Starting phenix.real_space_refine on Thu Mar 5 23:58:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k8z_22736/03_2026/7k8z_22736_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k8z_22736/03_2026/7k8z_22736.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 { model { file = "/net/cci-nas-00/data/ceres_data/7k8z_22736/03_2026/7k8z_22736_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k8z_22736/03_2026/7k8z_22736_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7k8z_22736/03_2026/7k8z_22736.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k8z_22736/03_2026/7k8z_22736.map" } 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= 0.002 sd= 0.016 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 110 5.16 5 C 16542 2.51 5 N 4278 2.21 5 O 5085 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 162 residue(s): 0.02s 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: 26015 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 7401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 967, 7401 Classifications: {'peptide': 967} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 47, 'TRANS': 919} Chain breaks: 12 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 216 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASN:plan1': 5, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 10, 'TYR:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 120 Chain: "B" Number of atoms: 6865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 6865 Classifications: {'peptide': 949} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PTRANS': 46, 'TRANS': 902} Chain breaks: 13 Unresolved non-hydrogen bonds: 576 Unresolved non-hydrogen angles: 742 Unresolved non-hydrogen dihedrals: 481 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'ASP:plan': 13, 'ASN:plan1': 17, 'GLU:plan': 12, 'GLN:plan1': 9, 'ARG:plan': 9, 'PHE:plan': 9, 'TYR:plan': 13, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 382 Chain: "C" Number of atoms: 7341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7341 Classifications: {'peptide': 972} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PTRANS': 47, 'TRANS': 924} Chain breaks: 10 Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 345 Unresolved non-hydrogen dihedrals: 222 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ASN:plan1': 9, 'ASP:plan': 13, 'GLN:plan1': 3, 'GLU:plan': 13, 'ARG:plan': 2, 'TYR:plan': 3, 'PHE:plan': 3} Unresolved non-hydrogen planarities: 179 Chain: "H" Number of atoms: 916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 916 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "L" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 818 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 910 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "N" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 818 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" 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: "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: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" 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 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 5.46, per 1000 atoms: 0.21 Number of scatterers: 26015 At special positions: 0 Unit cell: (131.252, 127.072, 196.46, 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 110 16.00 O 5085 8.00 N 4278 7.00 C 16542 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 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=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 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=2.02 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 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.06 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 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=2.06 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=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA K 3 " - " MAN K 4 " ALPHA1-6 " BMA K 3 " - " MAN K 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " 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 V 2 " - " BMA V 3 " BETA1-6 " NAG K 1 " - " FUC K 6 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG V 1 " - " FUC V 4 " 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 603 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 343 " " NAG B1307 " - " ASN B 603 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 657 " " NAG B1310 " - " ASN B 709 " " NAG B1311 " - " ASN B 717 " " NAG B1312 " - " ASN B1074 " " NAG B1313 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 282 " " 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 C1310 " - " ASN C 165 " " NAG C1311 " - " ASN C 331 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN A 165 " " NAG K 1 " - " ASN A 343 " " NAG O 1 " - " ASN B 801 " " NAG P 1 " - " ASN B1098 " " NAG Q 1 " - " ASN B1134 " " NAG R 1 " - " ASN C 717 " " NAG S 1 " - " ASN C 801 " " NAG T 1 " - " ASN C1098 " " NAG U 1 " - " ASN C1134 " " NAG V 1 " - " ASN C 343 " Time building additional restraints: 2.06 Conformation dependent library (CDL) restraints added in 1.1 seconds 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6244 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 52 sheets defined 25.1% alpha, 27.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.634A pdb=" N ASN A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.227A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.362A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.999A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.514A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.566A pdb=" N TYR A 873 " --> pdb=" O MET A 869 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.913A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 907 removed outlier: 3.900A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 910 No H-bonds generated for 'chain 'A' and resid 908 through 910' Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.833A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.544A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (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 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.688A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.088A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 341 Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.761A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.819A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.689A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 removed outlier: 3.518A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.516A pdb=" N LEU B 878 " --> pdb=" O THR B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.973A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.923A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.920A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.527A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (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 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.980A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.034A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.758A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.282A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 389 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.592A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.512A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.813A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.828A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.503A pdb=" N MET C 902 " --> pdb=" O PHE C 898 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.699A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.542A pdb=" N GLN C 965 " --> pdb=" O THR C 961 " (cutoff:3.500A) 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: 3.610A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.385A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.117A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 100A through 103 removed outlier: 3.896A pdb=" N TRP H 103 " --> pdb=" O SER H 100B" (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.021A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 61 through 64 Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'M' and resid 100A through 103 removed outlier: 3.716A pdb=" N TRP M 103 " --> pdb=" O SER M 100B" (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 removed outlier: 4.021A pdb=" N PHE N 83 " --> pdb=" O PRO N 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.927A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.555A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.585A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 118 through 121 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.107A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.822A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.550A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 538 through 543 removed outlier: 5.680A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.137A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 703 through 