Starting phenix.real_space_refine on Sun Jul 5 10:21:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7z86_14544/07_2026/7z86_14544.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z86_14544/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/7z86_14544/07_2026/7z86_14544.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z86_14544/07_2026/7z86_14544.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7z86_14544/07_2026/7z86_14544.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7z86_14544/07_2026/7z86_14544.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z86_14544/07_2026/7z86_14544.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z86_14544/07_2026/7z86_14544.map" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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 chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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 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 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 chiralities: 8 Time building chain proxies: 6.23, per 1000 atoms: 0.23 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: 2.66 Conformation dependent library (CDL) restraints added in 1.3 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: 1.28 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: 8.65 Time building geometry restraints manager: 3.51 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 - 17.82: 14845 17.82 - 35.65: 765 35.65 - 53.47: 183 53.47 - 71.29: 67 71.29 - 89.12: 27 Dihedral angle restraints: 15887 sinusoidal: 6163 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 15884 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: 2.760 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: 0.030 Extract box with map and model: 0.320 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 30.020 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.110 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:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 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 : 12.773 89.116 9517 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/Z covalent geometry : bond 0.00815 / 0.51 (27662) covalent geometry : angle 1.19294 / 0.75 (37614) SS BOND : bond 0.01740 / 1.11 ( 42) SS BOND : angle 2.12738 / 1.33 ( 84) hydrogen bonds : bond 0.13308 / 8.93 ( 1156) hydrogen bonds : angle 6.85125 / 4.79 ( 3090) link_BETA1-4 : bond 0.00436 / 0.30 ( 20) link_BETA1-4 : angle 1.55803 / 1.05 ( 60) link_NAG-ASN : bond 0.01460 / 0.94 ( 45) link_NAG-ASN : angle 6.00086 / 3.91 ( 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 : 0.937 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: 0.1847 time to fit residues: 138.2041 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 : 0.993 ------------------------------------------------------------------------------- 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... 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 = 0.205258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.163031 restraints weight = 33135.455| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 2.13 r_work: 0.3376 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27769 Z= 0.148 Angle : 0.673 11.300 37893 Z= 0.324 Chirality : 0.047 0.227 4439 Planarity : 0.004 0.051 4765 Dihedral : 4.930 52.103 3622 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.48 % Allowed : 8.17 % Favored : 90.34 % 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: 0.03 (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 0.000 ARG C 319 TYR 0.024 0.001 TYR A 369 PHE 0.026 0.002 PHE B 541 TRP 0.011 0.001 TRP Z 53 HIS 0.010 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (27662) covalent geometry : angle 0.64513 / 0.32 (37614) SS BOND : bond 0.00366 / 0.20 ( 42) SS BOND : angle 1.67421 / 1.03 ( 84) hydrogen bonds : bond 0.04738 / 3.11 ( 1156) hydrogen bonds : angle 5.64343 / 3.98 ( 3090) link_BETA1-4 : bond 0.00273 / 0.16 ( 20) link_BETA1-4 : angle 1.48011 / 0.97 ( 60) link_NAG-ASN : bond 0.00534 / 0.33 ( 45) link_NAG-ASN : angle 2.87876 / 1.89 ( 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 318 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 275 time to evaluate : 0.975 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: 0.6722 (m-80) cc_final: 0.6398 (m-80) REVERT: A 190 ARG cc_start: 0.7989 (mtt90) cc_final: 0.7060 (mtp180) REVERT: A 281 GLU cc_start: 0.7031 (pt0) cc_final: 0.6594 (tt0) REVERT: A 558 LYS cc_start: 0.8658 (mmtt) cc_final: 0.8345 (mmmt) REVERT: A 869 MET cc_start: 0.8643 (mtt) cc_final: 0.8404 (mtp) REVERT: B 52 GLN cc_start: 0.7913 (tt0) cc_final: 0.7453 (pp30) REVERT: B 169 GLU cc_start: 0.6136 (tt0) cc_final: 0.5680 (tm-30) REVERT: B 755 GLN cc_start: 0.7544 (mt0) cc_final: 0.7283 (mm110) REVERT: B 994 ASP cc_start: 0.7387 (t70) cc_final: 0.6997 (t0) REVERT: C 317 ASN cc_start: 0.8362 (m-40) cc_final: 0.8015 (m-40) REVERT: C 408 ARG cc_start: 0.6967 (ptm-80) cc_final: 0.6389 (mtp-110) REVERT: C 529 LYS cc_start: 0.7290 (tptp) cc_final: 0.6824 (mtmt) REVERT: C 532 ASN cc_start: 0.7833 (t0) cc_final: 0.7373 (p0) REVERT: X 12 MET cc_start: 0.2791 (tpp) cc_final: 0.2371 (tpp) REVERT: Z 12 MET cc_start: 0.3488 (mmp) cc_final: 0.3047 (mmp) REVERT: Z 83 MET cc_start: 0.2153 (mtt) cc_final: 0.1949 (mpp) outliers start: 43 outliers final: 27 residues processed: 306 average time/residue: 0.1779 time to fit residues: 87.2627 Evaluate side-chains 225 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 198 time to evaluate : 0.930 ------------------------------------------------------------------------------- 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: 8.9990 chunk 281 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 51 optimal weight: 0.9980 chunk 201 optimal weight: 0.4980 chunk 224 optimal weight: 9.9990 chunk 320 optimal weight: 8.9990 chunk 268 optimal weight: 0.7980 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 710 ASN C 913 GLN C 969 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.193761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.148486 restraints weight = 33224.573| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 2.53 r_work: 0.3158 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 27769 Z= 0.223 Angle : 0.700 10.115 37893 Z= 0.350 Chirality : 0.049 0.304 4439 Planarity : 0.005 0.164 4765 Dihedral : 4.673 49.247 3602 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.34 % Allowed : 9.41 % Favored : 88.24 % 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: 0.16 (0.14), residues: 3288 helix: 1.35 (0.20), residues: 667 sheet: 0.46 (0.17), residues: 785 loop : -0.49 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG X 52 TYR 0.020 0.002 TYR A 369 PHE 0.027 0.002 PHE B 565 TRP 0.013 0.002 TRP C1102 HIS 0.007 0.002 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.22 (27662) covalent geometry : angle 0.67441 / 0.34 (37614) SS BOND : bond 0.00455 / 0.30 ( 42) SS BOND : angle 2.02623 / 1.33 ( 84) hydrogen bonds : bond 0.05530 / 3.67 ( 1156) hydrogen bonds : angle 5.58778 / 3.90 ( 3090) link_BETA1-4 : bond 0.00535 / 0.29 ( 20) link_BETA1-4 : angle 1.58427 / 0.99 ( 60) link_NAG-ASN : bond 0.00515 / 0.35 ( 45) link_NAG-ASN : angle 2.65809 / 1.78 ( 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 315 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 247 time to evaluate : 0.986 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 32 PHE cc_start: 0.8416 (m-80) cc_final: 0.8170 (m-10) REVERT: A 53 ASP cc_start: 0.8684 (t0) cc_final: 0.8466 (t70) REVERT: A 170 TYR cc_start: 0.6818 (t80) cc_final: 0.6500 (t80) REVERT: A 190 ARG cc_start: 0.8102 (mtt90) cc_final: 0.7339 (mtp180) REVERT: A 278 LYS cc_start: 0.8878 (tttt) cc_final: 0.8615 (ttpp) REVERT: A 281 GLU cc_start: 0.7229 (pt0) cc_final: 0.6773 (tt0) REVERT: A 355 ARG cc_start: 0.6445 (ttm-80) cc_final: 0.6122 (ttm170) REVERT: A 365 TYR cc_start: 0.7231 (m-80) cc_final: 0.6813 (m-80) REVERT: A 558 LYS cc_start: 0.9006 (mmtt) cc_final: 0.8682 (mmmt) REVERT: A 1073 LYS cc_start: 0.8597 (mttt) cc_final: 0.8397 (mtpp) REVERT: B 237 ARG cc_start: 0.7060 (mtm180) cc_final: 0.6852 (mtm180) REVERT: B 415 THR cc_start: 0.7467 (t) cc_final: 0.7219 (t) REVERT: B 614 ASP cc_start: 0.7735 (m-30) cc_final: 0.7147 (t0) REVERT: B 994 ASP cc_start: 0.8121 (t70) cc_final: 0.7574 (t0) REVERT: B 1106 GLN cc_start: 0.9270 (OUTLIER) cc_final: 0.9032 (pt0) REVERT: C 529 LYS cc_start: 0.7405 (tptp) cc_final: 0.6978 (mtmt) REVERT: C 532 ASN cc_start: 0.7792 (t0) cc_final: 0.7498 (p0) REVERT: C 574 ASP cc_start: 0.8383 (t0) cc_final: 0.8131 (t0) REVERT: Y 83 MET cc_start: 0.3350 (mtm) cc_final: 0.1871 (tmm) REVERT: Z 83 MET cc_start: 0.2080 (mtt) cc_final: 0.1724 (mpp) outliers start: 68 outliers final: 50 residues processed: 306 average time/residue: 0.1697 time to fit residues: 84.7279 Evaluate side-chains 245 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 194 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 532 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 620 VAL 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 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 878 LEU 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: 4.9990 chunk 49 optimal weight: 2.9990 chunk 233 optimal weight: 8.9990 chunk 303 optimal weight: 8.9990 chunk 154 optimal weight: 2.9990 chunk 174 optimal weight: 0.8980 chunk 142 optimal weight: 0.7980 chunk 305 optimal weight: 10.0000 chunk 159 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS ** B 239 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 