Starting phenix.real_space_refine on Sun Jul 5 08:07:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xix_33211/07_2026/7xix_33211.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xix_33211/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7xix_33211/07_2026/7xix_33211.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xix_33211/07_2026/7xix_33211.cif" model { file = "/net/cci-nas-00/data/ceres_data/7xix_33211/07_2026/7xix_33211.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xix_33211/07_2026/7xix_33211.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xix_33211/07_2026/7xix_33211.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xix_33211/07_2026/7xix_33211.map" } 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-6108/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 10 Time building chain proxies: 5.44, per 1000 atoms: 0.20 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: 2.11 Conformation dependent library (CDL) restraints added in 2.1 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: 0.98 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: 5.32 Time building geometry restraints manager: 2.74 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 - 17.95: 14155 17.95 - 35.91: 1223 35.91 - 53.86: 184 53.86 - 71.82: 41 71.82 - 89.77: 36 Dihedral angle restraints: 15639 sinusoidal: 6072 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 15636 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: 0.04 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: 1.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.290 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 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 : 14.116 89.769 9387 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/Z covalent geometry : bond 0.00405 / 0.19 (27216) covalent geometry : angle 0.61378 / 0.31 (37065) SS BOND : bond 0.00135 / 0.08 ( 36) SS BOND : angle 1.23873 / 0.81 ( 72) hydrogen bonds : bond 0.13056 / 8.20 ( 805) hydrogen bonds : angle 5.31872 / 3.61 ( 2145) link_BETA1-4 : bond 0.00422 / 0.25 ( 18) link_BETA1-4 : angle 1.58000 / 0.91 ( 54) link_NAG-ASN : bond 0.00608 / 0.39 ( 48) link_NAG-ASN : angle 3.10488 / 2.02 ( 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 : 0.841 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: 0.1670 time to fit residues: 75.7242 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 : 1.008 ------------------------------------------------------------------------------- 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... 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 = 0.3931 r_free = 0.3931 target = 0.168844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.132299 restraints weight = 32708.277| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.76 r_work: 0.3152 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.0675 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= 0.105 Angle : 0.573 12.359 37335 Z= 0.281 Chirality : 0.046 0.326 4365 Planarity : 0.004 0.061 4719 Dihedral : 4.088 17.106 3528 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.35 % Allowed : 6.27 % Favored : 93.38 % 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: -1.08 (0.14), residues: 3267 helix: 0.79 (0.22), residues: 636 sheet: 0.05 (0.19), residues: 711 loop : -1.62 (0.13), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 190 TYR 0.019 0.001 TYR C 170 PHE 0.031 0.001 PHE A 133 TRP 0.009 0.001 TRP C 886 HIS 0.002 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 (27216) covalent geometry : angle 0.54580 / 0.28 (37065) SS BOND : bond 0.00174 / 0.10 ( 36) SS BOND : angle 0.98592 / 0.62 ( 72) hydrogen bonds : bond 0.03675 / 2.42 ( 805) hydrogen bonds : angle 4.69580 / 3.23 ( 2145) link_BETA1-4 : bond 0.00418 / 0.25 ( 18) link_BETA1-4 : angle 0.99466 / 0.62 ( 54) link_NAG-ASN : bond 0.00560 / 0.37 ( 48) link_NAG-ASN : angle 2.77278 / 1.81 ( 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 254 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 244 time to evaluate : 1.034 Fit