Starting phenix.real_space_refine on Fri Mar 6 00:30:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xix_33211/03_2026/7xix_33211.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xix_33211/03_2026/7xix_33211.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xix_33211/03_2026/7xix_33211.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xix_33211/03_2026/7xix_33211.map" model { file = "/net/cci-nas-00/data/ceres_data/7xix_33211/03_2026/7xix_33211.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xix_33211/03_2026/7xix_33211.cif" } resolution = 3.25 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= -0.001 sd= 0.095 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 114 5.16 5 C 16935 2.51 5 N 4338 2.21 5 O 5199 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 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: 26586 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1095, 8554 Classifications: {'peptide': 1095} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 58, 'TRANS': 1036} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 8554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1095, 8554 Classifications: {'peptide': 1095} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 58, 'TRANS': 1036} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 8554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1095, 8554 Classifications: {'peptide': 1095} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 58, 'TRANS': 1036} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 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: "H" 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 6.24, per 1000 atoms: 0.23 Number of scatterers: 26586 At special positions: 0 Unit cell: (157.29, 144.45, 182.97, 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 114 16.00 O 5199 8.00 N 4338 7.00 C 16935 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 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 480 " - pdb=" SG CYS A 488 " 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=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 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 480 " - pdb=" SG CYS B 488 " 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=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 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 480 " - pdb=" SG CYS C 488 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 234 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 343 " " NAG A1304 " - " ASN A 61 " " NAG A1305 " - " ASN A 122 " " NAG A1306 " - " ASN A 165 " " NAG A1307 " - " ASN A 282 " " NAG A1308 " - " ASN A 603 " " NAG A1309 " - " ASN A 657 " " NAG A1310 " - " ASN A1074 " " NAG B1301 " - " ASN B 234 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 343 " " NAG B1304 " - " ASN B 61 " " NAG B1305 " - " ASN B 122 " " NAG B1306 " - " ASN B 165 " " NAG B1307 " - " ASN B 282 " " NAG B1308 " - " ASN B 603 " " NAG B1309 " - " ASN B 657 " " NAG B1310 " - " ASN B1074 " " NAG C1301 " - " ASN C 234 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 343 " " NAG C1304 " - " ASN C 61 " " NAG C1305 " - " ASN C 122 " " NAG C1306 " - " ASN C 165 " " NAG C1307 " - " ASN C 282 " " NAG C1308 " - " ASN C 603 " " NAG C1309 " - " ASN C 657 " " NAG C1310 " - " ASN C1074 " " NAG D 1 " - " ASN A 616 " " NAG E 1 " - " ASN A 709 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG H 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN B 616 " " NAG K 1 " - " ASN B 709 " " NAG L 1 " - " ASN B 717 " " NAG M 1 " - " ASN B 801 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN B1134 " " NAG P 1 " - " ASN C 616 " " NAG Q 1 " - " ASN C 709 " " NAG R 1 " - " ASN C 717 " " NAG S 1 " - " ASN C 801 " " NAG T 1 " - " ASN C1098 " " NAG U 1 " - " ASN C1134 " Time building additional restraints: 2.17 Conformation dependent library (CDL) restraints added in 1.4 seconds 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6144 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 50 sheets defined 23.7% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 4.432A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.694A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.124A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.741A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 624 removed outlier: 4.047A pdb=" N VAL A 622 " --> pdb=" O THR A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 747 through 756 Processing helix chain 'A' and resid 758 through 782 removed outlier: 3.738A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG A 765 " --> pdb=" O THR A 761 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR A 768 " --> pdb=" O LYS A 764 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU A 780 " --> pdb=" O LYS A 776 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.792A pdb=" N TYR A 873 " --> pdb=" O MET A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.528A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 932 Processing helix chain 'A' and resid 933 through 941 Processing helix chain 'A' and resid 946 through 965 removed outlier: 3.755A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA A 956 " --> pdb=" O VAL A 952 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN A 957 " --> pdb=" O ASN A 953 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA A 958 " --> pdb=" O HIS A 954 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 993 removed outlier: 4.220A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1033 removed outlier: 3.686A pdb=" N THR A 998 " --> pdb=" O ASP A 994 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLY A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR A1006 " --> pdb=" O GLN A1002 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL A1008 " --> pdb=" O