239 GLN ** 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 = 0.4170 r_free = 0.4170 target = 0.195719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.151367 restraints weight = 33083.905| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 2.52 r_work: 0.3170 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 27769 Z= 0.127 Angle : 0.595 16.035 37893 Z= 0.290 Chirality : 0.045 0.390 4439 Planarity : 0.004 0.058 4765 Dihedral : 4.298 46.752 3602 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.72 % Allowed : 10.97 % Favored : 87.31 % 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: 0.41 (0.14), residues: 3288 helix: 1.76 (0.21), residues: 657 sheet: 0.50 (0.17), residues: 796 loop : -0.34 (0.14), residues: 1835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 237 TYR 0.018 0.001 TYR A 369 PHE 0.019 0.001 PHE B 541 TRP 0.012 0.001 TRP A 436 HIS 0.004 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (27662) covalent geometry : angle 0.56131 / 0.28 (37614) SS BOND : bond 0.00253 / 0.15 ( 42) SS BOND : angle 2.08477 / 1.18 ( 84) hydrogen bonds : bond 0.04450 / 2.94 ( 1156) hydrogen bonds : angle 5.27333 / 3.69 ( 3090) link_BETA1-4 : bond 0.00244 / 0.13 ( 20) link_BETA1-4 : angle 1.38144 / 0.89 ( 60) link_NAG-ASN : bond 0.00696 / 0.31 ( 45) link_NAG-ASN : angle 2.83730 / 2.04 ( 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 270 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 220 time to evaluate : 0.889 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 32 PHE cc_start: 0.8395 (m-80) cc_final: 0.8184 (m-10) REVERT: A 53 ASP cc_start: 0.8596 (t0) cc_final: 0.8353 (t0) REVERT: A 190 ARG cc_start: 0.8033 (mtt90) cc_final: 0.7267 (mtp180) REVERT: A 278 LYS cc_start: 0.8908 (tttt) cc_final: 0.8646 (ttpt) REVERT: A 281 GLU cc_start: 0.7139 (pt0) cc_final: 0.6731 (tt0) REVERT: A 298 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7715 (tp30) REVERT: A 355 ARG cc_start: 0.6397 (ttm-80) cc_final: 0.6059 (ttm170) REVERT: A 558 LYS cc_start: 0.8963 (mmtt) cc_final: 0.8678 (mmmt) REVERT: A 1133 VAL cc_start: 0.9270 (OUTLIER) cc_final: 0.9026 (m) REVERT: B 237 ARG cc_start: 0.7051 (mtm180) cc_final: 0.6822 (mtm180) REVERT: B 271 GLN cc_start: 0.7521 (mt0) cc_final: 0.7316 (mt0) REVERT: B 415 THR cc_start: 0.7545 (t) cc_final: 0.7108 (t) REVERT: B 614 ASP cc_start: 0.7699 (m-30) cc_final: 0.7158 (t0) REVERT: B 619 GLU cc_start: 0.6159 (mt-10) cc_final: 0.5804 (mt-10) REVERT: B 811 LYS cc_start: 0.5081 (OUTLIER) cc_final: 0.4536 (tttt) REVERT: B 859 THR cc_start: 0.8985 (p) cc_final: 0.8735 (m) REVERT: B 994 ASP cc_start: 0.7884 (t70) cc_final: 0.7353 (t0) REVERT: C 271 GLN cc_start: 0.7593 (mt0) cc_final: 0.7236 (mm-40) REVERT: C 529 LYS cc_start: 0.7369 (tptp) cc_final: 0.6933 (mtmt) REVERT: C 532 ASN cc_start: 0.8031 (t0) cc_final: 0.7632 (p0) REVERT: C 574 ASP cc_start: 0.8310 (t0) cc_final: 0.8051 (t0) REVERT: Y 34 MET cc_start: 0.4565 (mtm) cc_final: 0.4061 (ptt) REVERT: Y 83 MET cc_start: 0.3294 (mtm) cc_final: 0.1922 (tmm) REVERT: Z 12 MET cc_start: 0.3432 (mmp) cc_final: 0.3118 (mmp) outliers start: 50 outliers final: 36 residues processed: 257 average time/residue: 0.1704 time to fit residues: 70.6867 Evaluate side-chains 235 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 197 time to evaluate : 0.840 ------------------------------------------------------------------------------- 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 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 1100 THR Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR 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 532 ASN 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 392 PHE Chi-restraints excluded: chain C residue 430 THR 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 Y residue 28 THR Chi-restraints excluded: chain Y residue 111 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 327 optimal weight: 8.9990 chunk 208 optimal weight: 7.9990 chunk 205 optimal weight: 3.9990 chunk 230 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 302 optimal weight: 0.0670 chunk 285 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 198 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 overall best weight: 1.