49.29 - 65.72: 75 65.72 - 82.15: 17 Dihedral angle restraints: 18956 sinusoidal: 8081 harmonic: 10875 Sorted by residual: dihedral pdb=" CA TRP C 152 " pdb=" C TRP C 152 " pdb=" N MET C 153 " pdb=" CA MET C 153 " ideal model delta harmonic sigma weight residual 180.00 133.51 46.49 0 5.00e+00 4.00e-02 8.65e+01 dihedral pdb=" CA GLU B 96 " pdb=" C GLU B 96 " pdb=" N LYS B 97 " pdb=" CA LYS B 97 " ideal model delta harmonic sigma weight residual 180.00 134.14 45.86 0 5.00e+00 4.00e-02 8.41e+01 dihedral pdb=" CA GLU A 96 " pdb=" C GLU A 96 " pdb=" N LYS A 97 " pdb=" CA LYS A 97 " ideal model delta harmonic sigma weight residual 180.00 134.19 45.81 0 5.00e+00 4.00e-02 8.40e+01 ... (remaining 18953 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.183: 4834 0.183 - 0.367: 25 0.367 - 0.550: 3 0.550 - 0.734: 0 0.734 - 0.917: 2 Chirality restraints: 4864 Sorted by residual: chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN B 234 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.48 -0.92 2.00e-01 2.50e+01 2.10e+01 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN A 234 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.48 -0.92 2.00e-01 2.50e+01 2.10e+01 chirality pdb=" C1 NAG B1308 " pdb=" ND2 ASN B 657 " pdb=" C2 NAG B1308 " pdb=" O5 NAG B1308 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.14e+00 ... (remaining 4861 not shown) Planarity restraints: 5365 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 64 " -0.040 2.00e-02 2.50e+03 2.24e-02 1.25e+01 pdb=" CG TRP A 64 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP A 64 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 64 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP A 64 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 64 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 64 " 0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 64 " -0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 64 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 64 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 64 " -0.040 2.00e-02 2.50e+03 2.23e-02 1.24e+01 pdb=" CG TRP B 64 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP B 64 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP B 64 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP B 64 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 64 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 64 " 0.013 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 64 " -0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 64 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 64 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 64 " -0.030 2.00e-02 2.50e+03 1.97e-02 9.70e+00 pdb=" CG TRP C 64 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP C 64 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP C 64 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 64 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP C 64 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP C 64 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 64 " -0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 64 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP C 64 " 0.000 2.00e-02 2.50e+03 ... (remaining 5362 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 565 2.53 - 3.13: 27788 3.13 - 3.72: 46285 3.72 - 4.31: 68053 4.31 - 4.90: 108811 Nonbonded interactions: 251502 Sorted by model distance: nonbonded pdb=" NZ LYS A 811 " pdb=" OD2 ASP A 820 " model vdw 1.944 3.120 nonbonded pdb=" NZ LYS B 811 " pdb=" OD2 ASP B 820 " model vdw 1.965 3.120 nonbonded pdb=" O GLY C 880 " pdb=" OG SER C 884 " model vdw 2.011 3.040 nonbonded pdb=" NH2 ARG A 34 " pdb=" O PRO A 217 " model vdw 2.032 3.120 nonbonded pdb=" NH2 ARG B 34 " pdb=" O PRO B 217 " model vdw 2.033 3.120 ... (remaining 251497 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 25 through 335 or (resid 336 and (name N or name CA or nam \ e C or name O or name CB )) or resid 337 through 1309)) selection = (chain 'B' and (resid 25 through 335 or (resid 336 and (name N or name CA or nam \ e C or name O or name CB )) or resid 337 through 1309)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } 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 group one per residue 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: 5.350 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: 0.040 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 29.010 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6467 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 : 0.014 0.137 30744 Z= 0.638 Angle : 1.259 16.887 41930 Z= 0.657 Chirality : 0.065 0.917 4864 Planarity : 0.007 0.070 5321 Dihedral : 10.999 82.154 11870 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 32.62 Ramachandran Plot: Outliers : 0.57 % Allowed : 11.18 % Favored : 88.25 % Rotamer: Outliers : 0.19 % Allowed : 0.87 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.90 % 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 are not related in a simple way. whole: -4.93 (0.10), residues: 3702 helix: -4.75 (0.09), residues: 628 sheet: -3.16 (0.14), residues: 801 loop : -2.97 (0.10), residues: 2273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 355 TYR 0.046 0.004 TYR C 917 PHE 0.044 0.005 PHE C 86 TRP 0.053 0.005 TRP A 64 HIS 0.028 0.005 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.01396 (30645) covalent geometry : angle 1.22213 (41677) SS BOND : bond 0.00877 ( 38) SS BOND : angle 1.64296 ( 76) hydrogen bonds : bond 0.32080 ( 785) hydrogen bonds : angle 12.56361 ( 2079) Misc. bond : bond 0.00106 ( 2) link_BETA1-4 : bond 0.00914 ( 15) link_BETA1-4 : angle 3.46551 ( 45) link_NAG-ASN : bond 0.01489 ( 44) link_NAG-ASN : angle 5.15959 ( 132) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 419 time to evaluate : 