Starting phenix.real_space_refine on Sun Jul 5 10:10:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7z6v_14531/07_2026/7z6v_14531.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z6v_14531/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7z6v_14531/07_2026/7z6v_14531.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z6v_14531/07_2026/7z6v_14531.map" model { file = "/net/cci-nas-00/data/ceres_data/7z6v_14531/07_2026/7z6v_14531.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z6v_14531/07_2026/7z6v_14531.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7z6v_14531/07_2026/7z6v_14531.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7z6v_14531/07_2026/7z6v_14531.cif" } 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-6108/lib/python3.11/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 chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 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 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 chiralities: 9 Time building chain proxies: 6.48, per 1000 atoms: 0.24 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: 2.64 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.32 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: 8.67 Time building geometry restraints manager: 3.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 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 - 17.88: 14620 17.88 - 35.77: 1067 35.77 - 53.65: 196 53.65 - 71.54: 56 71.54 - 89.42: 12 Dihedral angle restraints: 15951 sinusoidal: 6197 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 15948 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: 1.750 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: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 30.080 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.150 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 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 : 13.333 89.424 9562 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/Z covalent geometry : bond 0.00994 / 0.63 (27742) covalent geometry : angle 1.64433 / 1.07 (37718) SS BOND : bond 0.15471 / 11.39 ( 41) SS BOND : angle 7.38140 / 5.62 ( 82) hydrogen bonds : bond 0.17333 / 11.57 ( 1171) hydrogen bonds : angle 7.73360 / 5.47 ( 3141) link_BETA1-4 : bond 0.00548 / 0.29 ( 19) link_BETA1-4 : angle 2.07965 / 1.42 ( 57) link_NAG-ASN : bond 0.01323 / 0.80 ( 47) link_NAG-ASN : angle 5.36734 / 3.63 ( 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 : 0.999 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: 0.1971 time to fit residues: 161.1025 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 : 0.959 ------------------------------------------------------------------------------- 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... 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 388 ASN ** 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: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.199238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.149673 restraints weight = 32952.944| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.37 r_work: 0.3078 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 27849 Z= 0.145 Angle : 0.653 12.087 37998 Z= 0.329 Chirality : 0.046 0.442 4456 Planarity : 0.004 0.035 4782 Dihedral : 4.682 34.465 3617 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.31 % Allowed : 9.55 % 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: 0.57 (0.17), residues: 818 loop : -0.46 (0.14), residues: 1811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 357 TYR 0.022 0.001 TYR A 369 PHE 0.022 0.002 PHE B 192 TRP 0.014 0.001 TRP C 436 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (27742) covalent geometry : angle 0.62588 / 0.32 (37718) SS BOND : bond 0.00457 / 0.32 ( 41) SS BOND : angle 1.60938 / 1.14 ( 82) hydrogen bonds : bond 0.04957 / 3.36 ( 1171) hydrogen bonds : angle 6.11884 / 4.31 ( 3141) link_BETA1-4 : bond 0.00521 / 0.25 ( 19) link_BETA1-4 : angle 1.31831 / 0.89 ( 57) link_NAG-ASN : bond 0.00381 / 0.21 ( 47) link_NAG-ASN : angle 2.79950 / 1.98 ( 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 375 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 337 time to evaluate : 1.038 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: 0.8197 (m-80) cc_final: 0.7968 (m-80) REVERT: A 133 PHE cc_start: 0.7062 (m-80) cc_final: 0.6685 (t80) REVERT: A 200 TYR cc_start: 0.5699 (p90) cc_final: 0.5238 (p90) REVERT: A 343 ASN cc_start: 0.5826 (m-40) cc_final: 0.4894 (t0) REVERT: A 697 MET cc_start: 0.8937 (ptm) cc_final: 0.8599 (ptm) REVERT: B 332 ILE cc_start: 0.8338 (mm) cc_final: 0.8063 (mm) REVERT: B 403 ARG cc_start: 0.7216 (ptt180) cc_final: 0.6536 (ptt180) REVERT: B 453 TYR cc_start: 0.7563 (p90) cc_final: 0.7359 (p90) REVERT: B 616 ASN cc_start: 0.7469 (OUTLIER) cc_final: 0.6955 (m-40) REVERT: C 140 PHE cc_start: 0.6696 (p90) cc_final: 0.6468 (p90) REVERT: C 198 ASP cc_start: 0.7543 (m-30) cc_final: 0.7252 (m-30) REVERT: C 239 GLN cc_start: 0.7767 (pt0) cc_final: 0.7311 (mt0) REVERT: C 353 TRP cc_start: 0.5965 (p-90) cc_final: 0.5684 (p-90) REVERT: C 356 LYS cc_start: 0.7493 (tptt) cc_final: 0.7269 (tptp) REVERT: C 378 LYS cc_start: 0.8082 (tttt) cc_final: 0.7571 (tptp) REVERT: C 396 TYR cc_start: 0.8257 (m-80) cc_final: 0.7742 (m-80) REVERT: C 433 VAL cc_start: 0.7917 (t) cc_final: 0.7573 (m) REVERT: C 869 MET cc_start: 0.8986 (mtt) cc_final: 0.8656 (mtp) REVERT: C 950 ASP cc_start: 0.8697 (t70) cc_final: 0.8344 (m-30) REVERT: C 1045 LYS cc_start: 0.8627 (mttt) cc_final: 0.8302 (tmtt) REVERT: Y 83 MET cc_start: 0.3981 (mtm) cc_final: 0.3569 (mtm) REVERT: Y 103 ARG cc_start: 0.8251 (mmm160) cc_final: 0.7038 (mmm-85) REVERT: Y 104 SER cc_start: 0.7925 (t) cc_final: 0.7670 (m) outliers start: 38 outliers final: 20 residues processed: 365 average time/residue: 0.1784 time to fit residues: 104.0729 Evaluate side-chains 272 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 251 time to evaluate : 0.990 ------------------------------------------------------------------------------- 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 C residue 88 ASP Chi-restraints excluded: chain C residue 317 ASN 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: 0.5980 chunk 93 optimal weight: 0.7980 chunk 40 optimal weight: 30.0000 chunk 263 optimal weight: 2.9990 chunk 202 optimal weight: 8.9990 chunk 166 optimal weight: 0.7980 chunk 254 optimal weight: 3.9990 chunk 317 optimal weight: 20.0000 chunk 72 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.195307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.142173 restraints weight = 33192.974| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.43 r_work: 0.3024 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 27849 Z= 0.170 Angle : 0.600 10.920 37998 Z= 0.305 Chirality : 0.046 0.450 4456 Planarity : 0.004 0.052 4782 Dihedral : 4.392 46.932 3613 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.72 % Allowed : 10.96 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.14), residues: 3304 helix: 2.07 (0.20), residues: 663 sheet: 0.53 (0.17), residues: 851 loop : -0.41 (0.14), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1107 TYR 0.026 0.001 TYR B 380 PHE 0.019 0.002 PHE A 898 TRP 0.024 0.001 TRP C 436 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 (27742) covalent geometry : angle 0.58073 / 0.30 (37718) SS BOND : bond 0.00495 / 0.36 ( 41) SS BOND : angle 1.68497 / 1.19 ( 82) hydrogen bonds : bond 0.04576 / 3.09 ( 1171) hydrogen bonds : angle 5.72685 / 4.02 ( 3141) link_BETA1-4 : bond 0.00284 / 0.16 ( 19) link_BETA1-4 : angle 1.21115 / 0.80 ( 57) link_NAG-ASN : bond 0.00329 / 0.20 ( 47) link_NAG-ASN : angle 2.11229 / 1.52 ( 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 324 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 274 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.8151 (m-80) cc_final: 0.7948 (m-80) REVERT: A 102 ARG cc_start: 0.6943 (mmm160) cc_final: 0.6653 (mmt180) REVERT: A 133 PHE cc_start: 0.7241 (m-80) cc_final: 0.6425 (t80) REVERT: A 343 ASN cc_start: 0.5837 (m-40) cc_final: 0.4867 (t0) REVERT: A 697 MET cc_start: 0.9026 (ptm) cc_final: 0.8646 (ptm) REVERT: A 1127 ASP cc_start: 0.8379 (m-30) cc_final: 0.8158 (m-30) REVERT: B 117 LEU cc_start: 0.7953 (tp) cc_final: 0.7162 (mp) REVERT: B 403 ARG cc_start: 0.7194 (ptt180) cc_final: 0.6531 (ptt180) REVERT: B 616 ASN cc_start: 0.7557 (OUTLIER) cc_final: 0.7122 (m-40) REVERT: B 780 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8207 (tt0) REVERT: B 988 GLU cc_start: 0.8222 (mt-10) cc_final: 0.8010 (pt0) REVERT: B 1050 MET cc_start: 0.9029 (ptm) cc_final: 0.8760 (ptm) REVERT: B 1106 GLN cc_start: 0.9389 (OUTLIER) cc_final: 0.9124 (pt0) REVERT: C 140 PHE cc_start: 0.6907 (p90) cc_final: 0.6599 (p90) REVERT: C 239 GLN cc_start: 0.8011 (pt0) cc_final: 0.7752 (tt0) REVERT: C 351 TYR cc_start: 0.6686 (p90) cc_final: 0.5983 (p90) REVERT: C 378 LYS cc_start: 0.8099 (tttt) cc_final: 0.7495 (tptp) REVERT: C 433 VAL cc_start: 0.7999 (t) cc_final: 0.7663 (m) REVERT: C 950 ASP cc_start: 0.8500 (t70) cc_final: 0.8226 (m-30) REVERT: C 1045 LYS cc_start: 0.8602 (mttt) cc_final: 0.8340 (tmtt) REVERT: Y 83 MET cc_start: 0.4140 (mtm) cc_final: 0.3745 (mtm) REVERT: Y 103 ARG cc_start: 0.8300 (mmm160) cc_final: 0.7530 (mmm160) outliers start: 50 outliers final: 34 residues processed: 307 average time/residue: 0.1793 time to fit residues: 88.3525 Evaluate side-chains 267 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 231 time to evaluate : 0.969 ------------------------------------------------------------------------------- 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 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 705 VAL 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 554 GLU 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 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 512 VAL 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 859 THR Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 916 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 48 optimal weight: 8.9990 chunk 236 optimal weight: 20.0000 chunk 61 optimal weight: 5.9990 chunk 19 optimal weight: 0.3980 chunk 194 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 122 optimal weight: 7.9990 chunk 305 optimal weight: 50.0000 chunk 215 optimal weight: 0.5980 chunk 83 optimal weight: 0.7980 chunk 255 optimal weight: 5.