704 removed outlier: 7.466A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.542A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.542A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 735 Processing sheet with id=AB6, first strand: chain 'A' and resid 789 through 790 removed outlier: 3.713A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.090A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1097 removed outlier: 3.643A pdb=" N VAL A1104 " --> pdb=" O GLN A1113 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 31 removed outlier: 4.206A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.489A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.723A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.651A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 318 removed outlier: 3.686A pdb=" N GLY B 311 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.266A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AC7, first strand: chain 'B' and resid 538 through 542 Processing sheet with id=AC8, first strand: chain 'B' and resid 565 through 566 removed outlier: 6.616A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.111A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.203A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 735 Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.609A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 31 removed outlier: 4.068A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.523A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.434A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.993A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.057A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.373A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.473A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.506A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.487A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.395A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE C1052 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE8, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AE9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AF1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.597A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.544A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.539A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AF5, first strand: chain 'M' and resid 58 through 59 removed outlier: 6.547A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N VAL M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N MET M 34 " --> pdb=" O VAL M 50 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.544A pdb=" N VAL N 19 " --> pdb=" O ILE N 75 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU N 70 " --> pdb=" O SER N 67 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.539A pdb=" N LEU N 11 " --> pdb=" O GLU N 105 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) 1063 hydrogen bonds defined for protein. 2841 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.15 Time building geometry restraints manager: 2.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8233 1.34 - 1.46: 6768 1.46 - 1.59: 11416 1.59 - 1.71: 1 1.71 - 1.83: 140 Bond restraints: 26558 Sorted by residual: bond pdb=" C1 MAN K 4 " pdb=" O5 MAN K 4 " ideal model delta sigma weight residual 1.399 1.491 -0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" C1 MAN K 4 " pdb=" C2 MAN K 4 " ideal model delta sigma weight residual 1.526 1.601 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C VAL B 860 " pdb=" N LEU B 861 " ideal model delta sigma weight residual 1.331 1.259 0.072 2.07e-02 2.33e+03 1.21e+01 bond pdb=" C3 BMA K 3 " pdb=" O3 BMA K 3 " ideal model delta sigma weight residual 1.406 1.467 -0.061 2.00e-02 2.50e+03 9.40e+00 bond pdb=" C VAL A 860 " pdb=" N LEU A 861 " ideal model delta sigma weight residual 1.331 1.247 0.084 2.83e-02 1.25e+03 8.80e+00 ... (remaining 26553 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.18: 35859 3.18 - 6.37: 297 6.37 - 9.55: 29 9.55 - 12.73: 7 12.73 - 15.91: 4 Bond angle restraints: 36196 Sorted by residual: angle pdb=" CG ARG N 24 " pdb=" CD ARG N 24 " pdb=" NE ARG N 24 " ideal model delta sigma weight residual 112.00 127.91 -15.91 2.20e+00 2.07e-01 5.23e+01 angle pdb=" CG ARG L 24 " pdb=" CD ARG L 24 " pdb=" NE ARG L 24 " ideal model delta sigma weight residual 112.00 127.90 -15.90 2.20e+00 2.07e-01 5.22e+01 angle pdb=" CA GLU L 50 " pdb=" CB GLU L 50 " pdb=" CG GLU L 50 " ideal model delta sigma weight residual 114.10 127.38 -13.28 2.00e+00 2.50e-01 4.41e+01 angle pdb=" CA GLU N 50 " pdb=" CB GLU N 50 " pdb=" CG GLU N 50 " ideal model delta sigma weight residual 114.10 127.33 -13.23 2.00e+00 2.50e-01 4.38e+01 angle pdb=" CD ARG N 24 " pdb=" NE ARG N 24 " pdb=" CZ ARG N 24 " ideal model delta sigma weight residual 124.40 132.92 -8.52 1.40e+00 5.10e-01 3.70e+01 ... (remaining 36191 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.50: 15712 21.50 - 43.01: 683 43.01 - 64.51: 159 64.51 - 86.02: 43 86.02 - 107.52: 14 Dihedral angle restraints: 16611 sinusoidal: 6941 harmonic: 9670 Sorted by residual: dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual 93.00 4.69 88.31 1 1.00e+01 1.00e-02 9.32e+01 dihedral pdb=" CA ILE L 29 " pdb=" C ILE L 29 " pdb=" N SER L 30 " pdb=" CA SER L 30 " ideal model delta harmonic sigma weight residual -180.00 -132.00 -48.00 0 5.00e+00 4.00e-02 9.21e+01 dihedral pdb=" CA ILE N 29 " pdb=" C ILE N 29 " pdb=" N SER N 30 " pdb=" CA SER N 30 " ideal model delta harmonic sigma weight residual 180.00 -132.05 -47.95 0 5.00e+00 4.00e-02 9.20e+01 ... (remaining 16608 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.154: 4364 0.154 - 0.308: 36 0.308 - 0.462: 1 0.462 - 0.616: 0 0.616 - 0.770: 1 Chirality restraints: 4402 Sorted by residual: chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.63 -0.77 2.00e-01 2.50e+01 1.48e+01 chirality pdb=" C1 NAG C1311 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG C1311 " pdb=" O5 NAG C1311 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" C3 BMA K 3 " pdb=" C2 BMA K 3 " pdb=" C4 BMA K 3 " pdb=" O3 BMA K 3 " both_signs ideal model delta sigma weight residual False 2.41 2.11 0.30 2.00e-01 2.50e+01 2.19e+00 ... (remaining 4399 not shown) Planarity restraints: 4621 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE M 100 " 0.036 2.00e-02 2.50e+03 2.77e-02 1.34e+01 pdb=" CG PHE M 100 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE M 100 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE M 100 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE M 100 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE M 100 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE M 100 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 61 " 0.029 2.00e-02 2.50e+03 2.82e-02 9.95e+00 pdb=" CG ASN A 61 " -0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN A 61 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A 61 " -0.035 2.00e-02 2.50e+03 pdb=" C1 NAG A1301 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE C 329 " -0.050 5.00e-02 4.00e+02 7.66e-02 9.38e+00 pdb=" N PRO C 330 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO C 330 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 330 " -0.042 5.00e-02 4.00e+02 ... (remaining 4618 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 490 2.66 - 3.22: 25463 3.22 - 3.78: 39633 3.78 - 4.34: 53824 4.34 - 4.90: 87570 Nonbonded interactions: 206980 Sorted by model distance: nonbonded pdb=" OE1 GLU B 725 " pdb=" NE2 HIS B1064 " model vdw 2.103 3.120 nonbonded pdb=" OE1 GLU A 725 " pdb=" NE2 HIS A1064 " model vdw 2.135 3.120 nonbonded pdb=" NE2 GLN B 949 " pdb=" OD1 ASN B 953 " model vdw 2.146 3.120 nonbonded pdb=" OD1 ASN B 616 " pdb=" N CYS B 617 " model vdw 2.147 3.120 nonbonded pdb=" OE1 GLU C 725 " pdb=" NE2 HIS C1064 " model vdw 2.156 3.120 ... (remaining 206975 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 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 52 or (resid 53 and (name N or nam \ e CA or name C or name O or name CB )) or resid 54 through 66 or resid 82 throug \ h 87 or (resid 88 and (name N or name CA or name C or name O or name CB )) or re \ sid 89 through 95 or (resid 96 through 97 and (name N or name CA or name C or na \ me O or name CB )) or resid 98 through 109 or (resid 110 through 113 and (name N \ or name CA or name C or name O or name CB )) or resid 116 through 124 or (resid \ 125 and (name N or name CA or name C or name O or name CB )) or resid 126 throu \ gh 131 or (resid 132 and (name N or name CA or name C or name O or name CB )) or \ resid 133 or (resid 134 through 138 and (name N or name CA or name C or name O \ or name CB )) or resid 139 through 140 or resid 165 through 168 or (resid 169 an \ d (name N or name CA or name C or name O or name CB )) or resid 170 through 171 \ or (resid 172 and (name N or name CA or name C or name O or name CB )) or resid \ 186 through 190 or (resid 191 and (name N or name CA or name C or name O or name \ CB )) or resid 192 through 196 or resid 200 through 210 or (resid 211 and (name \ N or name CA or name C or name O or