side-chains REVERT: A 52 GLN cc_start: 0.7759 (tm-30) cc_final: 0.7486 (tm-30) REVERT: A 332 ILE cc_start: 0.7349 (mm) cc_final: 0.7042 (mt) REVERT: A 386 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8076 (mttt) REVERT: A 739 THR cc_start: 0.8311 (m) cc_final: 0.8046 (p) REVERT: A 1002 GLN cc_start: 0.8554 (tt0) cc_final: 0.8197 (tt0) REVERT: A 1029 MET cc_start: 0.9018 (tpp) cc_final: 0.8740 (tpp) REVERT: B 88 ASP cc_start: 0.8119 (m-30) cc_final: 0.7753 (p0) REVERT: B 170 TYR cc_start: 0.7626 (t80) cc_final: 0.7392 (t80) REVERT: B 191 GLU cc_start: 0.8291 (mt-10) cc_final: 0.8078 (mt-10) REVERT: B 332 ILE cc_start: 0.7478 (mm) cc_final: 0.7210 (mt) REVERT: B 755 GLN cc_start: 0.8620 (tt0) cc_final: 0.8386 (tt0) REVERT: B 1128 VAL cc_start: 0.8598 (t) cc_final: 0.8355 (p) REVERT: C 332 ILE cc_start: 0.7435 (mm) cc_final: 0.7166 (mt) outliers start: 10 outliers final: 8 residues processed: 249 average time/residue: 0.1735 time to fit residues: 70.9447 Evaluate side-chains 231 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 222 time to evaluate : 1.006 ------------------------------------------------------------------------------- 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: 10.0000 chunk 289 optimal weight: 3.9990 chunk 199 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 104 optimal weight: 0.5980 chunk 310 optimal weight: 0.8980 chunk 274 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 209 optimal weight: 0.0770 chunk 89 optimal weight: 3.9990 chunk 80 optimal weight: 0.0030 overall best weight: 1.1150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.167206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.130079 restraints weight = 32915.400| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.73 r_work: 0.3134 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.0830 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= 0.127 Angle : 0.574 11.825 37335 Z= 0.282 Chirality : 0.047 0.331 4365 Planarity : 0.004 0.061 4719 Dihedral : 4.119 18.595 3528 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.98 % Allowed : 8.40 % Favored : 90.62 % 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: -1.15 (0.14), residues: 3267 helix: 0.65 (0.22), residues: 645 sheet: 0.03 (0.20), residues: 702 loop : -1.65 (0.13), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 995 TYR 0.018 0.001 TYR B1067 PHE 0.016 0.001 PHE B 906 TRP 0.010 0.001 TRP C 886 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (27216) covalent geometry : angle 0.54667 / 0.28 (37065) SS BOND : bond 0.00310 / 0.23 ( 36) SS BOND : angle 1.03730 / 0.67 ( 72) hydrogen bonds : bond 0.03926 / 2.59 ( 805) hydrogen bonds : angle 4.59374 / 3.16 ( 2145) link_BETA1-4 : bond 0.00338 / 0.19 ( 18) link_BETA1-4 : angle 1.06032 / 0.65 ( 54) link_NAG-ASN : bond 0.00535 / 0.36 ( 48) link_NAG-ASN : angle 2.72869 / 1.77 ( 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 261 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 233 time to evaluate : 0.998 Fit side-chains REVERT: A 52 GLN cc_start: 0.7826 (tm-30) cc_final: 0.7493 (tm-30) REVERT: A 332 ILE cc_start: 0.7360 (mm) cc_final: 0.7052 (mt) REVERT: A 739 THR cc_start: 0.8233 (m) cc_final: 0.7961 (p) REVERT: A 1002 GLN cc_start: 0.8600 (tt0) cc_final: 0.8225 (tt0) REVERT: B 88 ASP cc_start: 0.8096 (m-30) cc_final: 0.7782 (p0) REVERT: B 170 TYR cc_start: 0.7704 (t80) cc_final: 0.7400 (t80) REVERT: B 332 ILE cc_start: 0.7460 (mm) cc_final: 0.7195 (mt) REVERT: B 1128 VAL cc_start: 0.8569 (t) cc_final: 0.8271 (p) REVERT: C 332 ILE cc_start: 0.7450 (mm) cc_final: 0.7180 (mt) outliers start: 28 outliers final: 21 residues processed: 248 average time/residue: 0.1645 time to fit residues: 67.4598 Evaluate side-chains 243 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 222 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1128 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 1096 VAL 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 731 MET 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: 4.9990 chunk 