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN C 450 ASN ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.190819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.144753 restraints weight = 33004.896| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.16 r_work: 0.3153 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 27769 Z= 0.201 Angle : 0.628 11.275 37893 Z= 0.312 Chirality : 0.046 0.208 4439 Planarity : 0.004 0.051 4765 Dihedral : 4.425 46.940 3602 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.76 % Allowed : 10.97 % Favored : 86.28 % 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: 0.24 (0.14), residues: 3288 helix: 1.48 (0.20), residues: 666 sheet: 0.50 (0.17), residues: 799 loop : -0.47 (0.14), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 319 TYR 0.018 0.002 TYR A 369 PHE 0.026 0.002 PHE A 392 TRP 0.011 0.001 TRP A 436 HIS 0.006 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.20 (27662) covalent geometry : angle 0.60320 / 0.30 (37614) SS BOND : bond 0.00604 / 0.41 ( 42) SS BOND : angle 1.97732 / 1.19 ( 84) hydrogen bonds : bond 0.05111 / 3.40 ( 1156) hydrogen bonds : angle 5.30083 / 3.69 ( 3090) link_BETA1-4 : bond 0.00368 / 0.21 ( 20) link_BETA1-4 : angle 1.44931 / 0.94 ( 60) link_NAG-ASN : bond 0.00570 / 0.27 ( 45) link_NAG-ASN : angle 2.45694 / 1.72 ( 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 289 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 209 time to evaluate : 0.862 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 32 PHE cc_start: 0.8469 (m-80) cc_final: 0.8154 (m-10) REVERT: A 53 ASP cc_start: 0.8694 (t0) cc_final: 0.8407 (t0) REVERT: A 129 LYS cc_start: 0.7131 (pttt) cc_final: 0.6885 (pttt) REVERT: A 190 ARG cc_start: 0.8055 (mtt90) cc_final: 0.7341 (mtp180) REVERT: A 278 LYS cc_start: 0.8844 (tttt) cc_final: 0.8572 (ttpt) REVERT: A 281 GLU cc_start: 0.7113 (pt0) cc_final: 0.6742 (tt0) REVERT: A 298 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7777 (tp30) REVERT: A 355 ARG cc_start: 0.6479 (ttm-80) cc_final: 0.6181 (ttm170) REVERT: A 365 TYR cc_start: 0.7655 (m-80) cc_final: 0.7278 (m-80) REVERT: A 558 LYS cc_start: 0.8908 (mmtt) cc_final: 0.8653 (mmmt) REVERT: A 646 ARG cc_start: 0.8087 (mtm180) cc_final: 0.7849 (tpp80) REVERT: A 902 MET cc_start: 0.8812 (tpt) cc_final: 0.8378 (tpt) REVERT: A 916 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8614 (tp) REVERT: A 1133 VAL cc_start: 0.9257 (OUTLIER) cc_final: 0.9011 (m) REVERT: B 237 ARG cc_start: 0.7112 (mtm180) cc_final: 0.6799 (mtm180) REVERT: B 415 THR cc_start: 0.7526 (t) cc_final: 0.7325 (t) REVERT: B 614 ASP cc_start: 0.7460 (m-30) cc_final: 0.6976 (t0) REVERT: B 811 LYS cc_start: 0.5096 (OUTLIER) cc_final: 0.4477 (tttt) REVERT: B 1106 GLN cc_start: 0.9219 (OUTLIER) cc_final: 0.8983 (pt0) REVERT: C 271 GLN cc_start: 0.7491 (mt0) cc_final: 0.7157 (mm-40) REVERT: C 532 ASN cc_start: 0.8036 (t0) cc_final: 0.7635 (p0) REVERT: C 796 ASP cc_start: 0.8135 (p0) cc_final: 0.7805 (p0) REVERT: Y 34 MET cc_start: 0.5098 (mtm) cc_final: 0.4141 (ptt) REVERT: Y 83 MET cc_start: 0.3387 (mtm) cc_final: 0.2001 (tmm) REVERT: Z 12 MET cc_start: 0.3650 (mmp) cc_final: 0.3067 (mmt) outliers start: 80 outliers final: 59 residues processed: 274 average time/residue: 0.1586 time to fit residues: 70.4221 Evaluate side-chains 258 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 195 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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 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 132 GLU 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 316 SER Chi-restraints excluded: chain A residue 359 SER 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 916 LEU 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 33 THR 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 235 ILE 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 759 PHE Chi-restraints excluded: chain B residue 811 LYS 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 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 430 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 711 SER 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 1141 LEU Chi-restraints excluded: chain X residue 79 VAL Chi-restraints excluded: chain Y residue 28 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 123 optimal weight: 5.9990 chunk 221 optimal weight: 5.9990 chunk 180 optimal weight: 0.5980 chunk 232 optimal weight: 6.9990 chunk 184 optimal weight: 0.6980 chunk 235 optimal weight: 4.9990 chunk 225 optimal weight: 5.9990 chunk 152 optimal weight: 6.9990 chunk 166 optimal weight: 3.9990 chunk 233 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN ** 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 = 0.4187 r_free = 0.4187 target = 0.196669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.160420 restraints weight = 32974.047| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 1.87 r_work: 0.3475 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.4623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 27769 Z= 0.160 Angle : 0.576 10.056 37893 Z= 0.286 Chirality : 0.044 0.196 4439 Planarity : 0.004 0.048 4765 Dihedral : 4.303 47.735 3602 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.52 % Allowed : 12.03 % Favored : 85.45 % 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: 