1.125 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.5414 (m-10) cc_final: 0.4945 (m-80) REVERT: A 380 TYR cc_start: 0.6875 (m-10) cc_final: 0.6642 (m-10) REVERT: A 387 LEU cc_start: 0.7508 (mt) cc_final: 0.7209 (mt) REVERT: A 860 VAL cc_start: 0.7045 (t) cc_final: 0.6729 (p) REVERT: B 30 ASN cc_start: 0.5406 (t0) cc_final: 0.5174 (t0) REVERT: B 902 MET cc_start: 0.8320 (mmm) cc_final: 0.8112 (mmm) REVERT: B 1029 MET cc_start: 0.7885 (tpp) cc_final: 0.7582 (tpp) REVERT: C 106 PHE cc_start: 0.7333 (OUTLIER) cc_final: 0.7119 (m-10) REVERT: C 396 TYR cc_start: 0.6901 (m-80) cc_final: 0.6531 (m-80) REVERT: I 11 LEU cc_start: 0.3760 (mp) cc_final: 0.3313 (tt) outliers start: 6 outliers final: 1 residues processed: 423 average time/residue: 0.2366 time to fit residues: 150.2146 Evaluate side-chains 204 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 202 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1089 PHE Chi-restraints excluded: chain C residue 106 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 99 ASN A 164 ASN A 207 HIS A 239 GLN A 317 ASN A 437 ASN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 641 ASN A 658 ASN A 901 GLN A 913 GLN A 935 GLN A 957 GLN A1119 ASN B 30 ASN B 66 HIS B 164 ASN B 196 ASN B 207 HIS B 239 GLN B 245 HIS B 437 ASN B 501 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN B 655 HIS B 658 ASN B 901 GLN B 913 GLN B 935 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN B1119 ASN C 66 HIS C 99 ASN C 134 GLN C 196 ASN C 207 HIS C 334 ASN C 437 ASN C 448 ASN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN C 955 ASN C1010 GLN D 57 GLN E 31 ASN F 57 GLN H 56 ASN H 57 GLN H 93 GLN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.095067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.072134 restraints weight = 119082.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.073448 restraints weight = 66674.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.073480 restraints weight = 44185.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.074110 restraints weight = 38937.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.074129 restraints weight = 32100.724| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 30744 Z= 0.194 Angle : 0.873 18.435 41930 Z= 0.442 Chirality : 0.052 0.681 4864 Planarity : 0.006 0.076 5321 Dihedral : 9.610 58.975 5284 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.21 % Favored : 93.54 % Rotamer: Outliers : 1.36 % Allowed : 5.42 % Favored : 93.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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 are not related in a simple way. whole: -3.61 (0.12), residues: 3702 helix: -2.02 (0.17), residues: 628 sheet: -2.63 (0.14), residues: 850 loop : -2.48 (0.12), residues: 2224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 100 TYR 0.038 0.002 TYR G 57 PHE 0.033 0.002 PHE H 35 TRP 0.024 0.002 TRP C 64 HIS 0.007 0.002 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00424 (30645) covalent geometry : angle 0.82858 (41677) SS BOND : bond 0.00252 ( 38) SS BOND : angle 1.73177 ( 76) hydrogen bonds : bond 0.05561 ( 785) hydrogen bonds : angle 7.73593 ( 2079) Misc. bond : bond 0.00057 ( 2) link_BETA1-4 : bond 0.00454 ( 15) link_BETA1-4 : angle 2.12420 ( 45) link_NAG-ASN : bond 0.00996 ( 44) link_NAG-ASN : angle 4.69919 ( 132) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 255 time to evaluate : 1.066 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 146 HIS cc_start: 0.6586 (t-90) cc_final: 0.6373 (t70) REVERT: A 200 TYR cc_start: 0.7773 (OUTLIER) cc_final: 0.6230 (t80) REVERT: A 207 HIS cc_start: 0.5665 (m-70) cc_final: 0.5005 (t70) REVERT: A 408 ARG cc_start: 0.7053 (mtm-85) cc_final: 0.6796 (ptp-170) REVERT: A 409 GLN cc_start: 0.5142 (tt0) cc_final: 0.4787 (tm-30) REVERT: A 860 VAL cc_start: 0.7883 (t) cc_final: 0.7409 (p) REVERT: B 30 ASN cc_start: 0.6452 (OUTLIER) cc_final: 0.6084 (t0) REVERT: B 133 PHE cc_start: 0.5551 (p90) cc_final: 0.5043 (p90) REVERT: B 456 PHE cc_start: 0.7508 (OUTLIER) cc_final: 0.7277 (t80) REVERT: B 1050 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.8063 (ptm) REVERT: C 207 HIS cc_start: 0.6769 (OUTLIER) cc_final: 0.6543 (m90) REVERT: C 396 TYR cc_start: 0.6177 (m-80) cc_final: 0.5797 (m-10) REVERT: C 489 TYR cc_start: 0.7113 (OUTLIER) cc_final: 0.6626 (m-80) REVERT: C 556 ASN cc_start: 0.8097 (p0) cc_final: 0.7821 (p0) REVERT: E 44 ARG cc_start: 0.4759 (ptm-80) cc_final: 0.4537 (ptm160) REVERT: E 83 MET cc_start: 0.2422 (tpt) cc_final: 0.2154 (tpt) REVERT: G 19 ARG cc_start: 0.5779 (ttp80) cc_final: 0.5381 (mtp85) REVERT: I 11 LEU cc_start: 0.6246 (mp) cc_final: 0.5635 (tt) REVERT: I 109 TYR cc_start: 0.8387 (m-80) cc_final: 0.7978 (m-80) outliers start: 44 outliers final: 22 residues processed: 283 average time/residue: 0.2231 time to fit residues: 97.3524 Evaluate side-chains 209 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 181 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1135 ASN Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain D residue 35 PHE Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 35 PHE Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain H residue 31 TYR Chi-restraints excluded: chain I residue 115 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 170 optimal weight: 2.9990 chunk 301 optimal weight: 4.9990 chunk 340 optimal weight: 6.9990 chunk 215 optimal weight: 0.6980 chunk 267 optimal weight: 0.7980 chunk 235 optimal weight: 8.9990 chunk 177 optimal weight: 1.9990 chunk 371 optimal weight: 0.0980 chunk 256 optimal weight: 8.9990 chunk 233 optimal weight: 1.9990 chunk 293 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN A1119 ASN B 99 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B 913 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN C 137 ASN C 245 HIS C 437 ASN C 506 GLN C 519 HIS ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN H 57 GLN H 92 GLN ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.096743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.073860 restraints weight = 122204.