9 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 214 optimal weight: 0.1980 chunk 112 optimal weight: 1.9990 chunk 238 optimal weight: 0.6980 chunk 294 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 217 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 ASN A 675 GLN ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 804 GLN B 935 GLN ** 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 = 0.3905 r_free = 0.3905 target = 0.166479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.129233 restraints weight = 32728.816| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.75 r_work: 0.3112 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.0949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27318 Z= 0.129 Angle : 0.570 9.534 37335 Z= 0.280 Chirality : 0.047 0.341 4365 Planarity : 0.004 0.062 4719 Dihedral : 4.115 17.319 3528 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.61 % Allowed : 10.08 % Favored : 88.31 % 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: -1.14 (0.14), residues: 3267 helix: 0.70 (0.22), residues: 651 sheet: -0.00 (0.19), residues: 723 loop : -1.66 (0.13), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 190 TYR 0.017 0.001 TYR B1067 PHE 0.016 0.001 PHE C 377 TRP 0.010 0.001 TRP C 886 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 (27216) covalent geometry : angle 0.54259 / 0.27 (37065) SS BOND : bond 0.00216 / 0.15 ( 36) SS BOND : angle 1.09953 / 0.72 ( 72) hydrogen bonds : bond 0.03849 / 2.54 ( 805) hydrogen bonds : angle 4.55057 / 3.13 ( 2145) link_BETA1-4 : bond 0.00330 / 0.19 ( 18) link_BETA1-4 : angle 1.03676 / 0.64 ( 54) link_NAG-ASN : bond 0.00530 / 0.36 ( 48) link_NAG-ASN : angle 2.70632 / 1.75 ( 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 276 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 230 time to evaluate : 0.842 Fit side-chains REVERT: A 52 GLN cc_start: 0.7751 (tm-30) cc_final: 0.7387 (tm-30) REVERT: A 332 ILE cc_start: 0.7423 (mm) cc_final: 0.7114 (mt) REVERT: A 1002 GLN cc_start: 0.8613 (tt0) cc_final: 0.8234 (tt0) REVERT: A 1146 ASP cc_start: 0.6452 (m-30) cc_final: 0.5975 (t0) REVERT: B 88 ASP cc_start: 0.8092 (m-30) cc_final: 0.7814 (p0) REVERT: B 170 TYR cc_start: 0.7709 (t80) cc_final: 0.7373 (t80) REVERT: B 190 ARG cc_start: 0.8289 (mtt-85) cc_final: 0.7788 (mtt180) REVERT: B 332 ILE cc_start: 0.7469 (mm) cc_final: 0.7208 (mt) REVERT: B 1128 VAL cc_start: 0.8566 (t) cc_final: 0.8283 (p) REVERT: C 332 ILE cc_start: 0.7458 (mm) cc_final: 0.7196 (mt) outliers start: 46 outliers final: 34 residues processed: 261 average time/residue: 0.1660 time to fit residues: 71.2542 Evaluate side-chains 255 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 221 time to evaluate : 1.508 ------------------------------------------------------------------------------- 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 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 A residue 1128 VAL Chi-restraints excluded: chain B residue 130 VAL 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 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 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 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 1096 VAL 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: 0.9990 chunk 4 optimal weight: 2.9990 chunk 264 optimal weight: 10.0000 chunk 257 optimal weight: 5.9990 chunk 170 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 235 optimal weight: 0.9990 chunk 160 optimal weight: 5.9990 chunk 322 optimal weight: 0.9990 chunk 166 optimal weight: 0.8980 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 675 GLN 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 = 0.3894 r_free = 0.3894 target = 0.165436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.128275 restraints weight = 32784.112| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.74 r_work: 0.3109 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 27318 Z= 0.143 Angle : 0.581 9.564 37335 Z= 0.287 Chirality : 0.047 0.347 4365 Planarity : 0.004 0.062 