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS B 370 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.197661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.144142 restraints weight = 32920.818| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.39 r_work: 0.3057 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27849 Z= 0.115 Angle : 0.533 7.759 37998 Z= 0.271 Chirality : 0.043 0.412 4456 Planarity : 0.003 0.041 4782 Dihedral : 4.185 49.307 3613 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.51 % Allowed : 12.13 % Favored : 86.36 % 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: 0.68 (0.14), residues: 3304 helix: 2.37 (0.20), residues: 644 sheet: 0.62 (0.17), residues: 815 loop : -0.30 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 408 TYR 0.029 0.001 TYR B 453 PHE 0.016 0.001 PHE B 456 TRP 0.021 0.001 TRP C 436 HIS 0.005 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (27742) covalent geometry : angle 0.51678 / 0.27 (37718) SS BOND : bond 0.00403 / 0.28 ( 41) SS BOND : angle 1.33654 / 0.90 ( 82) hydrogen bonds : bond 0.03930 / 2.65 ( 1171) hydrogen bonds : angle 5.49981 / 3.85 ( 3141) link_BETA1-4 : bond 0.00283 / 0.17 ( 19) link_BETA1-4 : angle 1.12104 / 0.76 ( 57) link_NAG-ASN : bond 0.00267 / 0.15 ( 47) link_NAG-ASN : angle 1.87786 / 1.35 ( 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 305 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 261 time to evaluate : 0.954 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: 0.8140 (m-80) cc_final: 0.7904 (m-80) REVERT: A 102 ARG cc_start: 0.6992 (mmm160) cc_final: 0.6714 (mmt180) REVERT: A 133 PHE cc_start: 0.7269 (m-80) cc_final: 0.6384 (t80) REVERT: A 191 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8530 (mt-10) REVERT: A 343 ASN cc_start: 0.5944 (m-40) cc_final: 0.4872 (t0) REVERT: A 985 ASP cc_start: 0.7917 (m-30) cc_final: 0.7613 (m-30) REVERT: A 1127 ASP cc_start: 0.8402 (m-30) cc_final: 0.8169 (m-30) REVERT: B 117 LEU cc_start: 0.7935 (tp) cc_final: 0.7182 (mp) REVERT: B 403 ARG cc_start: 0.7125 (ptt180) cc_final: 0.6486 (ptt180) REVERT: B 616 ASN cc_start: 0.7515 (OUTLIER) cc_final: 0.6992 (m-40) REVERT: B 988 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7974 (pt0) REVERT: C 140 PHE cc_start: 0.6874 (p90) cc_final: 0.6602 (p90) REVERT: C 207 HIS cc_start: 0.7977 (m170) cc_final: 0.7745 (m-70) REVERT: C 239 GLN cc_start: 0.8075 (pt0) cc_final: 0.7392 (mt0) REVERT: C 351 TYR cc_start: 0.6771 (p90) cc_final: 0.6087 (p90) REVERT: C 378 LYS cc_start: 0.8091 (tttt) cc_final: 0.7440 (tptp) REVERT: C 433 VAL cc_start: 0.7986 (t) cc_final: 0.7676 (m) REVERT: C 532 ASN cc_start: 0.8435 (t0) cc_final: 0.7620 (m110) REVERT: C 950 ASP cc_start: 0.8428 (t70) cc_final: 0.8135 (m-30) REVERT: C 1045 LYS cc_start: 0.8426 (mttt) cc_final: 0.8220 (tmtt) REVERT: X 34 MET cc_start: 0.2046 (ptp) cc_final: -0.0096 (tpt) REVERT: Y 83 MET cc_start: 0.3909 (mtm) cc_final: 0.3571 (mtm) REVERT: Y 103 ARG cc_start: 0.8345 (mmm160) cc_final: 0.7563 (mmm160) outliers start: 44 outliers final: 30 residues processed: 290 average time/residue: 0.1761 time to fit residues: 83.1609 Evaluate side-chains 270 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 238 time to evaluate : 0.980 ------------------------------------------------------------------------------- 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 580 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 859 THR 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 302 THR 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 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 739 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 896 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 66 optimal weight: 3.9990 chunk 305 optimal weight: 50.0000 chunk 56 optimal weight: 6.9990 chunk 116 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 279 optimal weight: 4.9990 chunk 160 optimal weight: 5.9990 chunk 154 optimal weight: 0.0770 chunk 259 optimal weight: 0.4980 chunk 183 optimal weight: 1.9990 chunk 332 optimal weight: 7.9990 overall best weight: 1.5144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 544 ASN A 779 GLN A1005 GLN B 125 ASN B 370 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C 804 GLN C1054 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.194261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.141314 restraints weight = 32883.289| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.33 r_work: 0.3014 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 27849 Z= 0.159 Angle : 0.555 8.198 37998 Z= 0.280 Chirality : 0.044 0.420 4456 Planarity : 0.003 0.043 4782 Dihedral : 4.214 59.660 3613 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.03 % Allowed : 12.26 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.14), residues: 3304 helix: 2.26 (0.20), residues: 644 sheet: 0.61 (0.17), residues: 826 loop : -0.27 (0.14), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 408 TYR 0.039 0.001 TYR B 453 PHE 0.016 0.001 PHE C 898 TRP 0.024 0.001 TRP C 436 HIS 0.005 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (27742) covalent geometry : angle 0.54003 / 0.28 (37718) SS BOND : bond 0.00401 / 0.28 ( 41) SS BOND : angle 1.29497 / 0.92 ( 82) hydrogen bonds : bond 0.04207 / 2.84 ( 1171) hydrogen bonds : angle 5.44018 / 3.80 ( 3141) link_BETA1-4 : bond 0.00275 / 0.16 ( 19) link_BETA1-4 : angle 1.25994 / 0.85 ( 57) link_NAG-ASN : bond 0.00246 / 0.14 ( 47) link_NAG-ASN : angle 1.81805 / 1.30 ( 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 320 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 261 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.8150 (m-80) cc_final: 0.7876 (m-80) REVERT: A 133 PHE cc_start: 0.7304 (m-80) cc_final: 0.6347 (t80) REVERT: A 191 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8609 (mt-10) REVERT: A 343 ASN cc_start: 0.6069 (m-40) cc_final: 0.5190 (t0) REVERT: A 1127 ASP cc_start: 0.8485 (m-30) cc_final: 0.8225 (m-30) REVERT: B 106 PHE cc_start: 0.7184 (m-80) cc_final: 0.6979 (m-80) REVERT: B 380 TYR cc_start: 0.8489 (m-80) cc_final: 0.8128 (m-10) REVERT: B 403 ARG cc_start: 0.7231 (ptt180) cc_final: 0.6569 (ptt180) REVERT: B 616 ASN cc_start: 0.7535 (OUTLIER) cc_final: 0.7012 (m-40) REVERT: B 619 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7571 (mp0) REVERT: B 1106 GLN cc_start: 0.9440 (OUTLIER) cc_final: 0.8562 (pt0) REVERT: C 140 PHE cc_start: 0.6813 (p90) cc_final: 0.6548 (p90) REVERT: C 239 GLN cc_start: 0.7960 (pt0) cc_final: 0.7747 (tt0) REVERT: C 351 TYR cc_start: 0.6830 (p90) cc_final: 0.6175 (p90) REVERT: C 359 SER cc_start: 0.8304 (p) cc_final: 0.8088 (m) REVERT: C 378 LYS cc_start: 0.8187 (tttt) cc_final: 0.7532 (tptp) REVERT: C 388 ASN cc_start: 0.7687 (m110) cc_final: 0.7426 (t0) REVERT: C 396 TYR cc_start: 0.8474 (m-80) cc_final: 0.8159 (m-80) REVERT: C 433 VAL cc_start: 0.8058 (t) cc_final: 0.7782 (m) REVERT: C 468 ILE cc_start: 0.2782 (OUTLIER) cc_final: 0.2302 (pp) REVERT: C 532 ASN cc_start: 0.8429 (t0) cc_final: 0.7658 (m110) REVERT: C 950 ASP cc_start: 0.8486 (t70) cc_final: 0.8194 (m-30) REVERT: X 34 MET cc_start: 0.2212 (ptp) cc_final: -0.0037 (tpp) REVERT: Y 103 ARG cc_start: 0.8448 (mmm160) cc_final: 0.7646 (mmm160) outliers start: 59 outliers final: 39 residues processed: 302 average time/residue: 0.1770 time to fit residues: 86.8686 Evaluate side-chains 284 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 240 time to evaluate : 0.985 ------------------------------------------------------------------------------- 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 118 LEU 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 544 ASN Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 878 LEU 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 332 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 554 GLU 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 B residue 859 THR Chi-restraints excluded: chain B residue 1021 SER 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 112 SER Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 392 PHE 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 645 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 896 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 214 optimal weight: 1.9990 chunk 205 optimal weight: 0.7980 chunk 115 optimal weight: 5.9990 chunk 217 optimal weight: 0.8980 chunk 143 optimal weight: 3.9990 chunk 209 optimal weight: 10.0000 chunk 158 optimal weight: 3.9990 chunk 324 optimal weight: 50.0000 chunk 316 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 109 optimal weight: 9.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 544 ASN A 580 GLN A 779 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 388 ASN C 450 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.191488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.146017 restraints weight = 32844.522| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.22 r_work: 0.3017 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 27849 Z= 0.213 Angle : 0.589 11.071 37998 Z= 0.298 Chirality : 0.046 0.418 4456 Planarity : 0.004 0.045 4782 Dihedral : 4.226 22.097 3610 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.06 % Allowed : 12.99 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.14), residues: 3304 helix: 2.07 (0.20), residues: 646 sheet: 0.49 (0.17), residues: 829 loop : -0.35 (0.14), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 408 TYR 0.026 0.001 TYR B 453 PHE 0.017 0.002 PHE A 898 TRP 0.022 0.001 TRP C 436 HIS 0.006 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.21 (27742) covalent geometry : angle 0.57235 / 0.29 (37718) SS BOND : bond 0.00599 / 0.42 ( 41) SS BOND : angle 1.59204 / 1.10 ( 82) hydrogen bonds : bond 0.04481 / 3.03 ( 1171) hydrogen bonds : angle 5.51545 / 3.85 ( 3141) link_BETA1-4 : bond 0.00353 / 0.21 ( 19) link_BETA1-4 : angle 1.33947 / 0.93 ( 57) link_NAG-ASN : bond 0.00247 / 0.15 ( 47) link_NAG-ASN : angle 1.89363 / 