name CB )) or (resid 215 and (name N or nam \ e CA or name C or name O or name CB )) or resid 216 through 217 or (resid 218 an \ d (name N or name CA or name C or name O or name CB )) or resid 219 through 223 \ or (resid 224 and (name N or name CA or name C or name O or name CB )) or resid \ 225 through 238 or (resid 239 and (name N or name CA or name C or name O or name \ CB )) or resid 240 through 263 or resid 265 through 308 or (resid 309 and (name \ N or name CA or name C or name O or name CB )) or resid 310 through 323 or (res \ id 324 and (name N or name CA or name C or name O or name CB )) or resid 325 thr \ ough 332 or (resid 333 through 334 and (name N or name CA or name C or name O or \ name CB )) or resid 335 through 345 or (resid 346 through 360 and (name N or na \ me CA or name C or name O or name CB )) or resid 361 or (resid 362 through 378 a \ nd (name N or name CA or name C or name O or name CB )) or resid 379 or (resid 3 \ 80 and (name N or name CA or name C or name O or name CB )) or resid 381 or (res \ id 382 through 383 and (name N or name CA or name C or name O or name CB )) or r \ esid 384 or (resid 385 through 390 and (name N or name CA or name C or name O or \ name CB )) or resid 391 or (resid 392 through 403 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 404 through 411 and (name N or name CA or \ name C or name O or name CB )) or resid 412 through 413 or (resid 414 through 41 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 416 or (resi \ d 417 through 425 and (name N or name CA or name C or name O or name CB )) or re \ sid 426 through 427 or (resid 428 through 430 and (name N or name CA or name C o \ r name O or name CB )) or resid 431 through 432 or (resid 433 through 454 and (n \ ame N or name CA or name C or name O or name CB )) or (resid 462 and (name N or \ name CA or name C or name O or name CB )) or resid 463 or (resid 464 through 466 \ and (name N or name CA or name C or name O or name CB )) or resid 491 or (resid \ 492 through 495 and (name N or name CA or name C or name O or name CB )) or res \ id 496 or (resid 497 through 498 and (name N or name CA or name C or name O or n \ ame CB )) or resid 499 or (resid 500 through 503 and (name N or name CA or name \ C or name O or name CB )) or (resid 504 through 506 and (name N or name CA or na \ me C or name O or name CB )) or resid 507 or (resid 508 through 515 and (name N \ or name CA or name C or name O or name CB )) or (resid 522 through 524 and (name \ N or name CA or name C or name O or name CB )) or resid 525 through 528 or (res \ id 529 and (name N or name CA or name C or name O or name CB )) or resid 530 thr \ ough 553 or (resid 554 and (name N or name CA or name C or name O or name CB )) \ or resid 555 through 793 or (resid 794 and (name N or name CA or name C or name \ O or name CB )) or resid 795 or (resid 796 and (name N or name CA or name C or n \ ame O or name CB )) or resid 797 through 810 or (resid 811 and (name N or name C \ A or name C or name O or name CB )) or resid 813 through 827 or resid 856 throug \ h 866 or (resid 867 through 868 and (name N or name CA or name C or name O or na \ me CB )) or resid 869 through 939 or (resid 940 and (name N or name CA or name C \ or name O or name CB )) or resid 941 through 984 or (resid 985 and (name N or n \ ame CA or name C or name O or name CB )) or resid 986 through 987 or (resid 988 \ through 989 and (name N or name CA or name C or name O or name CB )) or resid 99 \ 0 through 1141 or (resid 1142 and (name N or name CA or name C or name O or name \ CB )) or resid 1143 through 1144 or (resid 1145 through 1146 and (name N or nam \ e CA or name C or name O or name CB )) or resid 1147 through 1309)) selection = (chain 'B' and (resid 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 66 or resid 82 through 87 or (resi \ d 88 and (name N or name CA or name C or name O or name CB )) or resid 89 throug \ h 96 or (resid 97 and (name N or name CA or name C or name O or name CB )) or re \ sid 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or \ resid 100 through 109 or (resid 110 through 113 and (name N or name CA or name C \ or name O or name CB )) or resid 116 through 128 or (resid 129 and (name N or n \ ame CA or name C or name O or name CB )) or resid 130 through 134 or (resid 135 \ through 138 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 9 through 140 or resid 165 through 168 or (resid 169 and (name N or name CA or n \ ame C or name O or name CB )) or resid 170 through 187 or (resid 188 and (name N \ or name CA or name C or name O or name CB )) or resid 189 through 190 or (resid \ 191 and (name N or name CA or name C or name O or name CB )) or resid 192 throu \ gh 195 or (resid 196 and (name N or name CA or name C or name O or name CB )) or \ resid 200 through 210 or (resid 211 through 215 and (name N or name CA or name \ C or name O or name CB )) or resid 216 through 241 or (resid 242 through 263 and \ (name N or name CA or name C or name O or name CB )) or resid 265 through 280 o \ r (resid 281 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 82 through 323 or (resid 324 and (name N or name CA or name C or name O or name \ CB )) or resid 325 through 442 or resid 448 through 501 or resid 503 through 567 \ or (resid 568 and (name N or name CA or name C or name O or name CB )) or resid \ 569 through 570 or (resid 571 and (name N or name CA or name C or name O or nam \ e CB )) or resid 572 through 581 or (resid 582 through 583 and (name N or name C \ A or name C or name O or name CB )) or resid 584 through 585 or (resid 586 and ( \ name N or name CA or name C or name O or name CB )) or resid 587 through 613 or \ (resid 614 and (name N or name CA or name C or name O or name CB )) or resid 615 \ through 618 or (resid 619 and (name N or name CA or name C or name O or name CB \ )) or resid 620 through 676 or resid 690 through 744 or (resid 745 and (name N \ or name CA or name C or name O or name CB )) or resid 746 through 810 or (resid \ 811 and (name N or name CA or name C or name O or name CB )) or resid 813 throug \ h 827 or resid 856 through 866 or (resid 867 through 868 and (name N or name CA \ or name C or name O or name CB )) or resid 869 through 920 or (resid 921 and (na \ me N or name CA or name C or name O or name CB )) or resid 922 through 939 or (r \ esid 940 and (name N or name CA or name C or name O or name CB )) or resid 941 t \ hrough 984 or (resid 985 and (name N or name CA or name C or name O or name CB ) \ ) or resid 986 through 987 or (resid 988 through 989 and (name N or name CA or n \ ame C or name O or name CB )) or resid 990 through 1072 or (resid 1073 and (name \ N or name CA or name C or name O or name CB )) or resid 1074 through 1117 or (r \ esid 1118 and (name N or name CA or name C or name O or name CB )) or resid 1119 \ through 1143 or (resid 1144 through 1146 and (name N or name CA or name C or na \ me O or name CB )) or resid 1147 through 1309)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or re \ sid 100 through 110 or (resid 111 through 113 and (name N or name CA or name C o \ r name O or name CB )) or resid 116 through 134 or (resid 135 through 138 and (n \ ame N or name CA or name C or name O or name CB )) or resid 139 through 140 or r \ esid 165 through 187 or (resid 188 and (name N or name CA or name C or name O or \ name CB )) or resid 189 through 195 or (resid 196 and (name N or name CA or nam \ e C or name O or name CB )) or resid 200 through 211 or resid 215 through 217 or \ (resid 218 and (name N or name CA or name C or name O or name CB )) or resid 21 \ 9 through 223 or (resid 224 and (name N or name CA or name C or name O or name C \ B )) or resid 225 through 238 or (resid 239 and (name N or name CA or name C or \ name O or name CB )) or resid 240 through 308 or (resid 309 and (name N or name \ CA or name C or name O or name CB )) or resid 310 through 332 or (resid 333 thro \ ugh 334 and (name N or name CA or name C or name O or name CB )) or resid 335 th \ rough 344 or (resid 345 through 360 and (name N or name CA or name C or name O o \ r name CB )) or resid 361 or (resid 362 through 378 and (name N or name CA or na \ me C or name O or name CB )) or resid 379 or (resid 380 and (name N or name CA o \ r name C or name O or name CB )) or resid 381 or (resid 382 through 383 and (nam \ e N or name CA or name C or name O or name CB )) or resid 384 or (resid 385 thro \ ugh 390 and (name N or name CA or name C or name O or name CB )) or resid 391 or \ (resid 392 through 403 and (name N or name CA or name C or name O or name CB )) \ or (resid 404 through 411 and (name N or name CA or name C or name O or name CB \ )) or resid 412 through 413 or (resid 414 through 415 and (name N or name CA or \ name C or name O or name CB )) or (resid 416 through 425 and (name N or name CA \ or name C or name O or name CB )) or resid 426 or (resid 427 through 430 and (n \ ame N or name CA or name C or name O or name CB )) or resid 431 through 432 or ( \ resid 433 through 442 and (name N or name CA or name C or name O or name CB )) o \ r (resid 448 through 454 and (name N or name CA or name C or name O or name CB ) \ ) or resid 462 through 463 or (resid 464 through 466 and (name N or name CA or n \ ame C or name O or name CB )) or resid 491 or (resid 492 through 495 and (name N \ or name CA or name C or name O or name CB )) or resid 496 or (resid 497 through \ 498 and (name N or name CA or name C or name O or name CB )) or resid 499 throu \ gh 500 or (resid 501 and (name N or name CA or name C or name O or name CB )) or \ (resid 503 and (name N or name CA or name C or name O or name CB )) or (resid 5 \ 04 through 506 and (name N or name CA or name C or name O or name CB )) or resid \ 507 or (resid 508 through 515 and (name N or name CA or name C or name O or nam \ e CB )) or (resid 522 through 524 and (name N or name CA or name C or name O or \ name CB )) or resid 525 through 527 or (resid 528 through 529 and (name N or nam \ e CA or name C or name O or name CB )) or resid 530 through 553 or (resid 554 an \ d (name N or name CA or name C or name O or name CB )) or resid 555 through 567 \ or (resid 568 and (name N or name CA or name C or name O or name CB )) or resid \ 569 through 570 or (resid 571 and (name N or name CA or name C or name O or name \ CB )) or resid 572 through 581 or (resid 582 through 583 and (name N or name CA \ or name C or name O or name CB )) or resid 584 through 585 or (resid 586 and (n \ ame N or name CA or name C or name O or name CB )) or resid 587 through 618 or ( \ resid 619 and (name N or name CA or name C or name O or name CB )) or resid 620 \ through 645 or (resid 646 through 647 and (name N or name CA or name C or name O \ or name CB )) or resid 648 through 793 or (resid 794 and (name N or name CA or \ name C or name O or name CB )) or resid 795 or (resid 796 and (name N or name CA \ or name C or name O or name CB )) or resid 797 through 920 or (resid 921 and (n \ ame N or name CA or name C or name O or name CB )) or resid 922 through 1072 or \ (resid 1073 and (name N or name CA or name C or name O or name CB )) or resid 10 \ 74 through 1117 or (resid 1118 and (name N or name CA or name C or name O or nam \ e CB )) or resid 1119 through 1141 or (resid 1142 and (name N or name CA or name \ C or name O or name CB )) or resid 1143 or (resid 1144 through 1146 and (name N \ or name CA or name C or name O or name CB )) or resid 1147 through 1309)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } ncs_group { reference = (chain 'H' and resid 1 through 111) selection = chain 'M' } ncs_group { reference = chain 'L' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.070 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 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 : 0.007 0.092 26666 Z= 0.337 Angle : 0.896 15.915 36481 Z= 0.472 Chirality : 0.053 0.770 4402 Planarity : 0.005 0.077 4573 Dihedral : 13.100 107.520 10250 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.52 % Favored : 95.42 % Rotamer: Outliers : 1.06 % Allowed : 0.49 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.14), residues: 3251 helix: -0.40 (0.19), residues: 675 sheet: -0.11 (0.17), residues: 841 loop : -0.62 (0.14), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.035 0.001 ARG A 346 TYR 0.030 0.002 TYR L 49 PHE 0.060 0.003 PHE M 100 TRP 0.046 0.003 TRP L 32 HIS 0.007 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00737 (26558) covalent geometry : angle 0.86429 (36196) SS BOND : bond 0.00752 ( 39) SS BOND : angle 2.12337 ( 78) hydrogen bonds : bond 0.25434 ( 1060) hydrogen bonds : angle 9.91211 ( 2841) link_ALPHA1-3 : bond 0.03250 ( 1) link_ALPHA1-3 : angle 7.74508 ( 3) link_ALPHA1-6 : bond 0.00110 ( 1) link_ALPHA1-6 : angle 1.89040 ( 3) link_BETA1-4 : bond 0.00293 ( 17) link_BETA1-4 : angle 1.85009 ( 51) link_BETA1-6 : bond 0.00675 ( 2) link_BETA1-6 : angle 1.70847 ( 6) link_NAG-ASN : bond 0.00621 ( 48) link_NAG-ASN : angle 3.21092 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 309 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 950 ASP cc_start: 0.8511 (m-30) cc_final: 0.8285 (m-30) REVERT: B 110 LEU cc_start: 0.8005 (mp) cc_final: 0.6933 (tt) REVERT: B 274 THR cc_start: 0.8489 (m) cc_final: 0.8267 (m) REVERT: B 342 PHE cc_start: 0.7735 (m-10) cc_final: 0.7386 (m-80) REVERT: C 45 SER cc_start: 0.7367 (p) cc_final: 0.7137 (t) REVERT: C 140 PHE cc_start: 0.7570 (p90) cc_final: 0.7257 (p90) REVERT: C 902 MET cc_start: 0.8286 (mmm) cc_final: 0.7845 (mmt) REVERT: H 3 GLN cc_start: 0.7992 (mp10) cc_final: 0.7784 (mp10) REVERT: H 29 PHE cc_start: 0.7586 (t80) cc_final: 0.7034 (t80) REVERT: H 82 MET cc_start: 0.9183 (mtm) cc_final: 0.8362 (mtm) REVERT: H 82 LEU cc_start: 0.7770 (mt) cc_final: 0.7283 (mp) REVERT: L 2 ILE cc_start: 0.7935 (tp) cc_final: 0.7681 (tp) REVERT: L 35 TRP cc_start: 0.6530 (m100) cc_final: 0.5351 (m100) REVERT: L 78 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7160 (tp) REVERT: M 6 GLU cc_start: 0.3125 (mp0) cc_final: 0.2783 (mp0) REVERT: M 34 MET cc_start: 0.8081 (mmp) cc_final: 0.7254 (mmm) REVERT: M 35 HIS cc_start: 0.8105 (m90) cc_final: 0.7592 (m170) REVERT: N 3 GLN cc_start: 0.8591 (tp40) cc_final: 0.8351 (tp-100) REVERT: N 24 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.7409 (mmm160) REVERT: N 47 LEU cc_start: 0.8649 (mp) cc_final: 0.8413 (mp) REVERT: N 55 GLU cc_start: 0.8143 (tp30) cc_final: 0.7701 (tp30) REVERT: N 97 THR cc_start: 0.8173 (p) cc_final: 0.7825 (p) outliers start: 28 outliers final: 6 residues processed: 320 average time/residue: 0.1563 time to fit residues: 80.6898 Evaluate side-chains 210 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 202 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 50 GLU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 24 ARG Chi-restraints excluded: chain N residue 50 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.0070 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 7.9990 overall best weight: 1.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 388 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN A1011 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN ** H 100AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 76 ASN ** N 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.111138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.077375 restraints weight = 64039.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.081088 restraints weight = 33250.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.082045 restraints weight = 18081.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.082932 restraints weight = 14272.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.083012 restraints weight = 12683.986| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26666 Z= 0.156 Angle : 0.675 14.596 36481 Z= 0.344 Chirality : 0.048 0.574 4402 Planarity : 0.005 0.061 4573 Dihedral : 8.273 89.811 4979 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.33 % Allowed : 6.30 % Favored : 92.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.14), residues: 3251 helix: 0.91 (0.20), residues: 698 sheet: 0.03 (0.16), residues: 879 loop : -0.47 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG N 61 TYR 0.022 0.002 TYR B 873 PHE 0.035 0.002 PHE M 100 TRP 0.026 0.002 TRP L 32 HIS 0.007 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00341 (26558) covalent geometry : angle 0.64744 (36196) SS BOND : bond 0.00421 ( 39) SS BOND : angle 1.51927 ( 78) hydrogen bonds : bond 0.04996 ( 1060) hydrogen bonds : angle 6.78639 ( 2841) link_ALPHA1-3 : bond 0.03444 ( 1) link_ALPHA1-3 : angle 8.90347 ( 3) link_ALPHA1-6 : bond 0.00366 ( 1) link_ALPHA1-6 : angle 2.24806 ( 3) link_BETA1-4 : bond 0.00485 ( 17) link_BETA1-4 : angle 1.62598 ( 51) link_BETA1-6 : bond 0.00470 ( 2) link_BETA1-6 : angle 1.98002 ( 6) link_NAG-ASN : bond 0.00503 ( 48) link_NAG-ASN : angle 2.43820 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 262 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 TYR cc_start: 0.8073 (t80) cc_final: 0.7816 (t80) REVERT: A 698 SER cc_start: 0.8989 (t) cc_final: 0.8644 (p) REVERT: A 1050 MET cc_start: 0.7588 (ptt) cc_final: 0.7030 (ptt) REVERT: A 1111 GLU cc_start: 0.8126 (tt0) cc_final: 0.7833 (tt0) REVERT: B 274 THR cc_start: 0.8588 (m) cc_final: 0.8249 (m) REVERT: B 342 PHE cc_start: 0.7717 (m-10) cc_final: 0.7373 (m-80) REVERT: B 869 MET cc_start: 0.8101 (mtp) cc_final: 0.7577 (mtp) REVERT: C 45 SER cc_start: 0.7204 (p) cc_final: 0.6957 (t) REVERT: C 697 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.7733 (ptm) REVERT: C 1107 ARG cc_start: 0.8087 (mmt90) cc_final: 0.7453 (mpt-90) REVERT: H 34 MET cc_start: 0.8165 (tpp) cc_final: 0.7716 (tpp) REVERT: H 36 TRP cc_start: 0.8436 (m100) cc_final: 0.8218 (m100) REVERT: H 46 GLU cc_start: 0.9051 (tp30) cc_final: 0.8849 (tp30) REVERT: H 82 MET cc_start: 0.9229 (mtm) cc_final: 0.8567 (mpp) REVERT: H 86 ASP cc_start: 0.7874 (m-30) cc_final: 0.7531 (t70) REVERT: L 35 TRP cc_start: 0.6585 (m100) cc_final: 0.5668 (m100) REVERT: M 29 PHE cc_start: 0.6144 (t80) cc_final: 0.5802 (t80) REVERT: M 34 MET cc_start: 0.7957 (mmp) cc_final: 0.7483 (mmm) REVERT: M 35 HIS cc_start: 0.7856 (m90) cc_final: 0.7207 (m170) REVERT: M 83 ARG cc_start: 0.8526 (mpp80) cc_final: 0.8156 (mpp80) REVERT: N 24 ARG cc_start: 0.8502 (mmm160) cc_final: 0.7951 (mmm-85) REVERT: N 70 GLU cc_start: 0.9105 (tp30) cc_final: 0.8689 (tp30) outliers start: 35 outliers final: 16 residues processed: 278 average time/residue: 0.1504 time to fit residues: 69.2066 Evaluate side-chains 214 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 197 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 50 GLU Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 106 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 189 optimal weight: 0.9980 chunk 147 optimal weight: 6.9990 chunk 327 optimal weight: 9.9990 chunk 149 optimal weight: 2.9990 chunk 277 optimal weight: 4.9990 chunk 271 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 171 optimal weight: 4.9990 chunk 301 optimal weight: 20.0000 chunk 25 optimal weight: 6.9990 chunk 318 optimal weight: 9.