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.073764 restraints weight = 78206.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.073716 restraints weight = 57776.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.074013 restraints weight = 55782.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.074284 restraints weight = 45478.299| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 30744 Z= 0.165 Angle : 0.754 15.445 41930 Z= 0.383 Chirality : 0.048 0.566 4864 Planarity : 0.005 0.048 5321 Dihedral : 8.344 55.668 5280 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.29 % Favored : 93.49 % Rotamer: Outliers : 2.05 % Allowed : 7.22 % Favored : 90.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 are not related in a simple way. whole: -2.80 (0.13), residues: 3702 helix: -0.45 (0.21), residues: 639 sheet: -2.10 (0.15), residues: 863 loop : -2.26 (0.12), residues: 2200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 87 TYR 0.029 0.002 TYR D 52 PHE 0.040 0.002 PHE H 35 TRP 0.025 0.002 TRP B 64 HIS 0.023 0.002 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00363 (30645) covalent geometry : angle 0.72116 (41677) SS BOND : bond 0.00336 ( 38) SS BOND : angle 2.00961 ( 76) hydrogen bonds : bond 0.04227 ( 785) hydrogen bonds : angle 6.74143 ( 2079) Misc. bond : bond 0.00065 ( 2) link_BETA1-4 : bond 0.00292 ( 15) link_BETA1-4 : angle 1.92566 ( 45) link_NAG-ASN : bond 0.00603 ( 44) link_NAG-ASN : angle 3.57839 ( 132) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 218 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 HIS cc_start: 0.6638 (t-90) cc_final: 0.6358 (t-170) REVERT: A 200 TYR cc_start: 0.7964 (OUTLIER) cc_final: 0.6553 (t80) REVERT: A 207 HIS cc_start: 0.5770 (m-70) cc_final: 0.5090 (t70) REVERT: A 406 GLU cc_start: 0.6000 (mt-10) cc_final: 0.5555 (mt-10) REVERT: A 408 ARG cc_start: 0.7020 (mtm-85) cc_final: 0.6797 (ptp-170) REVERT: A 409 GLN cc_start: 0.5181 (tt0) cc_final: 0.4947 (tm-30) REVERT: A 925 ASN cc_start: 0.8063 (t0) cc_final: 0.7741 (t0) REVERT: B 133 PHE cc_start: 0.5760 (p90) cc_final: 0.5111 (p90) REVERT: B 374 PHE cc_start: 0.6499 (p90) cc_final: 0.6086 (p90) REVERT: B 456 PHE cc_start: 0.7746 (OUTLIER) cc_final: 0.7510 (t80) REVERT: B 1050 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.8050 (ptm) REVERT: C 346 ARG cc_start: 0.6128 (mmm-85) cc_final: 0.5817 (tpt-90) REVERT: C 473 TYR cc_start: 0.6009 (t80) cc_final: 0.5721 (t80) REVERT: C 489 TYR cc_start: 0.6990 (OUTLIER) cc_final: 0.6671 (m-80) REVERT: G 19 ARG cc_start: 0.5994 (ttp80) cc_final: 0.5534 (mmm160) REVERT: G 100 ARG cc_start: 0.6475 (ttp80) cc_final: 0.6113 (ttp80) REVERT: H 36 MET cc_start: 0.6366 (OUTLIER) cc_final: 0.5651 (mmm) REVERT: H 62 PRO cc_start: 0.3946 (Cg_exo) cc_final: 0.3655 (Cg_endo) REVERT: I 2 VAL cc_start: 0.5461 (t) cc_final: 0.4673 (p) REVERT: I 11 LEU cc_start: 0.6121 (mp) cc_final: 0.5578 (tt) REVERT: I 83 MET cc_start: 0.7895 (mmm) cc_final: 0.7578 (ttm) REVERT: I 109 TYR cc_start: 0.8401 (m-80) cc_final: 0.8065 (m-80) outliers start: 66 outliers final: 28 residues processed: 265 average time/residue: 0.2117 time to fit residues: 88.1274 Evaluate side-chains 206 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 173 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain F residue 35 PHE Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain H residue 31 TYR Chi-restraints excluded: chain H residue 36 MET Chi-restraints excluded: chain I residue 115 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 169 optimal weight: 6.9990 chunk 154 optimal weight: 0.2980 chunk 4 optimal weight: 0.7980 chunk 149 optimal weight: 5.9990 chunk 245 optimal weight: 6.9990 chunk 240 optimal weight: 0.0670 chunk 184 optimal weight: 0.2980 chunk 189 optimal weight: 5.9990 chunk 159 optimal weight: 6.9990 chunk 190 optimal weight: 0.7980 chunk 221 optimal weight: 0.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 164 ASN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN B 99 ASN B 164 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN B 755 GLN B1002 GLN C 207 HIS C 437 ASN C 448 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 ASN C1088 HIS D 56 ASN ** F 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.095211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.071779 restraints weight = 117233.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.073807 restraints weight = 68581.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.073656 restraints weight = 40883.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.074155 restraints weight = 38251.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.074292 restraints weight = 32762.280| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 30744 Z= 0.124 Angle : 0.692 14.109 41930 Z= 0.348 Chirality : 0.047 0.559 4864 Planarity : 0.004 0.064 5321 Dihedral : 7.488 53.058 5280 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.97 % Favored : 93.87 % Rotamer: Outliers : 2.05 % Allowed : 8.68 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % 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 are not related in a simple way. whole: -2.25 (0.13), residues: 3702 helix: 0.37 (0.21), residues: 627 sheet: -1.72 (0.16), residues: 875 loop : -2.02 (0.12), residues: 2200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 67 TYR 0.020 0.001 TYR G 57 PHE 0.026 0.002 PHE H 101 TRP 0.014 0.002 TRP B 64 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00269 (30645) covalent geometry : angle 0.66220 (41677) SS BOND : bond 0.00368 ( 38) SS BOND : angle 1.80586 ( 76) hydrogen bonds : bond 0.03651 ( 785) hydrogen bonds : angle 6.21297 ( 2079) Misc. bond : bond 0.00012 ( 2) link_BETA1-4 : bond 0.00360 ( 15) link_BETA1-4 : angle 1.83905 ( 45) link_NAG-ASN : bond 0.00611 ( 44) link_NAG-ASN : angle 3.22754 ( 132) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 214 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ASN cc_start: 0.8513 (OUTLIER) cc_final: 0.8213 (t0) REVERT: A 146 HIS cc_start: 0.7178 (t-90) cc_final: 0.6738 (t70) REVERT: A 200 TYR cc_start: 0.7948 (OUTLIER) cc_final: 0.6574 (t80) REVERT: A 207 HIS cc_start: 0.5813 (m-70) cc_final: 0.5368 (t70) REVERT: A 406 GLU cc_start: 0.5948 (mt-10) cc_final: 0.5031 (mt-10) REVERT: A 904 TYR cc_start: 0.7627 (m-10) cc_final: 0.7355 (m-10) REVERT: A 925 ASN cc_start: 0.8090 (t0) cc_final: 0.7714 (t0) REVERT: B 133 PHE cc_start: 0.5735 (p90) cc_final: 0.4969 (p90) REVERT: B 374 PHE cc_start: 0.6293 (p90) cc_final: 0.5998 (p90) REVERT: B 1050 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7977 (ptm) REVERT: C 489 TYR cc_start: 0.7120 (OUTLIER) cc_final: 0.6700 (m-80) REVERT: C 900 MET cc_start: 0.7131 (OUTLIER) cc_final: 0.6803 (ttm) REVERT: E 44 ARG cc_start: 0.4670 (ptm-80) cc_final: 0.4462 (ptm160) REVERT: F 36 MET cc_start: 0.4999 (OUTLIER) cc_final: 0.3480 (ttp) REVERT: G 67 ARG cc_start: 0.8117 (tpm170) cc_final: 0.7795 (tpm170) REVERT: G 83 MET cc_start: 0.4086 (tpp) cc_final: 0.3871 (tpp) REVERT: H 62 PRO cc_start: 0.4454 (Cg_exo) cc_final: 0.4090 (Cg_endo) REVERT: I 11 LEU cc_start: 0.5886 (mp) cc_final: 0.5367 (tt) REVERT: I 109 TYR cc_start: 0.8335 (m-80) cc_final: 0.8010 (m-80) outliers start: 66 outliers final: 32 residues processed: 262 average time/residue: 0.2096 time to fit residues: 86.6426 Evaluate side-chains 207 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 169 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain D residue 35 PHE Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain F residue 35 PHE Chi-restraints excluded: chain F residue 36 MET Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 101 PHE Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain H residue 31 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 244 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 325 optimal weight: 30.0000 chunk 77 optimal weight: 1.9990 chunk 158 optimal weight: 0.4980 chunk 149 optimal weight: 0.1980 chunk 352 optimal weight: 8.9990 chunk 123 optimal weight: 3.9990 chunk 212 optimal weight: 0.7980 chunk 308 optimal weight: 0.2980 chunk 63 optimal weight: 3.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 188 ASN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN A 955 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B 913 GLN C 437 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 56 ASN I 31 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.095196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.071843 restraints weight = 117316.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.074047 restraints weight = 68714.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.073917 restraints weight = 40211.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.074303 restraints weight = 34705.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.074520 restraints weight = 31349.206| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.4476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 30744 Z= 0.118 Angle : 0.654 13.732 41930 Z= 0.330 Chirality : 0.046 0.543 4864 Planarity : 0.004 0.066 5321 Dihedral : 6.949 53.638 5280 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.78 % Favored : 93.98 % Rotamer: Outliers : 1.83 % Allowed : 9.58 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % 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 are not related in a simple way. whole: -1.91 (0.13), residues: 3702 helix: 0.87 (0.22), residues: 608 sheet: -1.48 (0.16), residues: 888 loop : -1.86 (0.13), residues: 2206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 19 TYR 0.031 0.001 TYR B 451 PHE 0.027 0.001 PHE H 101 TRP 0.016 0.001 TRP G 47 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00261 (30645) covalent geometry : angle 0.62571 (41677) SS BOND : bond 0.00231 ( 38) SS BOND : angle 1.64081 ( 76) hydrogen bonds : bond 0.03445 ( 785) hydrogen bonds : angle 5.91924 ( 2079) Misc. bond : bond 0.00012 ( 2) link_BETA1-4 : bond 0.00362 ( 15) link_BETA1-4 : angle 1.87699 ( 45) link_NAG-ASN : bond 0.00508 ( 44) link_NAG-ASN : angle 3.08864 ( 132) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 191 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.6694 (p0) cc_final: 0.6396 (p0) REVERT: A 146 HIS cc_start: 0.7062 (t-90) cc_final: 0.6682 (t-170) REVERT: A 200 TYR cc_start: 0.8016 (OUTLIER) cc_final: 0.6661 (t80) REVERT: A 207 HIS cc_start: 0.5854 (m-70) cc_final: 0.5511 (t70) REVERT: A 387 LEU cc_start: 0.7201 (mt) cc_final: 0.6900 (mt) REVERT: A 904 TYR cc_start: 0.7644 (m-10) cc_final: 0.7358 (m-10) REVERT: A 925 ASN cc_start: 0.8139 (t0) cc_final: 0.7743 (t0) REVERT: A 1145 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7496 (tt) REVERT: B 133 PHE cc_start: 0.5692 (p90) cc_final: 0.4978 (p90) REVERT: B 374 PHE cc_start: 0.6330 (p90) cc_final: 0.6026 (p90) REVERT: C 355 ARG cc_start: 0.6248 (ttt90) cc_final: 0.4965 (ttt180) REVERT: C 489 TYR cc_start: 0.7103 (OUTLIER) cc_final: 0.6724 (m-80) REVERT: C 900 MET cc_start: 0.7111 (OUTLIER) cc_final: 0.6651 (ttm) REVERT: E 34 MET cc_start: 0.6207 (mmm) cc_final: 0.5988 (mmp) REVERT: E 100 ARG cc_start: 0.7656 (ttp-170) cc_final: 0.7428 (ttp-170) REVERT: F 36 MET cc_start: 0.4804 (OUTLIER) cc_final: 0.3323 (ttp) REVERT: G 67 ARG cc_start: 0.8218 (tpm170) cc_final: 0.7884 (tpm170) REVERT: G 100 ARG cc_start: 0.6120 (ttp80) cc_final: 