4719 Dihedral : 4.177 17.563 3528 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.79 % Allowed : 11.03 % Favored : 87.18 % 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: 0.74 (0.22), residues: 633 sheet: 0.03 (0.19), residues: 756 loop : -1.76 (0.13), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 190 TYR 0.017 0.001 TYR B1067 PHE 0.015 0.001 PHE C1121 TRP 0.010 0.001 TRP C 886 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.14 (27216) covalent geometry : angle 0.55442 / 0.28 (37065) SS BOND : bond 0.00195 / 0.13 ( 36) SS BOND : angle 1.17969 / 0.76 ( 72) hydrogen bonds : bond 0.04083 / 2.70 ( 805) hydrogen bonds : angle 4.54034 / 3.12 ( 2145) link_BETA1-4 : bond 0.00329 / 0.19 ( 18) link_BETA1-4 : angle 1.08999 / 0.67 ( 54) link_NAG-ASN : bond 0.00527 / 0.36 ( 48) link_NAG-ASN : angle 2.72002 / 1.76 ( 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: 51 poor density : 228 time to evaluate : 0.925 Fit side-chains REVERT: A 52 GLN cc_start: 0.7816 (tm-30) cc_final: 0.7458 (tm-30) REVERT: A 332 ILE cc_start: 0.7442 (mm) cc_final: 0.7147 (mt) REVERT: A 1002 GLN cc_start: 0.8619 (tt0) cc_final: 0.8249 (tt0) REVERT: B 88 ASP cc_start: 0.8178 (m-30) cc_final: 0.7890 (p0) REVERT: B 170 TYR cc_start: 0.7742 (t80) cc_final: 0.7421 (t80) REVERT: B 332 ILE cc_start: 0.7506 (mm) cc_final: 0.7251 (mt) REVERT: B 1128 VAL cc_start: 0.8640 (t) cc_final: 0.8315 (p) REVERT: C 190 ARG cc_start: 0.8177 (mtt-85) cc_final: 0.7880 (mtp180) REVERT: C 332 ILE cc_start: 0.7473 (mm) cc_final: 0.7217 (mt) outliers start: 51 outliers final: 38 residues processed: 265 average time/residue: 0.1551 time to fit residues: 68.0649 Evaluate side-chains 259 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 221 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET 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 991 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 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 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 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 130 VAL 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 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: 10.0000 chunk 153 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 230 optimal weight: 0.3980 chunk 151 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 222 optimal weight: 4.9990 chunk 86 optimal weight: 0.5980 chunk 263 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN A 853 GLN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN B 675 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.165843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.129033 restraints weight = 32773.990| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.74 r_work: 0.3121 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1138 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= 0.128 Angle : 0.569 9.652 37335 Z= 0.280 Chirality : 0.047 0.345 4365 Planarity : 0.004 0.060 4719 Dihedral : 4.138 17.257 3528 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.79 % Allowed : 11.87 % Favored : 86.34 % 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: -1.17 (0.14), residues: 3267 helix: 0.66 (0.22), residues: 651 sheet: 0.06 (0.19), residues: 753 loop : -1.74 (0.13), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 190 TYR 0.016 0.001 TYR B1067 PHE 0.014 0.001 PHE C1121 TRP 0.009 0.001 TRP C 886 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (27216) covalent geometry : angle 0.54201 / 0.27 (37065) SS BOND : bond 0.00171 / 0.11 ( 36) SS BOND : angle 1.13324 / 0.72 ( 72) hydrogen bonds : bond 0.03804 / 2.52 ( 805) hydrogen bonds : angle 4.49576 / 3.09 ( 2145) link_BETA1-4 : bond 0.00351 / 0.20 ( 18) link_BETA1-4 : angle 1.06488 / 0.65 ( 54) link_NAG-ASN : bond 0.00524 / 0.36 ( 48) link_NAG-ASN : angle 2.68420 / 1.73 ( 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 273 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 222 time to evaluate : 0.949 Fit side-chains REVERT: A 52 GLN cc_start: 0.7761 (tm-30) cc_final: 