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN A 949 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN C 955 ASN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN H 39 GLN H 100AHIS N 38 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.107729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.073891 restraints weight = 65406.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.077469 restraints weight = 35472.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.078323 restraints weight = 19846.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.078901 restraints weight = 15900.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.079005 restraints weight = 14350.856| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 26666 Z= 0.264 Angle : 0.719 14.216 36481 Z= 0.362 Chirality : 0.049 0.574 4402 Planarity : 0.005 0.057 4573 Dihedral : 7.360 83.801 4965 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.86 % Allowed : 8.46 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.14), residues: 3251 helix: 0.97 (0.20), residues: 673 sheet: -0.17 (0.17), residues: 873 loop : -0.61 (0.15), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 19 TYR 0.032 0.002 TYR A 904 PHE 0.034 0.003 PHE B 133 TRP 0.015 0.002 TRP N 32 HIS 0.008 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00607 (26558) covalent geometry : angle 0.69417 (36196) SS BOND : bond 0.00488 ( 39) SS BOND : angle 1.59713 ( 78) hydrogen bonds : bond 0.04849 ( 1060) hydrogen bonds : angle 6.48251 ( 2841) link_ALPHA1-3 : bond 0.03197 ( 1) link_ALPHA1-3 : angle 8.67251 ( 3) link_ALPHA1-6 : bond 0.00109 ( 1) link_ALPHA1-6 : angle 2.16682 ( 3) link_BETA1-4 : bond 0.00383 ( 17) link_BETA1-4 : angle 1.68713 ( 51) link_BETA1-6 : bond 0.00309 ( 2) link_BETA1-6 : angle 1.45244 ( 6) link_NAG-ASN : bond 0.00391 ( 48) link_NAG-ASN : angle 2.42402 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 213 time to evaluate : 1.664 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 369 TYR cc_start: 0.8231 (t80) cc_final: 0.7991 (t80) REVERT: A 389 ASP cc_start: 0.8607 (m-30) cc_final: 0.8273 (t0) REVERT: A 698 SER cc_start: 0.9046 (t) cc_final: 0.8675 (p) REVERT: A 1050 MET cc_start: 0.7686 (ptt) cc_final: 0.7074 (ptt) REVERT: B 101 ILE cc_start: 0.9319 (pt) cc_final: 0.9031 (tp) REVERT: B 274 THR cc_start: 0.8659 (m) cc_final: 0.8345 (m) REVERT: B 315 THR cc_start: 0.8362 (p) cc_final: 0.8099 (t) REVERT: C 508 TYR cc_start: 0.8358 (m-80) cc_final: 0.7394 (m-80) REVERT: H 36 TRP cc_start: 0.8252 (m100) cc_final: 0.8044 (m100) REVERT: H 82 MET cc_start: 0.9335 (mtm) cc_final: 0.8293 (mtm) REVERT: H 86 ASP cc_start: 0.8071 (m-30) cc_final: 0.7507 (t70) REVERT: L 55 GLU cc_start: 0.8524 (tp30) cc_final: 0.8090 (tp30) REVERT: M 34 MET cc_start: 0.8158 (mmp) cc_final: 0.7363 (mmm) REVERT: M 35 HIS cc_start: 0.7999 (m90) cc_final: 0.7338 (m170) REVERT: M 36 TRP cc_start: 0.7881 (m100) cc_final: 0.6487 (m100) REVERT: N 24 ARG cc_start: 0.8574 (mmm160) cc_final: 0.8008 (mmm-85) REVERT: N 37 GLN cc_start: 0.8784 (tt0) cc_final: 0.8160 (tt0) REVERT: N 70 GLU cc_start: 0.9116 (OUTLIER) cc_final: 0.8525 (mm-30) outliers start: 49 outliers final: 25 residues processed: 243 average time/residue: 0.1665 time to fit residues: 65.8286 Evaluate side-chains 212 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 186 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain N residue 106 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 162 optimal weight: 5.9990 chunk 289 optimal weight: 20.0000 chunk 151 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 83 optimal weight: 0.8980 chunk 122 optimal weight: 30.0000 chunk 248 optimal weight: 0.9980 chunk 174 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 106 optimal weight: 30.0000 chunk 313 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN H 100AHIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.109125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.075289 restraints weight = 64327.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.078905 restraints weight = 34827.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.079784 restraints weight = 19401.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.080369 restraints weight = 15433.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.080526 restraints weight = 13921.687| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 26666 Z= 0.149 Angle : 0.620 14.208 36481 Z= 0.311 Chirality : 0.047 0.568 4402 Planarity : 0.004 0.057 4573 Dihedral : 6.834 81.603 4962 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.40 % Allowed : 10.24 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.14), residues: 3251 helix: 1.33 (0.20), residues: 677 sheet: -0.11 (0.17), residues: 855 loop : -0.56 (0.15), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 71 TYR 0.021 0.001 TYR A 904 PHE 0.031 0.002 PHE H 29 TRP 0.015 0.001 TRP M 36 HIS 0.008 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00335 (26558) covalent geometry : angle 0.59287 (36196) SS BOND : bond 0.00350 ( 39) SS BOND : angle 1.57953 ( 78) hydrogen bonds : bond 0.04052 ( 1060) hydrogen bonds : angle 6.10866 ( 2841) link_ALPHA1-3 : bond 0.03439 ( 1) link_ALPHA1-3 : angle 8.70714 ( 3) link_ALPHA1-6 : bond 0.00246 ( 1) link_ALPHA1-6 : angle 2.25727 ( 3) link_BETA1-4 : bond 0.00458 ( 17) link_BETA1-4 : angle 1.52769 ( 51) link_BETA1-6 : bond 0.00374 ( 2) link_BETA1-6 : angle 1.52529 ( 6) link_NAG-ASN : bond 0.00360 ( 48) link_NAG-ASN : angle 2.24610 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 216 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 ILE cc_start: 0.9365 (tt) cc_final: 0.9136 (pt) REVERT: A 369 TYR cc_start: 0.8299 (t80) cc_final: 0.8093 (t80) REVERT: A 389 ASP cc_start: 0.8585 (m-30) cc_final: 0.8202 (t0) REVERT: A 698 SER cc_start: 0.9032 (t) cc_final: 0.8651 (p) REVERT: A 1050 MET cc_start: 0.7562 (ptt) cc_final: 0.6875 (ptt) REVERT: B 101 ILE cc_start: 0.9291 (pt) cc_final: 0.9017 (tp) REVERT: B 274 THR cc_start: 0.8740 (m) cc_final: 0.8337 (m) REVERT: B 315 THR cc_start: 0.8371 (p) cc_final: 0.8103 (t) REVERT: C 508 TYR cc_start: 0.8403 (m-80) cc_final: 0.7397 (m-80) REVERT: C 902 MET cc_start: 0.8163 (mmt) cc_final: 0.7636 (mmt) REVERT: C 1107 ARG cc_start: 0.8010 (mmt90) cc_final: 0.7775 (mmt90) REVERT: H 34 MET cc_start: 0.8343 (tpp) cc_final: 0.8088 (tpp) REVERT: H 39 GLN cc_start: 0.6915 (pp30) cc_final: 0.6667 (pp30) REVERT: H 78 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7067 (tp) REVERT: H 82 MET cc_start: 0.9245 (mtm) cc_final: 0.8089 (mpp) REVERT: H 86 ASP cc_start: 0.8042 (m-30) cc_final: 0.7487 (t70) REVERT: L 35 TRP cc_start: 0.6420 (m100) cc_final: 0.5498 (m100) REVERT: L 55 GLU cc_start: 0.8516 (tp30) cc_final: 0.8122 (tp30) REVERT: M 34 MET cc_start: 0.8218 (mmp) cc_final: 0.7413 (mmm) REVERT: M 35 HIS cc_start: 0.7891 (m90) cc_final: 0.7189 (m170) REVERT: M 36 TRP cc_start: 0.7521 (m100) cc_final: 0.7207 (m100) REVERT: M 79 TYR cc_start: 0.6941 (m-80) cc_final: 0.6700 (m-80) REVERT: N 24 ARG cc_start: 0.8468 (mmm160) cc_final: 0.8197 (mmm-85) REVERT: N 37 GLN cc_start: 0.8770 (tt0) cc_final: 0.8156 (tt0) REVERT: N 55 GLU cc_start: 0.8145 (tp30) cc_final: 0.7899 (tp30) REVERT: N 70 GLU cc_start: 0.9111 (OUTLIER) cc_final: 0.8425 (mm-30) outliers start: 37 outliers final: 21 residues processed: 241 average time/residue: 0.1574 time to fit residues: 62.0655 Evaluate side-chains 214 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 191 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain N residue 106 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 62 optimal weight: 0.8980 chunk 301 optimal weight: 30.0000 chunk 27 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 chunk 219 optimal weight: 4.9990 chunk 120 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 141 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 242 optimal weight: 6.9990 chunk 183 optimal weight: 4.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN H 3 GLN ** H 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 100AHIS M 76 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.108187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.074516 restraints weight = 64665.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.078033 restraints weight = 34938.