Starting phenix.real_space_refine on Fri Mar 6 02:00:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z6v_14531/03_2026/7z6v_14531.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z6v_14531/03_2026/7z6v_14531.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7z6v_14531/03_2026/7z6v_14531.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z6v_14531/03_2026/7z6v_14531.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z6v_14531/03_2026/7z6v_14531.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z6v_14531/03_2026/7z6v_14531.map" } resolution = 3.1 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= 0.004 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 17255 2.51 5 N 4445 2.21 5 O 5334 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27154 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 7732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 990, 7732 Classifications: {'peptide': 990} Link IDs: {'PTRANS': 49, 'TRANS': 940} Chain breaks: 8 Chain: "B" Number of atoms: 7761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 994, 7761 Classifications: {'peptide': 994} Link IDs: {'PTRANS': 49, 'TRANS': 944} Chain breaks: 7 Chain: "C" Number of atoms: 7749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 7749 Classifications: {'peptide': 992} Link IDs: {'PTRANS': 49, 'TRANS': 942} Chain breaks: 7 Chain: "X" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 996 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 2, 'TRANS': 125} Chain: "Y" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 996 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 2, 'TRANS': 125} Chain: "Z" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 996 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 2, 'TRANS': 125} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 6.03, per 1000 atoms: 0.22 Number of scatterers: 27154 At special positions: 0 Unit cell: (129.32, 136.74, 221.54, 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 5334 8.00 N 4445 7.00 C 17255 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.05 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.09 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.07 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.06 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.09 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.10 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=2.05 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.06 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.06 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.06 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.07 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.09 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.10 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.01 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.05 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.01 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.10 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.08 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=1.07 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.05 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=1.86 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.00 Simple disulfide: pdb=" SG CYS X 22 " - pdb=" SG CYS X 96 " distance=2.04 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Y 96 " distance=2.04 Simple disulfide: pdb=" SG CYS Z 22 " - pdb=" SG CYS Z 96 " distance=2.04 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-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A 165 " " NAG A1308 " - " ASN A 343 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " 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 B1311 " - " ASN B 234 " " NAG C1401 " - " ASN C 343 " " NAG C1402 " - " ASN C 61 " " NAG C1403 " - " ASN C 122 " " NAG C1404 " - " ASN C 234 " " NAG C1405 " - " ASN C 331 " " NAG C1406 " - " ASN C 603 " " NAG C1407 " - " ASN C 616 " " NAG C1408 " - " ASN C 657 " " NAG C1409 " - " ASN C 165 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 282 " " NAG F 1 " - " ASN A 331 " " NAG G 1 " - " ASN A 717 " " NAG H 1 " - " ASN A 801 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN A1134 " " NAG K 1 " - " ASN A1074 " " 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 282 " " NAG Q 1 " - " ASN C 709 " " NAG R 1 " - " ASN C 717 " " NAG S 1 " - " ASN C 801 " " NAG T 1 " - " ASN C1074 " " NAG U 1 " - " ASN C1098 " " NAG V 1 " - " ASN C1134 " Time building additional restraints: 2.35 Conformation dependent library (CDL) restraints added in 963.8 milliseconds 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6266 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 54 sheets defined 25.8% alpha, 28.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.935A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.552A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 385 through 390 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.370A 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 742 Processing helix chain 'A' and resid 746 through 756 removed outlier: 3.785A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.798A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 removed outlier: 3.625A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.004A 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 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.578A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.939A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.019A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.031A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 384 through 390 removed outlier: 3.790A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.273A 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 616 through 620 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.650A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.722A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.065A 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 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.872A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.984A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.004A 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 384 through 390 removed outlier: 3.737A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.190A 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 616 through 620 Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.637A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.780A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.068A 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 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.637A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.643A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.033A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'X' and resid 28 through 31 Processing helix chain 'X' and resid 87 through 91 Processing helix chain 'X' and resid 105 through 111 Processing helix chain 'Y' and resid 28 through 31 Processing helix chain 'Y' and resid 87 through 91 Processing helix chain 'Y' and resid 105 through 111 Processing helix chain 'Z' and