0.7374 (tm-30) REVERT: A 332 ILE cc_start: 0.7404 (mm) cc_final: 0.7156 (mt) REVERT: A 1002 GLN cc_start: 0.8611 (tt0) cc_final: 0.8246 (tt0) REVERT: B 88 ASP cc_start: 0.8161 (m-30) cc_final: 0.7904 (p0) REVERT: B 170 TYR cc_start: 0.7668 (t80) cc_final: 0.7332 (t80) REVERT: B 332 ILE cc_start: 0.7510 (mm) cc_final: 0.7249 (mt) REVERT: B 1128 VAL cc_start: 0.8670 (t) cc_final: 0.8358 (p) REVERT: C 190 ARG cc_start: 0.8222 (mtt-85) cc_final: 0.7801 (mtp180) REVERT: C 332 ILE cc_start: 0.7478 (mm) cc_final: 0.7221 (mt) outliers start: 51 outliers final: 46 residues processed: 257 average time/residue: 0.1562 time to fit residues: 66.4583 Evaluate side-chains 261 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 215 time to evaluate : 0.941 ------------------------------------------------------------------------------- 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 289 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 386 LYS 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 739 THR Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 991 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 A residue 1128 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 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 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 Chi-restraints excluded: chain C residue 1125 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 152 optimal weight: 7.9990 chunk 6 optimal weight: 0.5980 chunk 234 optimal weight: 6.9990 chunk 133 optimal weight: 1.9990 chunk 243 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 7 optimal weight: 9.9990 chunk 85 optimal weight: 0.3980 chunk 137 optimal weight: 2.9990 chunk 281 optimal weight: 0.7980 chunk 138 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN A 853 GLN A1088 HIS ** B 66 HIS ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.166699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.129281 restraints weight = 32589.077| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.76 r_work: 0.3137 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 27318 Z= 0.103 Angle : 0.555 9.567 37335 Z= 0.272 Chirality : 0.046 0.339 4365 Planarity : 0.004 0.059 4719 Dihedral : 4.059 19.500 3528 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.89 % Allowed : 12.71 % Favored : 85.40 % 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: -1.11 (0.14), residues: 3267 helix: 0.77 (0.22), residues: 651 sheet: 0.06 (0.19), residues: 753 loop : -1.71 (0.13), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 646 TYR 0.016 0.001 TYR B1067 PHE 0.017 0.001 PHE A 855 TRP 0.008 0.001 TRP C 886 HIS 0.002 0.000 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.10 (27216) covalent geometry : angle 0.52882 / 0.27 (37065) SS BOND : bond 0.00169 / 0.12 ( 36) SS BOND : angle 1.24325 / 0.87 ( 72) hydrogen bonds : bond 0.03382 / 2.25 ( 805) hydrogen bonds : angle 4.43732 / 3.05 ( 2145) link_BETA1-4 : bond 0.00379 / 0.22 ( 18) link_BETA1-4 : angle 1.03875 / 0.64 ( 54) link_NAG-ASN : bond 0.00530 / 0.36 ( 48) link_NAG-ASN : angle 2.61185 / 1.68 ( 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 282 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 228 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7741 (tm-30) cc_final: 0.7345 (tm-30) REVERT: A 332 ILE cc_start: 0.7381 (mm) cc_final: 0.7121 (mt) REVERT: A 1002 GLN cc_start: 0.8577 (tt0) cc_final: 0.8241 (tt0) REVERT: A 1146 ASP cc_start: 0.6472 (m-30) cc_final: 0.5974 (t0) REVERT: B 170 TYR cc_start: 0.7672 (t80) cc_final: 0.7286 (t80) REVERT: B 332 ILE cc_start: 0.7545 (mm) cc_final: 0.7287 (mt) REVERT: B 1128 VAL cc_start: 0.8610 (t) cc_final: 0.8311 (p) REVERT: C 190 ARG cc_start: 0.8219 (mtt-85) cc_final: 0.7769 (mtp180) REVERT: C 332 ILE cc_start: 0.7467 (mm) cc_final: 0.7205 (mt) REVERT: C 592 PHE cc_start: 0.8219 (p90) cc_final: 0.7950 (p90) outliers start: 54 outliers final: 43 residues processed: 267 average time/residue: 0.1623 time to fit residues: 72.1058 Evaluate side-chains 261 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 