LEU A1004 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER A1021 " --> pdb=" O GLU A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1148 removed outlier: 4.063A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE A1148 " --> pdb=" O GLU A1144 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.430A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 367 through 372 removed outlier: 3.975A pdb=" N ALA B 372 " --> pdb=" O TYR B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 3.688A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.085A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.716A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 624 removed outlier: 4.146A pdb=" N VAL B 622 " --> pdb=" O THR B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 747 through 756 Processing helix chain 'B' and resid 758 through 782 removed outlier: 3.732A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG B 765 " --> pdb=" O THR B 761 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR B 768 " --> pdb=" O LYS B 764 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU B 780 " --> pdb=" O LYS B 776 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.893A pdb=" N TYR B 873 " --> pdb=" O MET B 869 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.595A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 932 Processing helix chain 'B' and resid 933 through 941 Processing helix chain 'B' and resid 946 through 965 removed outlier: 3.756A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA B 956 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN B 957 " --> pdb=" O ASN B 953 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA B 958 " --> pdb=" O HIS B 954 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 993 removed outlier: 4.243A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 1032 removed outlier: 3.668A pdb=" N THR B 998 " --> pdb=" O ASP B 994 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR B1006 " --> pdb=" O GLN B1002 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL B1008 " --> pdb=" O LEU B1004 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE B1013 " --> pdb=" O THR B1009 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA B1016 " --> pdb=" O LEU B1012 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1148 removed outlier: 3.999A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE B1148 " --> pdb=" O GLU B1144 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.449A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.673A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.110A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.688A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 624 removed outlier: 4.050A pdb=" N VAL C 622 " --> pdb=" O THR C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 747 through 756 Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.762A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG C 765 " --> pdb=" O THR C 761 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU C 767 " --> pdb=" O LEU C 763 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR C 768 " --> pdb=" O LYS C 764 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU C 780 " --> pdb=" O LYS C 776 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.876A pdb=" N TYR C 873 " --> pdb=" O MET C 869 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.614A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 932 Processing helix chain 'C' and resid 933 through 941 Processing helix chain 'C' and resid 946 through 965 removed outlier: 3.738A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA C 956 " --> pdb=" O VAL C 952 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN C 957 " --> pdb=" O ASN C 953 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA C 958 " --> pdb=" O HIS C 954 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU C 959 " --> pdb=" O ASN C 955 " (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 Processing helix chain 'C' and resid 985 through 993 removed outlier: 4.177A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 1032 removed outlier: 3.586A pdb=" N THR C 998 " --> pdb=" O ASP C 994 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR C1006 " --> pdb=" O GLN C1002 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL C1008 " --> pdb=" O LEU C1004 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE C1013 " --> pdb=" O THR C1009 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER C1021 " --> pdb=" O GLU C1017 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1148 removed outlier: 4.012A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE C1148 " --> pdb=" O GLU C1144 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 31 removed outlier: 3.823A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.684A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.738A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 126 through 127 removed outlier: 3.518A pdb=" N ILE A 119 " --> pdb=" O TRP A 104 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 129 through 130 removed outlier: 3.780A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.427A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.203A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (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 473 through 474 removed outlier: 3.535A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 542 through 543 removed outlier: 3.591A pdb=" N PHE A 543 " --> pdb=" O LEU A 546 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 551 through 554 removed outlier: 