1.36 ( 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: 60 poor density : 246 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.6983 (m-80) cc_final: 0.6283 (t80) REVERT: A 191 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8539 (mt-10) REVERT: A 343 ASN cc_start: 0.6057 (m-40) cc_final: 0.5107 (t0) REVERT: A 1127 ASP cc_start: 0.8234 (m-30) cc_final: 0.8020 (m-30) REVERT: B 403 ARG cc_start: 0.7472 (ptt180) cc_final: 0.6877 (ptt180) REVERT: B 616 ASN cc_start: 0.7580 (OUTLIER) cc_final: 0.7099 (m-40) REVERT: B 1106 GLN cc_start: 0.9494 (OUTLIER) cc_final: 0.8693 (pt0) REVERT: C 239 GLN cc_start: 0.8007 (pt0) cc_final: 0.7523 (mt0) REVERT: C 351 TYR cc_start: 0.6946 (p90) cc_final: 0.6431 (p90) REVERT: C 378 LYS cc_start: 0.8214 (tttt) cc_final: 0.7592 (tptp) REVERT: C 396 TYR cc_start: 0.8570 (m-80) cc_final: 0.8314 (m-80) REVERT: C 468 ILE cc_start: 0.2871 (OUTLIER) cc_final: 0.2403 (pp) REVERT: C 532 ASN cc_start: 0.8360 (t0) cc_final: 0.7675 (m110) REVERT: C 537 LYS cc_start: 0.8192 (mttt) cc_final: 0.7846 (mmtp) REVERT: C 950 ASP cc_start: 0.8520 (t70) cc_final: 0.8259 (m-30) REVERT: Y 12 MET cc_start: 0.2070 (mmt) cc_final: 0.1399 (tpp) REVERT: Y 83 MET cc_start: 0.4008 (mtm) cc_final: 0.3717 (mtm) REVERT: Y 103 ARG cc_start: 0.8413 (mmm160) cc_final: 0.7681 (mmm160) outliers start: 60 outliers final: 47 residues processed: 288 average time/residue: 0.1746 time to fit residues: 82.2783 Evaluate side-chains 273 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 222 time to evaluate : 1.211 ------------------------------------------------------------------------------- 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 118 LEU 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 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 332 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1021 SER Chi-restraints excluded: chain B residue 1037 SER 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 112 SER 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 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 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 Chi-restraints excluded: chain Z residue 79 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 133 optimal weight: 9.9990 chunk 73 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 190 optimal weight: 0.9990 chunk 141 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 270 optimal weight: 0.7980 chunk 148 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 334 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN B 125 ASN B 370 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN B 955 ASN C 207 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.193606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.150558 restraints weight = 32517.243| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.09 r_work: 0.3087 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27849 Z= 0.121 Angle : 0.533 7.923 37998 Z= 0.269 Chirality : 0.043 0.398 4456 Planarity : 0.003 0.038 4782 Dihedral : 4.002 20.135 3610 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.65 % Allowed : 14.15 % Favored : 84.20 % 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: 2.22 (0.20), residues: 650 sheet: 0.51 (0.17), residues: 842 loop : -0.24 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 190 TYR 0.026 0.001 TYR B 453 PHE 0.024 0.001 PHE C 565 TRP 0.023 0.001 TRP C 436 HIS 0.005 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (27742) covalent geometry : angle 0.51926 / 0.27 (37718) SS BOND : bond 0.00328 / 0.23 ( 41) SS BOND : angle 1.25490 / 0.85 ( 82) hydrogen bonds : bond 0.03802 / 2.56 ( 1171) hydrogen bonds : angle 5.31701 / 3.71 ( 3141) link_BETA1-4 : bond 0.00314 / 0.17 ( 19) link_BETA1-4 : angle 1.20501 / 0.84 ( 57) link_NAG-ASN : bond 0.00242 / 0.15 ( 47) link_NAG-ASN : angle 1.69514 / 1.21 ( 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 300 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 252 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7080 (m-80) cc_final: 0.6459 (t80) REVERT: A 191 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.8683 (mt-10) REVERT: A 343 ASN cc_start: 0.5949 (m-40) cc_final: 0.5046 (t0) REVERT: A 1127 ASP cc_start: 0.8651 (m-30) cc_final: 0.8441 (m-30) REVERT: B 117 LEU cc_start: 0.8189 (tp) cc_final: 0.7396 (mp) REVERT: B 403 ARG cc_start: 0.7369 (ptt180) cc_final: 0.6931 (ptt180) REVERT: B 406 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7807 (mt-10) REVERT: B 616 ASN cc_start: 0.7797 (OUTLIER) cc_final: 0.7303 (m-40) REVERT: B 936 ASP cc_start: 0.7983 (m-30) cc_final: 0.7573 (m-30) REVERT: B 1106 GLN cc_start: 0.9412 (OUTLIER) cc_final: 0.8744 (pt0) REVERT: C 140 PHE cc_start: 0.7012 (p90) cc_final: 0.6715 (p90) REVERT: C 238 PHE cc_start: 0.7810 (p90) cc_final: 0.7349 (p90) REVERT: C 239 GLN cc_start: 0.8238 (pt0) cc_final: 0.7668 (mt0) REVERT: C 351 TYR cc_start: 0.6879 (p90) cc_final: 0.6138 (p90) REVERT: C 378 LYS cc_start: 0.8263 (tttt) cc_final: 0.7526 (tptp) REVERT: C 388 ASN cc_start: 0.8322 (t0) cc_final: 0.7969 (t0) REVERT: C 396 TYR cc_start: 