218 time to evaluate : 0.970 ------------------------------------------------------------------------------- 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 739 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 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 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 1008 VAL Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1125 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 151 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 236 optimal weight: 2.9990 chunk 224 optimal weight: 5.9990 chunk 312 optimal weight: 0.9990 chunk 97 optimal weight: 0.1980 chunk 299 optimal weight: 0.9980 chunk 222 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 311 optimal weight: 0.5980 chunk 12 optimal weight: 9.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 ASN A 675 GLN A 853 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.166923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.129666 restraints weight = 32919.725| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.76 r_work: 0.3142 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 27318 Z= 0.103 Angle : 0.556 9.923 37335 Z= 0.271 Chirality : 0.046 0.338 4365 Planarity : 0.004 0.058 4719 Dihedral : 4.013 18.247 3528 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.00 % Allowed : 12.99 % Favored : 85.01 % 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: 0.91 (0.22), residues: 633 sheet: -0.00 (0.19), residues: 726 loop : -1.66 (0.13), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 190 TYR 0.016 0.001 TYR C 265 PHE 0.017 0.001 PHE A 855 TRP 0.008 0.001 TRP C 886 HIS 0.002 0.000 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.10 (27216) covalent geometry : angle 0.53043 / 0.26 (37065) SS BOND : bond 0.00175 / 0.12 ( 36) SS BOND : angle 1.26591 / 0.87 ( 72) hydrogen bonds : bond 0.03292 / 2.18 ( 805) hydrogen bonds : angle 4.41321 / 3.03 ( 2145) link_BETA1-4 : bond 0.00371 / 0.22 ( 18) link_BETA1-4 : angle 1.04753 / 0.64 ( 54) link_NAG-ASN : bond 0.00529 / 0.36 ( 48) link_NAG-ASN : angle 2.57498 / 1.66 ( 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: 57 poor density : 227 time to evaluate : 0.980 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7745 (tm-30) cc_final: 0.7331 (tm-30) REVERT: A 1002 GLN cc_start: 0.8561 (tt0) cc_final: 0.8226 (tt0) REVERT: A 1146 ASP cc_start: 0.6492 (m-30) cc_final: 0.6000 (t0) REVERT: B 170 TYR cc_start: 0.7646 (t80) cc_final: 0.7258 (t80) REVERT: B 332 ILE cc_start: 0.7497 (mm) cc_final: 0.7230 (mt) REVERT: B 1128 VAL cc_start: 0.8565 (t) cc_final: 0.8277 (p) REVERT: C 52 GLN cc_start: 0.7725 (tm-30) cc_final: 0.7315 (tm-30) REVERT: C 332 ILE cc_start: 0.7454 (mm) cc_final: 0.7184 (mt) REVERT: C 592 PHE cc_start: 0.8189 (p90) cc_final: 0.7926 (p90) REVERT: C 988 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8118 (mt-10) outliers start: 57 outliers final: 47 residues processed: 270 average time/residue: 0.1498 time to fit residues: 67.6314 Evaluate side-chains 269 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 222 time to evaluate : 0.697 ------------------------------------------------------------------------------- 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 289 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 739 THR Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 1008 VAL 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 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 731 MET Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 1008 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 Chi-restraints excluded: chain C residue 1125 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 131 optimal weight: 0.5980 chunk 241 optimal weight: 20.0000 chunk 127 optimal weight: 3.9990 chunk 181 optimal weight: 0.6980 chunk 240 optimal weight: 0.0060 chunk 313 optimal weight: 0.6980 chunk 292 optimal weight: 0.4980 chunk 25 optimal weight: 0.6980 chunk 135 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 