0.32 (0.14), residues: 3288 helix: 1.65 (0.21), residues: 662 sheet: 0.53 (0.17), residues: 798 loop : -0.44 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 357 TYR 0.016 0.001 TYR B 369 PHE 0.024 0.002 PHE C 168 TRP 0.010 0.001 TRP A 436 HIS 0.005 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (27662) covalent geometry : angle 0.55351 / 0.28 (37614) SS BOND : bond 0.00349 / 0.23 ( 42) SS BOND : angle 1.72979 / 1.02 ( 84) hydrogen bonds : bond 0.04578 / 3.04 ( 1156) hydrogen bonds : angle 5.15050 / 3.59 ( 3090) link_BETA1-4 : bond 0.00330 / 0.17 ( 20) link_BETA1-4 : angle 1.42005 / 0.92 ( 60) link_NAG-ASN : bond 0.00349 / 0.19 ( 45) link_NAG-ASN : angle 2.22837 / 1.48 ( 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 279 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 206 time to evaluate : 0.764 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: 0.8024 (mtt90) cc_final: 0.7620 (mtp180) REVERT: A 281 GLU cc_start: 0.6860 (pt0) cc_final: 0.6553 (tt0) REVERT: A 298 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7886 (tp30) REVERT: A 355 ARG cc_start: 0.6864 (ttm-80) cc_final: 0.6605 (ttm170) REVERT: A 902 MET cc_start: 0.8741 (tpt) cc_final: 0.8220 (tpt) REVERT: A 916 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8627 (tp) REVERT: B 334 ASN cc_start: 0.6902 (t0) cc_final: 0.6671 (t0) REVERT: B 589 PRO cc_start: 0.7913 (Cg_endo) cc_final: 0.7643 (Cg_exo) REVERT: B 811 LYS cc_start: 0.5289 (OUTLIER) cc_final: 0.4871 (tttt) REVERT: B 994 ASP cc_start: 0.8045 (t70) cc_final: 0.7713 (t0) REVERT: C 796 ASP cc_start: 0.8200 (p0) cc_final: 0.7823 (p0) REVERT: Y 83 MET cc_start: 0.2816 (mtm) cc_final: 0.2042 (tmm) REVERT: Z 12 MET cc_start: 0.3507 (mmp) cc_final: 0.3124 (mmt) outliers start: 73 outliers final: 49 residues processed: 266 average time/residue: 0.1523 time to fit residues: 66.3801 Evaluate side-chains 232 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 181 time to evaluate : 0.960 ------------------------------------------------------------------------------- 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 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 302 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 511 VAL 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 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 916 LEU 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 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 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 240 THR Chi-restraints excluded: chain C residue 242 LEU 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 711 SER 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 79 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 43 optimal weight: 0.6980 chunk 92 optimal weight: 0.6980 chunk 235 optimal weight: 0.5980 chunk 256 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 327 optimal weight: 10.0000 chunk 195 optimal weight: 0.4980 chunk 134 optimal weight: 0.9980 chunk 251 optimal weight: 3.9990 chunk 87 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C1142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.198499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.163551 restraints weight = 32679.238| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 1.80 r_work: 0.3518 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.4739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 27769 Z= 0.108 Angle : 0.534 8.848 37893 Z= 0.266 Chirality : 0.043 0.204 4439 Planarity : 0.003 0.046 4765 Dihedral : 4.102 47.171 3602 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % 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: 0.50 (0.14), residues: 3288 helix: 1.79 (0.21), residues: 670 sheet: 0.62 (0.17), residues: 809 loop : -0.33 (0.14), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 355 TYR 0.017 0.001 TYR B 369 PHE 0.022 0.001 PHE A 392 TRP 0.011 0.001 TRP C 436 HIS 0.005 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (27662) covalent geometry : angle 0.51547 / 0.26 (37614) SS BOND : bond 0.00318 / 0.21 ( 42) SS BOND : angle 1.55145 / 0.90 ( 84) hydrogen bonds : bond 0.04061 / 2.68 ( 1156) hydrogen bonds : angle 5.00746 / 3.49 ( 3090) link_BETA1-4 : bond 0.00305 / 0.16 ( 20) link_BETA1-4 : angle 1.38049 / 0.90 ( 60) link_NAG-ASN : bond 0.00365 / 0.19 ( 45) link_NAG-ASN : angle 1.95136 / 1.31 ( 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: 60 poor density : 203 time to evaluate : 0.904 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 66 HIS cc_start: 0.3501 (OUTLIER) cc_final: 0.3183 (p-80) REVERT: A 190 ARG cc_start: 0.8037 (mtt90) cc_final: 0.7638 (mtp180) REVERT: A 298 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7858 (tp30) REVERT: A 355 ARG cc_start: 0.6967 (ttm-80) cc_final: 0.6663 (ttm170) REVERT: A 916 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8600 (tp) REVERT: B 589 PRO cc_start: 0.7926 (Cg_endo) cc_final: 0.7647 (Cg_exo) REVERT: B 811 LYS cc_start: 0.5454 (OUTLIER) cc_final: 0.5002 (tttt) REVERT: B 994 ASP cc_start: 0.7840 (t70) cc_final: 0.7512 (t0) REVERT: C 241 LEU cc_start: 0.8025 (mt) cc_final: 0.7755 (mt) REVERT: C 442 ASP cc_start: 0.4757 (m-30) cc_final: 0.4294 (m-30) REVERT: C 796 ASP cc_start: 0.8121 (p0) cc_final: 0.7735 (p0) REVERT: X 22 CYS cc_start: -0.0359 (OUTLIER) cc_final: -0.1230 (m) REVERT: Y 34 MET cc_start: 0.4840 (mtm) cc_final: 0.4290 (ptt) REVERT: Y 83 MET cc_start: 0.2747 (mtm) cc_final: 0.2068 (tmm) REVERT: Z 12 MET cc_start: 0.3788 (mmp) cc_final: 0.3089 (mmt) outliers start: 60 outliers final: 43 residues processed: 251 average time/residue: 0.1596 time to fit residues: 66.2573 Evaluate side-chains 233 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 186 time to evaluate : 0.901 ------------------------------------------------------------------------------- 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 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 791 THR Chi-restraints excluded: chain A residue 916 LEU 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 120 VAL 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 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 564 GLN Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 620 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 242 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 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 1141 LEU Chi-restraints excluded: chain X residue 22 CYS 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: 2.9990 chunk 191 optimal weight: 0.9980 chunk 257 optimal weight: 1.9990 chunk 294 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 152 optimal weight: 7.9990 chunk 132 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 238 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 450 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C1142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.193988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.159447 restraints weight = 32852.206| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 1.72 r_work: 0.3466 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.5137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 27769 Z= 0.211 Angle : 0.617 9.293 37893 Z= 0.310 Chirality : 0.046 0.202 4439 Planarity : 0.004 0.044 4765 Dihedral : 4.432 48.658 3601 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.10 % Allowed : 12.62 % Favored : 85.28 % 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: 0.26 (0.14), residues: 3288 helix: 1.49 (0.20), residues: 672 sheet: 0.56 (0.17), residues: 803 loop : -0.49 (0.14), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 509 TYR 0.024 0.002 TYR B 453 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/Z covalent geometry : bond 0.00521 / 0.21 (27662) covalent geometry : angle 0.59762 / 0.30 (37614) SS BOND : bond 0.00408 / 0.25 ( 42) SS BOND : angle 1.85532 / 1.06 ( 84) hydrogen bonds : bond 0.05228 / 3.50 ( 1156) hydrogen bonds : angle 5.24614 / 3.64 ( 3090) link_BETA1-4 : bond 0.00373 / 0.20 ( 20) link_BETA1-4 : angle 1.55528 / 1.01 ( 60) link_NAG-ASN : bond 0.00383 / 0.21 ( 45) link_NAG-ASN : angle 2.07145 / 1.40 ( 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 258 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 197 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.3603 (OUTLIER) cc_final: 0.3217 (p-80) REVERT: A 190 ARG cc_start: 0.8093 (mtt90) cc_final: 0.7724 (mtp180) REVERT: A 298 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7876 (tp30) REVERT: A 355 ARG cc_start: 0.7172 (ttm-80) cc_final: 0.6858 (ttm170) REVERT: B 334 ASN cc_start: 0.6952 (t0) cc_final: 0.6646 (t0) REVERT: B 589 PRO cc_start: 0.7870 (Cg_endo) cc_final: 0.7590 (Cg_exo) REVERT: B 811 LYS cc_start: 0.5430 (OUTLIER) cc_final: 0.4771 (tttt) REVERT: C 241 LEU cc_start: 0.7950 (mt) cc_final: 0.7726 (mt) REVERT: C 442 ASP cc_start: 0.4731 (m-30) cc_final: 0.4199 (m-30) REVERT: C 796 ASP cc_start: 0.8216 (p0) cc_final: 0.7828 (p0) REVERT: X 22 CYS cc_start: -0.0325 (OUTLIER) cc_final: -0.1298 (m) REVERT: Y 83 MET cc_start: 0.3141 (mtm) cc_final: 0.2476 (tmm) REVERT: Z 12 MET cc_start: 0.3811 (mmp) cc_final: 0.3105 (mmt) outliers start: 61 outliers final: 48 residues processed: 248 average time/residue: 0.1650 time to fit residues: 67.2936 Evaluate side-chains 235 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 184 time to evaluate : 0.799 ------------------------------------------------------------------------------- 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 302 THR 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 