0.5800 (ttp80) REVERT: H 62 PRO cc_start: 0.4446 (Cg_exo) cc_final: 0.4090 (Cg_endo) REVERT: I 11 LEU cc_start: 0.5886 (mp) cc_final: 0.5343 (tt) REVERT: I 109 TYR cc_start: 0.8346 (m-80) cc_final: 0.8007 (m-80) outliers start: 59 outliers final: 33 residues processed: 237 average time/residue: 0.2122 time to fit residues: 79.4677 Evaluate side-chains 209 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 171 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain D residue 35 PHE Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain F residue 35 PHE Chi-restraints excluded: chain F residue 36 MET Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain H residue 31 TYR Chi-restraints excluded: chain H residue 101 PHE Chi-restraints excluded: chain I residue 12 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 229 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 306 optimal weight: 8.9990 chunk 256 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 151 optimal weight: 0.0970 chunk 258 optimal weight: 4.9990 chunk 129 optimal weight: 20.0000 chunk 192 optimal weight: 3.9990 chunk 34 optimal weight: 0.3980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS B 99 ASN B 360 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 ASN I 31 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.094918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.071263 restraints weight = 116345.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.073517 restraints weight = 66573.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.073373 restraints weight = 41643.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.073824 restraints weight = 35183.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.074193 restraints weight = 31780.417| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.4721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 30744 Z= 0.122 Angle : 0.651 14.212 41930 Z= 0.326 Chirality : 0.046 0.542 4864 Planarity : 0.004 0.046 5321 Dihedral : 6.655 54.732 5280 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.65 % Favored : 94.11 % Rotamer: Outliers : 2.01 % Allowed : 10.13 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % 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 are not related in a simple way. whole: -1.75 (0.13), residues: 3702 helix: 0.95 (0.22), residues: 618 sheet: -1.32 (0.17), residues: 895 loop : -1.77 (0.13), residues: 2189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 19 TYR 0.024 0.001 TYR E 109 PHE 0.025 0.001 PHE H 101 TRP 0.014 0.001 TRP B 64 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00275 (30645) covalent geometry : angle 0.61913 (41677) SS BOND : bond 0.00198 ( 38) SS BOND : angle 2.28032 ( 76) hydrogen bonds : bond 0.03377 ( 785) hydrogen bonds : angle 5.73664 ( 2079) Misc. bond : bond 0.00012 ( 2) link_BETA1-4 : bond 0.00363 ( 15) link_BETA1-4 : angle 2.03740 ( 45) link_NAG-ASN : bond 0.00538 ( 44) link_NAG-ASN : angle 3.01992 ( 132) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 196 time to evaluate : 1.065 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: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.6851 (p0) cc_final: 0.6562 (p0) REVERT: A 115 GLN cc_start: 0.6301 (mm-40) cc_final: 0.6024 (mm-40) REVERT: A 146 HIS cc_start: 0.7059 (t-90) cc_final: 0.6717 (t-170) REVERT: A 200 TYR cc_start: 0.8117 (OUTLIER) cc_final: 0.6768 (t80) REVERT: A 207 HIS cc_start: 0.5855 (m-70) cc_final: 0.5580 (t70) REVERT: A 239 GLN cc_start: 0.7576 (tm-30) cc_final: 0.7358 (tm-30) REVERT: A 396 TYR cc_start: 0.6090 (m-80) cc_final: 0.5332 (m-10) REVERT: A 409 GLN cc_start: 0.5889 (tt0) cc_final: 0.5244 (tm-30) REVERT: A 904 TYR cc_start: 0.7683 (m-10) cc_final: 0.7402 (m-10) REVERT: A 925 ASN cc_start: 0.8108 (t0) cc_final: 0.7740 (t0) REVERT: A 1145 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7503 (tt) REVERT: B 133 PHE cc_start: 0.5715 (p90) cc_final: 0.5031 (p90) REVERT: C 462 LYS cc_start: 0.7691 (mmmt) cc_final: 0.7223 (mtmm) REVERT: C 489 TYR cc_start: 0.7079 (OUTLIER) cc_final: 0.6665 (m-80) REVERT: E 100 ARG cc_start: 0.7559 (ttp-170) cc_final: 0.7316 (ttp-170) REVERT: F 36 MET cc_start: 0.4822 (OUTLIER) cc_final: 0.3338 (ttp) REVERT: H 62 PRO cc_start: 0.4657 (Cg_exo) cc_final: 0.4291 (Cg_endo) REVERT: I 11 LEU cc_start: 0.5795 (mp) cc_final: 0.5212 (tt) REVERT: I 109 TYR cc_start: 0.8279 (m-80) cc_final: 0.7935 (m-80) outliers start: 65 outliers final: 37 residues processed: 245 average time/residue: 0.2005 time to fit residues: 77.7041 Evaluate side-chains 215 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 174 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain D residue 35 PHE Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain F residue 35 PHE Chi-restraints excluded: chain F residue 36 MET Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 101 PHE Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain H residue 31 TYR Chi-restraints excluded: chain H residue 101 PHE Chi-restraints excluded: chain I residue 12 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 282 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 330 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 369 optimal weight: 40.0000 chunk 52 optimal weight: 5.9990 chunk 256 optimal weight: 6.9990 chunk 180 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 288 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN B 450 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B 762 GLN C 218 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.102410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.078301 restraints weight = 114665.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.080032 restraints weight = 65909.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.080621 restraints weight = 40820.