chunk 165 optimal weight: 0.6980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 ASN A 675 GLN A 853 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.167835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.130886 restraints weight = 32700.703| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.78 r_work: 0.3139 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 27318 Z= 0.095 Angle : 0.557 14.116 37335 Z= 0.270 Chirality : 0.046 0.334 4365 Planarity : 0.004 0.058 4719 Dihedral : 3.941 17.342 3528 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.47 % Allowed : 13.59 % 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: -1.04 (0.14), residues: 3267 helix: 0.87 (0.22), residues: 651 sheet: 0.01 (0.19), residues: 726 loop : -1.62 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 190 TYR 0.015 0.001 TYR C 265 PHE 0.019 0.001 PHE A 855 TRP 0.008 0.001 TRP C 886 HIS 0.002 0.000 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.09 (27216) covalent geometry : angle 0.53268 / 0.26 (37065) SS BOND : bond 0.00158 / 0.11 ( 36) SS BOND : angle 1.19664 / 0.79 ( 72) hydrogen bonds : bond 0.03056 / 2.03 ( 805) hydrogen bonds : angle 4.38982 / 3.01 ( 2145) link_BETA1-4 : bond 0.00380 / 0.22 ( 18) link_BETA1-4 : angle 1.03294 / 0.63 ( 54) link_NAG-ASN : bond 0.00529 / 0.36 ( 48) link_NAG-ASN : angle 2.53070 / 1.63 ( 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 279 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 237 time to evaluate : 1.066 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7735 (tm-30) cc_final: 0.7343 (tm-30) REVERT: A 592 PHE cc_start: 0.7889 (p90) cc_final: 0.7607 (p90) REVERT: A 1002 GLN cc_start: 0.8651 (tt0) cc_final: 0.8349 (tt0) REVERT: A 1146 ASP cc_start: 0.6516 (m-30) cc_final: 0.6052 (t0) REVERT: B 52 GLN cc_start: 0.7720 (tm-30) cc_final: 0.7473 (tm-30) REVERT: B 170 TYR cc_start: 0.7697 (t80) cc_final: 0.7326 (t80) REVERT: B 752 LEU cc_start: 0.8812 (mp) cc_final: 0.8603 (mp) REVERT: B 1128 VAL cc_start: 0.8497 (t) cc_final: 0.8252 (p) REVERT: C 52 GLN cc_start: 0.7730 (tm-30) cc_final: 0.7370 (tm-30) REVERT: C 332 ILE cc_start: 0.7513 (mm) cc_final: 0.7225 (mt) REVERT: C 592 PHE cc_start: 0.8129 (p90) cc_final: 0.7872 (p90) REVERT: C 988 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8159 (mt-10) outliers start: 42 outliers final: 39 residues processed: 265 average time/residue: 0.1545 time to fit residues: 68.1032 Evaluate side-chains 271 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 232 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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 289 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 739 THR Chi-restraints excluded: chain A residue 853 GLN 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 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 739 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1125 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 56 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 192 optimal weight: 4.9990 chunk 248 optimal weight: 0.2980 chunk 43 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 260 optimal weight: 10.0000 chunk 174 optimal weight: 4.9990 chunk 225 optimal weight: 9.9990 chunk 216 optimal weight: 0.4980 chunk 316 optimal weight: 0.0870 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN C 853 GLN C1002 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.167795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.130408 restraints weight = 32699.418| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.78 r_work: 0.3154 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1359 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= 0.097 Angle : 0.550 13.079 37335 Z= 0.267 Chirality : 0.046 0.333 4365 Planarity : 0.004 0.059 4719 Dihedral : 3.903 16.639 3528 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.54 % Allowed : 13.73 % 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: -1.01 (0.14), residues: 3267 helix: 1.00 (0.22), residues: 633 sheet: 0.12 (0.20), residues: 696 loop : -1.63 (0.13), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 190 TYR 0.015 0.001 TYR C 265 PHE 0.020 0.001 PHE A 855 TRP 0.008 0.001 TRP C 886 HIS 0.002 0.000 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (27216) covalent geometry : angle 0.52556 / 0.26 (37065) SS BOND : bond 0.00149 / 0.10 ( 36) SS BOND : angle 1.11821 / 0.74 ( 72) hydrogen bonds : bond 0.03053 / 2.03 ( 805) hydrogen bonds : angle 4.35955 / 2.99 ( 2145) link_BETA1-4 : bond 0.00384 / 0.22 ( 18) link_BETA1-4 : angle 1.03934 / 0.64 ( 54) link_NAG-ASN : bond 0.00520 / 0.36 ( 48) link_NAG-ASN : angle 2.49935 / 1.61 ( 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 279 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 235 time to evaluate : 0.635 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7708 (tm-30) cc_final: 0.7295 (tm-30) REVERT: A 592 PHE cc_start: 0.7861 (p90) cc_final: 0.7584 (p90) REVERT: A 1002 GLN cc_start: 0.8585 (tt0) cc_final: 0.8244 (tt0) REVERT: A 1146 ASP cc_start: 0.6492 (m-30) cc_final: 0.6013 (t0) REVERT: B 52 GLN cc_start: 0.7722 (tm-30) cc_final: 0.7441 (tm-30) REVERT: B 170 TYR cc_start: 0.7600 (t80) cc_final: 0.7233 (t80) REVERT: B 190 ARG cc_start: 0.8366 (mtt-85) cc_final: 0.7882 (mtt-85) REVERT: B 752 LEU cc_start: 0.8773 (mp) cc_final: 0.8570 (mp) REVERT: B 1128 VAL cc_start: 0.8455 (t) cc_final: 0.8217 (p) REVERT: C 52 GLN cc_start: 0.7705 (tm-30) cc_final: 0.7314 (tm-30) REVERT: C 177 MET cc_start: 0.7842 (OUTLIER) cc_final: 0.6825 (mmp) REVERT: C 332 ILE cc_start: 0.7425 (mm) cc_final: 0.7135 (mt) REVERT: C 592 PHE cc_start: 0.8088 (p90) cc_final: 0.7830 (p90) REVERT: C 988 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8092 (mt-10) outliers start: 44 outliers final: 42 residues processed: 265 average time/residue: 0.1512 time to fit residues: 66.6242 Evaluate side-chains 275 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 232 time to evaluate : 0.955 ------------------------------------------------------------------------------- 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 289 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 853 GLN Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 1008 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 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 739 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1125 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 215 optimal weight: 1.9990 chunk 216 optimal weight: 0.9980 chunk 289 optimal weight: 2.9990 chunk 232 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 302 optimal weight: 2.9990 chunk 320 optimal weight: 0.5980 chunk 130 optimal weight: 4.9990 chunk 312 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.166704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.129437 restraints weight = 32747.139| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.74 r_work: 0.3140 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27318 Z= 0.122 Angle : 0.569 14.926 37335 Z= 0.276 Chirality : 0.046 0.338 4365 Planarity : 0.004 0.059 4719 Dihedral : 3.957 16.336 3528 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.47 % Allowed : 14.11 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.14), residues: 3267 helix: 0.92 (0.22), residues: 630 sheet: 0.08 (0.20), residues: 699 loop : -1.66 (0.13), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 905 TYR 0.018 0.001 TYR B 266 PHE 0.015 0.001 PHE C1121 TRP 0.008 0.001 TRP C 886 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.12 (27216) covalent geometry : angle 0.54534 / 0.27 (37065) SS BOND : bond 0.00187 / 0.12 ( 36) SS BOND : angle 1.25545 / 0.85 ( 72) hydrogen bonds : bond 0.03452 / 2.29 ( 805) hydrogen bonds : angle 4.40093 / 3.02 ( 2145) link_BETA1-4 : bond 0.00357 / 0.20 ( 18) link_BETA1-4 : angle 1.07069 / 0.66 ( 54) link_NAG-ASN : bond 0.00502 / 0.35 ( 48) link_NAG-ASN : angle 2.50987 / 1.61 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7063.67 seconds wall clock time: 136 minutes 48.25 seconds (8208.25 seconds total)