7.275A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.921A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.592A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.091A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.602A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.532A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.951A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC2, first strand: chain 'B' and resid 26 through 31 removed outlier: 3.770A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.738A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 126 through 127 removed outlier: 3.513A pdb=" N ILE B 119 " --> pdb=" O TRP B 104 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.407A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.187A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.537A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 542 through 543 removed outlier: 3.605A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 551 through 554 removed outlier: 7.297A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.939A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.772A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AD5, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.898A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.601A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.919A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD9, first strand: chain 'C' and resid 26 through 31 removed outlier: 3.762A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.732A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 126 through 127 removed outlier: 3.534A pdb=" N ILE C 119 " --> pdb=" O TRP C 104 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.462A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.179A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.535A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 542 through 543 removed outlier: 3.593A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.935A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AF2, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.086A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.563A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.881A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 1094 through 1097 805 hydrogen bonds defined for protein. 2145 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: 5.90 Time building geometry restraints manager: 2.92 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: 8403 1.34 - 1.46: 6446 1.46 - 1.58: 12223 1.58 - 1.70: 0 1.70 - 1.82: 144 Bond restraints: 27216 Sorted by residual: bond pdb=" C1 NAG K 1 " pdb=" O5 NAG K 1 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.00e+00 bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.77e+00 bond pdb=" C1 NAG Q 1 " pdb=" O5 NAG Q 1 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.75e+00 bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.73e+00 bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.73e+00 ... (remaining 27211 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 35859 1.54 - 3.07: 1065 3.07 - 4.61: 100 4.61 - 6.15: 31 6.15 - 7.68: 10 Bond angle restraints: 37065 Sorted by residual: angle pdb=" N VAL A1128 " pdb=" CA VAL A1128 " pdb=" C VAL A1128 " ideal model delta sigma weight residual 113.71 109.38 4.33 9.50e-01 1.11e+00 2.07e+01 angle pdb=" N GLY B 757 " pdb=" CA GLY B 757 " pdb=" C GLY B 757 " ideal model delta sigma weight residual 111.56 115.95 -4.39 1.01e+00 9.80e-01 1.89e+01 angle pdb=" CA PRO B 987 " pdb=" N PRO B 987 " pdb=" CD PRO B 987 " ideal model delta sigma weight residual 112.00 107.56 4.44 1.40e+00 5.10e-01 1.00e+01 angle pdb=" C GLY A 744 " pdb=" N ASP A 745 " pdb=" CA ASP A 745 " ideal model delta sigma weight residual 122.08 126.45 -4.37 1.47e+00 4.63e-01 8.85e+00 angle pdb=" C GLY C 744 " pdb=" N ASP C 745 " pdb=" CA ASP C 745 " ideal model delta sigma weight residual 122.08 126.40 -4.32 1.47e+00 4.63e-01 8.63e+00 ... (remaining 37060 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.25: 15902 23.25 - 46.49: 936 46.49 - 69.74: 94 69.74 - 92.98: 48 92.98 - 116.23: 45 Dihedral angle restraints: 17025 sinusoidal: 7458 harmonic: 9567 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -136.38 50.38 1 1.00e+01 1.00e-02 3.48e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -135.15 49.15 1 1.00e+01 1.00e-02 3.32e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -134.79 48.79 1 1.00e+01 1.00e-02 3.27e+01 ... (remaining 17022 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 3947 0.086 - 0.173: 403 0.173 - 0.259: 8 0.259 - 0.346: 4 0.346 - 0.432: 3 Chirality restraints: 4365 Sorted by residual: chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN B1134 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.67e+00 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A1134 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.67e+00 chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN C1134 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.63e+00 ... (remaining 4362 not shown) Planarity restraints: 4767 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 986 " 0.056 5.00e-02 4.00e+02 8.37e-02 1.12e+01 pdb=" N PRO B 987 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO B 987 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 987 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 560 " -0.051 5.00e-02 4.00e+02 7.68e-02 9.44e+00 pdb=" N PRO B 561 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO B 561 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 561 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 224 " -0.047 5.00e-02 4.00e+02 7.22e-02 8.35e+00 pdb=" N PRO A 225 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 225 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 225 " -0.040 5.00e-02 4.00e+02 ... (remaining 4764 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1736 2.74 - 3.28: 25195 3.28 - 3.82: 39538 3.82 - 4.36: 47813 4.36 - 4.90: 85934 Nonbonded interactions: 200216 Sorted by model distance: nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.195 3.040 nonbonded pdb=" O ALA A 67 " pdb=" OG1 THR A 250 " model vdw 2.237 3.040 nonbonded pdb=" O ALA B 67 " pdb=" OG1 THR B 250 " model vdw 2.252 3.040 nonbonded pdb=" O ALA C 67 " pdb=" OG1 THR C 250 " model vdw 2.253 3.040 nonbonded pdb=" NZ LYS B 386 " pdb=" O LEU C 984 " model vdw 2.256 3.120 ... (remaining 200211 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.990 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: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 25.450 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 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 : 0.004 0.051 27318 Z= 0.186 Angle : 0.646 10.273 37335 Z= 0.319 Chirality : 0.049 0.432 4365 Planarity : 0.005 0.084 4719 Dihedral : 15.679 116.227 10773 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.14), residues: 3267 helix: 0.40 (0.22), residues: 630 sheet: 0.01 (0.19), residues: 699 loop : -1.71 (0.13), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 905 TYR 0.017 0.001 TYR C 204 PHE 0.022 0.001 PHE B 906 TRP 0.015 0.001 TRP A 886 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00405 (27216) covalent geometry : angle 0.61378 (37065) SS BOND : bond 0.00135 ( 36) SS BOND : angle 1.23873 ( 72) hydrogen bonds : bond 0.13056 ( 805) hydrogen bonds : angle 5.31872 ( 2145) link_BETA1-4 : bond 0.00422 ( 18) link_BETA1-4 : angle 1.58000 ( 54) link_NAG-ASN : bond 0.00608 ( 48) link_NAG-ASN : angle 3.10488 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7470 (tm-30) cc_final: 0.7237 (tm-30) REVERT: A 332 ILE cc_start: 0.7465 (mm) cc_final: 0.7203 (mt) REVERT: A 739 THR cc_start: 0.7942 (m) cc_final: 0.7721 (p) REVERT: A 1002 GLN cc_start: 0.7743 (tt0) cc_final: 0.7504 (tt0) REVERT: B 332 ILE cc_start: 0.7591 (mm) cc_final: 0.7327 (mt) REVERT: B 1128 VAL cc_start: 0.8512 (t) cc_final: 0.8286 (p) REVERT: C 332 ILE cc_start: 0.7546 (mm) cc_final: 0.7332 (mt) outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 0.1546 time to fit residues: 70.4356 Evaluate side-chains 221 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 0.0470 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.0050 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 0.7980 overall best weight: 0.5694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A 935 GLN A 957 GLN B 804 GLN B 935 GLN B 957 GLN B1005 GLN B1088 HIS C 804 GLN ** C 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN C 955 ASN C 957 GLN C1002 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.168906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.132219 restraints weight = 32726.640| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.75 r_work: 0.3158 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.0691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 27318 Z= 0.104 Angle : 0.591 12.553 37335 Z= 0.285 Chirality : 0.047 0.318 4365 Planarity : 0.004 0.060 4719 Dihedral : 10.992 107.274 4914 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.35 % Allowed : 6.34 % Favored : 93.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.14), residues: 3267 helix: 0.78 (0.22), residues: 636 sheet: 0.05 (0.19), residues: 711 loop : -1.63 (0.13), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 190 TYR 0.018 0.001 TYR C 170 PHE 0.032 0.001 PHE A 133 TRP 0.008 0.001 TRP C 886 HIS 0.002 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00233 (27216) covalent geometry : angle 0.56076 (37065) SS BOND : bond 0.00172 ( 36) SS BOND : angle 0.94242 ( 72) hydrogen bonds : bond 0.03636 ( 805) hydrogen bonds : angle 4.70022 ( 2145) link_BETA1-4 : bond 0.00405 ( 18) link_BETA1-4 : angle 1.67500 ( 54) link_NAG-ASN : bond 0.00583 ( 48) link_NAG-ASN : angle 2.85108 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 243 time to evaluate : 0.887 Fit side-chains REVERT: A 52 GLN cc_start: 0.7751 (tm-30) cc_final: 0.7482 (tm-30) REVERT: A 332 ILE cc_start: 0.7339 (mm) cc_final: 0.7034 (mt) REVERT: A 386 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8069 (mttt) REVERT: A 739 THR cc_start: 0.8308 (m) cc_final: 0.8047 (p) REVERT: A 1002 GLN cc_start: 0.8556 (tt0) cc_final: 0.8208 (tt0) REVERT: A 1029 MET cc_start: 0.8994 (tpp) cc_final: 0.8595 (tpp) REVERT: B 88 ASP cc_start: 0.8136 (m-30) cc_final: 0.7775 (p0) REVERT: B 170 TYR cc_start: 0.7605 (t80) cc_final: 0.7364 (t80) REVERT: B 190 ARG cc_start: 0.8101 (mtt-85) cc_final: 0.7893 (mtt-85) REVERT: B 332 ILE cc_start: 0.7473 (mm) cc_final: 0.7206 (mt) REVERT: B 755 GLN cc_start: 0.8627 (tt0) cc_final: 0.8396 (tt0) REVERT: B 1128 VAL cc_start: 0.8591 (t) cc_final: 0.8346 (p) REVERT: C 332 ILE cc_start: 0.7438 (mm) cc_final: 0.7172 (mt) outliers start: 10 outliers final: 8 residues processed: 248 average time/residue: 0.1556 time to fit residues: 63.1747 Evaluate side-chains 229 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 220 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 1125 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 138 optimal weight: 6.9990 chunk 289 optimal weight: 6.9990 chunk 199 optimal weight: 0.5980 chunk 110 optimal weight: 5.9990 chunk 104 optimal weight: 0.2980 chunk 310 optimal weight: 1.9990 chunk 274 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 209 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 80 optimal weight: 0.0000 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS ** C 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.168737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.131746 restraints weight = 32875.852| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.73 r_work: 0.3149 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.0907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 