Starting phenix.real_space_refine on Thu Mar 5 12:45:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kec_22838/03_2026/7kec_22838.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kec_22838/03_2026/7kec_22838.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7kec_22838/03_2026/7kec_22838.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kec_22838/03_2026/7kec_22838.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kec_22838/03_2026/7kec_22838.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kec_22838/03_2026/7kec_22838.map" } resolution = 3.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.037 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 96 5.16 5 C 14228 2.51 5 N 3681 2.21 5 O 4332 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 173 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22337 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 7394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 966, 7394 Classifications: {'peptide': 966} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 45, 'TRANS': 920} Chain breaks: 12 Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASN:plan1': 5, 'ASP:plan': 11, 'PHE:plan': 2, 'GLU:plan': 10, 'TYR:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 117 Chain: "B" Number of atoms: 6863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 6863 Classifications: {'peptide': 949} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PTRANS': 44, 'TRANS': 904} Chain breaks: 13 Unresolved non-hydrogen bonds: 576 Unresolved non-hydrogen angles: 742 Unresolved non-hydrogen dihedrals: 481 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'ASP:plan': 13, 'ASN:plan1': 17, 'GLU:plan': 12, 'GLN:plan1': 9, 'ARG:plan': 9, 'PHE:plan': 9, 'TYR:plan': 13, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 382 Chain: "C" Number of atoms: 7282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 960, 7282 Classifications: {'peptide': 960} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 45, 'TRANS': 914} Chain breaks: 11 Unresolved non-hydrogen bonds: 220 Unresolved non-hydrogen angles: 274 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASN:plan1': 7, 'ASP:plan': 12, 'GLN:plan1': 3, 'GLU:plan': 13, 'ARG:plan': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 140 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 5.07, per 1000 atoms: 0.23 Number of scatterers: 22337 At special positions: 0 Unit cell: (134.366, 132.25, 170.338, 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 96 16.00 O 4332 8.00 N 3681 7.00 C 14228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, 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=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " 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=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.02 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.04 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.02 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.06 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG B1301 " - " ASN B 165 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 61 " " NAG B1307 " - " ASN B 122 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B 603 " " NAG B1310 " - " ASN B 709 " " NAG B1311 " - " ASN B 717 " " NAG B1312 " - " ASN B 657 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 122 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 657 " " NAG C1308 " - " ASN C 616 " " NAG C1309 " - " ASN C 234 " " NAG C1310 " - " ASN C1074 " " NAG C1311 " - " ASN C 709 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B1134 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN B1098 " " NAG L 1 " - " ASN C 717 " " NAG M 1 " - " ASN C 801 " " NAG N 1 " - " ASN C1098 " " NAG O 1 " - " ASN C1134 " Time building additional restraints: 1.97 Conformation dependent library (CDL) restraints added in 803.1 milliseconds 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5398 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 48 sheets defined 27.7% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 341 removed outlier: 3.543A pdb=" N GLU A 340 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.199A pdb=" N LEU A 368 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.756A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.558A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 441 No H-bonds generated for 'chain 'A' and resid 439 through 441' Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 756 removed outlier: 4.270A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 782 removed outlier: 3.826A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 785 No H-bonds generated for 'chain 'A' and resid 783 through 785' Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.327A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.990A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.593A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.790A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (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 968 Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.898A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 5.448A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1129 No H-bonds generated for 'chain 'A' and resid 1127 through 1129' Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.590A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 Processing helix chain 'B' and resid 371 through 375 Processing helix chain 'B' and resid 385 through 389 Processing helix chain 'B' and resid 403 through 409 Processing helix chain 'B' and resid 439 through 441 No H-bonds generated for 'chain 'B' and resid 439 through 441' Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.855A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.508A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.854A pdb=" N ASP B 820 " --> pdb=" O SER B 816 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.977A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.513A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.918A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 967 removed outlier: 4.004A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.491A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (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 1127 through 1129 No H-bonds generated for 'chain 'B' and resid 1127 through 1129' Processing helix chain 'B' and resid 1141 through 1146 removed outlier: 3.962A pdb=" N LEU B1145 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 364 through 370 removed outlier: 3.767A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 389 removed outlier: 3.677A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 408 Processing helix chain 'C' and resid 439 through 442 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 757 through 783 removed outlier: 3.951A pdb=" N THR C 761 " --> pdb=" O GLY C 757 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) 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 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.718A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (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 968 Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.627A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1127 through 1129 No H-bonds generated for 'chain 'C' and resid 1127 through 1129' Processing helix chain 'C' and resid 1142 