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.078953 restraints weight = 19759.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.079633 restraints weight = 15572.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.079751 restraints weight = 14042.913| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 26666 Z= 0.181 Angle : 0.634 13.634 36481 Z= 0.316 Chirality : 0.047 0.557 4402 Planarity : 0.004 0.061 4573 Dihedral : 6.639 77.185 4961 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.90 % Allowed : 10.81 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.15), residues: 3251 helix: 1.32 (0.20), residues: 679 sheet: -0.16 (0.17), residues: 855 loop : -0.61 (0.15), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 34 TYR 0.022 0.001 TYR A 904 PHE 0.030 0.002 PHE B 133 TRP 0.040 0.002 TRP H 36 HIS 0.008 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00417 (26558) covalent geometry : angle 0.60735 (36196) SS BOND : bond 0.00374 ( 39) SS BOND : angle 1.79667 ( 78) hydrogen bonds : bond 0.04030 ( 1060) hydrogen bonds : angle 6.02434 ( 2841) link_ALPHA1-3 : bond 0.03014 ( 1) link_ALPHA1-3 : angle 8.35507 ( 3) link_ALPHA1-6 : bond 0.00200 ( 1) link_ALPHA1-6 : angle 2.25845 ( 3) link_BETA1-4 : bond 0.00394 ( 17) link_BETA1-4 : angle 1.48240 ( 51) link_BETA1-6 : bond 0.00355 ( 2) link_BETA1-6 : angle 1.45715 ( 6) link_NAG-ASN : bond 0.00328 ( 48) link_NAG-ASN : angle 2.22231 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 218 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 ASP cc_start: 0.8623 (m-30) cc_final: 0.8245 (t0) REVERT: A 698 SER cc_start: 0.9004 (t) cc_final: 0.8609 (p) REVERT: A 790 LYS cc_start: 0.8422 (mmpt) cc_final: 0.7993 (mttm) REVERT: A 990 GLU cc_start: 0.8823 (tt0) cc_final: 0.8244 (tm-30) REVERT: A 1050 MET cc_start: 0.7542 (ptt) cc_final: 0.6857 (ptt) REVERT: B 101 ILE cc_start: 0.9327 (pt) cc_final: 0.9042 (tp) REVERT: B 274 THR cc_start: 0.8722 (m) cc_final: 0.8412 (m) REVERT: B 1107 ARG cc_start: 0.7989 (ptp-170) cc_final: 0.7666 (ptp90) REVERT: C 508 TYR cc_start: 0.8401 (m-80) cc_final: 0.7457 (m-80) REVERT: C 1107 ARG cc_start: 0.8023 (mmt90) cc_final: 0.7727 (mmt90) REVERT: H 39 GLN cc_start: 0.6784 (pp30) cc_final: 0.6581 (pp30) REVERT: H 82 MET cc_start: 0.9300 (mtm) cc_final: 0.8112 (mpp) REVERT: H 86 ASP cc_start: 0.8022 (m-30) cc_final: 0.7484 (t70) REVERT: L 55 GLU cc_start: 0.8585 (tp30) cc_final: 0.8165 (tp30) REVERT: M 6 GLU cc_start: 0.5391 (pm20) cc_final: 0.5077 (pm20) REVERT: M 13 GLN cc_start: 0.6918 (tp40) cc_final: 0.6336 (tp40) REVERT: M 29 PHE cc_start: 0.5863 (t80) cc_final: 0.5567 (t80) REVERT: M 34 MET cc_start: 0.8041 (mmp) cc_final: 0.7171 (mmm) REVERT: M 36 TRP cc_start: 0.7796 (m100) cc_final: 0.7460 (m100) REVERT: M 79 TYR cc_start: 0.6831 (m-80) cc_final: 0.6570 (m-80) REVERT: N 4 MET cc_start: 0.4955 (ptm) cc_final: 0.4222 (ttp) REVERT: N 24 ARG cc_start: 0.8390 (mmm160) cc_final: 0.7673 (mmm-85) REVERT: N 37 GLN cc_start: 0.8814 (tt0) cc_final: 0.8203 (tt0) REVERT: N 39 LYS cc_start: 0.8091 (mmtm) cc_final: 0.7790 (mptt) REVERT: N 55 GLU cc_start: 0.8244 (tp30) cc_final: 0.8044 (tp30) REVERT: N 70 GLU cc_start: 0.9149 (OUTLIER) cc_final: 0.8724 (tp30) outliers start: 50 outliers final: 29 residues processed: 254 average time/residue: 0.1579 time to fit residues: 65.3140 Evaluate side-chains 225 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 195 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain N residue 106 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 275 optimal weight: 1.9990 chunk 219 optimal weight: 4.9990 chunk 181 optimal weight: 0.9990 chunk 221 optimal weight: 5.9990 chunk 258 optimal weight: 7.9990 chunk 186 optimal weight: 0.7980 chunk 189 optimal weight: 1.9990 chunk 159 optimal weight: 0.3980 chunk 234 optimal weight: 0.9990 chunk 281 optimal weight: 7.9990 chunk 225 optimal weight: 9.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 HIS H 100AHIS ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 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 = 0.3912 r_free = 0.3912 target = 0.113373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.079011 restraints weight = 61021.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.081642 restraints weight = 30108.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.083330 restraints weight = 19334.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.084326 restraints weight = 14581.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.085033 restraints weight = 12267.987| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 26666 Z= 0.119 Angle : 0.591 13.500 36481 Z= 0.295 Chirality : 0.046 0.550 4402 Planarity : 0.004 0.061 4573 Dihedral : 6.317 74.008 4961 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.21 % Allowed : 12.06 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.15), residues: 3251 helix: 1.57 (0.21), residues: 674 sheet: -0.05 (0.17), residues: 861 loop : -0.51 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 19 TYR 0.014 0.001 TYR B1138 PHE 0.018 0.001 PHE M 29 TRP 0.024 0.001 TRP H 36 HIS 0.010 0.001 HIS M 35 Details of bonding type rmsd covalent geometry : bond 0.00265 (26558) covalent geometry : angle 0.56549 (36196) SS BOND : bond 0.00290 ( 39) SS BOND : angle 1.61610 ( 78) hydrogen bonds : bond 0.03700 ( 1060) hydrogen bonds : angle 5.77615 ( 2841) link_ALPHA1-3 : bond 0.03178 ( 1) link_ALPHA1-3 : angle 8.29501 ( 3) link_ALPHA1-6 : bond 0.00389 ( 1) link_ALPHA1-6 : angle 2.22490 ( 3) link_BETA1-4 : bond 0.00440 ( 17) link_BETA1-4 : angle 1.39172 ( 51) link_BETA1-6 : bond 0.00420 ( 2) link_BETA1-6 : angle 1.50833 ( 6) link_NAG-ASN : bond 0.00351 ( 48) link_NAG-ASN : angle 2.11696 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 231 time to evaluate : 0.936 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 389 ASP cc_start: 0.8606 (m-30) cc_final: 0.8261 (t0) REVERT: A 698 SER cc_start: 0.8997 (t) cc_final: 0.8552 (p) REVERT: A 790 LYS cc_start: 0.8428 (mmpt) cc_final: 0.7921 (mttm) REVERT: A 1050 MET cc_start: 0.7478 (ptt) cc_final: 0.6716 (ptt) REVERT: B 101 ILE cc_start: 0.9292 (pt) cc_final: 0.9042 (tp) REVERT: B 110 LEU cc_start: 0.7139 (OUTLIER) cc_final: 0.6868 (mm) REVERT: B 274 THR cc_start: 0.8609 (m) cc_final: 0.8187 (m) REVERT: B 697 MET cc_start: 0.8499 (tmm) cc_final: 0.8289 (tmm) REVERT: B 1107 ARG cc_start: 0.7989 (ptp-170) cc_final: 0.7445 (ptp90) REVERT: C 508 TYR cc_start: 0.8462 (m-80) cc_final: 0.7548 (m-80) REVERT: C 697 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.7640 (ptm) REVERT: C 758 SER cc_start: 0.9201 (m) cc_final: 0.8990 (p) REVERT: C 764 ASN cc_start: 0.9036 (t0) cc_final: 0.8807 (m-40) REVERT: C 1010 GLN cc_start: 0.8825 (tp-100) cc_final: 0.8389 (tp-100) REVERT: C 1107 ARG cc_start: 0.8070 (mmt90) cc_final: 0.7819 (mmt90) REVERT: H 39 GLN cc_start: 0.7110 (pp30) cc_final: 0.6770 (pp30) REVERT: H 82 MET cc_start: 0.9247 (mtm) cc_final: 0.8094 (mpp) REVERT: H 86 ASP cc_start: 0.7823 (m-30) cc_final: 0.7339 (t70) REVERT: L 55 GLU cc_start: 0.8573 (tp30) cc_final: 0.8178 (tp30) REVERT: M 19 ARG cc_start: 0.8616 (tmm-80) cc_final: 0.8399 (tpp80) REVERT: M 34 MET cc_start: 0.7834 (mmp) cc_final: 0.7122 (mmm) REVERT: M 35 HIS cc_start: 0.8080 (m90) cc_final: 0.7596 (m170) REVERT: M 36 TRP cc_start: 0.7931 (m100) cc_final: 0.7590 (m100) REVERT: M 79 TYR cc_start: 0.6854 (m-80) cc_final: 0.6380 (m-80) REVERT: N 4 MET cc_start: 0.5114 (ptm) cc_final: 0.4314 (ttp) REVERT: N 24 ARG cc_start: 0.8370 (mmm160) cc_final: 0.7921 (mmm-85) REVERT: N 37 GLN cc_start: 0.8808 (tt0) cc_final: 0.8370 (tt0) REVERT: N 47 LEU cc_start: 0.8804 (mp) cc_final: 0.8431 (pp) REVERT: N 55 GLU cc_start: 0.8273 (tp30) cc_final: 0.8057 (tp30) REVERT: N 70 GLU cc_start: 0.9164 (OUTLIER) cc_final: 0.8633 (mm-30) outliers start: 32 outliers final: 23 residues processed: 254 average time/residue: 0.1606 time to fit residues: 65.9112 Evaluate side-chains 226 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 200 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 91 TYR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 70 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 139 optimal weight: 10.0000 chunk 142 optimal weight: 4.9990 chunk 157 optimal weight: 6.9990 chunk 245 optimal weight: 8.9990 chunk 178 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 304 optimal weight: 30.0000 chunk 169 optimal weight: 6.9990 chunk 259 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 153 optimal weight: 0.4980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN B1119 ASN ** C 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 100AHIS ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.108304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.074864 restraints weight = 63102.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.077641 restraints weight = 30295.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.079481 restraints weight = 18972.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.080656 restraints weight = 13963.