27318 Z= 0.103 Angle : 0.579 11.905 37335 Z= 0.276 Chirality : 0.046 0.304 4365 Planarity : 0.004 0.059 4719 Dihedral : 9.966 102.644 4914 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.91 % Allowed : 8.30 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.14), residues: 3267 helix: 0.81 (0.22), residues: 639 sheet: 0.07 (0.19), residues: 711 loop : -1.60 (0.13), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 995 TYR 0.018 0.001 TYR B 91 PHE 0.016 0.001 PHE B 65 TRP 0.009 0.001 TRP C 886 HIS 0.002 0.000 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00238 (27216) covalent geometry : angle 0.54684 (37065) SS BOND : bond 0.00135 ( 36) SS BOND : angle 0.88428 ( 72) hydrogen bonds : bond 0.03448 ( 805) hydrogen bonds : angle 4.52650 ( 2145) link_BETA1-4 : bond 0.00342 ( 18) link_BETA1-4 : angle 2.03307 ( 54) link_NAG-ASN : bond 0.00556 ( 48) link_NAG-ASN : angle 2.80753 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 241 time to evaluate : 0.747 Fit side-chains REVERT: A 52 GLN cc_start: 0.7767 (tm-30) cc_final: 0.7415 (tm-30) REVERT: A 332 ILE cc_start: 0.7336 (mm) cc_final: 0.7028 (mt) REVERT: A 386 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8040 (ptpp) REVERT: A 739 THR cc_start: 0.8212 (m) cc_final: 0.7926 (p) REVERT: A 1002 GLN cc_start: 0.8542 (tt0) cc_final: 0.8194 (tt0) REVERT: A 1029 MET cc_start: 0.8979 (tpp) cc_final: 0.8609 (tpp) REVERT: A 1146 ASP cc_start: 0.6334 (m-30) cc_final: 0.5966 (t0) REVERT: B 88 ASP cc_start: 0.8125 (m-30) cc_final: 0.7854 (p0) REVERT: B 190 ARG cc_start: 0.8256 (mtt-85) cc_final: 0.7952 (mtt-85) REVERT: B 332 ILE cc_start: 0.7467 (mm) cc_final: 0.7202 (mt) REVERT: B 755 GLN cc_start: 0.8575 (tt0) cc_final: 0.8301 (tt0) REVERT: B 1128 VAL cc_start: 0.8487 (t) cc_final: 0.8224 (p) REVERT: C 332 ILE cc_start: 0.7436 (mm) cc_final: 0.7164 (mt) outliers start: 26 outliers final: 18 residues processed: 255 average time/residue: 0.1633 time to fit residues: 67.8472 Evaluate side-chains 249 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 230 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1125 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 219 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 214 optimal weight: 0.0870 chunk 112 optimal weight: 2.9990 chunk 238 optimal weight: 5.9990 chunk 294 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 13 optimal weight: 0.4980 chunk 217 optimal weight: 3.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 ASN A 853 GLN B 675 GLN ** C 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.167941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.133055 restraints weight = 32681.385| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.69 r_work: 0.3167 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 27318 Z= 0.100 Angle : 0.580 11.344 37335 Z= 0.273 Chirality : 0.046 0.312 4365 Planarity : 0.004 0.060 4719 Dihedral : 8.374 87.829 4914 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.30 % Allowed : 9.66 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.14), residues: 3267 helix: 0.89 (0.22), residues: 651 sheet: 0.07 (0.19), residues: 717 loop : -1.59 (0.13), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 190 TYR 0.015 0.001 TYR B1067 PHE 0.014 0.001 PHE A 318 TRP 0.009 0.001 TRP C 886 HIS 0.002 0.000 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00229 (27216) covalent geometry : angle 0.54167 (37065) SS BOND : bond 0.00137 ( 36) SS BOND : angle 0.90720 ( 72) hydrogen bonds : bond 0.03212 ( 805) hydrogen bonds : angle 4.40374 ( 2145) link_BETA1-4 : bond 0.00350 ( 18) link_BETA1-4 : angle 2.38905 ( 54) link_NAG-ASN : bond 0.00556 ( 48) link_NAG-ASN : angle 3.02078 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 247 time to evaluate : 1.012 Fit side-chains REVERT: A 52 GLN cc_start: 0.7687 (tm-30) cc_final: 0.7285 (tm-30) REVERT: A 332 ILE cc_start: 0.7327 (mm) cc_final: 0.7016 (mt) REVERT: A 386 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.7982 (ptpp) REVERT: A 489 TYR cc_start: 0.7771 (m-10) cc_final: 0.7555 (m-10) REVERT: A 739 THR cc_start: 0.8210 (m) cc_final: 0.7905 (p) REVERT: A 1002 GLN cc_start: 0.8552 (tt0) cc_final: 0.8209 (tt0) REVERT: A 1146 ASP cc_start: 0.6466 (m-30) cc_final: 0.6048 (t0) REVERT: B 52 GLN cc_start: 0.7661 (tm-30) cc_final: 0.7388 (tm-30) REVERT: B 88 ASP cc_start: 0.8144 (m-30) cc_final: 0.7825 (p0) REVERT: B 332 ILE cc_start: 0.7452 (mm) cc_final: 0.7178 (mt) REVERT: B 1128 VAL cc_start: 0.8493 (t) cc_final: 0.8231 (p) REVERT: C 190 ARG cc_start: 0.8087 (mtt-85) cc_final: 0.7879 (mtp180) REVERT: C 332 ILE cc_start: 0.7430 (mm) cc_final: 0.7152 (mt) REVERT: C 592 PHE cc_start: 0.8240 (p90) cc_final: 0.7935 (p90) outliers start: 37 outliers final: 21 residues processed: 269 average time/residue: 0.1540 time to fit residues: 68.7161 Evaluate side-chains 258 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 236 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 1125 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 87 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 264 optimal weight: 0.7980 chunk 257 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 chunk 88 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 235 optimal weight: 0.9980 chunk 160 optimal weight: 3.9990 chunk 322 optimal weight: 0.9990 chunk 166 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN A 853 GLN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 804 GLN B 935 GLN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.167153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.133954 restraints weight = 32741.632| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.67 r_work: 0.3157 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27318 