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.740A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.646A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.216A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 328 removed outlier: 5.828A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 348 through 349 removed outlier: 6.934A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.321A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 348 through 349 removed outlier: 6.934A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.321A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR A 430 " --> pdb=" O PHE A 515 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.589A 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 453 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 584 through 586 removed outlier: 6.728A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.223A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.091A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 720 Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 720 removed outlier: 3.605A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB8, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.417A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 5.586A pdb=" N VAL A1122 " --> pdb=" O PHE A1089 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N PHE A1089 " --> pdb=" O VAL A1122 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N GLY A1124 " --> pdb=" O ALA A1087 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1094 through 1097 removed outlier: 4.264A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.582A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.446A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 8.918A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.391A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.639A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.804A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N THR B 573 " --> pdb=" O ASP B 568 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ASP B 568 " --> pdb=" O THR B 573 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 357 through 358 Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.538A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 376 through 379 removed outlier: 4.003A pdb=" N TRP B 436 " --> pdb=" O ARG B 509 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 660 removed outlier: 5.982A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 703 through 704 Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.974A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD6, first strand: chain 'B' and resid 1081 through 1082 removed outlier: 4.869A pdb=" N GLY B1124 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N PHE B1089 " --> pdb=" O VAL B1122 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N VAL B1122 " --> pdb=" O PHE B1089 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD8, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.608A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.607A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AE2, first strand: chain 'C' and resid 309 through 313 removed outlier: 6.388A pdb=" N GLU C 309 " --> pdb=" O GLY C 601 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLY C 601 " --> pdb=" O GLU C 309 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 309 through 313 removed outlier: 6.388A pdb=" N GLU C 309 " --> pdb=" O GLY C 601 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLY C 601 " --> pdb=" O GLU C 309 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.849A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.682A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.391A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.724A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.414A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N THR C1066 " --> pdb=" O SER C 721 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.414A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N THR C1066 " --> pdb=" O SER C 721 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 5.519A pdb=" N VAL C1122 " --> pdb=" O PHE C1089 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N PHE C1089 " --> pdb=" O VAL C1122 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N GLY C1124 " --> pdb=" O ALA C1087 " (cutoff:3.500A) 987 hydrogen bonds defined for protein. 2679 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.34 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6252 1.33 - 1.46: 4289 1.46 - 1.58: 12124 1.58 - 1.70: 0 1.70 - 1.82: 120 Bond restraints: 22785 Sorted by residual: bond pdb=" C5 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.413 1.491 -0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" C5 NAG A1305 " pdb=" O5 NAG A1305 " ideal model delta sigma weight residual 1.413 1.491 -0.078 2.00e-02 2.50e+03 1.50e+01 bond pdb=" C5 NAG C1305 " pdb=" O5 NAG C1305 " ideal model delta sigma weight residual 1.413 1.490 -0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" C5 NAG C1302 " pdb=" O5 NAG C1302 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" C5 NAG B1305 " pdb=" O5 NAG B1305 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.42e+01 ... (remaining 22780 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 24559 2.24 - 4.47: 5953 4.47 - 6.70: 509 6.70 - 8.94: 30 8.94 - 11.17: 3 Bond angle restraints: 31054 Sorted by residual: angle pdb=" CD ARG A 319 " pdb=" NE ARG A 319 " pdb=" CZ ARG A 319 " ideal model delta sigma weight residual 124.40 134.39 -9.99 1.40e+00 5.10e-01 5.09e+01 angle pdb=" CA PHE A 817 " pdb=" CB PHE A 817 " pdb=" CG PHE A 817 " ideal model delta sigma weight residual 113.80 120.92 -7.12 1.00e+00 1.00e+00 5.08e+01 angle pdb=" CA PHE A 377 " pdb=" CB PHE A 377 " pdb=" CG PHE A 377 " ideal model delta sigma weight residual 113.80 120.61 -6.81 1.00e+00 1.00e+00 4.64e+01 angle pdb=" CA ASN A 122 " pdb=" CB ASN A 122 " pdb=" CG ASN A 122 " ideal model delta sigma weight residual 112.60 118.87 -6.27 1.00e+00 1.00e+00 3.93e+01 angle pdb=" CA PHE A 201 " pdb=" CB PHE A 201 " pdb=" CG PHE A 201 " ideal model delta sigma weight residual 113.80 119.94 -6.14 1.00e+00 1.00e+00 3.77e+01 ... (remaining 31049 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 12984 17.88 - 35.76: 1013 35.76 - 53.63: 169 53.63 - 71.51: 50 71.51 - 89.39: 36 Dihedral angle restraints: 14252 sinusoidal: 5911 harmonic: 8341 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -169.26 83.26 1 1.00e+01 1.00e-02 8.47e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -165.11 79.11 1 1.00e+01 1.00e-02 7.79e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -162.34 76.34 1 1.00e+01 1.00e-02 7.33e+01 ... (remaining 14249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2165 0.077 - 0.154: 1277 0.154 - 0.231: 318 0.231 - 0.307: 45 0.307 - 0.384: 7 Chirality restraints: 3812 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 6.94e+01 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.76e+01 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.06e+01 ... (remaining 3809 not shown) Planarity restraints: 3972 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 603 " -0.207 2.00e-02 2.50e+03 3.22e-01 1.30e+03 pdb=" CG ASN B 603 " 0.144 2.00e-02 2.50e+03 pdb=" OD1 ASN B 603 " -0.098 2.00e-02 2.50e+03 pdb=" ND2 ASN B 603 " 0.545 2.00e-02 2.50e+03 pdb=" C1 NAG B1309 " -0.384 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 603 " -0.217 2.00e-02 2.50e+03 3.16e-01 1.25e+03 pdb=" CG ASN A 603 " 0.150 