Starting phenix.real_space_refine on Fri Mar 6 02:06:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z86_14544/03_2026/7z86_14544.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z86_14544/03_2026/7z86_14544.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7z86_14544/03_2026/7z86_14544.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z86_14544/03_2026/7z86_14544.map" model { file = "/net/cci-nas-00/data/ceres_data/7z86_14544/03_2026/7z86_14544.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z86_14544/03_2026/7z86_14544.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 120 5.16 5 C 17216 2.51 5 N 4414 2.21 5 O 5321 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27071 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 7712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 987, 7712 Classifications: {'peptide': 987} Link IDs: {'PTRANS': 49, 'TRANS': 937} Chain breaks: 9 Chain: "B" Number of atoms: 7745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 7745 Classifications: {'peptide': 992} Link IDs: {'PTRANS': 49, 'TRANS': 942} Chain breaks: 8 Chain: "C" Number of atoms: 7738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 991, 7738 Classifications: {'peptide': 991} Link IDs: {'PTRANS': 49, 'TRANS': 941} Chain breaks: 7 Chain: "X" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 984 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "Y" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 984 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "Z" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 984 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 6.50, per 1000 atoms: 0.24 Number of scatterers: 27071 At special positions: 0 Unit cell: (128.64, 136.144, 214.4, 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 120 16.00 O 5321 8.00 N 4414 7.00 C 17216 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.01 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.06 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.05 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.05 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.05 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=1.99 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.07 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=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.02 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.05 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.05 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.05 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.04 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.01 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 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 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.07 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.06 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS X 22 " - pdb=" SG CYS X 96 " distance=2.01 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Y 96 " distance=2.01 Simple disulfide: pdb=" SG CYS Z 22 " - pdb=" SG CYS Z 96 " distance=2.01 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 V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 603 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A 165 " " NAG A1308 " - " ASN A 343 " " NAG B1301 " - " ASN B 61 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B 343 " " NAG C1401 " - " ASN C 343 " " NAG C1402 " - " ASN C 61 " " NAG C1403 " - " ASN C 234 " " NAG C1404 " - " ASN C 331 " " NAG C1405 " - " ASN C 603 " " NAG C1406 " - " ASN C 616 " " NAG C1407 " - " ASN C 657 " " NAG C1408 " - " ASN C 165 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 234 " " NAG F 1 " - " ASN A 282 " " NAG G 1 " - " ASN A 331 " " NAG H 1 " - " ASN A 717 " " NAG I 1 " - " ASN A 801 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN A1134 " " 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 122 " " NAG Q 1 " - " ASN C 282 " " NAG R 1 " - " ASN C 709 " " NAG S 1 " - " ASN C 717 " " NAG T 1 " - " ASN C 801 " " NAG U 1 " - " ASN C1074 " " NAG V 1 " - " ASN C1098 " " NAG W 1 " - " ASN C1134 " Time building additional restraints: 2.48 Conformation dependent library (CDL) restraints added in 1.2 seconds 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6244 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 55 sheets defined 25.0% alpha, 28.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.959A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 388 removed outlier: 4.188A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.350A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.602A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.216A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.935A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 982 removed outlier: 4.008A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.670A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.954A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 390 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.331A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.083A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.827A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.259A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.671A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.523A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.616A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.283A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.021A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 388 removed outlier: 4.084A pdb=" N ASN C 388 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.060A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.563A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.673A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.248A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.609A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.555A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.065A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.158A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'X' and resid 62 through 65 Processing helix chain 'X' and resid 87 through 91 Processing helix chain 'X' and resid 105 through 111 Processing helix chain 'Y' and resid 62 through 65 Processing helix chain 'Y' and resid 87 through 91 Processing helix chain 'Y' and resid 105 through 111 Processing helix chain 