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.081377 restraints weight = 11442.631| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26666 Z= 0.138 Angle : 0.599 13.386 36481 Z= 0.298 Chirality : 0.046 0.546 4402 Planarity : 0.004 0.060 4573 Dihedral : 6.172 77.507 4961 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.56 % Allowed : 12.63 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.15), residues: 3251 helix: 1.58 (0.21), residues: 676 sheet: -0.04 (0.17), residues: 878 loop : -0.50 (0.15), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 16 TYR 0.015 0.001 TYR A 421 PHE 0.021 0.001 PHE B1103 TRP 0.017 0.001 TRP H 36 HIS 0.007 0.001 HIS M 35 Details of bonding type rmsd covalent geometry : bond 0.00316 (26558) covalent geometry : angle 0.57350 (36196) SS BOND : bond 0.00336 ( 39) SS BOND : angle 1.65684 ( 78) hydrogen bonds : bond 0.03732 ( 1060) hydrogen bonds : angle 5.71520 ( 2841) link_ALPHA1-3 : bond 0.03048 ( 1) link_ALPHA1-3 : angle 8.21055 ( 3) link_ALPHA1-6 : bond 0.00384 ( 1) link_ALPHA1-6 : angle 2.17879 ( 3) link_BETA1-4 : bond 0.00387 ( 17) link_BETA1-4 : angle 1.38110 ( 51) link_BETA1-6 : bond 0.00394 ( 2) link_BETA1-6 : angle 1.42841 ( 6) link_NAG-ASN : bond 0.00330 ( 48) link_NAG-ASN : angle 2.09425 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 212 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 ASP cc_start: 0.8612 (m-30) cc_final: 0.8306 (t0) REVERT: A 698 SER cc_start: 0.9014 (t) cc_final: 0.8601 (p) REVERT: A 790 LYS cc_start: 0.8425 (mmpt) cc_final: 0.7901 (mttm) REVERT: A 990 GLU cc_start: 0.8826 (tt0) cc_final: 0.8271 (tm-30) REVERT: A 1050 MET cc_start: 0.7541 (ptt) cc_final: 0.6746 (ptt) REVERT: B 101 ILE cc_start: 0.9302 (pt) cc_final: 0.9076 (tp) REVERT: B 110 LEU cc_start: 0.7058 (OUTLIER) cc_final: 0.6791 (mm) REVERT: B 274 THR cc_start: 0.8576 (m) cc_final: 0.8270 (m) REVERT: C 508 TYR cc_start: 0.8477 (m-80) cc_final: 0.7599 (m-80) REVERT: C 764 ASN cc_start: 0.8951 (t0) cc_final: 0.8719 (m-40) REVERT: C 1107 ARG cc_start: 0.8086 (mmt90) cc_final: 0.7781 (mmt90) REVERT: H 82 MET cc_start: 0.9271 (mtm) cc_final: 0.8027 (mpp) REVERT: H 86 ASP cc_start: 0.7825 (m-30) cc_final: 0.7280 (t70) REVERT: L 32 TRP cc_start: 0.8278 (m100) cc_final: 0.8068 (m100) REVERT: L 55 GLU cc_start: 0.8589 (tp30) cc_final: 0.8127 (tp30) REVERT: L 78 LEU cc_start: 0.8537 (mm) cc_final: 0.7919 (tp) REVERT: M 34 MET cc_start: 0.7665 (mmp) cc_final: 0.6999 (mmm) REVERT: M 35 HIS cc_start: 0.8076 (m90) cc_final: 0.7855 (m170) REVERT: M 36 TRP cc_start: 0.7935 (m100) cc_final: 0.7668 (m100) REVERT: N 4 MET cc_start: 0.5182 (ptm) cc_final: 0.4352 (ttp) REVERT: N 18 ARG cc_start: 0.8305 (tpt90) cc_final: 0.7695 (tpt90) REVERT: N 24 ARG cc_start: 0.8265 (mmm160) cc_final: 0.7840 (mmm-85) REVERT: N 37 GLN cc_start: 0.8819 (tt0) cc_final: 0.8397 (tt0) REVERT: N 47 LEU cc_start: 0.8865 (mp) cc_final: 0.8488 (pp) REVERT: N 55 GLU cc_start: 0.8258 (tp30) cc_final: 0.7951 (tp30) REVERT: N 70 GLU cc_start: 0.9153 (OUTLIER) cc_final: 0.8530 (mm-30) outliers start: 41 outliers final: 29 residues processed: 243 average time/residue: 0.1628 time to fit residues: 64.2282 Evaluate side-chains 225 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 194 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 91 TYR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain N residue 106 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 207 optimal weight: 6.9990 chunk 231 optimal weight: 9.9990 chunk 308 optimal weight: 5.9990 chunk 179 optimal weight: 4.9990 chunk 148 optimal weight: 4.9990 chunk 54 optimal weight: 8.9990 chunk 203 optimal weight: 6.9990 chunk 153 optimal weight: 0.9990 chunk 326 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 chunk 93 optimal weight: 0.5980 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN B1119 ASN C 655 HIS ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN H 100AHIS ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.106339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.072761 restraints weight = 64106.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.075438 restraints weight = 31134.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.077214 restraints weight = 19733.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.078342 restraints weight = 14685.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.079104 restraints weight = 12115.462| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 26666 Z= 0.220 Angle : 0.671 12.841 36481 Z= 0.334 Chirality : 0.048 0.558 4402 Planarity : 0.005 0.061 4573 Dihedral : 6.339 82.627 4961 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.86 % Allowed : 12.75 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.15), residues: 3251 helix: 1.37 (0.20), residues: 661 sheet: -0.20 (0.17), residues: 888 loop : -0.59 (0.15), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG M 16 TYR 0.026 0.002 TYR A 904 PHE 0.024 0.002 PHE C1089 TRP 0.026 0.002 TRP C 104 HIS 0.007 0.001 HIS M 35 Details of bonding type rmsd covalent geometry : bond 0.00509 (26558) covalent geometry : angle 0.64727 (36196) SS BOND : bond 0.00374 ( 39) SS BOND : angle 1.77005 ( 78) hydrogen bonds : bond 0.04030 ( 1060) hydrogen bonds : angle 5.89356 ( 2841) link_ALPHA1-3 : bond 0.02959 ( 1) link_ALPHA1-3 : angle 7.90011 ( 3) link_ALPHA1-6 : bond 0.00400 ( 1) link_ALPHA1-6 : angle 2.10124 ( 3) link_BETA1-4 : bond 0.00364 ( 17) link_BETA1-4 : angle 1.44187 ( 51) link_BETA1-6 : bond 0.00357 ( 2) link_BETA1-6 : angle 1.28252 ( 6) link_NAG-ASN : bond 0.00309 ( 48) link_NAG-ASN : angle 2.21602 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 204 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ILE cc_start: 0.5426 (mt) cc_final: 0.5213 (mt) REVERT: A 312 ILE cc_start: 0.9445 (OUTLIER) cc_final: 0.9233 (pt) REVERT: A 389 ASP cc_start: 0.8594 (m-30) cc_final: 0.8269 (t0) REVERT: A 698 SER cc_start: 0.9036 (t) cc_final: 0.8649 (p) REVERT: A 790 LYS cc_start: 0.8358 (mmpt) cc_final: 0.7870 (mttm) REVERT: A 990 GLU cc_start: 0.8882 (tt0) cc_final: 0.8300 (tm-30) REVERT: B 274 THR cc_start: 0.8477 (m) cc_final: 0.8082 (m) REVERT: C 104 TRP cc_start: 0.7644 (m-90) cc_final: 0.7366 (m-90) REVERT: C 508 TYR cc_start: 0.8514 (m-80) cc_final: 0.7633 (m-80) REVERT: C 758 SER cc_start: 0.9286 (m) cc_final: 0.9073 (p) REVERT: C 1050 MET cc_start: 0.6777 (ptt) cc_final: 0.6554 (ptt) REVERT: H 34 MET cc_start: 0.8482 (tpp) cc_final: 0.8181 (tpp) REVERT: H 82 MET cc_start: 0.9233 (mtm) cc_final: 0.7904 (mpp) REVERT: H 86 ASP cc_start: 0.7864 (m-30) cc_final: 0.7291 (t70) REVERT: L 55 GLU cc_start: 0.8628 (tp30) cc_final: 0.8184 (tp30) REVERT: M 34 MET cc_start: 0.7790 (mmp) cc_final: 0.7245 (mmm) REVERT: M 36 TRP cc_start: 0.7964 (m100) cc_final: 0.7717 (m100) REVERT: N 4 MET cc_start: 0.5249 (ptm) cc_final: 0.4516 (ttp) REVERT: N 18 ARG cc_start: 0.8350 (tpt90) cc_final: 0.7738 (tpt90) REVERT: N 24 ARG cc_start: 0.8235 (mmm160) cc_final: 0.7755 (mmm-85) REVERT: N 47 LEU cc_start: 0.8818 (mp) cc_final: 0.8513 (pp) REVERT: N 50 GLU cc_start: 0.7996 (mp0) cc_final: 0.7770 (mp0) REVERT: N 55 GLU cc_start: 0.8267 (tp30) cc_final: 0.7943 (tp30) REVERT: N 70 GLU cc_start: 0.9171 (OUTLIER) cc_final: 0.8510 (mm-30) outliers start: 49 outliers final: 32 residues processed: 241 average time/residue: 0.1606 time to fit residues: 62.3374 Evaluate side-chains 227 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 193 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain N residue 106 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 226 optimal weight: 9.9990 chunk 277 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 192 optimal weight: 1.9990 chunk 253 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 223 optimal weight: 2.9990 chunk 326 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN H 3 GLN H 100AHIS ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 100 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.109279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.075498 restraints weight = 63136.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.078276 restraints weight = 30373.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.080088 restraints weight = 19181.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.081270 restraints weight = 14223.