0.8557 (m-80) cc_final: 0.8325 (m-80) REVERT: C 468 ILE cc_start: 0.3195 (OUTLIER) cc_final: 0.2677 (pp) REVERT: C 532 ASN cc_start: 0.8478 (t0) cc_final: 0.7736 (m110) REVERT: C 537 LYS cc_start: 0.8228 (mttt) cc_final: 0.7883 (mmtp) REVERT: C 950 ASP cc_start: 0.8822 (t70) cc_final: 0.8416 (m-30) REVERT: Y 12 MET cc_start: 0.2223 (mmt) cc_final: 0.1435 (tpp) REVERT: Y 83 MET cc_start: 0.3718 (mtm) cc_final: 0.3329 (mtm) REVERT: Y 103 ARG cc_start: 0.8305 (mmm160) cc_final: 0.7564 (mmm160) outliers start: 48 outliers final: 30 residues processed: 283 average time/residue: 0.1751 time to fit residues: 80.5785 Evaluate side-chains 265 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 231 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 118 LEU 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 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 859 THR Chi-restraints excluded: chain B residue 878 LEU 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 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 614 ASP Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 645 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 243 optimal weight: 1.9990 chunk 277 optimal weight: 3.9990 chunk 219 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 172 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 195 optimal weight: 3.9990 chunk 248 optimal weight: 0.8980 chunk 177 optimal weight: 6.9990 chunk 206 optimal weight: 4.9990 chunk 142 optimal weight: 10.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN A 334 ASN A 450 ASN A 762 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN C 30 ASN C 207 HIS C 613 GLN ** Y 77 ASN ** 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 = 0.4112 r_free = 0.4112 target = 0.190856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.145211 restraints weight = 32853.747| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.16 r_work: 0.3025 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 27849 Z= 0.216 Angle : 0.606 13.711 37998 Z= 0.303 Chirality : 0.046 0.427 4456 Planarity : 0.004 0.040 4782 Dihedral : 4.233 22.612 3610 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.86 % Allowed : 14.05 % Favored : 84.09 % 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: 0.44 (0.14), residues: 3304 helix: 1.89 (0.20), residues: 658 sheet: 0.43 (0.17), residues: 855 loop : -0.34 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 190 TYR 0.025 0.002 TYR B 453 PHE 0.019 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/Z covalent geometry : bond 0.00523 / 0.22 (27742) covalent geometry : angle 0.58952 / 0.30 (37718) SS BOND : bond 0.00562 / 0.40 ( 41) SS BOND : angle 1.74257 / 1.19 ( 82) hydrogen bonds : bond 0.04551 / 3.08 ( 1171) hydrogen bonds : angle 5.46939 / 3.81 ( 3141) link_BETA1-4 : bond 0.00267 / 0.16 ( 19) link_BETA1-4 : angle 1.40754 / 0.97 ( 57) link_NAG-ASN : bond 0.00253 / 0.16 ( 47) link_NAG-ASN : angle 1.88027 / 1.35 ( 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 274 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 220 time to evaluate : 0.936 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: 0.7556 (mmt180) cc_final: 0.7150 (mmp-170) REVERT: A 133 PHE cc_start: 0.6817 (m-80) cc_final: 0.6082 (t80) REVERT: A 191 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8490 (mt-10) REVERT: A 202 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8581 (mttp) REVERT: A 326 ILE cc_start: 0.7796 (OUTLIER) cc_final: 0.7447 (tt) REVERT: A 343 ASN cc_start: 0.6188 (m-40) cc_final: 0.5131 (t0) REVERT: A 1127 ASP cc_start: 0.8245 (m-30) cc_final: 0.8032 (m-30) REVERT: B 117 LEU cc_start: 0.8194 (tp) cc_final: 0.7480 (mp) REVERT: B 403 ARG cc_start: 0.7512 (ptt180) cc_final: 0.7032 (ptt180) REVERT: B 616 ASN cc_start: 0.7599 (OUTLIER) cc_final: 0.7210 (m-40) REVERT: B 936 ASP cc_start: 0.7718 (m-30) cc_final: 0.7282 (m-30) REVERT: B 1106 GLN cc_start: 0.9511 (OUTLIER) cc_final: 0.8579 (pt0) REVERT: C 140 PHE cc_start: 0.6848 (p90) cc_final: 0.6624 (p90) REVERT: C 239 GLN cc_start: 0.8044 (pt0) cc_final: 0.7502 (mt0) REVERT: C 378 LYS cc_start: 0.8297 (tttt) cc_final: 0.7634 (tptp) REVERT: C 468 ILE cc_start: 0.3143 (OUTLIER) cc_final: 0.2654 (pp) REVERT: C 532 ASN cc_start: 0.8383 (t0) cc_final: 0.7736 (m110) REVERT: C 537 LYS cc_start: 0.8206 (mttt) cc_final: 0.7871 (mmtp) REVERT: C 950 ASP cc_start: 0.8520 (t70) cc_final: 0.8276 (m-30) REVERT: X 34 MET cc_start: 0.2307 (ptp) cc_final: -0.0242 (tpp) REVERT: Y 83 MET cc_start: 0.4131 (mtm) cc_final: 0.3784 (mtm) REVERT: Y 103 ARG cc_start: 0.8378 (mmm160) cc_final: 0.7656 (mmm160) outliers start: 54 outliers final: 41 residues processed: 261 average time/residue: 0.1807 time to fit residues: 76.6871 Evaluate side-chains 254 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 207 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 202 LYS 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 878 LEU 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 430 THR Chi-restraints excluded: chain B residue 452 LEU 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 804 