'Z' and resid 62 through 65 Processing helix chain 'Z' and resid 87 through 91 Processing helix chain 'Z' and resid 105 through 111 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.675A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.144A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.501A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.333A pdb=" N PHE A 43 " --> pdb=" O ARG B 567 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.542A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.646A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 327 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.545A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.452A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.084A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.933A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.705A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.983A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.194A 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: 5.720A pdb=" N ILE A 788 " --> pdb=" O ASN B 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: 4.426A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.268A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.272A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.172A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.725A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 169 through 171 Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.683A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.602A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 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 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.889A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.983A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 719 through 728 removed outlier: 6.030A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.240A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 788 through 790 removed outlier: 5.538A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.444A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.707A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.298A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.225A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.959A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.574A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.119A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE3, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.209A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.011A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.974A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 719 through 728 removed outlier: 7.000A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.132A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.550A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'X' and resid 3 through 8 Processing sheet with id=AF3, first strand: chain 'X' and resid 10 through 13 removed outlier: 6.301A pdb=" N GLY X 10 " --> pdb=" O THR X 124 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N SER X 126 " --> pdb=" O GLY X 10 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N MET X 12 " --> pdb=" O SER X 126 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ARG X 38 " --> pdb=" O PHE X 47 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N PHE X 47 " --> pdb=" O ARG X 38 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'X' and resid 10 through 13 removed outlier: 6.301A pdb=" N GLY X 10 " --> pdb=" O THR X 124 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N SER X 126 " --> pdb=" O GLY X 10 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N MET X 12 " --> pdb=" O SER X 126 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Y' and resid 3 through 8 Processing sheet with id=AF6, first strand: chain 'Y' and resid 10 through 13 removed outlier: 6.301A pdb=" N GLY Y 10 " --> pdb=" O THR Y 124 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N SER Y 126 " --> pdb=" O GLY Y 10 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N MET Y 12 " --> pdb=" O SER Y 126 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ARG Y 38 " --> pdb=" O PHE Y 47 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N PHE Y 47 " --> pdb=" O ARG Y 38 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Y' and resid 10 through 13 removed outlier: 6.301A pdb=" N GLY Y 10 " --> pdb=" O THR Y 124 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N SER Y 126 " --> pdb=" O GLY Y 10 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N MET Y 12 " --> pdb=" O SER Y 126 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Z' and resid 3 through 8 Processing sheet with id=AF9, first strand: chain 'Z' and resid 10 through 13 removed outlier: 6.301A pdb=" N GLY Z 10 " --> pdb=" O THR Z 124 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N SER Z 126 " --> pdb=" O GLY Z 10 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N MET Z 12 " --> pdb=" O SER Z 126 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ARG Z 38 " --> pdb=" O PHE Z 47 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N PHE Z 47 " --> pdb=" O ARG Z 38 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Z' and resid 10 through 13 removed outlier: 6.301A pdb=" N GLY Z 10 " --> pdb=" O THR Z 124 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N SER Z 126 " --> pdb=" O GLY Z 10 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N MET Z 12 " --> pdb=" O SER Z 126 " (cutoff:3.500A) 1168 hydrogen bonds defined for protein. 3090 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.96 Time building geometry restraints manager: 3.