Z= 0.110 Angle : 0.573 11.363 37335 Z= 0.274 Chirality : 0.046 0.313 4365 Planarity : 0.004 0.060 4719 Dihedral : 7.714 74.698 4914 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.40 % Allowed : 10.89 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.14), residues: 3267 helix: 0.87 (0.22), residues: 651 sheet: 0.07 (0.19), residues: 714 loop : -1.61 (0.13), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 190 TYR 0.016 0.001 TYR B1067 PHE 0.015 0.001 PHE C 377 TRP 0.008 0.001 TRP C 886 HIS 0.002 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00260 (27216) covalent geometry : angle 0.52978 (37065) SS BOND : bond 0.00323 ( 36) SS BOND : angle 1.11050 ( 72) hydrogen bonds : bond 0.03384 ( 805) hydrogen bonds : angle 4.39368 ( 2145) link_BETA1-4 : bond 0.00354 ( 18) link_BETA1-4 : angle 2.33644 ( 54) link_NAG-ASN : bond 0.00584 ( 48) link_NAG-ASN : angle 3.21888 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 239 time to evaluate : 0.891 Fit side-chains REVERT: A 52 GLN cc_start: 0.7707 (tm-30) cc_final: 0.7297 (tm-30) REVERT: A 332 ILE cc_start: 0.7322 (mm) cc_final: 0.7013 (mt) REVERT: A 386 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.7992 (ptpp) REVERT: A 739 THR cc_start: 0.8224 (m) cc_final: 0.7938 (p) REVERT: A 1002 GLN cc_start: 0.8562 (tt0) cc_final: 0.8214 (tt0) REVERT: A 1146 ASP cc_start: 0.6484 (m-30) cc_final: 0.6019 (t0) REVERT: B 88 ASP cc_start: 0.8170 (m-30) cc_final: 0.7890 (p0) REVERT: B 332 ILE cc_start: 0.7447 (mm) cc_final: 0.7170 (mt) REVERT: B 1128 VAL cc_start: 0.8516 (t) cc_final: 0.8259 (p) REVERT: C 52 GLN cc_start: 0.7773 (tm-30) cc_final: 0.7372 (tm-30) REVERT: C 190 ARG cc_start: 0.8166 (mtt-85) cc_final: 0.7792 (mtp180) REVERT: C 332 ILE cc_start: 0.7446 (mm) cc_final: 0.7165 (mt) REVERT: C 592 PHE cc_start: 0.8204 (p90) cc_final: 0.7908 (p90) REVERT: C 619 GLU cc_start: 0.7606 (mp0) cc_final: 0.7402 (mp0) outliers start: 40 outliers final: 29 residues processed: 269 average time/residue: 0.1593 time to fit residues: 70.6942 Evaluate side-chains 253 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 223 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1125 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 51 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 153 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 230 optimal weight: 0.0470 chunk 151 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 222 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 263 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 overall best weight: 2.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 ASN A 675 GLN A 804 GLN ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN ** C 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN C1002 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.164517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.127667 restraints weight = 32919.127| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.73 r_work: 0.3096 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 27318 Z= 0.191 Angle : 0.635 11.772 37335 Z= 0.311 Chirality : 0.049 0.329 4365 Planarity : 0.005 0.067 4719 Dihedral : 7.728 66.884 4914 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 1.68 % Allowed : 12.04 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.14), residues: 3267 helix: 0.60 (0.22), residues: 636 sheet: 0.01 (0.19), residues: 753 loop : -1.79 (0.13), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 905 TYR 0.019 0.002 TYR C 265 PHE 0.020 0.002 PHE A 855 TRP 0.012 0.001 TRP C 886 HIS 0.006 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00482 (27216) covalent geometry : angle 0.59787 (37065) SS BOND : bond 0.00254 ( 36) SS BOND : angle 1.55766 ( 72) hydrogen bonds : bond 0.04690 ( 805) hydrogen bonds : angle 4.60590 ( 2145) link_BETA1-4 : bond 0.00332 ( 18) link_BETA1-4 : angle 2.04721 ( 54) link_NAG-ASN : bond 0.00582 ( 48) link_NAG-ASN : angle 3.11775 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 228 time to evaluate : 0.977 Fit side-chains REVERT: A 52 GLN cc_start: 0.7795 (tm-30) cc_final: 0.7400 (tm-30) REVERT: A 332 ILE cc_start: 0.7436 (mm) cc_final: 0.7139 (mt) REVERT: A 1002 GLN cc_start: 0.8647 (tt0) cc_final: 0.8282 (tt0) REVERT: B 88 ASP cc_start: 0.8195 (m-30) cc_final: 0.7922 (p0) REVERT: B 332 ILE cc_start: 0.7505 (mm) cc_final: 0.7254 (mt) REVERT: B 1128 VAL cc_start: 0.8676 (t) cc_final: 0.8349 (p) REVERT: C 52 GLN cc_start: 0.7780 (tm-30) cc_final: 0.7374 (tm-30) REVERT: C 332 ILE cc_start: 0.7496 (mm) cc_final: 0.7250 (mt) REVERT: C 619 GLU cc_start: 0.7670 (mp0) cc_final: 0.7356 (mp0) outliers start: 48 outliers final: 37 residues processed: 260 average time/residue: 0.1494 time to fit residues: 65.2063 Evaluate side-chains 261 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 224 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 152 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 234 optimal weight: 7.9990 chunk 133 optimal weight: 6.9990 chunk 243 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 7 optimal weight: 9.9990 chunk 85 optimal weight: 0.4980 chunk 137 optimal weight: 1.9990 chunk 281 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN ** C 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.166272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.129173 restraints weight = 32714.990| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.77 r_work: 0.3110 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 27318 Z= 0.119 Angle : 0.581 11.483 37335 Z= 0.281 Chirality : 0.046 0.318 4365 Planarity : 0.004 0.062 4719 Dihedral : 7.321 59.482 4914 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.68 % Allowed : 12.85 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.14), residues: 3267 helix: 0.65 (0.22), residues: 