resid 28 through 31 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: 3.738A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.334A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 8.906A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY A 89 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.437A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.822A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.124A 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 removed outlier: 5.584A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.458A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 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 654 through 655 removed outlier: 6.094A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.771A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.780A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.350A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.699A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.105A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.824A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.092A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.368A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.713A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.724A pdb=" N ASN B 125 " --> pdb=" O ASN B 122 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.828A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.458A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.095A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.770A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 719 through 727 removed outlier: 5.783A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.309A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 788 through 790 removed outlier: 5.699A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.716A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.727A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.622A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.836A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.230A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.303A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.096A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.771A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.221A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.326A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF1, first strand: chain 'X' and resid 2 through 7 Processing sheet with id=AF2, first strand: chain 'X' and resid 10 through 13 removed outlier: 6.307A pdb=" N GLY X 10 " --> pdb=" O THR X 124 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N SER X 126 " --> pdb=" O GLY X 10 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N MET X 12 " --> pdb=" O SER X 126 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ARG X 38 " --> pdb=" O PHE X 47 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N PHE X 47 " --> pdb=" O ARG X 38 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'X' and resid 10 through 13 removed outlier: 6.307A pdb=" N GLY X 10 " --> pdb=" O THR X 124 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N SER X 126 " --> pdb=" O GLY X 10 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N MET X 12 " --> pdb=" O SER X 126 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Y' and resid 2 through 7 Processing sheet with id=AF5, first strand: chain 'Y' and resid 10 through 13 removed outlier: 6.303A pdb=" N GLY Y 10 " --> pdb=" O THR Y 124 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N SER Y 126 " --> pdb=" O GLY Y 10 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N MET Y 12 " --> pdb=" O SER Y 126 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ARG Y 38 " --> pdb=" O PHE Y 47 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N PHE Y 47 " --> pdb=" O ARG Y 38 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Y' and resid 10 through 13 removed outlier: 6.303A pdb=" N GLY Y 10 " --> pdb=" O THR Y 124 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N SER Y 126 " --> pdb=" O GLY Y 10 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N MET Y 12 " --> pdb=" O SER Y 126 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Z' and resid 2 through 7 Processing sheet with id=AF8, first strand: chain 'Z' and resid 10 through 13 removed outlier: 6.308A pdb=" N GLY Z 10 " --> pdb=" O THR Z 124 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N SER Z 126 " --> pdb=" O GLY Z 10 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N MET Z 12 " --> pdb=" O SER Z 126 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ARG Z 38 " --> pdb=" O PHE Z 47 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N PHE Z 47 " --> pdb=" O ARG Z 38 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Z' and resid 10 through 13 removed outlier: 6.308A pdb=" N GLY Z 10 " --> pdb=" O THR Z 124 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N SER Z 126 " --> pdb=" O GLY Z 10 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N MET Z 12 " --> pdb=" O SER Z 126 " (cutoff:3.500A) 1183 hydrogen bonds defined for protein. 3141 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: 8.16 Time building geometry restraints manager: 3.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4853 1.32 - 1.46: 9956 1.46 - 1.59: 12780 1.59 - 1.73: 1 1.73 - 1.86: 152 Bond restraints: 27742 Sorted by residual: bond pdb=" CA SER C1021 " pdb=" CB SER C1021 " ideal model delta sigma weight residual 1.528 1.455 0.073 1.56e-02 4.11e+03 2.20e+01 bond pdb=" CE1 HIS B 49 " pdb=" NE2 HIS B 49 " ideal model delta sigma weight residual 1.321 1.365 -0.044 1.00e-02 1.00e+04 1.97e+01 bond pdb=" CA SER A1021 " pdb=" CB SER A1021 " ideal model delta sigma weight residual 1.528 1.460 0.069 1.56e-02 4.11e+03 1.95e+01 bond pdb=" CA SER B1030 " pdb=" CB SER B1030 " ideal model delta sigma weight residual 1.529 1.462 0.067 1.55e-02 4.16e+03 1.87e+01 bond pdb=" CA SER A 721 " pdb=" CB SER A 721 " ideal model delta sigma weight residual 1.532 1.453 0.078 1.82e-02 3.02e+03 1.86e+01 ... (remaining 27737 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.24: 35658 3.24 - 6.47: 1932 6.47 - 9.71: 116 9.71 - 12.94: 11 12.94 - 16.18: 1 Bond angle restraints: 37718 Sorted by residual: angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 120.62 -9.92 1.22e+00 6.72e-01 6.61e+01 angle pdb=" N GLN B 901 " pdb=" CA GLN B 901 " pdb=" C GLN B 901 " ideal model delta sigma weight residual 111.14 102.66 8.48 1.08e+00 8.57e-01 6.16e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 119.41 -8.71 1.22e+00 6.72e-01 5.10e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 119.26 -8.56 1.22e+00 6.72e-01 4.93e+01 angle pdb=" CB GLN B 804 " pdb=" CG GLN B 804 " pdb=" CD GLN B 804 " ideal model delta sigma weight residual 112.60 123.77 -11.17 1.70e+00 3.46e-01 4.32e+01 ... (remaining 37713 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.60: 16290 21.60 - 43.20: 876 43.20 - 64.80: 116 64.80 - 86.40: 16 86.40 - 108.00: 39 Dihedral angle restraints: 17337 sinusoidal: 7583 harmonic: 9754 Sorted by residual: dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual -86.00 -170.95 84.95 1 1.00e+01 1.00e-02 8.75e+01 dihedral pdb=" CB