2.00e-02 2.50e+03 pdb=" OD1 ASN A 603 " -0.090 2.00e-02 2.50e+03 pdb=" ND2 ASN A 603 " 0.531 2.00e-02 2.50e+03 pdb=" C1 NAG A1306 " -0.374 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B1074 " 0.204 2.00e-02 2.50e+03 2.33e-01 6.80e+02 pdb=" CG ASN B1074 " -0.121 2.00e-02 2.50e+03 pdb=" OD1 ASN B1074 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN B1074 " -0.370 2.00e-02 2.50e+03 pdb=" C1 NAG B1308 " 0.280 2.00e-02 2.50e+03 ... (remaining 3969 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3600 2.80 - 3.33: 24475 3.33 - 3.85: 38758 3.85 - 4.38: 46774 4.38 - 4.90: 75422 Nonbonded interactions: 189029 Sorted by model distance: nonbonded pdb=" OE1 GLN C 607 " pdb=" CE1 TYR C 674 " model vdw 2.280 3.340 nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.526 3.040 nonbonded pdb=" OG SER B1123 " pdb=" OE2 GLU C 918 " model vdw 2.548 3.040 nonbonded pdb=" O5 NAG M 1 " pdb=" O6 NAG M 1 " model vdw 2.553 2.432 nonbonded pdb=" OE1 GLN A 607 " pdb=" CE1 TYR A 674 " model vdw 2.557 3.340 ... (remaining 189024 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 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 52 or (resid 53 and (name N or nam \ e CA or name C or name O or name CB )) or resid 54 through 66 or resid 82 throug \ h 87 or (resid 88 and (name N or name CA or name C or name O or name CB )) or re \ sid 89 through 95 or (resid 96 through 97 and (name N or name CA or name C or na \ me O or name CB )) or resid 98 through 109 or (resid 110 through 113 and (name N \ or name CA or name C or name O or name CB )) or resid 116 through 124 or (resid \ 125 and (name N or name CA or name C or name O or name CB )) or resid 126 throu \ gh 131 or (resid 132 and (name N or name CA or name C or name O or name CB )) or \ resid 133 or (resid 134 through 138 and (name N or name CA or name C or name O \ or name CB )) or resid 139 through 140 or resid 166 through 168 or (resid 169 an \ d (name N or name CA or name C or name O or name CB )) or resid 170 through 171 \ or (resid 172 and (name N or name CA or name C or name O or name CB )) or resid \ 186 through 190 or (resid 191 and (name N or name CA or name C or name O or name \ CB )) or resid 192 through 196 or resid 200 through 210 or (resid 211 and (name \ N or name CA or name C or name O or name CB )) or (resid 215 and (name N or nam \ e CA or name C or name O or name CB )) or resid 216 through 217 or (resid 218 an \ d (name N or name CA or name C or name O or name CB )) or resid 219 through 223 \ or (resid 224 and (name N or name CA or name C or name O or name CB )) or resid \ 225 through 238 or (resid 239 and (name N or name CA or name C or name O or name \ CB )) or resid 240 through 263 or resid 265 through 308 or (resid 309 and (name \ N or name CA or name C or name O or name CB )) or resid 310 through 323 or (res \ id 324 and (name N or name CA or name C or name O or name CB )) or resid 325 thr \ ough 332 or (resid 333 through 334 and (name N or name CA or name C or name O or \ name CB )) or resid 335 through 345 or (resid 346 through 360 and (name N or na \ me CA or name C or name O or name CB )) or resid 361 or (resid 362 through 378 a \ nd (name N or name CA or name C or name O or name CB )) or resid 379 or (resid 3 \ 80 and (name N or name CA or name C or name O or name CB )) or resid 381 or (res \ id 382 through 383 and (name N or name CA or name C or name O or name CB )) or r \ esid 384 or (resid 385 through 390 and (name N or name CA or name C or name O or \ name CB )) or resid 391 or (resid 392 through 403 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 404 through 411 and (name N or name CA or \ name C or name O or name CB )) or resid 412 through 413 or (resid 414 through 41 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 416 or (resi \ d 417 through 425 and (name N or name CA or name C or name O or name CB )) or re \ sid 426 through 427 or (resid 428 through 430 and (name N or name CA or name C o \ r name O or name CB )) or resid 431 through 432 or (resid 433 through 442 and (n \ ame N or name CA or name C or name O or name CB )) or (resid 450 through 451 and \ (name N or name CA or name C or name O or name CB )) or (resid 453 and (name N \ or name CA or name C or name O or name CB )) or resid 463 or (resid 464 through \ 466 and (name N or name CA or name C or name O or name CB )) or resid 491 or (re \ sid 492 through 495 and (name N or name CA or name C or name O or name CB )) or \ resid 496 or (resid 497 through 498 and (name N or name CA or name C or name O o \ r name CB )) or resid 499 or (resid 500 through 503 and (name N or name CA or na \ me C or name O or name CB )) or (resid 504 through 506 and (name N or name CA or \ name C or name O or name CB )) or resid 507 or (resid 508 through 515 and (name \ N or name CA or name C or name O or name CB )) or (resid 522 through 524 and (n \ ame N or name CA or name C or name O or name CB )) or resid 525 through 528 or ( \ resid 529 and (name N or name CA or name C or name O or name CB )) or resid 530 \ through 553 or (resid 554 and (name N or name CA or name C or name O or name CB \ )) or resid 555 through 793 or (resid 794 and (name N or name CA or name C or na \ me O or name CB )) or resid 795 or (resid 796 and (name N or name CA or name C o \ r name O or name CB )) or resid 797 through 810 or (resid 811 and (name N or nam \ e CA or name C or name O or name CB )) or resid 813 through 827 or resid 856 thr \ ough 866 or (resid 867 through 868 and (name N or name CA or name C or name O or \ name CB )) or resid 869 through 939 or (resid 940 and (name N or name CA or nam \ e C or name O or name CB )) or resid 941 through 984 or (resid 985 and (name N o \ r name CA or name C or name O or name CB )) or resid 986 through 987 or (resid 9 \ 88 through 989 and (name N or name CA or name C or name O or name CB )) or resid \ 990 through 1141 or (resid 1142 and (name N or name CA or name C or name O or n \ ame CB )) or resid 1143 through 1144 or (resid 1145 through 1146 and (name N or \ name CA or name C or name O or name CB )) or resid 1147 through 1310)) selection = (chain 'B' and (resid 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 66 or resid 82 through 87 or (resi \ d 88 and (name N or name CA or name C or name O or name CB )) or resid 89 throug \ h 96 or (resid 97 and (name N or name CA or name C or name O or name CB )) or re \ sid 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or \ resid 100 through 109 or (resid 110 through 113 and (name N or name CA or name C \ or name O or name CB )) or resid 116 through 128 or (resid 129 and (name N or n \ ame CA or name C or name O or name CB )) or resid 130 through 134 or (resid 135 \ through 138 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 9 through 140 or resid 166 through 168 or (resid 169 and (name N or name CA or n \ ame C or name O or name CB )) or resid 170 through 187 or (resid 188 and (name N \ or name CA or name C or name O or name CB )) or resid 189 through 190 or (resid \ 191 and (name N or name CA or name C or name O or name CB )) or resid 192 throu \ gh 195 or (resid 196 and (name N or name CA or name C or name O or name CB )) or \ resid 200 through 210 or (resid 211 through 215 and (name N or name CA or name \ C or name O or name CB )) or resid 216 through 241 or (resid 242 through 263 and \ (name N or name CA or name C or name O or name CB )) or resid 265 through 280 o \ r (resid 281 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 82 through 323 or (resid 324 and (name