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5205 1.33 - 1.46: 9895 1.46 - 1.59: 12409 1.59 - 1.72: 0 1.72 - 1.84: 153 Bond restraints: 27662 Sorted by residual: bond pdb=" CE1 HIS B 49 " pdb=" NE2 HIS B 49 " ideal model delta sigma weight residual 1.321 1.351 -0.030 1.00e-02 1.00e+04 9.19e+00 bond pdb=" CA SER A 325 " pdb=" CB SER A 325 " ideal model delta sigma weight residual 1.531 1.486 0.045 1.52e-02 4.33e+03 8.77e+00 bond pdb=" CE1 HIS C1058 " pdb=" NE2 HIS C1058 " ideal model delta sigma weight residual 1.321 1.350 -0.029 1.00e-02 1.00e+04 8.38e+00 bond pdb=" C ASN A 81 " pdb=" N PRO A 82 " ideal model delta sigma weight residual 1.328 1.365 -0.036 1.26e-02 6.30e+03 8.27e+00 bond pdb=" CE1 HIS B1101 " pdb=" NE2 HIS B1101 " ideal model delta sigma weight residual 1.321 1.349 -0.028 1.00e-02 1.00e+04 8.07e+00 ... (remaining 27657 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 34873 2.10 - 4.21: 2542 4.21 - 6.31: 170 6.31 - 8.41: 22 8.41 - 10.52: 7 Bond angle restraints: 37614 Sorted by residual: angle pdb=" CA PHE B 565 " pdb=" CB PHE B 565 " pdb=" CG PHE B 565 " ideal model delta sigma weight residual 113.80 120.06 -6.26 1.00e+00 1.00e+00 3.91e+01 angle pdb=" C LYS A 113 " pdb=" CA LYS A 113 " pdb=" CB LYS A 113 " ideal model delta sigma weight residual 110.06 118.90 -8.84 1.44e+00 4.82e-01 3.77e+01 angle pdb=" CA ASP C 198 " pdb=" CB ASP C 198 " pdb=" CG ASP C 198 " ideal model delta sigma weight residual 112.60 118.02 -5.42 1.00e+00 1.00e+00 2.93e+01 angle pdb=" CA PHE B 86 " pdb=" CB PHE B 86 " pdb=" CG PHE B 86 " ideal model delta sigma weight residual 113.80 119.08 -5.28 1.00e+00 1.00e+00 2.79e+01 angle pdb=" C ASN A 81 " pdb=" CA ASN A 81 " pdb=" CB ASN A 81 " ideal model delta sigma weight residual 110.10 119.36 -9.26 1.90e+00 2.77e-01 2.38e+01 ... (remaining 37609 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.79: 16187 20.79 - 41.57: 770 41.57 - 62.35: 220 62.35 - 83.14: 48 83.14 - 103.92: 48 Dihedral angle restraints: 17273 sinusoidal: 7549 harmonic: 9724 Sorted by residual: dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual -86.00 -165.77 79.77 1 1.00e+01 1.00e-02 7.90e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 170.80 -77.80 1 1.00e+01 1.00e-02 7.57e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 168.96 -75.96 1 1.00e+01 1.00e-02 7.27e+01 ... (remaining 17270 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.630: 4435 0.630 - 1.260: 3 1.260 - 1.889: 0 1.889 - 2.519: 0 2.519 - 3.149: 1 Chirality restraints: 4439 Sorted by residual: chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN B 801 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 0.75 -3.15 2.00e-01 2.50e+01 2.48e+02 chirality pdb=" C1 NAG W 2 " pdb=" O4 NAG W 1 " pdb=" C2 NAG W 2 " pdb=" O5 NAG W 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-02 2.50e+03 1.91e+02 chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-02 2.50e+03 1.11e+02 ... (remaining 4436 not shown) Planarity restraints: 4810 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1306 " 0.350 2.00e-02 2.50e+03 3.01e-01 1.13e+03 pdb=" C7 NAG A1306 " -0.086 2.00e-02 2.50e+03 pdb=" C8 NAG A1306 " 0.140 2.00e-02 2.50e+03 pdb=" N2 NAG A1306 " -0.534 2.00e-02 2.50e+03 pdb=" O7 NAG A1306 " 0.131 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG U 2 " 0.341 2.00e-02 2.50e+03 2.96e-01 1.10e+03 pdb=" C7 NAG U 2 " -0.075 2.00e-02 2.50e+03 pdb=" C8 NAG U 2 " 0.094 2.00e-02 2.50e+03 pdb=" N2 NAG U 2 " -0.529 2.00e-02 2.50e+03 pdb=" O7 NAG U 2 " 0.168 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " 0.339 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" C7 NAG D 1 " -0.073 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " 0.072 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " -0.522 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " 0.184 2.00e-02 2.50e+03 ... (remaining 4807 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 41 2.41 - 3.03: 16466 3.03 - 3.66: 39261 3.66 - 4.28: 62317 4.28 - 4.90: 103799 Nonbonded interactions: 221884 Sorted by model distance: nonbonded pdb=" O GLN B 613 " pdb=" OD1 ASP B 614 " model vdw 1.791 3.040 nonbonded pdb=" OD1 ASN A 81 " pdb=" CD PRO A 82 " model vdw 1.855 3.440 nonbonded pdb=" CB PHE B 342 " pdb=" O7 NAG B1310 " model vdw 2.118 3.440 nonbonded pdb=" O TRP X 53 " pdb=" CZ ARG X 72 " model vdw 2.123 3.270 nonbonded pdb=" O TRP Y 53 " pdb=" CZ ARG Y 72 " model vdw 2.124 3.270 ... (remaining 221879 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 66 or resid 82 through 113 or resid 116 through \ 140 or resid 166 through 263 or resid 265 through 676 or resid 690 through 827 \ or resid 856 through 1308)) selection = (chain 'B' and (resid 27 through 66 or resid 82 through 140 or resid 166 through \ 196 or resid 200 through 211 or resid 215 through 263 or resid 265 through 827 \ or resid 856 through 1308)) selection = (chain 'C' and (resid 27 through 66 or resid 82 through 113 or resid 116 through \ 140 or resid 166 through 196 or resid 200 through 211 or resid 215 through 1408 \ )) } 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' selection = chain 'V' selection = chain 'W' } ncs_group { reference = chain 'X' selection = chain 'Y' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 27.810 Find NCS groups from input model: 0.790 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: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6687 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 : 0.008 0.053 27769 Z= 0.509 Angle : 1.247 14.466 37893 Z= 0.760 Chirality : 0.101 3.149 4439 Planarity : 0.023 0.301 4765 Dihedral : 14.675 103.925 10903 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.97 % Allowed : 4.10 % Favored : 93.93 % Cbeta Deviations : 0.10 % 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: -0.77 (0.14), residues: 3288 helix: 0.18 (0.20), residues: 676 sheet: -0.13 (0.17), residues: 789 loop : -0.93 (0.13), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.003 ARG C1091 TYR 0.042 0.008 TYR A 904 PHE 0.041 0.007 PHE B 565 TRP 0.042 0.006 TRP C 104 HIS 0.030 0.006 HIS C 655 Details of bonding type rmsd covalent geometry : bond 0.00815 (27662) covalent geometry : angle 1.19294 (37614) SS BOND : bond 0.01740 ( 42) SS BOND : angle 2.12738 ( 84) hydrogen bonds : bond 0.13308 ( 1156) hydrogen bonds : angle 6.85125 ( 3090) link_BETA1-4 : bond 0.00436 ( 20) link_BETA1-4 : angle 1.55803 ( 60) link_NAG-ASN : bond 0.01460 ( 45) link_NAG-ASN : angle 6.00086 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 431 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 SER cc_start: 0.6495 (p) cc_final: 0.6292 (t) REVERT: A 190 ARG cc_start: 0.6635 (mtt90) cc_final: 0.6016 (mtp180) REVERT: A 298 GLU cc_start: 0.7245 (mt-10) cc_final: 0.6805 (mm-30) REVERT: A 389 ASP cc_start: 0.7670 (OUTLIER) cc_final: 0.7171 (m-30) REVERT: A 558 LYS cc_start: 0.7870 (mmtt) cc_final: 0.7609 (mmmt) REVERT: A 591 SER cc_start: 0.8260 (t) cc_final: 0.7772 (p) REVERT: A 646 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7413 (mtm180) REVERT: A 654 GLU cc_start: 0.7052 (mt-10) cc_final: 0.6698 (tt0) REVERT: A 661 GLU cc_start: 0.8319 (pm20) cc_final: 0.8035 (pt0) REVERT: A 1050 MET cc_start: 