CYS C 743 " pdb=" SG CYS C 743 " pdb=" SG CYS C 749 " pdb=" CB CYS C 749 " ideal model delta sinusoidal sigma weight residual -86.00 -16.73 -69.27 1 1.00e+01 1.00e-02 6.20e+01 dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual -86.00 -18.68 -67.32 1 1.00e+01 1.00e-02 5.90e+01 ... (remaining 17334 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.541: 4446 0.541 - 1.082: 8 1.082 - 1.622: 0 1.622 - 2.163: 0 2.163 - 2.704: 2 Chirality restraints: 4456 Sorted by residual: chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-02 2.50e+03 2.11e+02 chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-02 2.50e+03 2.08e+02 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 0.30 -2.70 2.00e-01 2.50e+01 1.83e+02 ... (remaining 4453 not shown) Planarity restraints: 4829 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " -0.331 2.00e-02 2.50e+03 2.83e-01 1.00e+03 pdb=" C7 NAG F 1 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " -0.174 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " 0.499 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " -0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1406 " -0.320 2.00e-02 2.50e+03 2.79e-01 9.76e+02 pdb=" C7 NAG C1406 " 0.073 2.00e-02 2.50e+03 pdb=" C8 NAG C1406 " -0.112 2.00e-02 2.50e+03 pdb=" N2 NAG C1406 " 0.500 2.00e-02 2.50e+03 pdb=" O7 NAG C1406 " -0.142 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1307 " 0.294 2.00e-02 2.50e+03 2.54e-01 8.05e+02 pdb=" C7 NAG A1307 " -0.075 2.00e-02 2.50e+03 pdb=" C8 NAG A1307 " 0.168 2.00e-02 2.50e+03 pdb=" N2 NAG A1307 " -0.445 2.00e-02 2.50e+03 pdb=" O7 NAG A1307 " 0.058 2.00e-02 2.50e+03 ... (remaining 4826 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 50 2.53 - 3.12: 19829 3.12 - 3.71: 40856 3.71 - 4.31: 64481 4.31 - 4.90: 101992 Nonbonded interactions: 227208 Sorted by model distance: nonbonded pdb=" CA ILE B 101 " pdb=" CD2 LEU B 242 " model vdw 1.932 3.890 nonbonded pdb=" CG1 ILE B 101 " pdb=" CD2 LEU B 242 " model vdw 1.957 3.860 nonbonded pdb=" O TRP X 53 " pdb=" CZ ARG X 72 " model vdw 1.963 3.270 nonbonded pdb=" O TRP Y 53 " pdb=" CZ ARG Y 72 " model vdw 1.964 3.270 nonbonded pdb=" O TRP Z 53 " pdb=" CZ ARG Z 72 " model vdw 1.965 3.270 ... (remaining 227203 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 140 or resid 166 through \ 263 or resid 265 through 676 or resid 690 through 827 or resid 855 through 1308 \ )) selection = (chain 'B' and (resid 27 through 66 or resid 82 through 140 or resid 166 through \ 211 or resid 215 through 263 or resid 265 through 1308)) selection = (chain 'C' and (resid 27 through 66 or resid 82 through 140 or resid 166 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' } 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: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 27.100 Find NCS groups from input model: 0.920 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: 0.010 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 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 : 0.012 0.957 27849 Z= 0.695 Angle : 1.707 45.478 37998 Z= 1.082 Chirality : 0.137 2.704 4456 Planarity : 0.020 0.283 4782 Dihedral : 13.892 107.998 10948 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.85 % Favored : 97.06 % Rotamer: Outliers : 0.45 % Allowed : 7.18 % Favored : 92.37 % Cbeta Deviations : 0.96 % 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: -0.18 (0.13), residues: 3304 helix: 0.98 (0.18), residues: 682 sheet: 0.29 (0.17), residues: 803 loop : -0.72 (0.13), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.003 ARG C1039 TYR 0.053 0.009 TYR B 741 PHE 0.062 0.010 PHE B 565 TRP 0.032 0.006 TRP B 104 HIS 0.025 0.007 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00994 (27742) covalent geometry : angle 1.64433 (37718) SS BOND : bond 0.15471 ( 41) SS BOND : angle 7.38140 ( 82) hydrogen bonds : bond 0.17333 ( 1171) hydrogen bonds : angle 7.73360 ( 3141) link_BETA1-4 : bond 0.00548 ( 19) link_BETA1-4 : angle 2.07965 ( 57) link_NAG-ASN : bond 0.01323 ( 47) link_NAG-ASN : angle 5.36734 ( 141) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 519 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7807 (mttm) cc_final: 0.7493 (mppt) REVERT: A 65 PHE cc_start: 0.8216 (m-80) cc_final: 0.7853 (m-10) REVERT: A 133 PHE cc_start: 0.6701 (m-80) cc_final: 0.6235 (t80) REVERT: A 136 CYS cc_start: 0.6402 (m) cc_final: 0.6149 (t) REVERT: A 137 ASN cc_start: 0.6847 (m-40) cc_final: 0.6482 (p0) REVERT: A 169 GLU cc_start: 0.8473 (tt0) cc_final: 0.8070 (tm-30) REVERT: A 200 TYR cc_start: 0.5632 (p90) cc_final: 0.5093 (p90) REVERT: A 343 ASN cc_start: 0.4844 (m-40) cc_final: 0.4272 (t0) REVERT: A 568 ASP cc_start: 0.8472 (t0) cc_final: 0.8118 (p0) REVERT: A 697 MET cc_start: 0.9103 (ptm) cc_final: 0.8856 (ptm) REVERT: A 702 GLU cc_start: 0.8643 (tm-30) cc_final: 0.8395 (mm-30) REVERT: A 811 LYS cc_start: 0.5386 (mttt) cc_final: 0.5083 (tttm) REVERT: A 825 LYS cc_start: 0.8279 (mmtt) cc_final: 0.8056 (mmmt) REVERT: A 859 THR cc_start: 0.9221 (p) cc_final: 0.8833 (t) REVERT: A 1045 LYS cc_start: 0.9239 (mmtt) cc_final: 0.8721 (mmtm) REVERT: A 1113 GLN cc_start: 0.9021 (mm-40) cc_final: 0.8664 (mt0) REVERT: B 117 LEU cc_start: 0.7671 (tp) cc_final: 0.7017 (mp) REVERT: B 129 LYS cc_start: 0.7202 (mttt) cc_final: 0.6913 (pttp) REVERT: B 131 CYS cc_start: 0.6812 (m) cc_final: 0.6521 (t) REVERT: B 191 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8259 (mt-10) REVERT: B 235 ILE cc_start: 0.7046 (mt) cc_final: 0.6540 (mm) REVERT: B 357 ARG cc_start: 0.8617 (ttp80) cc_final: 0.8225 (ttm170) REVERT: B 403 ARG cc_start: 0.7052 (ptt180) cc_final: 0.6459 (ptt-90) REVERT: B 427 ASP cc_start: 0.8047 (m-30) cc_final: 0.7545 (m-30) REVERT: B 449 TYR cc_start: 0.6693 (m-80) cc_final: 0.6468 (m-80) REVERT: B 453 TYR cc_start: 0.7581 (p90) cc_final: 0.7175 (p90) REVERT: B 535 LYS cc_start: 0.8420 (mttt) cc_final: 0.8138 (mtmt) REVERT: B 558 LYS cc_start: 0.7831 (mmtt) cc_final: 0.7617 (mttt) REVERT: B 586 ASP cc_start: 0.8096 (m-30) cc_final: 0.7864 (t0) REVERT: B 661 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8597 (tt0) REVERT: B 675 GLN cc_start: 0.7833 (mt0) cc_final: 0.7449 (pp30) REVERT: B 745 ASP cc_start: 0.7800 (m-30) cc_final: 0.7582 (t70) REVERT: B 755 GLN cc_start: 0.8747 (mt0) cc_final: 0.8381 (mm-40) REVERT: B 868 GLU cc_start: 0.8389 (pp20) cc_final: 0.8104 (mm-30) REVERT: B 985 ASP cc_start: 0.7691 (m-30) cc_final: 0.7142 (p0) REVERT: B 1073 LYS cc_start: 0.8609 (mttt) cc_final: 0.8392 (mtpp) REVERT: B 1081 ILE cc_start: 0.9069 (pt) cc_final: 0.8862 (pt) REVERT: B 1092 GLU cc_start: 0.9005 (mt-10) cc_final: 0.8583 (pt0) REVERT: C 85 PRO cc_start: 0.7383 (Cg_exo) cc_final: 0.7162 (Cg_endo) REVERT: C 113 LYS cc_start: 0.6827 (mttm) cc_final: 0.6601 (tptp) REVERT: C 198 ASP cc_start: 0.8158 (m-30) cc_final: 0.7633 (p0) REVERT: C 353 TRP cc_start: 0.5665 (p-90) cc_final: 0.5284 (p-90) REVERT: C 360 ASN cc_start: 0.8389 (t0) cc_final: 0.8063 (m-40) REVERT: C 364 ASP cc_start: 0.8358 (t0) cc_final: 0.8138 (t70) REVERT: C 378 LYS cc_start: 0.7303 (tttt) cc_final: 0.6959 (tptp) REVERT: C 380 TYR cc_start: 0.8058 (m-80) cc_final: 0.7580 (m-80) REVERT: C 433 VAL cc_start: 0.7662 (t) cc_final: 0.7168 (m) REVERT: C 532 ASN cc_start: 0.8579 (t0) cc_final: 0.7960 (m110) REVERT: C 646 ARG cc_start: 0.8898 (tpp80) cc_final: 0.8434 (tpt-90) REVERT: C 675 GLN cc_start: 0.8264 (mt0) cc_final: 0.7342 (pp30) REVERT: C 734 THR cc_start: 0.9022 (m) cc_final: 0.8628 (p) REVERT: C 745 ASP cc_start: 0.8076 (m-30) cc_final: 0.7789 (p0) REVERT: C 868 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8386 (mp0) REVERT: C 869 MET cc_start: 0.9235 (mtt) cc_final: 0.8974 (mtp) REVERT: C 950 ASP cc_start: 0.8779 (t70) cc_final: 0.8317 (m-30) REVERT: C 960 ASN cc_start: 0.8305 (m-40) cc_final: 0.7979 (t0) REVERT: C 985 ASP cc_start: 0.7639 (m-30) cc_final: 0.7183 (p0) REVERT: C 1045 LYS cc_start: 0.9192 (mttt) cc_final: 0.8412 (tmtt) REVERT: C 1081 ILE cc_start: 0.9061 (pt) cc_final: 0.8734 (mt) REVERT: Y 85 SER cc_start: 0.4982 (m) cc_final: 0.4774 (p) REVERT: Y 103 ARG cc_start: 0.7383 (mmm160) cc_final: 0.6486 (mmm-85) REVERT: Z 34 MET cc_start: 0.1237 (mmm) cc_final: 0.0968 (ptp) outliers start: 13 outliers final: 3 residues processed: 529 average time/residue: 0.1784 time to fit residues: 145.3579 Evaluate side-chains 297 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 294 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain B residue 87 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.0870 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 9.9990 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 87 ASN A 125 ASN A 239 GLN A 334 ASN A 901 GLN A 907 ASN A 914 ASN A 954 GLN A1011 GLN A1113 GLN B 121 ASN B 207 HIS B 271 GLN B 360 ASN B 607 GLN B 690 GLN B 762 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN B1010 GLN B1011 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN C 207 HIS ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN C 787 GLN C 901 GLN C 957 GLN C1010 GLN C1011 GLN C1036 GLN C1048 HIS ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.199162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.149998 restraints weight = 32946.725| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.37 r_work: 0.3072 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27849 Z= 0.144 Angle : 0.650 11.997 37998 Z= 0.329 Chirality : 0.046 0.312 4456 Planarity : 0.004 0.034 4782 Dihedral : 8.032 95.578 5003 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.41 % Allowed : 9.45 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.14), residues: 3304 helix: 2.04 (0.20), residues: 675 sheet: 0.53 (0.17), residues: 823 loop : -0.44 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 357 TYR 0.022 0.001 TYR B1067 PHE 0.022 0.002 PHE B 192 TRP 0.013 0.001 TRP C 436 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00319 (27742) covalent geometry : angle 0.62146 (37718) SS BOND : bond 0.00558 ( 41) SS BOND : angle 1.62541 ( 82) hydrogen bonds : bond 0.05067 ( 1171) hydrogen bonds : angle 6.13212 ( 3141) link_BETA1-4 : bond 0.00642 ( 19) link_BETA1-4 : angle 1.44904 ( 57) link_NAG-ASN : bond 0.00377 ( 47) link_NAG-ASN : angle 2.87589 ( 141) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 339 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.8185 (m-80) cc_final: 0.7972 (m-80) REVERT: A 133 PHE cc_start: 0.7035 (m-80) cc_final: 0.6690 (t80) REVERT: A 200 TYR cc_start: 0.5676 (p90) cc_final: 0.5249 (p90) REVERT: A 343 ASN cc_start: 0.5798 (m-40) cc_final: 0.4986 (t0) REVERT: A 697 MET cc_start: 0.8924 (ptm) cc_final: 0.8603 (ptm) REVERT: B 235 ILE cc_start: 0.7222 (mt) cc_final: 0.6823 (mm) REVERT: B 332 ILE cc_start: 0.8342 (mm) cc_final: 0.8082 (mm) REVERT: B 394 ASN cc_start: 0.7242 (m-40) cc_final: 0.6866 (m-40) REVERT: B 403 ARG cc_start: 0.7250 (ptt180) cc_final: 0.6579 (ptt180) REVERT: B 616 ASN cc_start: 0.7399 (OUTLIER) cc_final: 0.6881 (m-40) REVERT: B 1081 ILE cc_start: 0.8860 (pt) cc_final: 0.8658 (pt) REVERT: C 140 PHE cc_start: 0.6725 (p90) cc_final: 0.6489 (p90) REVERT: C 198 ASP cc_start: 0.7474 (m-30) cc_final: 0.7195 (m-30) REVERT: C 239 GLN cc_start: 0.7755 (pt0) cc_final: 0.7322 (mt0) REVERT: C 353 TRP cc_start: 0.5989 (p-90) cc_final: 0.5711 (p-90) REVERT: C 378 LYS cc_start: 0.8083 (tttt) cc_final: 0.7585 (tptp) REVERT: C 396 TYR cc_start: 0.8238 (m-80) cc_final: 0.7734 (m-80) REVERT: C 433 VAL cc_start: 0.7910 (t) cc_final: 0.7568 (m) REVERT: C 869 MET cc_start: 0.8992 (mtt) cc_final: 0.8662 (mtp) REVERT: C 950 ASP cc_start: 0.8666 (t70) cc_final: 0.8338 (m-30) REVERT: C 1045 LYS cc_start: 0.8662 (mttt) cc_final: 0.8326 (tmtt) REVERT: Y 83 MET cc_start: 0.4033 (mtm) cc_final: 0.3625 (mtm) REVERT: Y 103 ARG cc_start: 0.8264 (mmm160) cc_final: 0.7058 (mmm-85) REVERT: Y 104 SER cc_start: 0.7935 (t) cc_final: 0.7708 (m) outliers start: 41 outliers final: 22 residues processed: 368 average time/residue: 0.1634 time to fit residues: 96.1699 Evaluate side-chains 269 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 246 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 859 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 84 optimal weight: 2.9990 chunk 284 optimal weight: 2.9990 chunk 55 optimal weight: 0.0470 chunk 93 optimal weight: 1.9990 chunk 40 optimal weight: 30.0000 chunk 263 optimal weight: 2.9990 chunk 202 optimal weight: 9.9990 chunk 166 optimal weight: 0.0970 chunk 254 optimal weight: 3.9990 chunk 317 optimal weight: 20.0000 chunk 72 optimal weight: 4.9990 overall best weight: 1.6282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 ASN A 779 GLN A 955 ASN A1048 HIS B 901 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1048 HIS B1106 GLN C 66 HIS C1010 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.196455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.146382 restraints weight = 33146.157| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.38 r_work: 0.2980 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 27849 Z= 0.172 Angle : 0.605 12.812 37998 Z= 0.306 Chirality : 0.045 0.252 4456 Planarity : 0.004 0.041 4782 Dihedral : 6.674 83.618 4999 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.82 % Allowed : 10.82 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.14), residues: 3304 helix: 2.03 (0.20), residues: 669 sheet: 0.55 (0.17), residues: 847 loop : -0.39 (0.14), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 408 TYR 0.025 0.001 TYR B 380 PHE 0.020 0.002 PHE B 456 TRP 0.023 0.001 TRP C 436 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00409 (27742) covalent geometry : angle 0.58077 (37718) SS BOND : bond 0.00509 ( 41) SS BOND : angle 1.58034 ( 82) hydrogen bonds : bond 0.04576 ( 1171) hydrogen bonds : angle 5.74811 ( 3141) link_BETA1-4 : bond 0.00278 ( 19) link_BETA1-4 : angle 1.50157 ( 57) link_NAG-ASN : bond 0.00398 ( 47) link_NAG-ASN : angle 2.48471 ( 141) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 272 time to evaluate : 0.875 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 65 PHE cc_start: 0.8126 (m-80) cc_final: 0.7925 (m-80) REVERT: A 102 ARG cc_start: 0.6950 (mmm160) cc_final: 0.6653 (mmt180) REVERT: A 133 PHE cc_start: 0.7223 (m-80) cc_final: 0.6429 (t80) REVERT: A 343 ASN cc_start: 0.5846 (m-40) cc_final: 0.4878 (t0) REVERT: A 697 MET cc_start: 0.9026 (ptm) cc_final: 0.8644 (ptm) REVERT: A 1127 ASP cc_start: 0.8332 (m-30) cc_final: 0.8120 (m-30) REVERT: B 117 LEU cc_start: 0.7861 (tp) cc_final: 0.7090 (mp) REVERT: B 235 ILE cc_start: 0.7288 (mt) cc_final: 0.6838 (mm) REVERT: B 403 ARG cc_start: 0.7159 (ptt180) cc_final: 0.6488 (ptt180) REVERT: B 616 ASN cc_start: 0.7496 (OUTLIER) cc_final: 0.7104 (m-40) REVERT: B 780 GLU cc_start: 0.8334 (mt-10) cc_final: 0.8107 (tt0) REVERT: B 1050 MET cc_start: 0.9047 (ptm) cc_final: 0.8751 (ptm) REVERT: B 1106 GLN cc_start: 0.9397 (OUTLIER) cc_final: 0.9131 (pt0) REVERT: C 140 PHE cc_start: 0.6879 (p90) cc_final: 0.6609 (p90) REVERT: C 239 GLN cc_start: 0.8012 (pt0) cc_final: 0.7761 (tt0) REVERT: C 351 TYR cc_start: 0.6658 (p90) cc_final: 0.5947 (p90) REVERT: C 378 LYS cc_start: 0.8111 (tttt) cc_final: 0.7526 (tptp) REVERT: C 433 VAL cc_start: 0.7963 (t) cc_final: 0.7638 (m) REVERT: C 950 ASP cc_start: 0.8556 (t70) cc_final: 0.8238 (m-30) REVERT: C 1045 LYS cc_start: 0.8633 (mttt) cc_final: 0.8355 (tmtt) REVERT: Y 83 MET cc_start: 0.4034 (mtm) cc_final: 0.3626 (mtm) REVERT: Y 103 ARG cc_start: 0.8270 (mmm160) cc_final: 0.7490 (mmm160) outliers start: 53 outliers final: 37 residues processed: 306 average time/residue: 0.1632 time to fit residues: 81.4449 Evaluate side-chains 270 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 231 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 896 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 48 optimal weight: 5.9990 chunk 236 optimal weight: 20.0000 chunk 61 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 194 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 122 optimal weight: 7.9990 chunk 305 optimal weight: 6.9990 chunk 215 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 chunk 255 optimal weight: 5.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 370 ASN B 394 ASN C 66 HIS C 360 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.194539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.140625 restraints weight = 32865.693| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.39 r_work: 0.2994 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 27849 Z= 0.216 Angle : 0.607 8.926 37998 Z= 0.307 Chirality : 0.046 0.239 4456 Planarity : 0.004 0.043 4782 Dihedral : 6.182 70.146 4999 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.92 % Allowed : 11.78 % Favored : 86.29 % 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: 0.48 (0.14), residues: 3304 helix: 2.06 (0.20), residues: 642 sheet: 0.51 (0.17), residues: 824 loop : -0.38 (0.14), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 408 TYR 0.027 0.002 TYR B 380 PHE 0.018 0.002 PHE A 898 TRP 0.021 0.001 TRP C 436 HIS 0.007 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00523 (27742) covalent geometry : angle 0.58545 (37718) SS BOND : bond 0.00543 ( 41) SS BOND : angle 1.70610 ( 82) hydrogen bonds : bond 0.04673 ( 1171) hydrogen bonds : angle 5.67149 ( 3141) link_BETA1-4 : bond 0.00337 ( 19) link_BETA1-4 : angle 1.60888 ( 57) link_NAG-ASN : bond 0.00331 ( 47) link_NAG-ASN : angle 2.17737 ( 141) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 258 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7030 (mmm160) cc_final: 0.6764 (mmt180) REVERT: A 133 PHE cc_start: 0.7258 (m-80) cc_final: 0.6429 (t80) REVERT: A 191 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8591 (mt-10) REVERT: A 343 ASN cc_start: 0.6143 (m-40) cc_final: 0.5249 (t0) REVERT: A 1127 ASP cc_start: 0.8383 (m-30) cc_final: 0.8156 (m-30) REVERT: B 129 LYS cc_start: 0.7509 (pttp) cc_final: 0.7124 (pptt) REVERT: B 403 ARG cc_start: 0.7240 (ptt180) cc_final: 0.6602 (ptt180) REVERT: B 616 ASN cc_start: 0.7623 (OUTLIER) cc_final: 0.7165 (m-40) REVERT: B 780 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8204 (tt0) REVERT: C 191 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8105 (mm-30) REVERT: C 239 GLN cc_start: 0.8019 (pt0) cc_final: 0.7444 (mt0) REVERT: C 273 ARG cc_start: 0.8162 (mmt90) cc_final: 0.7845 (mtt180) REVERT: C 351 TYR cc_start: 0.6845 (p90) cc_final: 0.6202 (p90) REVERT: C 378 LYS cc_start: 0.8124 (tttt) cc_final: 0.7482 (tptp) REVERT: C 433 VAL cc_start: 0.8088 (t) cc_final: 0.7809 (m) REVERT: C 532 ASN cc_start: 0.8494 (t0) cc_final: 0.7711 (m110) REVERT: C 950 ASP cc_start: 0.8571 (t70) cc_final: 0.8266 (m-30) REVERT: X 34 MET cc_start: 0.2261 (ptp) cc_final: -0.0084 (tpt) REVERT: Y 83 MET cc_start: 0.4068 (mtm) cc_final: 0.3670 (mtm) REVERT: Y 103 ARG cc_start: 0.8427 (mmm160) cc_final: 0.7631 (mmm160) outliers start: 56 outliers final: 44 residues processed: 296 average time/residue: 0.1580 time to fit residues: 76.4208 Evaluate side-chains 280 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 234 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1021 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain Z residue 79 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 66 optimal weight: 0.0570 chunk 305 optimal weight: 50.0000 chunk 56 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 279 optimal weight: 3.9990 chunk 160 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 259 optimal weight: 0.8980 chunk 183 optimal weight: 0.7980 chunk 332 optimal weight: 4.9990 overall best weight: 1.5502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 334 ASN A 580 GLN B 370 ASN C 207 HIS C 388 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.194425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.145028 restraints weight = 32892.316| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.31 r_work: 0.3029 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 27849 Z= 0.158 Angle : 0.557 9.123 37998 Z= 0.282 Chirality : 0.044 0.247 4456 Planarity : 0.004 0.042 4782 Dihedral : 5.607 58.789 4996 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.03 % Favored : 97.94 % Rotamer: Outliers : 2.06 % Allowed : 12.68 % Favored : 85.26 % 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: 0.55 (0.14), residues: 3304 helix: 2.12 (0.20), residues: 648 sheet: 0.53 (0.17), residues: 816 loop : -0.31 (0.14), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 408 TYR 0.033 0.001 TYR B 453 PHE 0.025 0.001 PHE A 32 TRP 0.022 0.001 TRP C 436 HIS 0.005 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00375 (27742) covalent geometry : angle 0.53929 (37718) SS BOND : bond 0.00420 ( 41) SS BOND : angle 1.32470 ( 82) hydrogen bonds : bond 0.04199 ( 1171) hydrogen bonds : angle 5.51613 ( 3141) link_BETA1-4 : bond 0.00287 ( 19) link_BETA1-4 : angle 1.58397 ( 57) link_NAG-ASN : bond 0.00271 ( 47) link_NAG-ASN : angle 1.98015 ( 141) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 255 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7095 (mmm160) cc_final: 0.6834 (mmt180) REVERT: A 120 VAL cc_start: 0.9197 (t) cc_final: 0.8988 (m) REVERT: A 133 PHE cc_start: 0.7256 (m-80) cc_final: 0.6411 (t80) REVERT: A 343 ASN cc_start: 0.6045 (m-40) cc_final: 0.5213 (t0) REVERT: A 985 ASP cc_start: 0.7928 (m-30) cc_final: 0.7634 (m-30) REVERT: A 1127 ASP cc_start: 0.8253 (m-30) cc_final: 0.8036 (m-30) REVERT: B 129 LYS cc_start: 0.7639 (pttp) cc_final: 0.7347 (pptt) REVERT: B 403 ARG cc_start: 0.7359 (ptt180) cc_final: 0.6510 (ptt180) REVERT: B 406 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7598 (mt-10) REVERT: B 567 ARG cc_start: 0.7974 (mtt180) cc_final: 0.7733 (mtt180) REVERT: B 616 ASN cc_start: 0.7590 (OUTLIER) cc_final: 0.6888 (m-40) REVERT: B 619 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7358 (mp0) REVERT: C 140 PHE cc_start: 0.6974 (p90) cc_final: 0.6737 (p90) REVERT: C 239 GLN cc_start: 0.8036 (pt0) cc_final: 0.7499 (mt0) REVERT: C 273 ARG cc_start: 0.8144 (mmt90) cc_final: 0.7809 (mtt180) REVERT: C 351 TYR cc_start: 0.6874 (p90) cc_final: 0.6284 (p90) REVERT: C 357 ARG cc_start: 0.7850 (ttp80) cc_final: 0.7568 (ttp80) REVERT: C 359 SER cc_start: 0.8322 (p) cc_final: 0.8006 (m) REVERT: C 378 LYS cc_start: 0.8140 (tttt) cc_final: 0.7513 (tptp) REVERT: C 388 ASN cc_start: 0.7846 (m-40) cc_final: 0.7617 (t0) REVERT: C 433 VAL cc_start: 0.8074 (t) cc_final: 0.7794 (m) REVERT: C 468 ILE cc_start: 0.2650 (OUTLIER) cc_final: 0.2156 (pp) REVERT: C 532 ASN cc_start: 0.8500 (t0) cc_final: 0.7722 (m110) REVERT: C 950 ASP cc_start: 0.8662 (t70) cc_final: 0.8294 (m-30) REVERT: X 34 MET cc_start: 0.2300 (ptp) cc_final: 0.0004 (tpp) REVERT: Y 83 MET cc_start: 0.4122 (mtm) cc_final: 0.3756 (mtm) REVERT: Y 103 ARG cc_start: 0.8492 (mmm160) cc_final: 0.7654 (mmm160) outliers start: 60 outliers final: 43 residues processed: 298 average time/residue: 0.1577 time to fit residues: 76.6826 Evaluate side-chains 286 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 240 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1021 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 1072 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 214 optimal weight: 0.9980 chunk 205 optimal weight: 7.9990 chunk 115 optimal weight: 7.9990 chunk 217 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 209 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 324 optimal weight: 50.0000 chunk 316 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 109 optimal weight: 0.0980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN B 125 ASN B 370 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 450 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.193562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.144075 restraints weight = 32950.021| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.28 r_work: 0.2963 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 27849 Z= 0.173 Angle : 0.563 10.607 37998 Z= 0.285 Chirality : 0.044 0.214 4456 Planarity : 0.004 0.040 4782 Dihedral : 5.249 53.882 4996 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.54 % Favored : 97.43 % Rotamer: Outliers : 2.10 % Allowed : 12.99 % Favored : 84.92 % 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: 0.53 (0.14), residues: 3304 helix: 2.05 (0.20), residues: 655 sheet: 0.51 (0.17), residues: 828 loop : -0.33 (0.14), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 190 TYR 0.029 0.001 TYR B 453 PHE 0.015 0.001 PHE C 898 TRP 0.024 0.001 TRP C 436 HIS 0.008 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00415 (27742) covalent geometry : angle 0.54376 (37718) SS BOND : bond 0.00463 ( 41) SS BOND : angle 1.50829 ( 82) hydrogen bonds : bond 0.04239 ( 1171) hydrogen bonds : angle 5.48683 ( 3141) link_BETA1-4 : bond 0.00277 ( 19) link_BETA1-4 : angle 1.71214 ( 57) link_NAG-ASN : bond 0.00271 ( 47) link_NAG-ASN : angle 1.97150 ( 141) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 245 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7227 (mmm160) cc_final: 0.6919 (mmt180) REVERT: A 133 PHE cc_start: 0.7071 (m-80) cc_final: 0.6168 (t80) REVERT: A 191 GLU cc_start: 0.9008 (OUTLIER) cc_final: 0.8691 (mt-10) REVERT: A 343 ASN cc_start: 0.6016 (m-40) cc_final: 0.5106 (t0) REVERT: A 1127 ASP cc_start: 0.8533 (m-30) cc_final: 0.8301 (m-30) REVERT: B 117 LEU cc_start: 0.8025 (tp) cc_final: 0.7220 (mp) REVERT: B 403 ARG cc_start: 0.7297 (ptt180) cc_final: 0.6574 (ptt180) REVERT: B 616 ASN cc_start: 0.7788 (OUTLIER) cc_final: 0.7203 (m-40) REVERT: B 619 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7655 (mp0) REVERT: C 140 PHE cc_start: 0.6989 (p90) cc_final: 0.6720 (p90) REVERT: C 239 GLN cc_start: 0.8259 (pt0) cc_final: 0.7609 (mt0) REVERT: C 273 ARG cc_start: 0.8257 (mmt90) cc_final: 0.7846 (mtt180) REVERT: C 351 TYR cc_start: 0.6708 (p90) cc_final: 0.5959 (p90) REVERT: C 359 SER cc_start: 0.8305 (p) cc_final: 0.8025 (m) REVERT: C 378 LYS cc_start: 0.8168 (tttt) cc_final: 0.7400 (tptp) REVERT: C 433 VAL cc_start: 0.8114 (t) cc_final: 0.7811 (m) REVERT: C 468 ILE cc_start: 0.3048 (OUTLIER) cc_final: 0.2630 (pp) REVERT: C 532 ASN cc_start: 0.8501 (t0) cc_final: 0.7775 (m110) REVERT: C 565 PHE cc_start: 0.7370 (p90) cc_final: 0.7017 (p90) REVERT: C 950 ASP cc_start: 0.8894 (t70) cc_final: 0.8426 (m-30) REVERT: X 34 MET cc_start: 0.1613 (ptp) cc_final: -0.0644 (tpp) REVERT: Y 12 MET cc_start: 0.2045 (mmt) cc_final: 0.1360 (tpp) REVERT: Y 103 ARG cc_start: 0.8051 (mmm160) cc_final: 0.7268 (mmm160) outliers start: 61 outliers final: 48 residues processed: 288 average time/residue: 0.1590 time to fit residues: 74.1407 Evaluate side-chains 279 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 227 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1021 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 896 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 133 optimal weight: 6.9990 chunk 73 optimal weight: 0.0980 chunk 107 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 190 optimal weight: 0.8980 chunk 141 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 270 optimal weight: 2.9990 chunk 148 optimal weight: 7.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 334 ASN B 370 ASN C 207 HIS C 388 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.195906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.146233 restraints weight = 32715.294| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.32 r_work: 0.3053 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 27849 Z= 0.107 Angle : 0.530 13.827 37998 Z= 0.264 Chirality : 0.043 0.211 4456 Planarity : 0.003 0.048 4782 Dihedral : 4.880 54.212 4996 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.58 % Allowed : 13.95 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.14), residues: 3304 helix: 2.26 (0.20), residues: 657 sheet: 0.52 (0.17), residues: 842 loop : -0.23 (0.14), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 190 TYR 0.026 0.001 TYR B 453 PHE 0.016 0.001 PHE B 32 TRP 0.025 0.001 TRP C 436 HIS 0.004 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00244 (27742) covalent geometry : angle 0.51185 (37718) SS BOND : bond 0.00338 ( 41) SS BOND : angle 1.51923 ( 82) hydrogen bonds : bond 0.03618 ( 1171) hydrogen bonds : angle 5.30028 ( 3141) link_BETA1-4 : bond 0.00340 ( 19) link_BETA1-4 : angle 1.57849 ( 57) link_NAG-ASN : bond 0.00267 ( 47) link_NAG-ASN : angle 1.77556 ( 141) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 264 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7206 (mmm160) cc_final: 0.6942 (mmt180) REVERT: A 133 PHE cc_start: 0.6990 (m-80) cc_final: 0.6420 (t80) REVERT: A 191 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8487 (mt-10) REVERT: A 343 ASN cc_start: 0.5990 (m-40) cc_final: 0.5162 (t0) REVERT: A 1127 ASP cc_start: 0.8407 (m-30) cc_final: 0.8187 (m-30) REVERT: B 406 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7537 (mt-10) REVERT: B 616 ASN cc_start: 0.7461 (OUTLIER) cc_final: 0.6879 (m-40) REVERT: B 619 