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.081022 restraints weight = 31759.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.081255 restraints weight = 28070.675| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.4888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.107 30744 Z= 0.296 Angle : 0.829 12.975 41930 Z= 0.418 Chirality : 0.051 0.515 4864 Planarity : 0.006 0.119 5321 Dihedral : 7.605 59.456 5280 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.45 % Favored : 91.27 % Rotamer: Outliers : 2.29 % Allowed : 10.66 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % 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 are not related in a simple way. whole: -2.30 (0.13), residues: 3702 helix: 0.28 (0.21), residues: 611 sheet: -1.60 (0.16), residues: 917 loop : -2.09 (0.13), residues: 2174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 214 TYR 0.047 0.003 TYR E 109 PHE 0.035 0.003 PHE A 133 TRP 0.042 0.003 TRP B 64 HIS 0.010 0.002 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00672 (30645) covalent geometry : angle 0.79801 (41677) SS BOND : bond 0.00485 ( 38) SS BOND : angle 2.89625 ( 76) hydrogen bonds : bond 0.04269 ( 785) hydrogen bonds : angle 6.23876 ( 2079) Misc. bond : bond 0.00095 ( 2) link_BETA1-4 : bond 0.00396 ( 15) link_BETA1-4 : angle 2.04345 ( 45) link_NAG-ASN : bond 0.00813 ( 44) link_NAG-ASN : angle 3.33324 ( 132) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 195 time to evaluate : 1.113 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: A 40 ASP cc_start: 0.7584 (p0) cc_final: 0.7310 (p0) REVERT: A 134 GLN cc_start: 0.5853 (tm-30) cc_final: 0.5627 (tm-30) REVERT: A 146 HIS cc_start: 0.7110 (t-90) cc_final: 0.6784 (t-170) REVERT: A 200 TYR cc_start: 0.8409 (OUTLIER) cc_final: 0.7162 (t80) REVERT: A 207 HIS cc_start: 0.5961 (m-70) cc_final: 0.5541 (t-90) REVERT: A 394 ASN cc_start: 0.7068 (m-40) cc_final: 0.6535 (m-40) REVERT: A 1145 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7521 (tt) REVERT: B 133 PHE cc_start: 0.6220 (p90) cc_final: 0.5957 (p90) REVERT: B 160 TYR cc_start: 0.5799 (OUTLIER) cc_final: 0.5069 (p90) REVERT: B 374 PHE cc_start: 0.6660 (p90) cc_final: 0.6243 (p90) REVERT: C 144 TYR cc_start: 0.3513 (OUTLIER) cc_final: 0.1812 (t80) REVERT: C 462 LYS cc_start: 0.7656 (mmmt) cc_final: 0.7157 (mtmm) REVERT: C 592 PHE cc_start: 0.6308 (OUTLIER) cc_final: 0.5994 (t80) REVERT: C 697 MET cc_start: 0.6998 (ptm) cc_final: 0.6133 (ptt) REVERT: C 1089 PHE cc_start: 0.8639 (OUTLIER) cc_final: 0.8422 (m-80) REVERT: E 100 ARG cc_start: 0.7815 (ttp-170) cc_final: 0.7472 (ttp-170) REVERT: F 36 MET cc_start: 0.4935 (OUTLIER) cc_final: 0.3334 (ttp) outliers start: 74 outliers final: 54 residues processed: 248 average time/residue: 0.1951 time to fit residues: 76.1366 Evaluate side-chains 224 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 163 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 689 SER Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain D residue 35 PHE Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 35 PHE Chi-restraints excluded: chain F residue 36 MET Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 101 PHE Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain H residue 101 PHE Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 19 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 244 optimal weight: 0.3980 chunk 134 optimal weight: 6.9990 chunk 41 optimal weight: 0.0980 chunk 300 optimal weight: 0.9990 chunk 269 optimal weight: 0.6980 chunk 223 optimal weight: 0.4980 chunk 170 optimal weight: 5.9990 chunk 240 optimal weight: 0.0270 chunk 174 optimal weight: 0.8980 chunk 38 optimal weight: 8.9990 chunk 230 optimal weight: 0.5980 overall best weight: 0.3238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 675 GLN B 207 HIS ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN C 606 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 84 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.093487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.070164 restraints weight = 116266.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.071580 restraints weight = 63545.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.071653 restraints weight = 40572.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.072215 restraints weight = 37537.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.072269 restraints weight = 31227.464| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.5265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30744 Z= 0.116 Angle : 0.665 12.209 41930 Z= 0.336 Chirality : 0.046 0.515 4864 Planarity : 0.004 0.043 5321 Dihedral : 6.699 59.373 5280 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.00 % Favored : 93.71 % Rotamer: Outliers : 1.46 % Allowed : 11.81 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % 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 are not related in a simple way. whole: -1.82 (0.14), residues: 3702 helix: 0.94 (0.22), residues: 603 sheet: -1.35 (0.17), residues: 870 loop : -1.83 (0.13), residues: 2229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 408 TYR 0.030 0.001 TYR G 57 PHE 0.026 0.001 PHE C 157 TRP 0.020 0.002 TRP F 38 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00254 (30645) covalent geometry : angle 0.63778 (41677) SS BOND : bond 0.00329 ( 38) SS BOND : angle 2.05096 ( 76) hydrogen bonds : bond 0.03396 ( 785) hydrogen bonds : angle 5.76487 ( 2079) Misc. bond : bond 0.00027 ( 2) link_BETA1-4 : bond 0.00372 ( 15) link_BETA1-4 : angle 1.72963 ( 45) link_NAG-ASN : bond 0.00471 ( 44) link_NAG-ASN : angle 2.95957 ( 132) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 176 time to evaluate : 1.204 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 200 TYR cc_start: 0.8324 (OUTLIER) cc_final: 