651 sheet: 0.06 (0.19), residues: 753 loop : -1.76 (0.13), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 995 TYR 0.016 0.001 TYR B1067 PHE 0.013 0.001 PHE C 65 TRP 0.009 0.001 TRP C 886 HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00285 (27216) covalent geometry : angle 0.54541 (37065) SS BOND : bond 0.00193 ( 36) SS BOND : angle 1.21080 ( 72) hydrogen bonds : bond 0.03667 ( 805) hydrogen bonds : angle 4.50257 ( 2145) link_BETA1-4 : bond 0.00336 ( 18) link_BETA1-4 : angle 1.86535 ( 54) link_NAG-ASN : bond 0.00547 ( 48) link_NAG-ASN : angle 2.98179 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 233 time to evaluate : 0.751 Fit side-chains REVERT: A 52 GLN cc_start: 0.7783 (tm-30) cc_final: 0.7366 (tm-30) REVERT: A 332 ILE cc_start: 0.7448 (mm) cc_final: 0.7151 (mt) REVERT: A 1002 GLN cc_start: 0.8658 (tt0) cc_final: 0.8287 (tt0) REVERT: B 88 ASP cc_start: 0.8186 (m-30) cc_final: 0.7913 (p0) REVERT: B 332 ILE cc_start: 0.7500 (mm) cc_final: 0.7238 (mt) REVERT: B 1128 VAL cc_start: 0.8652 (t) cc_final: 0.8334 (p) REVERT: C 52 GLN cc_start: 0.7745 (tm-30) cc_final: 0.7357 (tm-30) REVERT: C 190 ARG cc_start: 0.8281 (mtt-85) cc_final: 0.7994 (mtt-85) REVERT: C 332 ILE cc_start: 0.7488 (mm) cc_final: 0.7237 (mt) REVERT: C 619 GLU cc_start: 0.7632 (mp0) cc_final: 0.7318 (mp0) outliers start: 48 outliers final: 38 residues processed: 268 average time/residue: 0.1477 time to fit residues: 66.2119 Evaluate side-chains 265 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 227 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 151 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 chunk 236 optimal weight: 2.9990 chunk 224 optimal weight: 5.9990 chunk 312 optimal weight: 1.9990 chunk 97 optimal weight: 0.2980 chunk 299 optimal weight: 0.6980 chunk 222 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 311 optimal weight: 0.4980 chunk 12 optimal weight: 8.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN ** C 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.166568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.129507 restraints weight = 32987.090| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.73 r_work: 0.3122 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27318 Z= 0.113 Angle : 0.575 11.690 37335 Z= 0.278 Chirality : 0.046 0.319 4365 Planarity : 0.004 0.061 4719 Dihedral : 6.819 58.000 4914 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.61 % Allowed : 13.45 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.14), residues: 3267 helix: 0.83 (0.22), residues: 633 sheet: 0.02 (0.20), residues: 723 loop : -1.69 (0.13), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 190 TYR 0.016 0.001 TYR B1067 PHE 0.013 0.001 PHE C 65 TRP 0.010 0.001 TRP C 886 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00268 (27216) covalent geometry : angle 0.54047 (37065) SS BOND : bond 0.00196 ( 36) SS BOND : angle 1.17788 ( 72) hydrogen bonds : bond 0.03507 ( 805) hydrogen bonds : angle 4.45380 ( 2145) link_BETA1-4 : bond 0.00341 ( 18) link_BETA1-4 : angle 1.75280 ( 54) link_NAG-ASN : bond 0.00537 ( 48) link_NAG-ASN : angle 2.94830 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 238 time to evaluate : 1.017 Fit side-chains REVERT: A 52 GLN cc_start: 0.7785 (tm-30) cc_final: 0.7356 (tm-30) REVERT: A 332 ILE cc_start: 0.7427 (mm) cc_final: 0.7125 (mt) REVERT: A 1002 GLN cc_start: 0.8602 (tt0) cc_final: 0.8235 (tt0) REVERT: A 1146 ASP cc_start: 0.6514 (m-30) cc_final: 0.6014 (t0) REVERT: B 88 ASP cc_start: 0.8159 (m-30) cc_final: 0.7901 (p0) REVERT: B 190 ARG cc_start: 0.8242 (mtt-85) cc_final: 0.7674 (mtt180) REVERT: B 332 ILE cc_start: 0.7511 (mm) cc_final: 0.7247 (mt) REVERT: B 1128 VAL cc_start: 0.8591 (t) cc_final: 0.8295 (p) REVERT: C 52 GLN cc_start: 0.7719 (tm-30) cc_final: 0.7332 (tm-30) REVERT: C 190 ARG cc_start: 0.8257 (mtt-85) cc_final: 0.7955 (mtt-85) REVERT: C 332 ILE cc_start: 0.7471 (mm) cc_final: 0.7210 (mt) REVERT: C 592 PHE cc_start: 0.8173 (p90) cc_final: 0.7922 (p90) REVERT: C 619 GLU cc_start: 0.7587 (mp0) cc_final: 0.7246 (mp0) REVERT: C 988 GLU cc_start: 0.8374 (mm-30) cc_final: 0.8047 (mt-10) outliers start: 46 outliers final: 40 residues processed: 272 average time/residue: 0.1572 time to fit residues: 70.6200 Evaluate side-chains 269 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 229 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 131 optimal weight: 8.9990 chunk 241 optimal weight: 20.0000 chunk 127 optimal weight: 3.9990 chunk 181 optimal weight: 0.0060 chunk 240 optimal weight: 20.0000 chunk 313 optimal weight: 0.4980 chunk 292 optimal weight: 0.7980 chunk 25 optimal weight: 6.9990 chunk 135 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 chunk 165 optimal weight: 6.9990 overall best weight: 1.4600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN ** C 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.165241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.128359 restraints weight = 32801.682| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.72 r_work: 0.3095 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 27318 Z= 0.150 Angle : 0.611 14.503 37335 Z= 0.296 Chirality : 0.047 0.328 4365 Planarity : 0.004 0.062 4719 Dihedral : 6.544 57.956 4914 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.54 % Allowed : 13.55 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.14), residues: 3267 helix: 0.53 (0.21), residues: 657 sheet: 0.01 (0.19), residues: 756 loop : -1.81 (0.13), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 905 TYR 0.023 0.001 TYR B 266 PHE 0.015 0.001 PHE C1121 TRP 0.010 0.001 TRP C 886 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00372 (27216) covalent geometry : angle 0.57581 (37065) SS BOND : bond 0.00251 ( 36) SS BOND : angle 1.52700 ( 