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7398 (mp0) REVERT: B 1119 ASN cc_start: 0.8349 (m-40) cc_final: 0.8092 (m110) REVERT: C 140 PHE cc_start: 0.6942 (p90) cc_final: 0.6681 (p90) REVERT: C 238 PHE cc_start: 0.7650 (p90) cc_final: 0.7229 (p90) REVERT: C 239 GLN cc_start: 0.8093 (pt0) cc_final: 0.7496 (mt0) REVERT: C 273 ARG cc_start: 0.8033 (mmt90) cc_final: 0.7762 (mtt180) REVERT: C 351 TYR cc_start: 0.6924 (p90) cc_final: 0.6227 (p90) REVERT: C 359 SER cc_start: 0.8264 (p) cc_final: 0.8009 (m) REVERT: C 378 LYS cc_start: 0.8125 (tttt) cc_final: 0.7453 (tptp) REVERT: C 433 VAL cc_start: 0.7946 (t) cc_final: 0.7654 (m) REVERT: C 468 ILE cc_start: 0.2982 (OUTLIER) cc_final: 0.2509 (pp) REVERT: C 532 ASN cc_start: 0.8390 (t0) cc_final: 0.7705 (m110) REVERT: C 565 PHE cc_start: 0.7140 (p90) cc_final: 0.6764 (p90) REVERT: C 950 ASP cc_start: 0.8515 (t70) cc_final: 0.8185 (m-30) REVERT: X 34 MET cc_start: 0.2080 (ptp) cc_final: -0.0322 (tpp) REVERT: Y 12 MET cc_start: 0.2124 (mmt) cc_final: 0.1425 (tpp) REVERT: Y 34 MET cc_start: 0.4369 (mmp) cc_final: 0.3445 (mmt) REVERT: Y 83 MET cc_start: 0.3441 (mtm) cc_final: 0.3065 (mtm) REVERT: Y 103 ARG cc_start: 0.8297 (mmm160) cc_final: 0.7547 (mmm160) outliers start: 46 outliers final: 29 residues processed: 293 average time/residue: 0.1582 time to fit residues: 75.8004 Evaluate side-chains 271 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 238 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 896 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 243 optimal weight: 7.9990 chunk 277 optimal weight: 0.9980 chunk 219 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 172 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 195 optimal weight: 3.9990 chunk 248 optimal weight: 2.9990 chunk 177 optimal weight: 5.9990 chunk 206 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 370 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN C 207 HIS ** Y 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.190806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.145512 restraints weight = 32912.608| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.14 r_work: 0.3031 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 27849 Z= 0.219 Angle : 0.600 12.824 37998 Z= 0.301 Chirality : 0.046 0.225 4456 Planarity : 0.004 0.038 4782 Dihedral : 5.061 54.335 4996 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.65 % Allowed : 14.39 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.14), residues: 3304 helix: 2.06 (0.20), residues: 646 sheet: 0.47 (0.17), residues: 850 loop : -0.31 (0.14), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 190 TYR 0.028 0.001 TYR B 380 PHE 0.017 0.002 PHE A 898 TRP 0.025 0.001 TRP C 436 HIS 0.006 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00535 (27742) covalent geometry : angle 0.57856 (37718) SS BOND : bond 0.00524 ( 41) SS BOND : angle 1.90714 ( 82) hydrogen bonds : bond 0.04499 ( 1171) hydrogen bonds : angle 5.47158 ( 3141) link_BETA1-4 : bond 0.00274 ( 19) link_BETA1-4 : angle 1.84253 ( 57) link_NAG-ASN : bond 0.00281 ( 47) link_NAG-ASN : angle 1.96185 ( 141) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 227 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7361 (mmm160) cc_final: 0.7108 (mmt180) REVERT: A 133 PHE cc_start: 0.6796 (m-80) cc_final: 0.6060 (t80) REVERT: A 191 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8515 (mt-10) REVERT: A 343 ASN cc_start: 0.6270 (m-40) cc_final: 0.5474 (t0) REVERT: A 740 MET cc_start: 0.8848 (OUTLIER) cc_final: 0.8640 (ttt) REVERT: A 1127 ASP cc_start: 0.8238 (m-30) cc_final: 0.7986 (m-30) REVERT: B 117 LEU cc_start: 0.8152 (tp) cc_final: 0.7412 (mp) REVERT: B 403 ARG cc_start: 0.7480 (ptt180) cc_final: 0.6749 (ptt180) REVERT: B 406 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7706 (mt-10) REVERT: B 616 ASN cc_start: 0.7532 (OUTLIER) cc_final: 0.7110 (m-40) REVERT: B 619 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7283 (mp0) REVERT: C 239 GLN cc_start: 0.8061 (pt0) cc_final: 0.7502 (mt0) REVERT: C 273 ARG cc_start: 0.8216 (mmt90) cc_final: 0.7826 (mtt180) REVERT: C 359 SER cc_start: 0.8255 (p) cc_final: 0.8027 (m) REVERT: C 378 LYS cc_start: 0.8215 (tttt) cc_final: 0.7599 (tptp) REVERT: C 468 ILE cc_start: 0.3122 (OUTLIER) cc_final: 0.2642 (pp) REVERT: C 532 ASN cc_start: 0.8392 (t0) cc_final: 0.7779 (m110) REVERT: C 537 LYS cc_start: 0.8218 (mttt) cc_final: 0.7880 (mmtp) REVERT: C 565 PHE cc_start: 0.7271 (p90) cc_final: 0.6976 (p90) REVERT: C 950 ASP cc_start: 0.8510 (t70) cc_final: 0.8262 (m-30) REVERT: X 34 MET cc_start: 0.2271 (ptp) cc_final: -0.0103 (tpp) REVERT: Y 83 MET cc_start: 0.3983 (mtm) cc_final: 0.3647 (mtm) REVERT: Y 103 ARG cc_start: 0.8374 (mmm160) cc_final: 0.7631 (mmm160) outliers start: 48 outliers final: 38 residues processed: 260 average time/residue: 0.1568 time to fit residues: 65.9959 Evaluate side-chains 257 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 214 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 1003 SER Chi-restraints excluded: chain Z residue 79 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 280 optimal weight: 2.9990 chunk 295 optimal weight: 3.9990 chunk 190 optimal weight: 0.8980 chunk 330 optimal weight: 20.0000 chunk 277 optimal weight: 0.9990 chunk 131 optimal weight: 4.9990 chunk 278 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 187 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 chunk 260 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 207 HIS ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN B 121 ASN B 370 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN C 207 HIS ** Y 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.193497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.148718 restraints weight = 32970.957| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.16 r_work: 0.3064 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27849 Z= 0.113 Angle : 0.525 11.803 37998 Z= 0.265 Chirality : 0.043 0.203 4456 Planarity : 0.003 0.041 4782 Dihedral : 4.740 53.875 4996 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.48 % Allowed : 14.46 % Favored : 84.06 % 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: 0.64 (0.14), residues: 3304 helix: 2.17 (0.20), residues: 663 sheet: 0.48 (0.17), residues: 857 loop : -0.23 (0.14), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 190 TYR 0.024 0.001 TYR B 453 PHE 0.019 0.001 PHE C 643 TRP 0.026 0.001 TRP C 436 HIS 0.003 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00261 (27742) covalent geometry : angle 0.50842 (37718) SS BOND : bond 0.00291 ( 41) SS BOND : angle 1.46255 ( 82) hydrogen bonds : bond 0.03689 ( 1171) hydrogen bonds : angle 5.25514 ( 3141) link_BETA1-4 : bond 0.00340 ( 19) link_BETA1-4 : angle 1.60716 ( 57) link_NAG-ASN : bond 0.00244 ( 47) link_NAG-ASN : angle 1.72468 ( 141) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 241 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.6754 (m-80) cc_final: 0.6184 (t80) REVERT: A 191 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8458 (mt-10) REVERT: A 233 ILE cc_start: 0.7313 (mm) cc_final: 0.7088 (mm) REVERT: A 326 ILE cc_start: 0.7675 (OUTLIER) cc_final: 0.7290 (tt) REVERT: A 343 ASN cc_start: 0.6234 (m-40) cc_final: 0.5488 (t0) REVERT: A 854 LYS cc_start: 0.5595 (tmtt) cc_final: 0.4558 (ptpt) REVERT: A 1001 LEU cc_start: 0.9001 (tp) cc_final: 0.8799 (tp) REVERT: A 1127 ASP cc_start: 0.8237 (m-30) cc_final: 0.8024 (m-30) REVERT: B 117 LEU cc_start: 0.8124 (tp) cc_final: 0.7417 (mp) REVERT: B 403 ARG cc_start: 0.7476 (ptt180) cc_final: 0.7087 (ptt180) REVERT: B 616 ASN cc_start: 0.7457 (OUTLIER) cc_final: 0.6963 (m-40) REVERT: C 238 PHE cc_start: 0.7669 (p90) cc_final: 0.7277 (p90) REVERT: C 239 GLN cc_start: 0.8069 (pt0) cc_final: 0.7495 (mt0) REVERT: C 273 ARG cc_start: 0.8072 (mmt90) cc_final: 0.7777 (mtt180) REVERT: C 351 TYR cc_start: 0.6717 (p90) cc_final: 0.6397 (p90) REVERT: C 359 SER cc_start: 0.8218 (p) cc_final: 0.8007 (m) REVERT: C 378 LYS cc_start: 0.8230 (tttt) cc_final: 0.7573 (tptp) REVERT: C 396 TYR cc_start: 0.8519 (m-80) cc_final: 0.8277 (m-80) REVERT: C 468 ILE cc_start: 0.3094 (OUTLIER) cc_final: 0.2626 (pp) REVERT: C 532 ASN cc_start: 0.8327 (t0) cc_final: 0.7703 (m110) REVERT: C 537 LYS cc_start: 0.8220 (mttt) cc_final: 0.7879 (mmtp) REVERT: C 565 PHE cc_start: 0.7089 (p90) cc_final: 0.6762 (p90) REVERT: C 950 ASP cc_start: 0.8452 (t70) cc_final: 0.8179 (m-30) REVERT: X 34 MET cc_start: 0.2296 (ptp) cc_final: 0.0007 (tpp) REVERT: Y 34 MET cc_start: 0.4286 (mmp) cc_final: 0.3167 (mmt) REVERT: Y 83 MET cc_start: 0.4062 (mtm) cc_final: 0.3685 (mtm) REVERT: Y 103 ARG cc_start: 0.8372 (mmm160) cc_final: 0.7676 (mmm160) outliers start: 43 outliers final: 28 residues processed: 272 average time/residue: 0.1674 time to fit residues: 73.1708 Evaluate side-chains 263 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 231 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain Z residue 79 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 21 optimal weight: 0.0070 chunk 240 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 31 optimal weight: 30.0000 chunk 278 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 210 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 185 optimal weight: 0.7980 chunk 169 optimal weight: 1.9990 chunk 174 optimal weight: 0.5980 overall best weight: 1.0802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 334 ASN B 370 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 804 GLN B 954 GLN C 207 HIS ** Y 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.192811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.147784 restraints weight = 32823.845| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.15 r_work: 0.3050 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27849 Z= 0.128 Angle : 0.535 10.930 37998 Z= 0.269 Chirality : 0.043 0.199 4456 Planarity : 0.004 0.042 4782 Dihedral : 4.641 54.017 4996 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.27 % Allowed : 14.57 % Favored : 84.16 % 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: 0.66 (0.14), residues: 3304 helix: 2.14 (0.20), residues: 670 sheet: 0.51 (0.17), residues: 857 loop : -0.22 (0.14), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 190 TYR 0.023 0.001 TYR B 453 PHE 0.019 0.001 PHE C 643 TRP 0.028 0.001 TRP C 436 HIS 0.004 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00304 (27742) covalent geometry : angle 0.51823 (37718) SS BOND : bond 0.00320 ( 41) SS BOND : angle 1.42357 ( 82) hydrogen bonds : bond 0.03776 ( 1171) hydrogen bonds : angle 5.23397 ( 3141) link_BETA1-4 : bond 0.00301 ( 19) link_BETA1-4 : angle 1.61090 ( 57) link_NAG-ASN : bond 0.00230 ( 47) link_NAG-ASN : angle 1.72763 ( 141) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6608 Ramachandran restraints generated. 3304 Oldfield, 0 Emsley, 3304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 233 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.6789 (m-80) cc_final: 0.6165 (t80) REVERT: A 191 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8460 (mt-10) REVERT: A 326 ILE cc_start: 0.7650 (OUTLIER) cc_final: 0.7237 (tt) REVERT: A 343 ASN cc_start: 0.6175 (m-40) cc_final: 0.5408 (t0) REVERT: A 854 LYS cc_start: 0.5606 (tmtt) cc_final: 0.4574 (ptpt) REVERT: A 1127 ASP cc_start: 0.8230 (m-30) cc_final: 0.8006 (m-30) REVERT: B 117 LEU cc_start: 0.8198 (tp) cc_final: 0.7496 (mp) REVERT: C 238 PHE cc_start: 0.7687 (p90) cc_final: 0.7286 (p90) REVERT: C 239 GLN cc_start: 0.8069 (pt0) cc_final: 0.7498 (mt0) REVERT: C 273 ARG cc_start: 0.8088 (mmt90) cc_final: 0.7791 (mtt180) REVERT: C 351 TYR cc_start: 0.6636 (p90) cc_final: 0.6310 (p90) REVERT: C 359 SER cc_start: 0.8212 (p) cc_final: 0.8001 (m) REVERT: C 378 LYS cc_start: 0.8227 (tttt) cc_final: 0.7645 (mmmt) REVERT: C 396 TYR cc_start: 0.8530 (m-80) cc_final: 0.8301 (m-80) REVERT: C 468 ILE cc_start: 0.3110 (OUTLIER) cc_final: 0.2641 (pp) REVERT: C 532 ASN cc_start: 0.8361 (t0) cc_final: 0.7756 (m110) REVERT: C 537 LYS cc_start: 0.8224 (mttt) cc_final: 0.7922 (mmtp) REVERT: C 565 PHE cc_start: 0.7140 (p90) cc_final: 0.6852 (p90) REVERT: C 950 ASP cc_start: 0.8499 (t70) cc_final: 0.8218 (m-30) REVERT: X 34 MET cc_start: 0.2316 (ptp) cc_final: 0.0031 (tpp) REVERT: Y 83 MET cc_start: 0.4110 (mtm) cc_final: 0.3639 (mtm) REVERT: Y 103 ARG cc_start: 0.8377 (mmm160) cc_final: 0.7693 (mmm160) outliers start: 37 outliers final: 28 residues processed: 259 average time/residue: 0.1655 time to fit residues: 69.4500 Evaluate side-chains 255 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 224 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain Z residue 79 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 18 optimal weight: 7.9990 chunk 285 optimal weight: 0.5980 chunk 24 optimal weight: 7.9990 chunk 216 optimal weight: 4.9990 chunk 108 optimal weight: 20.0000 chunk 152 optimal weight: 0.9980 chunk 109 optimal weight: 30.0000 chunk 8 optimal weight: 10.0000 chunk 199 optimal weight: 1.9990 chunk 244 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 334 ASN A 450 ASN B 370 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.191500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.146029 restraints weight = 32620.567| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.13 r_work: 0.3043 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 27849 Z= 0.182 Angle : 0.580 14.833 37998 Z= 0.290 Chirality : 0.045 0.402 4456 Planarity : 0.004 0.043 4782 Dihedral : 4.859 54.255 4996 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.69 % Favored : 97.28 % Rotamer: Outliers : 1.24 % Allowed : 14.81 % Favored : 83.96 % 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: 0.56 (0.14), residues: 3304 helix: 2.02 (0.20), residues: 663 sheet: 0.49 (0.17), residues: 862 loop : -0.28 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 190 TYR 0.023 0.001 TYR B 453 PHE 0.019 0.001 PHE C 643 TRP 0.027 0.001 TRP C 436 HIS 0.005 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00441 (27742) covalent geometry : angle 0.55526 (37718) SS BOND : bond 0.00449 ( 41) SS BOND : angle 1.62131 ( 82) hydrogen bonds : bond 0.04187 ( 1171) hydrogen bonds : angle 5.32959 ( 3141) link_BETA1-4 : bond 0.00300 ( 19) link_BETA1-4 : angle 1.74007 ( 57) link_NAG-ASN : bond 0.00279 ( 47) link_NAG-ASN : angle 2.31492 ( 141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6145.75 seconds wall clock time: 106 minutes 1.64 seconds (6361.64 seconds total)