N or name CA or name C or name O or name \ CB )) or resid 325 through 442 or resid 450 through 451 or resid 453 or resid 46 \ 3 through 501 or resid 503 through 567 or (resid 568 and (name N or name CA or n \ ame C or name O or name CB )) or resid 569 through 570 or (resid 571 and (name N \ or name CA or name C or name O or name CB )) or resid 572 through 581 or (resid \ 582 through 583 and (name N or name CA or name C or name O or name CB )) or res \ id 584 through 585 or (resid 586 and (name N or name CA or name C or name O or n \ ame CB )) or resid 587 through 618 or (resid 619 and (name N or name CA or name \ C or name O or name CB )) or resid 620 through 676 or resid 690 through 744 or ( \ resid 745 and (name N or name CA or name C or name O or name CB )) or resid 746 \ through 810 or (resid 811 and (name N or name CA or name C or name O or name CB \ )) or resid 813 through 827 or resid 856 through 866 or (resid 867 through 868 a \ nd (name N or name CA or name C or name O or name CB )) or resid 869 through 920 \ or (resid 921 and (name N or name CA or name C or name O or name CB )) or resid \ 922 through 939 or (resid 940 and (name N or name CA or name C or name O or nam \ e CB )) or resid 941 through 984 or (resid 985 and (name N or name CA or name C \ or name O or name CB )) or resid 986 through 987 or (resid 988 through 989 and ( \ name N or name CA or name C or name O or name CB )) or resid 990 through 1072 or \ (resid 1073 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 074 through 1117 or (resid 1118 and (name N or name CA or name C or name O or na \ me CB )) or resid 1119 through 1143 or (resid 1144 through 1146 and (name N or n \ ame CA or name C or name O or name CB )) or resid 1147 through 1310)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or re \ sid 100 through 110 or (resid 111 through 113 and (name N or name CA or name C o \ r name O or name CB )) or resid 116 through 134 or (resid 135 through 138 and (n \ ame N or name CA or name C or name O or name CB )) or resid 139 through 140 or r \ esid 166 through 187 or (resid 188 and (name N or name CA or name C or name O or \ name CB )) or resid 189 through 195 or (resid 196 and (name N or name CA or nam \ e C or name O or name CB )) or resid 200 through 211 or resid 215 through 217 or \ (resid 218 and (name N or name CA or name C or name O or name CB )) or resid 21 \ 9 through 223 or (resid 224 and (name N or name CA or name C or name O or name C \ B )) or resid 225 through 238 or (resid 239 and (name N or name CA or name C or \ name O or name CB )) or resid 240 through 308 or (resid 309 and (name N or name \ CA or name C or name O or name CB )) or resid 310 through 332 or (resid 333 thro \ ugh 334 and (name N or name CA or name C or name O or name CB )) or resid 335 th \ rough 344 or (resid 345 through 360 and (name N or name CA or name C or name O o \ r name CB )) or resid 361 or (resid 362 through 378 and (name N or name CA or na \ me C or name O or name CB )) or resid 379 or (resid 380 and (name N or name CA o \ r name C or name O or name CB )) or resid 381 or (resid 382 through 383 and (nam \ e N or name CA or name C or name O or name CB )) or resid 384 or (resid 385 thro \ ugh 390 and (name N or name CA or name C or name O or name CB )) or resid 391 or \ (resid 392 through 403 and (name N or name CA or name C or name O or name CB )) \ or (resid 404 through 411 and (name N or name CA or name C or name O or name CB \ )) or resid 412 through 413 or (resid 414 through 415 and (name N or name CA or \ name C or name O or name CB )) or (resid 416 through 425 and (name N or name CA \ or name C or name O or name CB )) or resid 426 or (resid 427 through 430 and (n \ ame N or name CA or name C or name O or name CB )) or resid 431 through 432 or ( \ resid 433 through 442 and (name N or name CA or name C or name O or name CB )) o \ r (resid 448 through 449 and (name N or name CA or name C or name O or name CB ) \ ) or (resid 451 and (name N or name CA or name C or name O or name CB )) or resi \ d 463 or (resid 464 through 466 and (name N or name CA or name C or name O or na \ me CB )) or resid 491 or (resid 492 through 495 and (name N or name CA or name C \ or name O or name CB )) or resid 496 or (resid 497 through 498 and (name N or n \ ame CA or name C or name O or name CB )) or resid 499 through 500 or (resid 501 \ and (name N or name CA or name C or name O or name CB )) or (resid 503 and (name \ N or name CA or name C or name O or name CB )) or (resid 504 through 506 and (n \ ame N or name CA or name C or name O or name CB )) or resid 507 or (resid 508 th \ rough 515 and (name N or name CA or name C or name O or name CB )) or (resid 522 \ through 524 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 25 through 527 or (resid 528 through 529 and (name N or name CA or name C or nam \ e O or name CB )) or resid 530 through 553 or (resid 554 and (name N or name CA \ or name C or name O or name CB )) or resid 555 through 567 or (resid 568 and (na \ me N or name CA or name C or name O or name CB )) or resid 569 through 570 or (r \ esid 571 and (name N or name CA or name C or name O or name CB )) or resid 572 t \ hrough 581 or (resid 582 through 583 and (name N or name CA or name C or name O \ or name CB )) or resid 584 through 585 or (resid 586 and (name N or name CA or n \ ame C or name O or name CB )) or resid 587 through 618 or (resid 619 and (name N \ or name CA or name C or name O or name CB )) or resid 620 through 645 or (resid \ 646 through 647 and (name N or name CA or name C or name O or name CB )) or res \ id 648 through 793 or (resid 794 and (name N or name CA or name C or name O or n \ ame CB )) or resid 795 or (resid 796 and (name N or name CA or name C or name O \ or name CB )) or resid 797 through 920 or (resid 921 and (name N or name CA or n \ ame C or name O or name CB )) or resid 922 through 1072 or (resid 1073 and (name \ N or name CA or name C or name O or name CB )) or resid 1074 through 1117 or (r \ esid 1118 and (name N or name CA or name C or name O or name CB )) or resid 1119 \ through 1141 or (resid 1142 and (name N or name CA or name C or name O or name \ CB )) or resid 1143 or (resid 1144 through 1146 and (name N or name CA or name C \ or name O or name CB )) or resid 1147 through 1310)) } 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' } 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 group one per residue 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: 1.820 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: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 21.230 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6418 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 : 0.013 0.078 22877 Z= 0.758 Angle : 1.835 11.175 31295 Z= 1.186 Chirality : 0.095 0.384 3812 Planarity : 0.017 0.264 3927 Dihedral : 13.963 89.392 8749 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 0.83 Ramachandran Plot: Outliers : 1.04 % Allowed : 9.05 % Favored : 89.92 % Rotamer: Outliers : 2.39 % Allowed : 5.94 % Favored : 91.67 % 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: -2.05 (0.14), residues: 2797 helix: -0.92 (0.17), residues: 652 sheet: -0.73 (0.24), residues: 369 loop : -1.74 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.002 ARG B 102 TYR 0.216 0.025 TYR C1138 PHE 0.089 0.014 PHE A 201 TRP 0.119 0.029 TRP A1102 HIS 0.019 0.004 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.01350 (22785) covalent geometry : angle 1.80799 (31054) SS