0.7181 (t80) REVERT: A 239 GLN cc_start: 0.7897 (tm-30) cc_final: 0.7641 (tm-30) REVERT: A 394 ASN cc_start: 0.6922 (m-40) cc_final: 0.6581 (m-40) REVERT: A 409 GLN cc_start: 0.5779 (tt0) cc_final: 0.5230 (tm-30) REVERT: A 904 TYR cc_start: 0.7562 (m-10) cc_final: 0.7283 (m-10) REVERT: A 925 ASN cc_start: 0.8192 (t0) cc_final: 0.7919 (t0) REVERT: A 1145 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7652 (tt) REVERT: B 133 PHE cc_start: 0.6079 (p90) cc_final: 0.5307 (p90) REVERT: B 238 PHE cc_start: 0.7178 (p90) cc_final: 0.6702 (p90) REVERT: B 242 LEU cc_start: 0.7725 (mm) cc_final: 0.7420 (mt) REVERT: B 374 PHE cc_start: 0.6617 (p90) cc_final: 0.6282 (p90) REVERT: C 355 ARG cc_start: 0.6146 (ttt90) cc_final: 0.5083 (ttt180) REVERT: C 462 LYS cc_start: 0.7588 (mmmt) cc_final: 0.7114 (mtmm) REVERT: E 100 ARG cc_start: 0.7651 (ttp-170) cc_final: 0.7297 (ttp-170) REVERT: F 36 MET cc_start: 0.4945 (mmp) cc_final: 0.3303 (ttp) REVERT: G 67 ARG cc_start: 0.7983 (tpm170) cc_final: 0.7590 (tpm170) REVERT: G 100 ARG cc_start: 0.5693 (ttp-170) cc_final: 0.5360 (ptm-80) REVERT: G 101 TYR cc_start: 0.5481 (m-80) cc_final: 0.5094 (m-80) REVERT: H 36 MET cc_start: 0.6525 (mmt) cc_final: 0.5928 (mmm) outliers start: 47 outliers final: 35 residues processed: 212 average time/residue: 0.2117 time to fit residues: 70.1647 Evaluate side-chains 201 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 164 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 52 TYR Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 35 PHE Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 101 PHE Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain I residue 12 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 309 optimal weight: 20.0000 chunk 310 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 371 optimal weight: 20.0000 chunk 75 optimal weight: 5.9990 chunk 147 optimal weight: 8.9990 chunk 117 optimal weight: 5.9990 chunk 321 optimal weight: 30.0000 chunk 326 optimal weight: 7.9990 chunk 138 optimal weight: 6.9990 chunk 350 optimal weight: 30.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A1142 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1142 GLN ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN D 41 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.088403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.065217 restraints weight = 116846.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.065119 restraints weight = 72943.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.065718 restraints weight = 58090.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.066488 restraints weight = 44158.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.066629 restraints weight = 36496.837| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.5370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.158 30744 Z= 0.549 Angle : 1.121 15.972 41930 Z= 0.568 Chirality : 0.060 0.469 4864 Planarity : 0.007 0.091 5321 Dihedral : 8.960 59.850 5280 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 19.51 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.43 % Favored : 88.22 % Rotamer: Outliers : 2.08 % Allowed : 11.78 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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 are not related in a simple way. whole: -3.12 (0.13), residues: 3702 helix: -0.86 (0.19), residues: 612 sheet: -2.17 (0.16), residues: 956 loop : -2.45 (0.12), residues: 2134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG A 403 TYR 0.046 0.004 TYR E 109 PHE 0.053 0.005 PHE A 133 TRP 0.055 0.004 TRP B 64 HIS 0.013 0.003 HIS B1101 Details of bonding type rmsd covalent geometry : bond 0.01236 (30645) covalent geometry : angle 1.09432 (41677) SS BOND : bond 0.00777 ( 38) SS BOND : angle 2.90990 ( 76) hydrogen bonds : bond 0.05317 ( 785) hydrogen bonds : angle 6.94484 ( 2079) Misc. bond : bond 0.00175 ( 2) link_BETA1-4 : bond 0.00603 ( 15) link_BETA1-4 : angle 2.38696 ( 45) link_NAG-ASN : bond 0.01319 ( 44) link_NAG-ASN : angle 3.80857 ( 132) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 172 time to evaluate : 0.971 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 134 GLN cc_start: 0.5904 (tm-30) cc_final: 0.5644 (tm-30) REVERT: A 146 HIS cc_start: 0.7338 (t-90) cc_final: 0.6902 (t-170) REVERT: A 239 GLN cc_start: 0.8017 (tm-30) cc_final: 0.7805 (tm-30) REVERT: A 394 ASN cc_start: 0.6877 (m-40) cc_final: 0.6573 (m-40) REVERT: A 400 PHE cc_start: 0.6438 (OUTLIER) cc_final: 0.5740 (p90) REVERT: A 409 GLN cc_start: 0.5860 (tt0) cc_final: 0.5431 (tm-30) REVERT: A 1145 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7488 (tt) REVERT: B 133 PHE cc_start: 0.6506 (p90) cc_final: 0.6006 (p90) REVERT: B 160 TYR cc_start: 0.6095 (OUTLIER) cc_final: 0.4054 (p90) REVERT: B 374 PHE cc_start: 0.6932 (p90) cc_final: 0.6490 (p90) REVERT: C 144 TYR cc_start: 0.3646 (OUTLIER) cc_final: 0.1852 (t80) REVERT: C 462 LYS cc_start: 0.7557 (mmmt) cc_final: 0.7073 (mtmm) REVERT: C 592 PHE cc_start: 0.6602 (OUTLIER) cc_final: 0.6344 (t80) REVERT: C 1089 PHE cc_start: 0.8820 (OUTLIER) cc_final: 0.7997 (m-80) REVERT: E 100 ARG cc_start: 0.7943 (ttp-170) cc_final: 0.7607 (ttp-170) REVERT: F 35 PHE cc_start: 0.4569 (OUTLIER) cc_final: 0.4068 (m-10) REVERT: F 36 MET cc_start: 0.4960 (mmp) cc_final: 0.3411 (ttp) REVERT: H 101 PHE cc_start: 0.7920 (OUTLIER) cc_final: 0.7609 (m-10) REVERT: I 2 VAL cc_start: 0.5224 (t) cc_final: 0.4955 (t) REVERT: I 109 TYR cc_start: 0.8314 (m-80) cc_final: 0.7858 (m-80) outliers start: 67 outliers final: 45 residues processed: 224 average time/residue: 0.1989 time to fit residues: 71.1797 Evaluate side-chains 206 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 153 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 689 SER Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 35 PHE Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 101 PHE Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 80 TYR Chi-restraints excluded: chain H residue 101 PHE Chi-restraints excluded: chain I residue 86 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 50 optimal weight: 2.9990 chunk 249 optimal weight: 8.9990 chunk 4 optimal weight: 0.0770 chunk 168 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 326 optimal weight: 6.9990 chunk 84 optimal weight: 0.8980 chunk 289 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 165 optimal weight: 0.0570 chunk 358 optimal weight: 7.9990 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN A 913 GLN B 164 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.091964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.068289 restraints weight = 114647.