791 THR 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 120 VAL 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 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 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 705 VAL Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 1004 LEU 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 236 THR 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 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 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: 4.9990 chunk 96 optimal weight: 0.9980 chunk 270 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 218 optimal weight: 0.0570 chunk 101 optimal weight: 0.9980 chunk 130 optimal weight: 0.0980 chunk 236 optimal weight: 20.0000 chunk 188 optimal weight: 0.6980 chunk 263 optimal weight: 0.7980 chunk 104 optimal weight: 6.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN ** 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 = 0.4185 r_free = 0.4185 target = 0.196438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.161292 restraints weight = 32699.151| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 1.77 r_work: 0.3504 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.5204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 27769 Z= 0.105 Angle : 0.533 9.932 37893 Z= 0.266 Chirality : 0.043 0.196 4439 Planarity : 0.003 0.044 4765 Dihedral : 4.068 46.391 3601 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.86 % Allowed : 13.07 % Favored : 85.07 % 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: 0.49 (0.14), residues: 3288 helix: 1.88 (0.21), residues: 661 sheet: 0.63 (0.17), residues: 822 loop : -0.39 (0.14), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 355 TYR 0.024 0.001 TYR B 453 PHE 0.021 0.001 PHE B 86 TRP 0.012 0.001 TRP A 353 HIS 0.005 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (27662) covalent geometry : angle 0.51582 / 0.26 (37614) SS BOND : bond 0.00337 / 0.23 ( 42) SS BOND : angle 1.54147 / 0.89 ( 84) hydrogen bonds : bond 0.03989 / 2.64 ( 1156) hydrogen bonds : angle 4.99043 / 3.47 ( 3090) link_BETA1-4 : bond 0.00323 / 0.19 ( 20) link_BETA1-4 : angle 1.40468 / 0.91 ( 60) link_NAG-ASN : bond 0.00311 / 0.19 ( 45) link_NAG-ASN : angle 1.80617 / 1.23 ( 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 258 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 204 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.3443 (OUTLIER) cc_final: 0.3122 (p-80) REVERT: A 190 ARG cc_start: 0.8016 (mtt90) cc_final: 0.7701 (mtp180) REVERT: A 207 HIS cc_start: 0.7412 (m90) cc_final: 0.7206 (m90) REVERT: A 298 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7633 (tp30) REVERT: A 355 ARG cc_start: 0.6965 (ttm-80) cc_final: 0.6566 (ttm170) REVERT: B 334 ASN cc_start: 0.6798 (t0) cc_final: 0.6517 (t0) REVERT: B 589 PRO cc_start: 0.7798 (Cg_endo) cc_final: 0.7540 (Cg_exo) REVERT: B 811 LYS cc_start: 0.5345 (OUTLIER) cc_final: 0.5020 (tttt) REVERT: C 442 ASP cc_start: 0.4535 (m-30) cc_final: 0.4070 (m-30) REVERT: C 796 ASP cc_start: 0.8045 (p0) cc_final: 0.7579 (t0) REVERT: X 22 CYS cc_start: -0.0290 (OUTLIER) cc_final: -0.1116 (m) REVERT: Y 83 MET cc_start: 0.2538 (mtm) cc_final: 0.2143 (tmm) REVERT: Z 12 MET cc_start: 0.3870 (mmp) cc_final: 0.3190 (mmt) outliers start: 54 outliers final: 41 residues processed: 245 average time/residue: 0.1648 time to fit residues: 66.8736 Evaluate side-chains 234 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 190 time to evaluate : 0.992 ------------------------------------------------------------------------------- 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 240 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 316 SER 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 1094 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 277 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 440 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 620 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 392 PHE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 525 CYS 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: 9.9990 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: 0.7980 chunk 54 optimal weight: 0.6980 chunk 268 optimal weight: 0.6980 chunk 317 optimal weight: 5.9990 chunk 255 optimal weight: 0.9990 chunk 166 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 804 GLN A 935 GLN ** 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 = 0.4169 r_free = 0.4169 target = 0.194973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.158869 restraints weight = 32507.219| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 1.78 r_work: 0.3514 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.5299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27769 