BOND : bond 0.00778 ( 35) SS BOND : angle 2.01582 ( 70) hydrogen bonds : bond 0.14121 ( 971) hydrogen bonds : angle 8.88506 ( 2679) link_BETA1-4 : bond 0.02363 ( 12) link_BETA1-4 : angle 4.57517 ( 36) link_NAG-ASN : bond 0.00992 ( 45) link_NAG-ASN : angle 4.62197 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 115 time to evaluate : 0.878 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: symmetry clash revert: symmetry clash REVERT: A 877 LEU cc_start: 0.7437 (mt) cc_final: 0.7188 (mt) REVERT: A 1084 ASP cc_start: 0.6308 (OUTLIER) cc_final: 0.6053 (m-30) REVERT: B 608 VAL cc_start: 0.5276 (OUTLIER) cc_final: 0.5073 (t) outliers start: 54 outliers final: 16 residues processed: 166 average time/residue: 0.1638 time to fit residues: 42.4532 Evaluate side-chains 68 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 50 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 1004 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 50.0000 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 926 GLN A 969 ASN A1005 GLN A1023 ASN B 188 ASN B 580 GLN ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN C 52 GLN C 606 ASN C 613 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.044194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.030310 restraints weight = 196990.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.031244 restraints weight = 119953.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.031828 restraints weight = 85330.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.032150 restraints weight = 67744.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.032442 restraints weight = 59316.384| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 22877 Z= 0.196 Angle : 0.818 11.206 31295 Z= 0.413 Chirality : 0.049 0.431 3812 Planarity : 0.005 0.139 3927 Dihedral : 8.511 87.343 4266 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.18 % Favored : 94.71 % Rotamer: Outliers : 2.13 % Allowed : 8.68 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.15), residues: 2797 helix: 0.18 (0.19), residues: 670 sheet: -1.08 (0.21), residues: 530 loop : -1.36 (0.15), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 237 TYR 0.028 0.002 TYR C 904 PHE 0.027 0.002 PHE B 759 TRP 0.022 0.002 TRP C 64 HIS 0.006 0.002 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00386 (22785) covalent geometry : angle 0.76075 (31054) SS BOND : bond 0.00919 ( 35) SS BOND : angle 1.69180 ( 70) hydrogen bonds : bond 0.06073 ( 971) hydrogen bonds : angle 7.01068 ( 2679) link_BETA1-4 : bond 0.00302 ( 12) link_BETA1-4 : angle 1.81944 ( 36) link_NAG-ASN : bond 0.00583 ( 45) link_NAG-ASN : angle 4.41428 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 63 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 LYS cc_start: 0.6361 (OUTLIER) cc_final: 0.6120 (pttm) REVERT: A 740 MET cc_start: 0.9264 (mmm) cc_final: 0.8727 (mmm) REVERT: A 873 TYR cc_start: 0.8424 (OUTLIER) cc_final: 0.7425 (t80) REVERT: A 1061 VAL cc_start: 0.9692 (OUTLIER) cc_final: 0.9415 (p) REVERT: B 29 THR cc_start: 0.8743 (OUTLIER) cc_final: 0.8491 (t) REVERT: B 763 LEU cc_start: 0.9776 (mt) cc_final: 0.9278 (pp) REVERT: B 869 MET cc_start: 0.8793 (mtp) cc_final: 0.8493 (ptp) REVERT: B 1029 MET cc_start: 0.9465 (tpp) cc_final: 0.9129 (mmm) REVERT: C 282 ASN cc_start: 0.8150 (OUTLIER) cc_final: 0.7917 (m-40) REVERT: C 390 LEU cc_start: 0.8988 (mt) cc_final: 0.8612 (mp) REVERT: C 731 MET cc_start: 0.8895 (mtp) cc_final: 0.8053 (ttt) REVERT: C 763 LEU cc_start: 0.9586 (OUTLIER) cc_final: 0.9286 (pp) REVERT: C 911 VAL cc_start: 0.9566 (t) cc_final: 0.9355 (p) REVERT: C 1002 GLN cc_start: 0.8945 (tp40) cc_final: 0.8565 (tp-100) outliers start: 48 outliers final: 16 residues processed: 104 average time/residue: 0.1417 time to fit residues: 24.8249 Evaluate side-chains 72 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 50 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1061 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 140 optimal weight: 0.5980 chunk 277 optimal weight: 7.9990 chunk 101 optimal weight: 40.0000 chunk 262 optimal weight: 9.9990 chunk 257 optimal weight: 9.9990 chunk 93 optimal weight: 4.9990 chunk 108 optimal weight: 20.0000 chunk 168 optimal weight: 6.9990 chunk 29 optimal weight: 30.0000 chunk 111 optimal weight: 20.0000 chunk 30 optimal weight: 20.0000 overall best weight: 6.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 872 GLN A 901 GLN A 914 ASN A 954 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN B 914 ASN B 926 GLN B 955 ASN B 965 GLN C 779 GLN C 914 ASN C 954 GLN C 955 ASN C1011 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1058 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.042726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.029237 restraints weight = 202320.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.030075 restraints weight = 124060.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.030612 restraints weight = 89029.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.031019 restraints weight = 70752.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.031243 restraints weight = 60962.299| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 22877 Z= 0.280 Angle : 0.782 12.796 31295 Z= 0.399 Chirality : 0.046 0.302 3812 Planarity : 0.005 0.098 3927 Dihedral : 7.928 87.694 4245 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.54 % Favored : 93.35 % Rotamer: Outliers : 2.44 % Allowed : 9.48 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.15), residues: 2797 helix: 0.52 (0.19), residues: 678 sheet: -1.32 (0.20), residues: 532 loop : -1.32 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 237 TYR 0.026 0.002 TYR A 423 PHE 0.029 0.002 PHE C 759 TRP 0.014 0.002 TRP A 104 HIS 0.007 0.002 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00554 (22785) covalent geometry : angle 0.73103 (31054) SS BOND : bond 0.00574 ( 35) SS BOND : angle 2.07371 ( 70) hydrogen bonds : bond 0.06001 ( 971) hydrogen bonds : angle 6.79608 ( 2679) link_BETA1-4 : bond 0.00536 ( 12) link_BETA1-4 : angle 1.79510 ( 36) link_NAG-ASN : bond 0.00613 ( 45) link_NAG-ASN : angle 3.98615 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 55 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 740 MET cc_start: 0.9205 (mmm) cc_final: 0.8979 (mmm) REVERT: A 873 TYR cc_start: 0.8497 (OUTLIER) cc_final: 0.7840 (t80) REVERT: A 1005 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8593 (pt0) REVERT: A 1050 MET cc_start: 0.8800 (ttp) cc_final: 0.8181 (ptp) REVERT: B 1029 MET cc_start: 0.9513 (tpp) cc_final: 0.9148 (mmm) REVERT: C 731 MET cc_start: 0.8901 (mtp) cc_final: 0.8474 (ttm) REVERT: C 763 LEU cc_start: 0.9579 (OUTLIER) cc_final: 0.9346 (pp) REVERT: C 872 GLN cc_start: 0.9384 (OUTLIER) cc_final: 0.8984 (tp-100) outliers start: 55 outliers final: 28 residues processed: 102 average time/residue: 0.1399 time to fit residues: 24.4203 Evaluate side-chains 80 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 48 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 872 GLN Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1061 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 1 optimal weight: 3.9990 chunk 133 optimal weight: 50.0000 chunk 272 optimal weight: 0.6980 chunk 242 optimal weight: 9.9990 chunk 136 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 151 optimal weight: 2.9990 chunk 251 optimal weight: 5.9990 chunk 124 optimal weight: 0.0070 chunk 71 optimal weight: 0.2980 chunk 24 optimal weight: 30.0000 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1113 GLN C 969 ASN C1048 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.044242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.030777 restraints weight = 196158.