72) hydrogen bonds : bond 0.04078 ( 805) hydrogen bonds : angle 4.55573 ( 2145) link_BETA1-4 : bond 0.00337 ( 18) link_BETA1-4 : angle 1.73733 ( 54) link_NAG-ASN : bond 0.00536 ( 48) link_NAG-ASN : angle 3.02482 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 237 time to evaluate : 0.819 Fit side-chains REVERT: A 52 GLN cc_start: 0.7812 (tm-30) cc_final: 0.7381 (tm-30) REVERT: A 332 ILE cc_start: 0.7425 (mm) cc_final: 0.7124 (mt) REVERT: A 1002 GLN cc_start: 0.8629 (tt0) cc_final: 0.8263 (tt0) REVERT: B 88 ASP cc_start: 0.8202 (m-30) cc_final: 0.7923 (p0) REVERT: B 190 ARG cc_start: 0.8293 (mtt-85) cc_final: 0.7680 (mtt180) REVERT: B 332 ILE cc_start: 0.7493 (mm) cc_final: 0.7229 (mt) REVERT: B 1128 VAL cc_start: 0.8676 (t) cc_final: 0.8356 (p) REVERT: C 52 GLN cc_start: 0.7792 (tm-30) cc_final: 0.7368 (tm-30) REVERT: C 190 ARG cc_start: 0.8301 (mtt-85) cc_final: 0.7980 (mtt-85) REVERT: C 332 ILE cc_start: 0.7493 (mm) cc_final: 0.7250 (mt) REVERT: C 592 PHE cc_start: 0.8259 (p90) cc_final: 0.8001 (p90) REVERT: C 619 GLU cc_start: 0.7601 (mp0) cc_final: 0.7237 (mp0) REVERT: C 988 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8090 (mt-10) outliers start: 44 outliers final: 43 residues processed: 267 average time/residue: 0.1431 time to fit residues: 64.2433 Evaluate side-chains 278 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 235 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 56 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 192 optimal weight: 3.9990 chunk 248 optimal weight: 0.0070 chunk 43 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 260 optimal weight: 6.9990 chunk 174 optimal weight: 4.9990 chunk 225 optimal weight: 9.9990 chunk 216 optimal weight: 1.9990 chunk 316 optimal weight: 2.9990 overall best weight: 1.5204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN B 675 GLN ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN ** C 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.164905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.127984 restraints weight = 32845.482| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.71 r_work: 0.3096 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 27318 Z= 0.153 Angle : 0.622 16.619 37335 Z= 0.302 Chirality : 0.047 0.329 4365 Planarity : 0.004 0.062 4719 Dihedral : 6.376 59.748 4914 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.61 % Allowed : 13.66 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.14), residues: 3267 helix: 0.47 (0.21), residues: 645 sheet: -0.01 (0.19), residues: 756 loop : -1.83 (0.13), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 454 TYR 0.022 0.001 TYR B 266 PHE 0.015 0.001 PHE C1121 TRP 0.010 0.001 TRP C 886 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00380 (27216) covalent geometry : angle 0.58730 (37065) SS BOND : bond 0.00266 ( 36) SS BOND : angle 1.60711 ( 72) hydrogen bonds : bond 0.04120 ( 805) hydrogen bonds : angle 4.61414 ( 2145) link_BETA1-4 : bond 0.00345 ( 18) link_BETA1-4 : angle 1.66270 ( 54) link_NAG-ASN : bond 0.00532 ( 48) link_NAG-ASN : angle 3.04479 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 235 time to evaluate : 0.823 Fit side-chains revert: symmetry clash REVERT: A 332 ILE cc_start: 0.7454 (mm) cc_final: 0.7163 (mt) REVERT: A 1002 GLN cc_start: 0.8638 (tt0) cc_final: 0.8271 (tt0) REVERT: B 190 ARG cc_start: 0.8321 (mtt-85) cc_final: 0.7685 (mtt180) REVERT: B 332 ILE cc_start: 0.7535 (mm) cc_final: 0.7286 (mt) REVERT: B 1128 VAL cc_start: 0.8684 (t) cc_final: 0.8358 (p) REVERT: C 52 GLN cc_start: 0.7831 (tm-30) cc_final: 0.7363 (tm-30) REVERT: C 190 ARG cc_start: 0.8316 (mtt-85) cc_final: 0.7992 (mtt-85) REVERT: C 332 ILE cc_start: 0.7508 (mm) cc_final: 0.7274 (mt) REVERT: C 592 PHE cc_start: 0.8263 (p90) cc_final: 0.8015 (p90) REVERT: C 988 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8087 (mt-10) outliers start: 46 outliers final: 43 residues processed: 265 average time/residue: 0.1561 time to fit residues: 68.8986 Evaluate side-chains 269 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 226 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 215 optimal weight: 0.9990 chunk 216 optimal weight: 0.8980 chunk 289 optimal weight: 0.9990 chunk 232 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 302 optimal weight: 1.9990 chunk 320 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 312 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 853 GLN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN ** C 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.166314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.129407 restraints weight = 32812.096| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.75 r_work: 0.3114 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27318 Z= 0.116 Angle : 0.594 15.490 37335 Z= 0.287 Chirality : 0.046 0.323 4365 Planarity : 0.004 0.060 4719 Dihedral : 6.098 56.792 4914 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.65 % Allowed : 13.83 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.14), residues: 3267 helix: 0.68 (0.22), residues: 654 sheet: 0.04 (0.19), residues: 756 loop : -1.80 (0.13), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 567 TYR 0.018 0.001 TYR B 266 PHE 0.014 0.001 PHE B 65 TRP 0.009 0.001 TRP C 886 HIS 0.002 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00277 (27216) covalent geometry : angle 0.55983 (37065) SS BOND : bond 0.00191 ( 36) SS BOND : angle 1.51352 ( 72) hydrogen bonds : bond 0.03533 ( 805) hydrogen bonds : angle 4.53861 ( 2145) link_BETA1-4 : bond 0.00377 ( 18) link_BETA1-4 : angle 1.52663 ( 54) link_NAG-ASN : bond 0.00531 ( 48) link_NAG-ASN : angle 2.96356 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6917.32 seconds wall clock time: 118 minutes 51.06 seconds (7131.06 seconds total)