GLN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1021 SER Chi-restraints excluded: chain B residue 1106 GLN 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 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 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 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: 5.9990 chunk 295 optimal weight: 4.9990 chunk 190 optimal weight: 0.6980 chunk 330 optimal weight: 6.9990 chunk 277 optimal weight: 0.2980 chunk 131 optimal weight: 0.9980 chunk 278 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 187 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 260 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN B 804 GLN C 207 HIS C 613 GLN ** Y 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.194066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.148667 restraints weight = 32946.002| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 2.24 r_work: 0.3059 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 27849 Z= 0.109 Angle : 0.534 13.727 37998 Z= 0.268 Chirality : 0.043 0.396 4456 Planarity : 0.003 0.041 4782 Dihedral : 3.948 19.335 3610 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.24 % Allowed : 14.70 % 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: 0.63 (0.14), residues: 3304 helix: 2.23 (0.20), residues: 656 sheet: 0.45 (0.17), residues: 853 loop : -0.24 (0.14), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 190 TYR 0.025 0.001 TYR B 453 PHE 0.021 0.001 PHE C 565 TRP 0.027 0.001 TRP C 436 HIS 0.003 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (27742) covalent geometry : angle 0.52105 / 0.26 (37718) SS BOND : bond 0.00301 / 0.22 ( 41) SS BOND : angle 1.44686 / 0.99 ( 82) hydrogen bonds : bond 0.03629 / 2.43 ( 1171) hydrogen bonds : angle 5.21818 / 3.63 ( 3141) link_BETA1-4 : bond 0.00353 / 0.19 ( 19) link_BETA1-4 : angle 1.19152 / 0.84 ( 57) link_NAG-ASN : bond 0.00267 / 0.16 ( 47) link_NAG-ASN : angle 1.60074 / 1.14 ( 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 273 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 237 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.6817 (m-80) cc_final: 0.6214 (t80) REVERT: A 191 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8488 (mt-10) REVERT: A 202 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8486 (mttp) REVERT: A 326 ILE cc_start: 0.7681 (OUTLIER) cc_final: 0.7285 (tt) REVERT: A 343 ASN cc_start: 0.6048 (m-40) cc_final: 0.5053 (t0) REVERT: A 985 ASP cc_start: 0.7832 (m-30) cc_final: 0.7540 (m-30) REVERT: A 1001 LEU cc_start: 0.9003 (tp) cc_final: 0.8797 (tp) REVERT: A 1127 ASP cc_start: 0.8326 (m-30) cc_final: 0.8089 (m-30) REVERT: B 106 PHE cc_start: 0.7412 (m-80) cc_final: 0.7206 (m-80) REVERT: B 117 LEU cc_start: 0.8157 (tp) cc_final: 0.7409 (mp) REVERT: B 616 ASN cc_start: 0.7471 (OUTLIER) cc_final: 0.7260 (m-40) REVERT: B 936 ASP cc_start: 0.7754 (m-30) cc_final: 0.7317 (m-30) REVERT: C 140 PHE cc_start: 0.6972 (p90) cc_final: 0.6744 (p90) REVERT: C 238 PHE cc_start: 0.7688 (p90) cc_final: 0.7260 (p90) REVERT: C 239 GLN cc_start: 0.8074 (pt0) cc_final: 0.7513 (mt0) REVERT: C 351 TYR cc_start: 0.6741 (p90) cc_final: 0.6401 (p90) REVERT: C 378 LYS cc_start: 0.8274 (tttt) cc_final: 0.7578 (tptp) REVERT: C 468 ILE cc_start: 0.3146 (OUTLIER) cc_final: 0.2703 (pp) REVERT: C 532 ASN cc_start: 0.8334 (t0) cc_final: 0.7687 (m110) REVERT: C 537 LYS cc_start: 0.8233 (mttt) cc_final: 0.7910 (mmtp) REVERT: C 950 ASP cc_start: 0.8464 (t70) cc_final: 0.8203 (m-30) REVERT: X 34 MET cc_start: 0.2288 (ptp) cc_final: -0.0005 (tpp) REVERT: Y 12 MET cc_start: 0.2329 (mmt) cc_final: 0.1637 (tpp) REVERT: Y 34 MET cc_start: 0.4260 (mmp) cc_final: 0.3150 (mmt) REVERT: Y 83 MET cc_start: 0.4128 (mtm) cc_final: 0.3785 (mtm) REVERT: Y 103 ARG cc_start: 0.8378 (mmm160) cc_final: 0.7698 (mmm160) outliers start: 36 outliers final: 25 residues processed: 264 average time/residue: 0.1743 time to fit residues: 75.3000 Evaluate side-chains 253 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 223 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 202 LYS 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 430 THR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1021 SER Chi-restraints excluded: chain C residue 54 LEU 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 735 SER Chi-restraints excluded: chain C residue 791 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: 0.8980 chunk 240 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 278 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 210 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 185 optimal weight: 1.9990 chunk 169 optimal weight: 0.8980 chunk 174 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN B 370 ASN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.193279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.147504 restraints weight = 32819.800| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.23 r_work: 0.3048 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 27849 Z= 0.132 Angle : 0.543 12.765 37998 Z= 0.273 Chirality : 0.044 0.409 4456 