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.031772 restraints weight = 116679.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.032368 restraints weight = 82219.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.032816 restraints weight = 64132.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.033074 restraints weight = 54457.491| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 22877 Z= 0.125 Angle : 0.666 13.172 31295 Z= 0.333 Chirality : 0.045 0.228 3812 Planarity : 0.004 0.072 3927 Dihedral : 6.812 57.581 4240 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.11 % Favored : 94.74 % Rotamer: Outliers : 1.91 % Allowed : 10.46 % Favored : 87.64 % 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: -0.95 (0.15), residues: 2797 helix: 0.82 (0.20), residues: 670 sheet: -0.96 (0.20), residues: 562 loop : -1.14 (0.15), residues: 1565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 237 TYR 0.021 0.001 TYR A 423 PHE 0.017 0.001 PHE B 32 TRP 0.012 0.001 TRP A 104 HIS 0.004 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00255 (22785) covalent geometry : angle 0.61978 (31054) SS BOND : bond 0.00245 ( 35) SS BOND : angle 1.54557 ( 70) hydrogen bonds : bond 0.04639 ( 971) hydrogen bonds : angle 6.31514 ( 2679) link_BETA1-4 : bond 0.00418 ( 12) link_BETA1-4 : angle 1.41715 ( 36) link_NAG-ASN : bond 0.00453 ( 45) link_NAG-ASN : angle 3.58131 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 58 time to evaluate : 0.822 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 740 MET cc_start: 0.9190 (mmm) cc_final: 0.8684 (mmm) REVERT: A 873 TYR cc_start: 0.8403 (OUTLIER) cc_final: 0.7832 (t80) REVERT: A 1005 GLN cc_start: 0.8950 (mt0) cc_final: 0.8567 (pt0) REVERT: A 1011 GLN cc_start: 0.9568 (OUTLIER) cc_final: 0.9288 (mm-40) REVERT: A 1123 SER cc_start: 0.6119 (OUTLIER) cc_final: 0.5571 (t) REVERT: B 912 THR cc_start: 0.8764 (OUTLIER) cc_final: 0.8285 (p) REVERT: B 1004 LEU cc_start: 0.9651 (OUTLIER) cc_final: 0.9448 (pp) REVERT: B 1029 MET cc_start: 0.9332 (tpp) cc_final: 0.8997 (mmm) REVERT: C 763 LEU cc_start: 0.9564 (mt) cc_final: 0.9351 (pp) REVERT: C 872 GLN cc_start: 0.9330 (OUTLIER) cc_final: 0.8823 (tp-100) outliers start: 43 outliers final: 22 residues processed: 96 average time/residue: 0.1422 time to fit residues: 23.3556 Evaluate side-chains 75 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 47 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1011 GLN Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 872 GLN Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1061 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 103 optimal weight: 40.0000 chunk 64 optimal weight: 7.9990 chunk 211 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 179 optimal weight: 10.0000 chunk 262 optimal weight: 9.9990 chunk 122 optimal weight: 50.0000 chunk 2 optimal weight: 10.0000 chunk 4 optimal weight: 8.9990 chunk 240 optimal weight: 20.0000 chunk 117 optimal weight: 10.0000 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 856 ASN ** C1106 GLN ** 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 = 0.3463 r_free = 0.3463 target = 0.041924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.028719 restraints weight = 205844.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.029546 restraints weight = 125561.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.030092 restraints weight = 90287.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.030372 restraints weight = 72287.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.030609 restraints weight = 63625.563| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 22877 Z= 0.360 Angle : 0.806 13.488 31295 Z= 0.412 Chirality : 0.046 0.203 3812 Planarity : 0.005 0.062 3927 Dihedral : 6.928 56.443 4233 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.54 % Favored : 93.35 % Rotamer: Outliers : 2.57 % Allowed : 11.61 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.15), residues: 2797 helix: 0.57 (0.19), residues: 679 sheet: -1.22 (0.20), residues: 540 loop : -1.38 (0.15), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 408 TYR 0.027 0.002 TYR A 423 PHE 0.025 0.002 PHE A1089 TRP 0.009 0.002 TRP A 104 HIS 0.008 0.002 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00713 (22785) covalent geometry : angle 0.76462 (31054) SS BOND : bond 0.00610 ( 35) SS BOND : angle 1.97016 ( 70) hydrogen bonds : bond 0.06014 ( 971) hydrogen bonds : angle 6.62555 ( 2679) link_BETA1-4 : bond 0.00598 ( 12) link_BETA1-4 : angle 1.83379 ( 36) link_NAG-ASN : bond 0.00742 ( 45) link_NAG-ASN : angle 3.62316 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 44 time to evaluate : 0.650 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 740 MET cc_start: 0.9222 (mmm) cc_final: 0.8990 (mmm) REVERT: A 873 TYR cc_start: 0.8503 (OUTLIER) cc_final: 0.7675 (t80) REVERT: B 912 THR cc_start: 0.8575 (OUTLIER) cc_final: 0.8053 (p) REVERT: B 1029 MET cc_start: 0.9557 (tpp) cc_final: 0.9150 (mmm) REVERT: B 1050 MET cc_start: 0.8703 (ptm) cc_final: 0.8491 (ptm) REVERT: C 731 MET cc_start: 0.9011 (ttm) cc_final: 0.8768 (ttm) REVERT: C 872 GLN cc_start: 0.9384 (OUTLIER) cc_final: 0.9010 (tp-100) outliers start: 58 outliers final: 38 residues processed: 95 average time/residue: 0.1341 time to fit residues: 22.2277 Evaluate side-chains 83 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 42 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 872 GLN Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1061 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 45 optimal weight: 8.9990 chunk 101 optimal weight: 30.0000 chunk 184 optimal weight: 7.9990 chunk 169 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 120 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 25 optimal weight: 40.0000 chunk 274 optimal weight: 5.9990 chunk 221 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.042626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.029308 restraints weight = 202374.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.030171 restraints weight = 122336.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.030760 restraints weight = 86612.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.031069 restraints weight = 68417.