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.069962 restraints weight = 64696.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.070427 restraints weight = 39651.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.071025 restraints weight = 30750.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.071113 restraints weight = 26529.932| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.5671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 30744 Z= 0.136 Angle : 0.727 13.691 41930 Z= 0.367 Chirality : 0.047 0.488 4864 Planarity : 0.004 0.048 5321 Dihedral : 7.271 59.016 5280 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.75 % Favored : 92.95 % Rotamer: Outliers : 1.30 % Allowed : 13.05 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 are not related in a simple way. whole: -2.34 (0.13), residues: 3702 helix: 0.32 (0.21), residues: 612 sheet: -1.81 (0.16), residues: 923 loop : -2.05 (0.13), residues: 2167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 23 TYR 0.023 0.002 TYR E 109 PHE 0.060 0.002 PHE D 35 TRP 0.025 0.002 TRP G 47 HIS 0.007 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00298 (30645) covalent geometry : angle 0.70108 (41677) SS BOND : bond 0.00450 ( 38) SS BOND : angle 2.02697 ( 76) hydrogen bonds : bond 0.03607 ( 785) hydrogen bonds : angle 5.97400 ( 2079) Misc. bond : bond 0.00047 ( 2) link_BETA1-4 : bond 0.00289 ( 15) link_BETA1-4 : angle 1.75732 ( 45) link_NAG-ASN : bond 0.00474 ( 44) link_NAG-ASN : angle 3.05153 ( 132) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 177 time to evaluate : 1.138 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 239 GLN cc_start: 0.7974 (tm-30) cc_final: 0.7720 (tm-30) REVERT: A 409 GLN cc_start: 0.5803 (tt0) cc_final: 0.5366 (tm-30) REVERT: A 1145 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7613 (tt) REVERT: B 133 PHE cc_start: 0.5633 (p90) cc_final: 0.5296 (p90) REVERT: B 238 PHE cc_start: 0.7207 (p90) cc_final: 0.6745 (p90) REVERT: B 374 PHE cc_start: 0.6802 (p90) cc_final: 0.6459 (p90) REVERT: C 214 ARG cc_start: 0.6728 (tpt90) cc_final: 0.6258 (mmm160) REVERT: C 462 LYS cc_start: 0.7525 (mmmt) cc_final: 0.7094 (mtmm) REVERT: E 100 ARG cc_start: 0.7899 (ttp-170) cc_final: 0.7466 (ttp-170) REVERT: F 36 MET cc_start: 0.4948 (OUTLIER) cc_final: 0.3314 (ttp) REVERT: I 109 TYR cc_start: 0.8379 (m-80) cc_final: 0.7880 (m-80) outliers start: 42 outliers final: 36 residues processed: 210 average time/residue: 0.2028 time to fit residues: 67.7226 Evaluate side-chains 196 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 158 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 35 PHE Chi-restraints excluded: chain F residue 36 MET Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 101 PHE Chi-restraints excluded: chain G residue 4 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 361 optimal weight: 20.0000 chunk 283 optimal weight: 4.9990 chunk 363 optimal weight: 8.9990 chunk 100 optimal weight: 4.9990 chunk 277 optimal weight: 6.9990 chunk 217 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 228 optimal weight: 0.5980 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.090282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.066345 restraints weight = 116615.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.068042 restraints weight = 66976.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.067974 restraints weight = 42477.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.068363 restraints weight = 38355.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.069085 restraints weight = 32431.953| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.5720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 30744 Z= 0.269 Angle : 0.804 13.882 41930 Z= 0.405 Chirality : 0.049 0.485 4864 Planarity : 0.005 0.079 5321 Dihedral : 7.660 59.475 5280 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.70 % Favored : 89.98 % Rotamer: Outliers : 1.58 % Allowed : 13.23 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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 are not related in a simple way. whole: -2.51 (0.13), residues: 3702 helix: 0.16 (0.21), residues: 602 sheet: -1.92 (0.16), residues: 949 loop : -2.14 (0.13), residues: 2151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 214 TYR 0.027 0.002 TYR E 109 PHE 0.059 0.003 PHE D 35 TRP 0.030 0.002 TRP B 64 HIS 0.007 0.002 HIS B1101 Details of bonding type rmsd covalent geometry : bond 0.00609 (30645) covalent geometry : angle 0.77896 (41677) SS BOND : bond 0.00462 ( 38) SS BOND : angle 2.13892 ( 76) hydrogen bonds : bond 0.04042 ( 785) hydrogen bonds : angle 6.14160 ( 2079) Misc. bond : bond 0.00068 ( 2) link_BETA1-4 : bond 0.00361 ( 15) link_BETA1-4 : angle 1.85077 ( 45) link_NAG-ASN : bond 0.00731 ( 44) link_NAG-ASN : angle 3.14144 ( 132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5247.93 seconds wall clock time: 91 minutes 59.87 seconds (5519.87 seconds total)