0.8229 (ptt) cc_final: 0.7843 (ptp) REVERT: A 1101 HIS cc_start: 0.6772 (m90) cc_final: 0.6547 (m170) REVERT: B 52 GLN cc_start: 0.7607 (tt0) cc_final: 0.6889 (pp30) REVERT: B 90 VAL cc_start: 0.5423 (OUTLIER) cc_final: 0.4890 (t) REVERT: B 169 GLU cc_start: 0.6165 (tt0) cc_final: 0.5630 (tm-30) REVERT: B 287 ASP cc_start: 0.7332 (t0) cc_final: 0.7005 (m-30) REVERT: B 360 ASN cc_start: 0.7214 (t0) cc_final: 0.6933 (m-40) REVERT: B 464 PHE cc_start: 0.7583 (m-80) cc_final: 0.7268 (m-80) REVERT: B 564 GLN cc_start: 0.6685 (tp40) cc_final: 0.6151 (mm110) REVERT: B 583 GLU cc_start: 0.7251 (pt0) cc_final: 0.6977 (pt0) REVERT: B 614 ASP cc_start: 0.7428 (p0) cc_final: 0.6950 (t0) REVERT: B 646 ARG cc_start: 0.8179 (ttt90) cc_final: 0.7426 (mmp-170) REVERT: B 661 GLU cc_start: 0.8333 (mm-30) cc_final: 0.7859 (mt-10) REVERT: B 740 MET cc_start: 0.7448 (ttt) cc_final: 0.6960 (mtt) REVERT: B 755 GLN cc_start: 0.6534 (mt0) cc_final: 0.6254 (mm110) REVERT: B 823 PHE cc_start: 0.7417 (m-80) cc_final: 0.7170 (m-80) REVERT: B 935 GLN cc_start: 0.6675 (mt0) cc_final: 0.6343 (mt0) REVERT: B 994 ASP cc_start: 0.7047 (t70) cc_final: 0.6628 (m-30) REVERT: B 995 ARG cc_start: 0.6653 (mtt90) cc_final: 0.6339 (mtm-85) REVERT: B 1050 MET cc_start: 0.8477 (ptt) cc_final: 0.8085 (ptm) REVERT: B 1113 GLN cc_start: 0.7190 (mt0) cc_final: 0.6923 (mm-40) REVERT: C 47 VAL cc_start: 0.7860 (p) cc_final: 0.7611 (m) REVERT: C 82 PRO cc_start: 0.7658 (Cg_endo) cc_final: 0.7446 (Cg_exo) REVERT: C 97 LYS cc_start: 0.5660 (OUTLIER) cc_final: 0.5387 (ttpt) REVERT: C 135 PHE cc_start: 0.4876 (m-80) cc_final: 0.4608 (m-80) REVERT: C 138 ASP cc_start: 0.7214 (OUTLIER) cc_final: 0.6769 (t0) REVERT: C 191 GLU cc_start: 0.8107 (pm20) cc_final: 0.7868 (pt0) REVERT: C 224 GLU cc_start: 0.7628 (pm20) cc_final: 0.7187 (mp0) REVERT: C 269 TYR cc_start: 0.7841 (m-80) cc_final: 0.7166 (m-80) REVERT: C 282 ASN cc_start: 0.8174 (m-40) cc_final: 0.7964 (m-40) REVERT: C 307 THR cc_start: 0.8064 (p) cc_final: 0.7746 (t) REVERT: C 309 GLU cc_start: 0.7307 (mt-10) cc_final: 0.7004 (mp0) REVERT: C 317 ASN cc_start: 0.8368 (m-40) cc_final: 0.8123 (m-40) REVERT: C 357 ARG cc_start: 0.7323 (ttt180) cc_final: 0.6889 (ttp-110) REVERT: C 532 ASN cc_start: 0.7052 (t0) cc_final: 0.6716 (p0) REVERT: C 646 ARG cc_start: 0.7829 (tpp80) cc_final: 0.7501 (ttt180) REVERT: C 1037 SER cc_start: 0.9044 (t) cc_final: 0.8823 (p) REVERT: C 1045 LYS cc_start: 0.8726 (mtpp) cc_final: 0.8200 (mptt) REVERT: C 1050 MET cc_start: 0.8437 (ptt) cc_final: 0.8059 (ptp) REVERT: X 12 MET cc_start: 0.2343 (tpp) cc_final: 0.2050 (tpp) REVERT: Y 83 MET cc_start: 0.3967 (mtp) cc_final: 0.3736 (mtm) outliers start: 57 outliers final: 6 residues processed: 478 average time/residue: 0.1977 time to fit residues: 146.7172 Evaluate side-chains 254 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 243 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 791 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS B 207 HIS B 314 GLN B 606 ASN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 HIS B1101 HIS ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN C 607 GLN C 954 GLN C 957 GLN C 969 ASN C1048 HIS C1119 ASN C1135 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.205293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.164707 restraints weight = 33131.766| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 2.10 r_work: 0.3360 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27769 Z= 0.150 Angle : 0.676 10.965 37893 Z= 0.325 Chirality : 0.048 0.327 4439 Planarity : 0.004 0.051 4765 Dihedral : 11.009 98.297 5008 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.48 % Allowed : 8.03 % Favored : 90.48 % 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: 0.03 (0.14), residues: 3288 helix: 1.30 (0.21), residues: 675 sheet: 0.12 (0.17), residues: 810 loop : -0.48 (0.14), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG Y 72 TYR 0.024 0.001 TYR A 369 PHE 0.026 0.001 PHE B 541 TRP 0.011 0.001 TRP Z 53 HIS 0.005 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00333 (27662) covalent geometry : angle 0.64592 (37614) SS BOND : bond 0.00581 ( 42) SS BOND : angle 1.53406 ( 84) hydrogen bonds : bond 0.04697 ( 1156) hydrogen bonds : angle 5.64005 ( 3090) link_BETA1-4 : bond 0.00553 ( 20) link_BETA1-4 : angle 2.09221 ( 60) link_NAG-ASN : bond 0.00493 ( 45) link_NAG-ASN : angle 2.91004 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 273 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.6682 (m-80) cc_final: 0.6374 (m-80) REVERT: A 190 ARG cc_start: 0.7988 (mtt90) cc_final: 0.7037 (mtp180) REVERT: A 281 GLU cc_start: 0.7100 (pt0) cc_final: 0.6628 (tt0) REVERT: A 355 ARG cc_start: 0.5901 (ttm-80) cc_final: 0.5622 (ttm-80) REVERT: A 558 LYS cc_start: 0.8639 (mmtt) cc_final: 0.8315 (mmmt) REVERT: A 869 MET cc_start: 0.8636 (mtt) cc_final: 0.8389 (mtp) REVERT: B 52 GLN cc_start: 0.7853 (tt0) cc_final: 0.7435 (pp30) REVERT: B 169 GLU cc_start: 0.6128 (tt0) cc_final: 0.5643 (tm-30) REVERT: B 332 ILE cc_start: 0.6872 (mt) cc_final: 0.6596 (pt) REVERT: B 464 PHE cc_start: 0.8349 (m-80) cc_final: 0.8097 (m-80) REVERT: B 755 GLN cc_start: 0.7570 (mt0) cc_final: 0.7278 (mm110) REVERT: B 994 ASP cc_start: 0.7354 (t70) cc_final: 0.6962 (t0) REVERT: C 317 ASN cc_start: 0.8355 (m-40) cc_final: 0.8005 (m-40) REVERT: C 408 ARG cc_start: 0.6931 (ptm-80) cc_final: 0.6349 (mtp-110) REVERT: C 529 LYS cc_start: 0.7266 (tptp) cc_final: 0.6806 (mtmt) REVERT: C 532 ASN cc_start: 0.7810 (t0) cc_final: 0.7351 (p0) REVERT: X 12 MET cc_start: 0.2819 (tpp) cc_final: 0.2374 (tpp) REVERT: Y 83 MET cc_start: 0.3671 (mtp) cc_final: 0.3454 (mtm) REVERT: Z 12 MET cc_start: 0.3543 (mmp) cc_final: 0.3097 (mmp) REVERT: Z 83 MET cc_start: 0.2067 (mtt) cc_final: 0.1833 (mpp) outliers start: 43 outliers final: 27 residues processed: 304 average time/residue: 0.1875 time to fit residues: 90.7683 Evaluate side-chains 224 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 197 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain Y residue 111 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 34 optimal weight: 10.0000 chunk 281 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 201 optimal weight: 0.9980 chunk 224 optimal weight: 9.9990 chunk 320 optimal weight: 10.0000 chunk 268 optimal weight: 1.