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.031326 restraints weight = 59645.000| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 22877 Z= 0.206 Angle : 0.682 12.791 31295 Z= 0.342 Chirality : 0.044 0.191 3812 Planarity : 0.004 0.054 3927 Dihedral : 6.625 57.173 4233 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.58 % Favored : 94.32 % Rotamer: Outliers : 1.99 % Allowed : 12.27 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.15), residues: 2797 helix: 0.77 (0.20), residues: 680 sheet: -1.22 (0.20), residues: 549 loop : -1.33 (0.15), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 357 TYR 0.024 0.002 TYR A 423 PHE 0.015 0.001 PHE B 32 TRP 0.011 0.001 TRP A 104 HIS 0.006 0.001 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00412 (22785) covalent geometry : angle 0.63786 (31054) SS BOND : bond 0.00373 ( 35) SS BOND : angle 2.08856 ( 70) hydrogen bonds : bond 0.05118 ( 971) hydrogen bonds : angle 6.37457 ( 2679) link_BETA1-4 : bond 0.00380 ( 12) link_BETA1-4 : angle 1.46676 ( 36) link_NAG-ASN : bond 0.00472 ( 45) link_NAG-ASN : angle 3.35650 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 47 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 727 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9052 (mp) REVERT: A 740 MET cc_start: 0.9195 (mmm) cc_final: 0.8963 (mmm) REVERT: A 873 TYR cc_start: 0.8414 (OUTLIER) cc_final: 0.7974 (t80) REVERT: A 900 MET cc_start: 0.7789 (mpp) cc_final: 0.7314 (mtt) REVERT: B 912 THR cc_start: 0.8625 (OUTLIER) cc_final: 0.8095 (p) REVERT: B 1029 MET cc_start: 0.9503 (tpp) cc_final: 0.9130 (mmm) REVERT: C 731 MET cc_start: 0.8990 (ttm) cc_final: 0.8643 (ttm) REVERT: C 872 GLN cc_start: 0.9361 (OUTLIER) cc_final: 0.8882 (tp-100) REVERT: C 1084 ASP cc_start: 0.9192 (OUTLIER) cc_final: 0.8892 (p0) outliers start: 45 outliers final: 28 residues processed: 86 average time/residue: 0.1293 time to fit residues: 19.9446 Evaluate side-chains 79 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 46 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 872 GLN Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1084 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 227 optimal weight: 30.0000 chunk 90 optimal weight: 6.9990 chunk 101 optimal weight: 30.0000 chunk 214 optimal weight: 4.9990 chunk 152 optimal weight: 8.9990 chunk 136 optimal weight: 10.0000 chunk 24 optimal weight: 0.0870 chunk 220 optimal weight: 6.9990 chunk 141 optimal weight: 10.0000 chunk 63 optimal weight: 8.9990 chunk 3 optimal weight: 9.9990 overall best weight: 5.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 GLN A 913 GLN A1011 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN B1011 GLN C 641 ASN C 856 ASN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.042094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.028909 restraints weight = 204212.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.029726 restraints weight = 124043.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.030274 restraints weight = 88298.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.030661 restraints weight = 70021.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.030896 restraints weight = 59582.988| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 22877 Z= 0.257 Angle : 0.699 12.388 31295 Z= 0.354 Chirality : 0.044 0.180 3812 Planarity : 0.004 0.059 3927 Dihedral : 6.597 56.881 4232 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.79 % Favored : 93.10 % Rotamer: Outliers : 2.22 % Allowed : 12.54 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.15), residues: 2797 helix: 0.68 (0.20), residues: 679 sheet: -1.28 (0.20), residues: 549 loop : -1.36 (0.15), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 408 TYR 0.021 0.002 TYR A 423 PHE 0.015 0.002 PHE A1089 TRP 0.009 0.002 TRP A 886 HIS 0.007 0.002 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00511 (22785) covalent geometry : angle 0.66067 (31054) SS BOND : bond 0.00325 ( 35) SS BOND : angle 1.74601 ( 70) hydrogen bonds : bond 0.05293 ( 971) hydrogen bonds : angle 6.45302 ( 2679) link_BETA1-4 : bond 0.00475 ( 12) link_BETA1-4 : angle 1.57950 ( 36) link_NAG-ASN : bond 0.00584 ( 45) link_NAG-ASN : angle 3.23510 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 47 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 740 MET cc_start: 0.9180 (mmm) cc_final: 0.8950 (mmm) REVERT: A 873 TYR cc_start: 0.8382 (OUTLIER) cc_final: 0.8034 (t80) REVERT: B 912 THR cc_start: 0.8582 (OUTLIER) cc_final: 0.8028 (p) REVERT: B 1029 MET cc_start: 0.9530 (tpp) cc_final: 0.9136 (mmm) REVERT: C 731 MET cc_start: 0.9008 (OUTLIER) cc_final: 0.8682 (ttm) REVERT: C 872 GLN cc_start: 0.9364 (OUTLIER) cc_final: 0.8949 (tp-100) outliers start: 50 outliers final: 34 residues processed: 89 average time/residue: 0.1325 time to fit residues: 20.9806 Evaluate side-chains 81 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 43 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 872 GLN Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1135 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 80 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 254 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 269 optimal weight: 1.9990 chunk 238 optimal weight: 9.9990 chunk 259 optimal weight: 6.9990 chunk 124 optimal weight: 50.0000 chunk 156 optimal weight: 0.8980 chunk 210 optimal weight: 6.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1113 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.042727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.029410 restraints weight = 199795.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.030299 restraints weight = 120193.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.030857 restraints weight = 84632.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.031255 restraints weight = 67182.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.031470 restraints weight = 57423.142| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22877 Z= 0.173 Angle : 0.637 12.407 31295 Z= 0.318 Chirality : 0.043 0.184 3812 Planarity : 0.004 0.059 3927 Dihedral : 6.271 56.796 4232 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.43 % Favored : 94.42 % Rotamer: Outliers : 1.82 % Allowed : 13.07 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.15), residues: 2797 helix: 0.89 (0.20), residues: 675 sheet: -1.20 (0.20), residues: 561 loop : -1.28 (0.15), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1000 TYR 0.016 0.001 TYR C1067 PHE 0.015 0.001 PHE C 888 TRP 0.011 0.001 TRP A 104 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00348 (22785) covalent geometry : angle 0.60148 (31054) SS BOND : bond 0.00262 ( 35) SS BOND : angle 1.47368 ( 70) hydrogen bonds : bond 0.04693 ( 971) hydrogen bonds : angle 6.19554 ( 2679) link_BETA1-4 : bond 0.00365 ( 12) link_BETA1-4 : angle 1.34736 ( 36) link_NAG-ASN : bond 0.00420 ( 45) link_NAG-ASN : angle 3.04686 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 48 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 727 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9082 (mp) REVERT: A 740 MET cc_start: 0.9193 (mmm) cc_final: 0.8982 (mmm) REVERT: A 873 TYR cc_start: 0.8425 (OUTLIER) cc_final: 0.8124 (t80) REVERT: A 900 MET cc_start: 0.7771 (mpp) cc_final: 0.7421 (mtt) REVERT: B 912 THR cc_start: 0.8714 (OUTLIER) cc_final: 0.8188 (p) REVERT: C 731 MET cc_start: 0.8958 (ttm) cc_final: 0.8733 (ttm) REVERT: C 872 GLN cc_start: 0.9363 (OUTLIER) cc_final: 0.8888 (tp-100) outliers start: 41 outliers final: 30 residues processed: 85 average time/residue: 0.1342 time to fit residues: 20.2386 Evaluate side-chains 81 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 47 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 872 GLN Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1084 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 70 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 chunk 226 optimal weight: 40.0000 chunk 109 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 235 optimal weight: 6.9990 chunk 178 optimal weight: 1.9990 chunk 128 optimal weight: 40.0000 chunk 98 optimal weight: 30.0000 chunk 107 optimal weight: 7.9990 chunk 127 optimal weight: 50.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.042437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.029453 restraints weight = 203462.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.030241 restraints weight = 121898.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.030825 restraints weight = 84878.