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.082013 restraints weight = 11713.469| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 26666 Z= 0.125 Angle : 0.628 16.280 36481 Z= 0.312 Chirality : 0.046 0.546 4402 Planarity : 0.004 0.065 4573 Dihedral : 6.068 88.053 4961 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.48 % Allowed : 13.32 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.15), residues: 3251 helix: 1.50 (0.21), residues: 680 sheet: -0.00 (0.17), residues: 857 loop : -0.54 (0.15), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG M 16 TYR 0.013 0.001 TYR B1067 PHE 0.030 0.001 PHE C 140 TRP 0.021 0.001 TRP C 104 HIS 0.006 0.001 HIS M 35 Details of bonding type rmsd covalent geometry : bond 0.00283 (26558) covalent geometry : angle 0.59813 (36196) SS BOND : bond 0.00289 ( 39) SS BOND : angle 2.50927 ( 78) hydrogen bonds : bond 0.03719 ( 1060) hydrogen bonds : angle 5.64873 ( 2841) link_ALPHA1-3 : bond 0.03001 ( 1) link_ALPHA1-3 : angle 7.95413 ( 3) link_ALPHA1-6 : bond 0.00582 ( 1) link_ALPHA1-6 : angle 2.09343 ( 3) link_BETA1-4 : bond 0.00453 ( 17) link_BETA1-4 : angle 1.37875 ( 51) link_BETA1-6 : bond 0.00438 ( 2) link_BETA1-6 : angle 1.42814 ( 6) link_NAG-ASN : bond 0.00351 ( 48) link_NAG-ASN : angle 2.08192 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 210 time to evaluate : 1.005 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 128 ILE cc_start: 0.5431 (mt) cc_final: 0.5224 (mt) REVERT: A 312 ILE cc_start: 0.9415 (OUTLIER) cc_final: 0.9207 (pt) REVERT: A 389 ASP cc_start: 0.8569 (m-30) cc_final: 0.8212 (t0) REVERT: A 698 SER cc_start: 0.8984 (t) cc_final: 0.8578 (p) REVERT: A 790 LYS cc_start: 0.8386 (mmpt) cc_final: 0.7890 (mttm) REVERT: A 1050 MET cc_start: 0.7313 (ptt) cc_final: 0.6564 (ptt) REVERT: B 110 LEU cc_start: 0.7051 (OUTLIER) cc_final: 0.6768 (mm) REVERT: B 274 THR cc_start: 0.8514 (m) cc_final: 0.8197 (m) REVERT: B 697 MET cc_start: 0.8493 (tmm) cc_final: 0.8293 (tmm) REVERT: C 104 TRP cc_start: 0.7646 (m-90) cc_final: 0.7359 (m-90) REVERT: C 508 TYR cc_start: 0.8508 (m-80) cc_final: 0.7614 (m-80) REVERT: C 758 SER cc_start: 0.9176 (m) cc_final: 0.8959 (p) REVERT: C 1050 MET cc_start: 0.6436 (ptt) cc_final: 0.6163 (ptt) REVERT: C 1107 ARG cc_start: 0.8081 (mmt90) cc_final: 0.7815 (mmt90) REVERT: H 39 GLN cc_start: 0.6747 (pp30) cc_final: 0.6477 (pp30) REVERT: H 82 MET cc_start: 0.9250 (mtm) cc_final: 0.8025 (mpp) REVERT: H 86 ASP cc_start: 0.7762 (m-30) cc_final: 0.7199 (t70) REVERT: L 55 GLU cc_start: 0.8653 (tp30) cc_final: 0.8247 (tp30) REVERT: M 34 MET cc_start: 0.7580 (mmp) cc_final: 0.7168 (mmm) REVERT: N 4 MET cc_start: 0.5030 (ptm) cc_final: 0.4344 (ttp) REVERT: N 18 ARG cc_start: 0.8335 (tpt90) cc_final: 0.7758 (tpt90) REVERT: N 24 ARG cc_start: 0.8169 (mmm160) cc_final: 0.7774 (mmm-85) REVERT: N 37 GLN cc_start: 0.8871 (tt0) cc_final: 0.8398 (tt0) REVERT: N 47 LEU cc_start: 0.8859 (mp) cc_final: 0.8463 (pp) REVERT: N 55 GLU cc_start: 0.8264 (tp30) cc_final: 0.7946 (tp30) REVERT: N 70 GLU cc_start: 0.9172 (OUTLIER) cc_final: 0.8464 (mm-30) outliers start: 39 outliers final: 31 residues processed: 234 average time/residue: 0.1757 time to fit residues: 65.9899 Evaluate side-chains 223 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 189 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain N residue 100 GLN Chi-restraints excluded: chain N residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 321 optimal weight: 9.9990 chunk 261 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 275 optimal weight: 3.9990 chunk 222 optimal weight: 10.0000 chunk 273 optimal weight: 0.9990 chunk 249 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 266 optimal weight: 8.9990 chunk 286 optimal weight: 7.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN H 100AHIS ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 76 ASN M 81 GLN ** N 100 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 = 0.3863 r_free = 0.3863 target = 0.108134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.074354 restraints weight = 63341.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.077052 restraints weight = 30846.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.078839 restraints weight = 19589.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.079978 restraints weight = 14588.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.080642 restraints weight = 12044.986| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 26666 Z= 0.183 Angle : 0.653 15.527 36481 Z= 0.325 Chirality : 0.047 0.537 4402 Planarity : 0.004 0.063 4573 Dihedral : 6.116 92.233 4961 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.44 % Allowed : 13.85 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.15), residues: 3251 helix: 1.49 (0.20), residues: 674 sheet: -0.05 (0.17), residues: 873 loop : -0.57 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG M 16 TYR 0.019 0.002 TYR B1138 PHE 0.024 0.002 PHE C 140 TRP 0.071 0.002 TRP H 36 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00424 (26558) covalent geometry : angle 0.62507 (36196) SS BOND : bond 0.00328 ( 39) SS BOND : angle 2.38930 ( 78) hydrogen bonds : bond 0.03845 ( 1060) hydrogen bonds : angle 5.72148 ( 2841) link_ALPHA1-3 : bond 0.02777 ( 1) link_ALPHA1-3 : angle 7.81242 ( 3) link_ALPHA1-6 : bond 0.00517 ( 1) link_ALPHA1-6 : angle 2.03633 ( 3) link_BETA1-4 : bond 0.00389 ( 17) link_BETA1-4 : angle 1.40384 ( 51) link_BETA1-6 : bond 0.00369 ( 2) link_BETA1-6 : angle 1.31867 ( 6) link_NAG-ASN : bond 0.00340 ( 48) link_NAG-ASN : angle 2.17068 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6502 Ramachandran restraints generated. 3251 Oldfield, 0 Emsley, 3251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 196 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ILE cc_start: 0.5473 (mt) cc_final: 0.5267 (mt) REVERT: A 312 ILE cc_start: 0.9435 (OUTLIER) cc_final: 0.9212 (pt) REVERT: A 389 ASP cc_start: 0.8564 (m-30) cc_final: 0.8221 (t0) REVERT: A 698 SER cc_start: 0.9006 (t) cc_final: 0.8603 (p) REVERT: A 790 LYS cc_start: 0.8392 (mmpt) cc_final: 0.7894 (mttm) REVERT: A 943 SER cc_start: 0.7548 (p) cc_final: 0.7330 (t) REVERT: A 990 GLU cc_start: 0.8855 (tt0) cc_final: 0.8268 (tm-30) REVERT: A 1050 MET cc_start: 0.7423 (ptt) cc_final: 0.6571 (ptt) REVERT: B 274 THR cc_start: 0.8553 (m) cc_final: 0.8243 (m) REVERT: B 697 MET cc_start: 0.8481 (tmm) cc_final: 0.8268 (tmm) REVERT: C 104 TRP cc_start: 0.7695 (m-90) cc_final: 0.7370 (m-90) REVERT: C 758 SER cc_start: 0.9238 (m) cc_final: 0.9009 (p) REVERT: C 1050 MET cc_start: 0.6640 (ptt) cc_final: 0.6421 (ptt) REVERT: C 1107 ARG cc_start: 0.8063 (mmt90) cc_final: 0.7744 (mmt90) REVERT: H 18 LEU cc_start: 0.8282 (tp) cc_final: 0.7854 (tt) REVERT: H 39 GLN cc_start: 0.6720 (pp30) cc_final: 0.6475 (pp30) REVERT: H 82 MET cc_start: 0.9275 (mtm) cc_final: 0.7968 (mpp) REVERT: H 86 ASP cc_start: 0.7787 (m-30) cc_final: 0.7196 (t70) REVERT: L 55 GLU cc_start: 0.8680 (tp30) cc_final: 0.8275 (tp30) REVERT: M 34 MET cc_start: 0.7293 (mmp) cc_final: 0.6447 (mmm) REVERT: M 36 TRP cc_start: 0.7630 (m100) cc_final: 0.7427 (m100) REVERT: M 83 ARG cc_start: 0.8802 (mpp80) cc_final: 0.8549 (mpp80) REVERT: N 4 MET cc_start: 0.5145 (ptm) cc_final: 0.4430 (ttp) REVERT: N 18 ARG cc_start: 0.8346 (tpt90) cc_final: 0.7763 (tpt90) REVERT: N 24 ARG cc_start: 0.8107 (mmm160) cc_final: 0.7663 (mmm-85) REVERT: N 37 GLN cc_start: 0.8855 (tt0) cc_final: 0.8377 (tt0) REVERT: N 47 LEU cc_start: 0.8835 (mp) cc_final: 0.8467 (pp) REVERT: N 55 GLU cc_start: 0.8198 (tp30) cc_final: 0.7892 (tp30) REVERT: N 70 GLU cc_start: 0.9185 (OUTLIER) cc_final: 0.8513 (mm-30) outliers start: 38 outliers final: 30 residues processed: 222 average time/residue: 0.1643 time to fit residues: 58.8423 Evaluate side-chains 222 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 190 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain N residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 294 optimal weight: 20.0000 chunk 174 optimal weight: 0.7980 chunk 138 optimal weight: 0.1980 chunk 279 optimal weight: 2.9990 chunk 301 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 127 optimal weight: 9.9990 chunk 295 optimal weight: 5.9990 chunk 235 optimal weight: 9.9990 chunk 113 optimal weight: 9.9990 chunk 218 optimal weight: 9.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN H 100AHIS ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.107316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.073715 restraints weight = 63506.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.076411 restraints weight = 30868.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.078193 restraints weight = 19555.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.079330 restraints weight = 14533.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.080051 restraints weight = 12020.206| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 26666 Z= 0.180 Angle : 0.643 14.229 36481 Z= 0.319 Chirality : 0.047 0.533 4402 Planarity : 0.004 0.062 4573 Dihedral : 6.178 98.696 4961 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.33 % Allowed : 14.15 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.15), residues: 3251 helix: 1.48 (0.21), residues: 673 sheet: -0.03 (0.17), residues: 850 loop : -0.62 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 16 TYR 0.019 0.001 TYR A 904 PHE 0.020 0.002 PHE C1089 TRP 0.053 0.002 TRP H 36 HIS 0.014 0.001 HIS M 35 Details of bonding type rmsd covalent geometry : bond 0.00417 (26558) covalent geometry : angle 0.61378 (36196) SS BOND : bond 0.00319 ( 39) SS BOND : angle 2.24495 ( 78) hydrogen bonds : bond 0.03845 ( 1060) hydrogen bonds : angle 5.72242 ( 2841) link_ALPHA1-3 : bond 0.02597 ( 1) link_ALPHA1-3 : angle 7.71248 ( 3) link_ALPHA1-6 : bond 0.00568 ( 1) link_ALPHA1-6 : angle 1.97877 ( 3) link_BETA1-4 : bond 0.00380 ( 17) link_BETA1-4 : angle 1.38226 ( 51) link_BETA1-6 : bond 0.00379 ( 2) link_BETA1-6 : angle 1.31221 ( 6) link_NAG-ASN : bond 0.00277 ( 48) link_NAG-ASN : angle 2.28010 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5445.41 seconds wall clock time: 94 minutes 22.26 seconds (5662.26 seconds total)