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN B 87 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B1048 HIS B1135 ASN C 81 ASN ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 710 ASN C 913 GLN C 969 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.190647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.144368 restraints weight = 33311.159| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.55 r_work: 0.3100 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.096 27769 Z= 0.308 Angle : 0.786 13.464 37893 Z= 0.392 Chirality : 0.052 0.272 4439 Planarity : 0.005 0.111 4765 Dihedral : 9.654 85.802 4988 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.45 % Allowed : 9.45 % Favored : 88.10 % 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: -0.09 (0.14), residues: 3288 helix: 1.08 (0.20), residues: 664 sheet: 0.29 (0.17), residues: 786 loop : -0.62 (0.14), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 357 TYR 0.021 0.002 TYR A 369 PHE 0.030 0.003 PHE B 565 TRP 0.016 0.002 TRP C1102 HIS 0.008 0.002 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00755 (27662) covalent geometry : angle 0.75577 (37614) SS BOND : bond 0.00512 ( 42) SS BOND : angle 2.33361 ( 84) hydrogen bonds : bond 0.06214 ( 1156) hydrogen bonds : angle 5.76029 ( 3090) link_BETA1-4 : bond 0.00556 ( 20) link_BETA1-4 : angle 2.45203 ( 60) link_NAG-ASN : bond 0.00896 ( 45) link_NAG-ASN : angle 2.87509 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 243 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.8191 (mtt90) cc_final: 0.7413 (mtp180) REVERT: A 355 ARG cc_start: 0.6258 (ttm-80) cc_final: 0.5921 (ttm170) REVERT: A 558 LYS cc_start: 0.9016 (mmtt) cc_final: 0.8676 (mmmt) REVERT: B 332 ILE cc_start: 0.7328 (mt) cc_final: 0.6988 (pt) REVERT: B 415 THR cc_start: 0.7506 (t) cc_final: 0.7288 (t) REVERT: B 614 ASP cc_start: 0.7686 (m-30) cc_final: 0.7329 (t0) REVERT: B 994 ASP cc_start: 0.8308 (t70) cc_final: 0.7719 (t0) REVERT: B 1106 GLN cc_start: 0.9301 (OUTLIER) cc_final: 0.9031 (pt0) REVERT: C 529 LYS cc_start: 0.7457 (tptp) cc_final: 0.7008 (mtmt) REVERT: C 532 ASN cc_start: 0.7961 (t0) cc_final: 0.7573 (p0) REVERT: C 574 ASP cc_start: 0.8333 (t0) cc_final: 0.8078 (t0) REVERT: Y 83 MET cc_start: 0.4204 (mtp) cc_final: 0.3816 (mtm) REVERT: Z 12 MET cc_start: 0.3242 (mmp) cc_final: 0.2938 (mmp) REVERT: Z 83 MET cc_start: 0.2072 (mtt) cc_final: 0.1662 (mpp) outliers start: 71 outliers final: 53 residues processed: 304 average time/residue: 0.1773 time to fit residues: 87.3677 Evaluate side-chains 242 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 188 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 710 ASN Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain Y residue 28 THR Chi-restraints excluded: chain Y residue 111 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 151 optimal weight: 0.9990 chunk 219 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 233 optimal weight: 9.9990 chunk 303 optimal weight: 9.9990 chunk 154 optimal weight: 4.9990 chunk 174 optimal weight: 0.8980 chunk 142 optimal weight: 0.5980 chunk 305 optimal weight: 7.9990 chunk 159 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C1005 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.193308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.148651 restraints weight = 33097.382| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.46 r_work: 0.3155 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 27769 Z= 0.142 Angle : 0.634 16.441 37893 Z= 0.305 Chirality : 0.046 0.363 4439 Planarity : 0.004 0.051 4765 Dihedral : 8.608 78.955 4988 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.14 % Allowed : 10.59 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.14), residues: 3288 helix: 1.51 (0.20), residues: 671 sheet: 0.52 (0.17), residues: 775 loop : -0.48 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 237 TYR 0.019 0.001 TYR A 369 PHE 0.020 0.001 PHE B 541 TRP 0.012 0.001 TRP A 436 HIS 0.005 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00325 (27662) covalent geometry : angle 0.59371 (37614) SS BOND : bond 0.00291 ( 42) SS BOND : angle 2.10243 ( 84) hydrogen bonds : bond 0.04740 ( 1156) hydrogen bonds : angle 5.35671 ( 3090) link_BETA1-4 : bond 0.00493 ( 20) link_BETA1-4 : angle 2.37353 ( 60) link_NAG-ASN : bond 0.00641 ( 45) link_NAG-ASN : angle 3.07149 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 210 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8650 (t0) cc_final: 0.8378 (t0) REVERT: A 190 ARG cc_start: 0.8094 (mtt90) cc_final: 0.7361 (mtp180) REVERT: A 278 LYS cc_start: 0.8809 (tttt) cc_final: 0.8547 (ttpt) REVERT: A 281 GLU cc_start: 0.7144 (pt0) cc_final: 0.6748 (tt0) REVERT: A 298 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7647 (tp30) REVERT: A 355 ARG cc_start: 0.6356 (ttm-80) cc_final: 0.5991 (ttm170) REVERT: A 509 ARG cc_start: 0.5123 (mtt-85) cc_final: 0.4776 (mtt-85) REVERT: A 558 LYS cc_start: 0.8966 (mmtt) cc_final: 0.8687 (mmmt) REVERT: A 1133 VAL cc_start: 0.9245 (OUTLIER) cc_final: 0.9033 (m) REVERT: B 86 PHE cc_start: 0.7088 (t80) cc_final: 0.6774 (t80) REVERT: B 229 LEU cc_start: 0.6090 (mt) cc_final: 0.5854 (mp) REVERT: B 271 GLN cc_start: 0.7635 (mt0) cc_final: 0.7421 (mt0) REVERT: B 393 THR cc_start: 0.6917 (OUTLIER) cc_final: 0.6599 (t) REVERT: B 415 THR cc_start: 0.7590 (t) cc_final: 0.7109 (t) REVERT: B 619 GLU cc_start: 0.6264 (mt-10) cc_final: 0.5909 (mt-10) REVERT: B 811 LYS cc_start: 0.5054 (OUTLIER) cc_final: 0.4581 (tttt) REVERT: B 994 ASP cc_start: 0.7966 (t70) cc_final: 0.7507 (t0) REVERT: C 355 ARG cc_start: 0.7753 (ttm-80) cc_final: 0.7524 (ttm170) REVERT: C 532 ASN cc_start: 0.8081 (t0) cc_final: 0.7690 (p0) REVERT: C 900 MET cc_start: 0.8796 (mtp) cc_final: 0.8585 (mtp) REVERT: Y 34 MET cc_start: 0.4604 (mtm) cc_final: 0.4111 (ptt) REVERT: Z 12 MET cc_start: 0.3425 (mmp) cc_final: 0.3128 (mmp) outliers start: 62 outliers final: 41 residues processed: 258 average time/residue: 0.1698 time to fit residues: 70.7330 Evaluate side-chains 231 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 187 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain Y residue 28 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 327 optimal weight: 9.9990 chunk 208 optimal weight: 6.9990 chunk 205 optimal weight: 3.9990 chunk 230 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 302 optimal weight: 0.0770 chunk 285 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 198 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 overall best weight: 1.3344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN C 317 ASN ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.197206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.162282 restraints weight = 33005.227| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 1.80 r_work: 0.3512 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.4435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 27769 Z= 0.159 Angle : 0.619 13.447 37893 Z= 0.298 Chirality : 0.046 0.243 4439 Planarity : 0.004 0.048 4765 Dihedral : 7.580 65.700 4988 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.69 % Allowed : 11.24 % Favored : 86.07 % 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: 0.31 (0.14), residues: 3288 helix: 1.56 (0.21), residues: 669 sheet: 0.54 (0.17), residues: 798 loop : -0.43 (0.14), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 34 TYR 0.018 0.001 TYR B 369 PHE 0.024 0.002 PHE A 392 TRP 0.011 0.001 TRP A 436 HIS 0.005 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00380 (27662) covalent geometry : angle 0.58691 (37614) SS BOND : bond 0.00336 ( 42) SS BOND : angle 1.81853 ( 84) hydrogen bonds : bond 0.04648 ( 1156) hydrogen bonds : angle 5.20011 ( 3090) link_BETA1-4 : bond 0.00442 ( 20) link_BETA1-4 : angle 2.52294 ( 60) link_NAG-ASN : bond 0.00585 ( 45) link_NAG-ASN : angle 2.59247 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 215 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8608 (t0) cc_final: 0.8406 (t0) REVERT: A 190 ARG cc_start: 0.7945 (mtt90) cc_final: 0.7543 (mtp180) REVERT: A 298 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7731 (tp30) REVERT: A 355 ARG cc_start: 0.6732 (ttm-80) cc_final: 0.6521 (ttm170) REVERT: A 916 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8476 (tp) REVERT: B 415 THR cc_start: 0.7637 (t) cc_final: 0.7409 (t) REVERT: B 614 ASP cc_start: 0.7380 (m-30) cc_final: 0.7015 (t0) REVERT: B 811 LYS cc_start: 0.5235 (OUTLIER) cc_final: 0.4756 (tttt) REVERT: C 532 ASN cc_start: 0.7949 (t0) cc_final: 0.7746 (p0) REVERT: C 796 ASP cc_start: 0.8088 (p0) cc_final: 0.7695 (p0) REVERT: Y 34 MET cc_start: 0.4308 (mtm) cc_final: 0.3975 (ptt) REVERT: Z 12 MET cc_start: 0.3333 (mmp) cc_final: 0.3047 (mmt) outliers start: 78 outliers final: 48 residues processed: 280 average time/residue: 0.1714 time to fit residues: 78.5819 Evaluate side-chains 235 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 185 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain X residue 79 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 123 optimal weight: 1.9990 chunk 221 optimal weight: 7.9990 chunk 180 optimal weight: 0.7980 chunk 232 optimal weight: 10.0000 chunk 184 optimal weight: 0.9980 chunk 235 optimal weight: 0.0770 chunk 225 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 166 optimal weight: 0.0050 chunk 233 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 overall best weight: 0.5552 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 804 GLN A 935 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 787 GLN B1106 GLN C 81 ASN ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C1142 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.199397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.163738 restraints weight = 32979.254| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 1.87 r_work: 0.3521 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.4582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 27769 Z= 0.106 Angle : 0.568 10.471 37893 Z= 0.273 Chirality : 0.044 0.235 4439 Planarity : 0.003 0.045 4765 Dihedral : 6.920 59.915 4988 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.07 % Allowed : 12.59 % Favored : 85.34 % 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: 0.52 (0.14), residues: 3288 helix: 1.81 (0.21), residues: 669 sheet: 0.63 (0.17), residues: 794 loop : -0.30 (0.14), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 237 TYR 0.017 0.001 TYR B 369 PHE 0.025 0.001 PHE A 392 TRP 0.010 0.001 TRP A 436 HIS 0.004 0.000 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00235 (27662) covalent geometry : angle 0.53746 (37614) SS BOND : bond 0.00308 ( 42) SS BOND : angle 1.74620 ( 84) hydrogen bonds : bond 0.04016 ( 1156) hydrogen bonds : angle 5.01373 ( 3090) link_BETA1-4 : bond 0.00303 ( 20) link_BETA1-4 : angle 2.49236 ( 60) link_NAG-ASN : bond 0.00455 ( 45) link_NAG-ASN : angle 2.29608 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 211 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.7913 (mtt90) cc_final: 0.7506 (mtp180) REVERT: A 298 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7739 (tp30) REVERT: A 355 ARG cc_start: 0.6770 (ttm-80) cc_final: 0.6477 (ttm170) REVERT: A 392 PHE cc_start: 0.6153 (m-10) cc_final: 0.5945 (m-10) REVERT: A 916 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8462 (tp) REVERT: B 415 THR cc_start: 0.7698 (t) cc_final: 0.7431 (t) REVERT: B 811 LYS cc_start: 0.4999 (OUTLIER) cc_final: 0.4728 (tttt) REVERT: C 81 ASN cc_start: 0.6030 (m-40) cc_final: 0.5776 (m110) REVERT: C 355 ARG cc_start: 0.8060 (ttm170) cc_final: 0.7720 (ttm170) REVERT: C 796 ASP cc_start: 0.8088 (p0) cc_final: 0.7706 (p0) REVERT: Y 34 MET cc_start: 0.4304 (mtm) cc_final: 0.3967 (ptt) REVERT: Z 12 MET cc_start: 0.3441 (mmp) cc_final: 0.3201 (mmt) outliers start: 60 outliers final: 45 residues processed: 262 average time/residue: 0.1590 time to fit residues: 69.9851 Evaluate side-chains 229 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 182 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain X residue 79 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 43 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 235 optimal weight: 0.2980 chunk 256 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 327 optimal weight: 20.0000 chunk 195 optimal weight: 0.5980 chunk 134 optimal weight: 1.9990 chunk 251 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.196561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.161316 restraints weight = 32724.145| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 1.81 r_work: 0.3487 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.4822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 27769 Z= 0.157 Angle : 0.594 10.095 37893 Z= 0.288 Chirality : 0.045 0.234 4439 Planarity : 0.004 0.041 4765 Dihedral : 6.648 57.116 4987 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.41 % Allowed : 12.17 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.14), residues: 