Z= 0.117 Angle : 0.537 10.635 37893 Z= 0.267 Chirality : 0.043 0.203 4439 Planarity : 0.004 0.046 4765 Dihedral : 4.018 46.116 3601 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.69 % Allowed : 13.14 % Favored : 85.17 % 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: 0.50 (0.14), residues: 3288 helix: 1.88 (0.21), residues: 664 sheet: 0.64 (0.17), residues: 822 loop : -0.38 (0.14), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 102 TYR 0.022 0.001 TYR B 453 PHE 0.022 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/Z covalent geometry : bond 0.00270 / 0.12 (27662) covalent geometry : angle 0.52026 / 0.26 (37614) SS BOND : bond 0.00327 / 0.22 ( 42) SS BOND : angle 1.54882 / 0.89 ( 84) hydrogen bonds : bond 0.04080 / 2.70 ( 1156) hydrogen bonds : angle 4.95356 / 3.45 ( 3090) link_BETA1-4 : bond 0.00322 / 0.17 ( 20) link_BETA1-4 : angle 1.40481 / 0.91 ( 60) link_NAG-ASN : bond 0.00278 / 0.16 ( 45) link_NAG-ASN : angle 1.74862 / 1.19 ( 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 242 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 193 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.8067 (mtt90) cc_final: 0.7720 (mtp180) REVERT: A 207 HIS cc_start: 0.7446 (m90) cc_final: 0.7236 (m90) REVERT: A 298 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7906 (tp30) REVERT: A 355 ARG cc_start: 0.7258 (ttm-80) cc_final: 0.6885 (ttm170) REVERT: B 237 ARG cc_start: 0.7233 (mtm180) cc_final: 0.6844 (mtm180) REVERT: B 334 ASN cc_start: 0.7040 (t0) cc_final: 0.6699 (t0) REVERT: B 589 PRO cc_start: 0.7854 (Cg_endo) cc_final: 0.7570 (Cg_exo) REVERT: B 811 LYS cc_start: 0.5238 (OUTLIER) cc_final: 0.4912 (tttt) REVERT: C 442 ASP cc_start: 0.4575 (m-30) cc_final: 0.4128 (m-30) REVERT: C 796 ASP cc_start: 0.8130 (p0) cc_final: 0.7657 (t0) REVERT: X 22 CYS cc_start: -0.0287 (OUTLIER) cc_final: -0.1439 (m) REVERT: Y 83 MET cc_start: 0.2940 (mtm) cc_final: 0.2409 (tmm) REVERT: Z 12 MET cc_start: 0.4208 (mmp) cc_final: 0.3405 (mmt) outliers start: 49 outliers final: 43 residues processed: 233 average time/residue: 0.1632 time to fit residues: 62.8662 Evaluate side-chains 231 residues out of total 2900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 186 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 316 SER 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 1004 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 124 THR 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 430 THR Chi-restraints excluded: chain B residue 440 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 620 VAL Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 1004 LEU 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 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 615 VAL Chi-restraints excluded: chain C residue 702 GLU 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 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: 0.9990 chunk 12 optimal weight: 7.9990 chunk 37 optimal weight: 0.0770 chunk 208 optimal weight: 8.9990 chunk 94 optimal weight: 2.9990 chunk 161 optimal weight: 0.8980 chunk 18 optimal weight: 9.9990 chunk 263 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 142 optimal weight: 0.5980 chunk 157 optimal weight: 1.9990 overall best weight: 0.9142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 804 GLN C 81 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 = 0.4199 r_free = 0.4199 target = 0.197499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.161973 restraints weight = 32335.898| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 3.16 r_work: 0.3396 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.5419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27769 Z= 0.120 Angle : 0.539 10.790 37893 Z= 0.268 Chirality : 0.043 0.201 4439 Planarity : 0.004 0.089 4765 Dihedral : 3.998 43.831 3601 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.72 % Allowed : 13.17 % Favored : 85.10 % 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: 0.50 (0.14), residues: 3288 helix: 1.85 (0.21), residues: 670 sheet: 0.67 (0.17), residues: 822 loop : -0.40 (0.15), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 237 TYR 0.025 0.001 TYR B 453 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/Z covalent geometry : bond 0.00280 / 0.12 (27662) covalent geometry : angle 0.52380 / 0.26 (37614) SS BOND : bond 0.00310 / 0.20 ( 42) SS BOND : angle 1.48798 / 0.86 ( 84) hydrogen bonds : bond 0.04077 / 2.70 ( 1156) hydrogen bonds : angle 4.91193 / 3.41 ( 3090) link_BETA1-4 : bond 0.00277 / 0.16 ( 20) link_BETA1-4 : angle 1.39148 / 0.90 ( 60) link_NAG-ASN : bond 0.00281 / 0.17 ( 45) link_NAG-ASN : angle 1.69923 / 1.17 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5565.28 seconds wall clock time: 96 minutes 30.57 seconds (5790.57 seconds total)