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.031134 restraints weight = 66241.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.031400 restraints weight = 57332.795| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 22877 Z= 0.201 Angle : 0.646 12.073 31295 Z= 0.324 Chirality : 0.043 0.188 3812 Planarity : 0.004 0.058 3927 Dihedral : 6.192 56.614 4232 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.22 % Favored : 93.64 % Rotamer: Outliers : 2.08 % Allowed : 12.80 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.15), residues: 2797 helix: 0.91 (0.20), residues: 673 sheet: -1.14 (0.20), residues: 563 loop : -1.28 (0.15), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1000 TYR 0.015 0.002 TYR C1067 PHE 0.037 0.001 PHE A 456 TRP 0.009 0.001 TRP A 886 HIS 0.005 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00402 (22785) covalent geometry : angle 0.61242 (31054) SS BOND : bond 0.00272 ( 35) SS BOND : angle 1.43729 ( 70) hydrogen bonds : bond 0.04796 ( 971) hydrogen bonds : angle 6.19659 ( 2679) link_BETA1-4 : bond 0.00368 ( 12) link_BETA1-4 : angle 1.40644 ( 36) link_NAG-ASN : bond 0.00472 ( 45) link_NAG-ASN : angle 2.99572 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 46 time to evaluate : 0.996 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 727 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9053 (mp) REVERT: A 740 MET cc_start: 0.9202 (mmm) cc_final: 0.8991 (mmm) REVERT: A 873 TYR cc_start: 0.8404 (OUTLIER) cc_final: 0.8100 (t80) REVERT: A 900 MET cc_start: 0.7892 (mpp) cc_final: 0.7382 (mtt) REVERT: B 912 THR cc_start: 0.8615 (OUTLIER) cc_final: 0.8069 (p) REVERT: B 1029 MET cc_start: 0.9497 (tpp) cc_final: 0.9139 (mmm) REVERT: C 731 MET cc_start: 0.9014 (OUTLIER) cc_final: 0.8725 (ttm) REVERT: C 872 GLN cc_start: 0.9368 (OUTLIER) cc_final: 0.8910 (tp-100) REVERT: C 902 MET cc_start: 0.8756 (tpp) cc_final: 0.8477 (tpp) REVERT: C 1050 MET cc_start: 0.8356 (ptp) cc_final: 0.8143 (ptp) outliers start: 47 outliers final: 33 residues processed: 90 average time/residue: 0.1325 time to fit residues: 21.4238 Evaluate side-chains 82 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 44 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 872 GLN Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 904 TYR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1084 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 76 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 257 optimal weight: 0.2980 chunk 157 optimal weight: 2.9990 chunk 250 optimal weight: 1.9990 chunk 276 optimal weight: 2.9990 chunk 217 optimal weight: 6.9990 chunk 120 optimal weight: 50.0000 chunk 148 optimal weight: 10.0000 chunk 107 optimal weight: 20.0000 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1002 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.042973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.029811 restraints weight = 201947.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.030690 restraints weight = 120104.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.031265 restraints weight = 84300.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.031692 restraints weight = 66015.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.031971 restraints weight = 56209.373| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22877 Z= 0.145 Angle : 0.620 13.345 31295 Z= 0.306 Chirality : 0.043 0.199 3812 Planarity : 0.004 0.055 3927 Dihedral : 5.944 56.600 4232 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.29 % Favored : 94.57 % Rotamer: Outliers : 1.86 % Allowed : 13.03 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.15), residues: 2797 helix: 0.92 (0.20), residues: 676 sheet: -1.05 (0.20), residues: 587 loop : -1.24 (0.15), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 273 TYR 0.016 0.001 TYR C1067 PHE 0.027 0.001 PHE A 456 TRP 0.011 0.001 TRP A 104 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00296 (22785) covalent geometry : angle 0.58849 (31054) SS BOND : bond 0.00248 ( 35) SS BOND : angle 1.33945 ( 70) hydrogen bonds : bond 0.04414 ( 971) hydrogen bonds : angle 6.05870 ( 2679) link_BETA1-4 : bond 0.00373 ( 12) link_BETA1-4 : angle 1.24156 ( 36) link_NAG-ASN : bond 0.00424 ( 45) link_NAG-ASN : angle 2.87065 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 49 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 727 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9096 (mp) REVERT: A 758 SER cc_start: 0.9733 (m) cc_final: 0.9434 (t) REVERT: A 873 TYR cc_start: 0.8418 (OUTLIER) cc_final: 0.8137 (t80) REVERT: A 900 MET cc_start: 0.7758 (mpp) cc_final: 0.7260 (mtt) REVERT: B 912 THR cc_start: 0.8729 (OUTLIER) cc_final: 0.8195 (p) REVERT: B 1029 MET cc_start: 0.9414 (tpp) cc_final: 0.9059 (mmm) REVERT: B 1050 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.7821 (ptm) REVERT: C 731 MET cc_start: 0.8936 (OUTLIER) cc_final: 0.8574 (tmm) REVERT: C 872 GLN cc_start: 0.9369 (OUTLIER) cc_final: 0.8916 (tp-100) REVERT: C 896 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8793 (tp) REVERT: C 902 MET cc_start: 0.8748 (tpp) cc_final: 0.8519 (tpp) outliers start: 42 outliers final: 28 residues processed: 86 average time/residue: 0.1352 time to fit residues: 20.7288 Evaluate side-chains 84 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 49 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 872 GLN Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1084 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 200 optimal weight: 9.9990 chunk 32 optimal weight: 50.0000 chunk 186 optimal weight: 9.9990 chunk 159 optimal weight: 4.9990 chunk 36 optimal weight: 8.9990 chunk 105 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 240 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 133 optimal weight: 50.0000 chunk 91 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.041802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.028911 restraints weight = 209449.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.029745 restraints weight = 125916.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.030299 restraints weight = 88607.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.030603 restraints weight = 69960.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.030854 restraints weight = 60952.259| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.4129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 22877 Z= 0.289 Angle : 0.727 14.043 31295 Z= 0.368 Chirality : 0.044 0.203 3812 Planarity : 0.005 0.055 3927 Dihedral : 6.267 56.599 4230 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.97 % Favored : 92.89 % Rotamer: Outliers : 1.73 % Allowed : 13.38 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.15), residues: 2797 helix: 0.64 (0.20), residues: 676 sheet: -1.12 (0.20), residues: 576 loop : -1.40 (0.15), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1000 TYR 0.021 0.002 TYR C 789 PHE 0.023 0.002 PHE A 456 TRP 0.009 0.002 TRP A 886 HIS 0.007 0.002 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00574 (22785) covalent geometry : angle 0.69043 (31054) SS BOND : bond 0.00409 ( 35) SS BOND : angle 2.43816 ( 70) hydrogen bonds : bond 0.05330 ( 971) hydrogen bonds : angle 6.36079 ( 2679) link_BETA1-4 : bond 0.00508 ( 12) link_BETA1-4 : angle 1.55855 ( 36) link_NAG-ASN : bond 0.00631 ( 45) link_NAG-ASN : angle 3.00142 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4402.26 seconds wall clock time: 76 minutes 53.66 seconds (4613.66 seconds total)