3288 helix: 1.70 (0.21), residues: 669 sheet: 0.65 (0.17), residues: 802 loop : -0.37 (0.14), residues: 1817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 403 TYR 0.023 0.001 TYR B 453 PHE 0.023 0.001 PHE B 456 TRP 0.010 0.001 TRP A 436 HIS 0.005 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00379 (27662) covalent geometry : angle 0.56475 (37614) SS BOND : bond 0.00366 ( 42) SS BOND : angle 1.83349 ( 84) hydrogen bonds : bond 0.04525 ( 1156) hydrogen bonds : angle 5.05562 ( 3090) link_BETA1-4 : bond 0.00365 ( 20) link_BETA1-4 : angle 2.60493 ( 60) link_NAG-ASN : bond 0.00374 ( 45) link_NAG-ASN : angle 2.22220 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 193 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.8013 (mtt90) cc_final: 0.7616 (mtp180) REVERT: A 298 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7986 (tp30) REVERT: A 355 ARG cc_start: 0.6819 (ttm-80) cc_final: 0.6525 (ttm170) REVERT: A 916 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8678 (tp) REVERT: B 334 ASN cc_start: 0.6811 (t0) cc_final: 0.6413 (t0) REVERT: B 415 THR cc_start: 0.7775 (t) cc_final: 0.7534 (t) REVERT: B 811 LYS cc_start: 0.5309 (OUTLIER) cc_final: 0.4871 (tttt) REVERT: B 994 ASP cc_start: 0.7976 (t0) cc_final: 0.7565 (t0) REVERT: C 355 ARG cc_start: 0.8076 (ttm170) cc_final: 0.7771 (ttm170) REVERT: C 442 ASP cc_start: 0.4857 (m-30) cc_final: 0.4328 (m-30) REVERT: C 796 ASP cc_start: 0.8143 (p0) cc_final: 0.7744 (p0) REVERT: X 22 CYS cc_start: -0.0423 (OUTLIER) cc_final: -0.1320 (m) REVERT: Y 83 MET cc_start: 0.3057 (mtt) cc_final: 0.2670 (tmm) REVERT: Z 12 MET cc_start: 0.3430 (mmp) cc_final: 0.3048 (mmt) outliers start: 70 outliers final: 55 residues processed: 248 average time/residue: 0.1628 time to fit residues: 67.1828 Evaluate side-chains 245 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 187 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain X residue 22 CYS Chi-restraints excluded: chain X residue 79 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 61 optimal weight: 2.9990 chunk 310 optimal weight: 9.9990 chunk 191 optimal weight: 0.7980 chunk 257 optimal weight: 0.9990 chunk 294 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 152 optimal weight: 0.9990 chunk 132 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 238 optimal weight: 9.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.194283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.159731 restraints weight = 32822.959| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 1.69 r_work: 0.3448 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.5241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 27769 Z= 0.191 Angle : 0.625 9.703 37893 Z= 0.306 Chirality : 0.046 0.257 4439 Planarity : 0.004 0.040 4765 Dihedral : 6.529 56.271 4987 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.28 % Allowed : 12.86 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.14), residues: 3288 helix: 1.54 (0.21), residues: 675 sheet: 0.59 (0.17), residues: 799 loop : -0.48 (0.14), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 403 TYR 0.019 0.001 TYR B 453 PHE 0.020 0.002 PHE A 392 TRP 0.010 0.001 TRP C 436 HIS 0.005 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00466 (27662) covalent geometry : angle 0.59562 (37614) SS BOND : bond 0.00396 ( 42) SS BOND : angle 1.97906 ( 84) hydrogen bonds : bond 0.04943 ( 1156) hydrogen bonds : angle 5.14980 ( 3090) link_BETA1-4 : bond 0.00328 ( 20) link_BETA1-4 : angle 2.62467 ( 60) link_NAG-ASN : bond 0.00380 ( 45) link_NAG-ASN : angle 2.29556 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 204 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.8078 (mtt90) cc_final: 0.7693 (mtp180) REVERT: A 298 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7948 (tp30) REVERT: A 355 ARG cc_start: 0.7047 (ttm-80) cc_final: 0.6612 (ttm170) REVERT: A 916 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8725 (tp) REVERT: B 117 LEU cc_start: 0.7994 (mp) cc_final: 0.7435 (tt) REVERT: B 334 ASN cc_start: 0.6925 (t0) cc_final: 0.6245 (m110) REVERT: B 449 TYR cc_start: 0.7426 (m-10) cc_final: 0.7175 (m-80) REVERT: B 495 TYR cc_start: 0.7177 (m-80) cc_final: 0.6827 (m-10) REVERT: B 811 LYS cc_start: 0.5375 (OUTLIER) cc_final: 0.4906 (tttt) REVERT: B 994 ASP cc_start: 0.8020 (t0) cc_final: 0.7631 (t0) REVERT: C 424 LYS cc_start: 0.7766 (tptt) cc_final: 0.7495 (tppt) REVERT: C 442 ASP cc_start: 0.4751 (m-30) cc_final: 0.4249 (m-30) REVERT: C 796 ASP cc_start: 0.8201 (p0) cc_final: 0.7813 (p0) REVERT: X 22 CYS cc_start: -0.0275 (OUTLIER) cc_final: -0.1270 (m) REVERT: Z 12 MET cc_start: 0.3669 (mmp) cc_final: 0.2971 (mmt) outliers start: 66 outliers final: 58 residues processed: 256 average time/residue: 0.1686 time to fit residues: 71.8495 Evaluate side-chains 248 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 187 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain X residue 22 CYS Chi-restraints excluded: chain X residue 79 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 2 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 270 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 218 optimal weight: 0.2980 chunk 101 optimal weight: 0.7980 chunk 130 optimal weight: 0.3980 chunk 236 optimal weight: 20.0000 chunk 188 optimal weight: 0.9980 chunk 263 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 762 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.197331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.162716 restraints weight = 32837.572| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 1.76 r_work: 0.3499 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.5326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 27769 Z= 0.108 Angle : 0.557 10.041 37893 Z= 0.272 Chirality : 0.044 0.255 4439 Planarity : 0.003 0.040 4765 Dihedral : 6.000 53.479 4987 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.14 % Allowed : 13.14 % Favored : 84.72 % 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: 0.47 (0.15), residues: 3288 helix: 1.84 (0.21), residues: 668 sheet: 0.58 (0.17), residues: 816 loop : -0.36 (0.15), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 403 TYR 0.024 0.001 TYR B 489 PHE 0.020 0.001 PHE A 392 TRP 0.012 0.001 TRP C 436 HIS 0.005 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00242 (27662) covalent geometry : angle 0.53184 (37614) SS BOND : bond 0.00314 ( 42) SS BOND : angle 1.66435 ( 84) hydrogen bonds : bond 0.04002 ( 