Planarity : 0.003 0.040 4782 Dihedral : 3.945 20.382 3610 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.06 % Allowed : 14.63 % Favored : 84.30 % 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: 0.63 (0.14), residues: 3304 helix: 2.16 (0.20), residues: 668 sheet: 0.48 (0.17), residues: 850 loop : -0.24 (0.14), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 190 TYR 0.027 0.001 TYR B 453 PHE 0.021 0.001 PHE B 456 TRP 0.028 0.001 TRP C 436 HIS 0.004 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (27742) covalent geometry : angle 0.52857 / 0.27 (37718) SS BOND : bond 0.00395 / 0.29 ( 41) SS BOND : angle 1.57588 / 1.05 ( 82) hydrogen bonds : bond 0.03808 / 2.56 ( 1171) hydrogen bonds : angle 5.21749 / 3.63 ( 3141) link_BETA1-4 : bond 0.00358 / 0.21 ( 19) link_BETA1-4 : angle 1.26539 / 0.87 ( 57) link_NAG-ASN : bond 0.00227 / 0.13 ( 47) link_NAG-ASN : angle 1.62972 / 1.16 ( 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 263 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 232 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.6857 (m-80) cc_final: 0.6204 (t80) REVERT: A 191 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8507 (mt-10) REVERT: A 202 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8518 (mttp) REVERT: A 326 ILE cc_start: 0.7700 (OUTLIER) cc_final: 0.7266 (tt) REVERT: A 343 ASN cc_start: 0.6181 (m-40) cc_final: 0.5208 (t0) REVERT: A 854 LYS cc_start: 0.5596 (tmtt) cc_final: 0.4577 (ptpt) REVERT: A 1001 LEU cc_start: 0.9007 (tp) cc_final: 0.8797 (tp) REVERT: A 1127 ASP cc_start: 0.8280 (m-30) cc_final: 0.8069 (m-30) REVERT: B 32 PHE cc_start: 0.8016 (m-10) cc_final: 0.7733 (m-10) REVERT: B 117 LEU cc_start: 0.8154 (tp) cc_final: 0.7436 (mp) REVERT: B 403 ARG cc_start: 0.7537 (ptp90) cc_final: 0.6933 (ptt180) REVERT: B 936 ASP cc_start: 0.7726 (m-30) cc_final: 0.7271 (m-30) REVERT: C 140 PHE cc_start: 0.6981 (p90) cc_final: 0.6752 (p90) REVERT: C 238 PHE cc_start: 0.7710 (p90) cc_final: 0.7284 (p90) REVERT: C 239 GLN cc_start: 0.8093 (pt0) cc_final: 0.7502 (mt0) REVERT: C 351 TYR cc_start: 0.6619 (p90) cc_final: 0.6287 (p90) REVERT: C 378 LYS cc_start: 0.8242 (tttt) cc_final: 0.7659 (mmmt) REVERT: C 468 ILE cc_start: 0.3142 (OUTLIER) cc_final: 0.2706 (pp) REVERT: C 532 ASN cc_start: 0.8353 (t0) cc_final: 0.7710 (m110) REVERT: C 537 LYS cc_start: 0.8234 (mttt) cc_final: 0.7912 (mmtp) REVERT: C 902 MET cc_start: 0.8491 (mmt) cc_final: 0.7942 (mmt) REVERT: C 950 ASP cc_start: 0.8455 (t70) cc_final: 0.8216 (m-30) REVERT: X 34 MET cc_start: 0.2323 (ptp) cc_final: 0.0027 (tpp) REVERT: Y 83 MET cc_start: 0.4511 (mtm) cc_final: 0.4037 (mtm) REVERT: Y 103 ARG cc_start: 0.8373 (mmm160) cc_final: 0.7706 (mmm160) outliers start: 31 outliers final: 25 residues processed: 255 average time/residue: 0.1785 time to fit residues: 73.8128 Evaluate side-chains 251 residues out of total 2911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 222 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 202 LYS 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 430 THR Chi-restraints excluded: chain B residue 452 LEU 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 54 LEU 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 735 SER Chi-restraints excluded: chain C residue 791 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: 8.9990 chunk 285 optimal weight: 0.5980 chunk 24 optimal weight: 10.0000 chunk 216 optimal weight: 2.9990 chunk 108 optimal weight: 0.0870 chunk 152 optimal weight: 0.9990 chunk 109 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 199 optimal weight: 0.8980 chunk 244 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 GLN ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN C 207 HIS ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.193454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.150928 restraints weight = 32635.467| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.07 r_work: 0.3091 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27849 Z= 0.129 Angle : 0.547 14.150 37998 Z= 0.272 Chirality : 0.044 0.410 4456 Planarity : 0.003 0.042 4782 Dihedral : 3.928 21.259 3610 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.36 % Favored : 97.61 % Rotamer: Outliers : 1.06 % Allowed : 14.98 % 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: 0.60 (0.14), residues: 3304 helix: 1.96 (0.20), residues: 692 sheet: 0.51 (0.17), residues: 833 loop : -0.24 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 190 TYR 0.026 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/Z covalent geometry : bond 0.00304 / 0.13 (27742) covalent geometry : angle 0.52780 / 0.27 (37718) SS BOND : bond 0.00334 / 0.24 ( 41) SS BOND : angle 1.53927 / 1.02 ( 82) hydrogen bonds : bond 0.03734 / 2.51 ( 1171) hydrogen bonds : angle 5.17918 / 3.60 ( 3141) link_BETA1-4 : bond 0.00318 / 0.19 ( 19) link_BETA1-4 : angle 1.22526 / 0.85 ( 57) link_NAG-ASN : bond 0.00239 / 0.15 ( 47) link_NAG-ASN : angle 2.06480 / 1.48 ( 141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6516.25 seconds wall clock time: 112 minutes 42.38 seconds (6762.38 seconds total)