1156) hydrogen bonds : angle 4.94366 ( 3090) link_BETA1-4 : bond 0.00317 ( 20) link_BETA1-4 : angle 2.45071 ( 60) link_NAG-ASN : bond 0.00323 ( 45) link_NAG-ASN : angle 1.98963 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 201 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.3459 (OUTLIER) cc_final: 0.3096 (p-80) REVERT: A 110 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7082 (mp) REVERT: A 190 ARG cc_start: 0.7891 (mtt90) cc_final: 0.7587 (mtp180) REVERT: A 298 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7742 (tp30) REVERT: A 355 ARG cc_start: 0.7062 (ttm-80) cc_final: 0.6644 (ttm170) REVERT: A 916 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8524 (tp) REVERT: B 117 LEU cc_start: 0.7671 (mp) cc_final: 0.7418 (tt) REVERT: B 334 ASN cc_start: 0.6896 (t0) cc_final: 0.6304 (m110) REVERT: B 449 TYR cc_start: 0.7240 (m-10) cc_final: 0.7001 (m-80) REVERT: B 811 LYS cc_start: 0.5101 (OUTLIER) cc_final: 0.4898 (tttt) REVERT: B 994 ASP cc_start: 0.7567 (t0) cc_final: 0.7240 (t0) REVERT: C 421 TYR cc_start: 0.5149 (m-80) cc_final: 0.4515 (m-80) REVERT: C 442 ASP cc_start: 0.4431 (m-30) cc_final: 0.4090 (m-30) REVERT: C 796 ASP cc_start: 0.8028 (p0) cc_final: 0.7570 (t0) REVERT: X 22 CYS cc_start: -0.0345 (OUTLIER) cc_final: -0.1301 (m) REVERT: Z 12 MET cc_start: 0.3858 (mmp) cc_final: 0.3207 (mmt) outliers start: 62 outliers final: 48 residues processed: 247 average time/residue: 0.1556 time to fit residues: 64.6786 Evaluate side-chains 244 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 191 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain X residue 22 CYS Chi-restraints excluded: chain X residue 79 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 10 optimal weight: 7.9990 chunk 104 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 167 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 54 optimal weight: 0.9980 chunk 268 optimal weight: 0.5980 chunk 317 optimal weight: 6.9990 chunk 255 optimal weight: 3.9990 chunk 166 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.195533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.161489 restraints weight = 32665.038| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 1.64 r_work: 0.3506 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.5464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 27769 Z= 0.148 Angle : 0.584 10.402 37893 Z= 0.285 Chirality : 0.045 0.254 4439 Planarity : 0.004 0.042 4765 Dihedral : 5.894 52.302 4987 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.97 % Allowed : 13.31 % Favored : 84.72 % 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: 0.40 (0.14), residues: 3288 helix: 1.71 (0.21), residues: 683 sheet: 0.51 (0.17), residues: 823 loop : -0.40 (0.15), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 403 TYR 0.023 0.001 TYR B 489 PHE 0.021 0.001 PHE A 392 TRP 0.010 0.001 TRP A 436 HIS 0.005 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00352 (27662) covalent geometry : angle 0.55844 (37614) SS BOND : bond 0.00355 ( 42) SS BOND : angle 1.71259 ( 84) hydrogen bonds : bond 0.04427 ( 1156) hydrogen bonds : angle 4.99918 ( 3090) link_BETA1-4 : bond 0.00320 ( 20) link_BETA1-4 : angle 2.52957 ( 60) link_NAG-ASN : bond 0.00319 ( 45) link_NAG-ASN : angle 2.03704 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 194 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.3672 (OUTLIER) cc_final: 0.3223 (p-80) REVERT: A 110 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7305 (mp) REVERT: A 190 ARG cc_start: 0.8047 (mtt90) cc_final: 0.7717 (mtp180) REVERT: A 298 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7934 (tp30) REVERT: A 355 ARG cc_start: 0.7150 (ttm-80) cc_final: 0.6774 (ttm170) REVERT: A 916 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8696 (tp) REVERT: B 117 LEU cc_start: 0.8014 (mp) cc_final: 0.7561 (tt) REVERT: B 334 ASN cc_start: 0.6931 (t0) cc_final: 0.6359 (m110) REVERT: B 449 TYR cc_start: 0.7293 (m-10) cc_final: 0.7013 (m-80) REVERT: B 811 LYS cc_start: 0.5208 (OUTLIER) cc_final: 0.4804 (tttt) REVERT: B 994 ASP cc_start: 0.7955 (t0) cc_final: 0.7567 (t0) REVERT: C 421 TYR cc_start: 0.5110 (m-80) cc_final: 0.4600 (m-80) REVERT: C 424 LYS cc_start: 0.7734 (tptt) cc_final: 0.7392 (tptt) REVERT: C 442 ASP cc_start: 0.4510 (m-30) cc_final: 0.4192 (m-30) REVERT: C 796 ASP cc_start: 0.8138 (p0) cc_final: 0.7617 (t0) REVERT: X 22 CYS cc_start: -0.0351 (OUTLIER) cc_final: -0.1340 (m) REVERT: Z 12 MET cc_start: 0.4130 (mmp) cc_final: 0.3353 (mmt) outliers start: 57 outliers final: 48 residues processed: 239 average time/residue: 0.1574 time to fit residues: 62.9699 Evaluate side-chains 241 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 188 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain X residue 22 CYS Chi-restraints excluded: chain X residue 79 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 113 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 37 optimal weight: 0.6980 chunk 208 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 161 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 263 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.194103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.163320 restraints weight = 32341.293| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 1.54 r_work: 0.3546 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.5662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 27769 Z= 0.186 Angle : 0.620 10.339 37893 Z= 0.305 Chirality : 0.046 0.249 4439 Planarity : 0.004 0.042 4765 Dihedral : 6.042 52.223 4987 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.00 % Allowed : 13.34 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.14), residues: 3288 helix: 1.64 (0.20), residues: 678 sheet: 0.47 (0.17), residues: 826 loop : -0.48 (0.14), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Y 52 TYR 0.030 0.001 TYR B 489 PHE 0.023 0.002 PHE A 392 TRP 0.012 0.001 TRP Y 53 HIS 0.005 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00456 (27662) covalent geometry : angle 0.59408 (37614) SS BOND : bond 0.00391 ( 42) SS BOND : angle 1.92733 ( 84) hydrogen bonds : bond 0.04780 ( 1156) hydrogen bonds : angle 5.10615 ( 3090) link_BETA1-4 : bond 0.00349 ( 20) link_BETA1-4 : angle 2.58699 ( 60) link_NAG-ASN : bond 0.00316 ( 45) link_NAG-ASN : angle 2.05744 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5643.42 seconds wall clock time: 97 minutes 49.04 seconds (5869.04 seconds total)