Starting phenix.real_space_refine on Tue Apr 7 08:39:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zoz_11331/04_2026/6zoz_11331.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zoz_11331/04_2026/6zoz_11331.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6zoz_11331/04_2026/6zoz_11331.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zoz_11331/04_2026/6zoz_11331.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6zoz_11331/04_2026/6zoz_11331.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zoz_11331/04_2026/6zoz_11331.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 123 5.16 5 C 16556 2.51 5 N 4240 2.21 5 O 5092 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 190 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26011 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 8332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1069, 8332 Classifications: {'peptide': 1069} Link IDs: {'PTRANS': 53, 'TRANS': 1015} Chain breaks: 5 Chain: "B" Number of atoms: 8332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1069, 8332 Classifications: {'peptide': 1069} Link IDs: {'PTRANS': 53, 'TRANS': 1015} Chain breaks: 5 Chain: "C" Number of atoms: 8336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1070, 8336 Classifications: {'peptide': 1070} Link IDs: {'PTRANS': 53, 'TRANS': 1016} Chain breaks: 5 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: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 225 Unusual residues: {'BLA': 1, 'NAG': 13} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 225 Unusual residues: {'BLA': 1, 'NAG': 13} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 225 Unusual residues: {'BLA': 1, 'NAG': 13} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 6.15, per 1000 atoms: 0.24 Number of scatterers: 26011 At special positions: 0 Unit cell: (126.259, 138.991, 164.455, 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 123 16.00 O 5092 8.00 N 4240 7.00 C 16556 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS B 981 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.02 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 734 " - pdb=" SG CYS A 756 " distance=2.02 Simple disulfide: pdb=" SG CYS A 739 " - pdb=" SG CYS A 745 " distance=2.03 Simple disulfide: pdb=" SG CYS A 836 " - pdb=" SG CYS A 847 " distance=2.03 Simple disulfide: pdb=" SG CYS A 981 " - pdb=" SG CYS C 383 " distance=2.06 Simple disulfide: pdb=" SG CYS A1028 " - pdb=" SG CYS A1039 " distance=2.02 Simple disulfide: pdb=" SG CYS A1078 " - pdb=" SG CYS A1122 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " 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=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS C 981 " distance=2.01 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.02 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 734 " - pdb=" SG CYS B 756 " distance=2.02 Simple disulfide: pdb=" SG CYS B 739 " - pdb=" SG CYS B 745 " distance=2.03 Simple disulfide: pdb=" SG CYS B 836 " - pdb=" SG CYS B 847 " distance=2.03 Simple disulfide: pdb=" SG CYS B1028 " - pdb=" SG CYS B1039 " distance=2.02 Simple disulfide: pdb=" SG CYS B1078 " - pdb=" SG CYS B1122 " distance=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.02 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 734 " - pdb=" SG CYS C 756 " distance=2.02 Simple disulfide: pdb=" SG CYS C 739 " - pdb=" SG CYS C 745 " distance=2.03 Simple disulfide: pdb=" SG CYS C 836 " - pdb=" SG CYS C 847 " distance=2.03 Simple disulfide: pdb=" SG CYS C1028 " - pdb=" SG CYS C1039 " distance=2.02 Simple disulfide: pdb=" SG CYS C1078 " - pdb=" SG CYS C1122 " 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 331 " " NAG A1304 " - " ASN A 603 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 705 " " NAG A1308 " - " ASN A1070 " " NAG A1309 " - " ASN A1094 " " NAG A1310 " - " ASN A 165 " " NAG A1311 " - " ASN A 282 " " NAG A1312 " - " ASN A 343 " " NAG A1313 " - " ASN A 17 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 331 " " NAG B1304 " - " ASN B 603 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B 705 " " NAG B1308 " - " ASN B1070 " " NAG B1309 " - " ASN B1094 " " NAG B1310 " - " ASN B 165 " " NAG B1311 " - " ASN B 282 " " NAG B1312 " - " ASN B 343 " " NAG B1313 " - " ASN B 17 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 705 " " NAG C1308 " - " ASN C1070 " " NAG C1309 " - " ASN C1094 " " NAG C1310 " - " ASN C 165 " " NAG C1311 " - " ASN C 282 " " NAG C1312 " - " ASN C 343 " " NAG C1313 " - " ASN C 17 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 713 " " NAG F 1 " - " ASN A 797 " " NAG G 1 " - " ASN A1130 " " NAG H 1 " - " ASN B 234 " " NAG I 1 " - " ASN B 713 " " NAG J 1 " - " ASN B 797 " " NAG K 1 " - " ASN B1130 " " NAG L 1 " - " ASN C 234 " " NAG M 1 " - " ASN C 713 " " NAG N 1 " - " ASN C 797 " " NAG O 1 " - " ASN C1130 " Time building additional restraints: 2.25 Conformation dependent library (CDL) restraints added in 993.7 milliseconds 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6012 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 45 sheets defined 26.2% alpha, 30.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 4.034A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 372 Processing helix chain 'A' and resid 383 through 388 removed outlier: 4.300A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 619 through 625 Processing helix chain 'A' and resid 626 through 629 Processing helix chain 'A' and resid 630 through 638 removed outlier: 4.189A pdb=" N TYR A 636 " --> pdb=" O THR A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 739 Processing helix chain 'A' and resid 742 through 751 removed outlier: 3.892A pdb=" N GLN A 751 " --> pdb=" O ASN A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 779 Processing helix chain 'A' and resid 812 through 822 Processing helix chain 'A' and resid 832 through 839 Processing helix chain 'A' and resid 844 through 851 Processing helix chain 'A' and resid 862 through 881 Processing helix chain 'A' and resid 893 through 905 Processing helix chain 'A' and resid 909 through 935 removed outlier: 3.536A pdb=" N TYR A 913 " --> pdb=" O GLN A 909 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N LYS A 917 " --> pdb=" O TYR A 913 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N LEU A 918 " --> pdb=" O GLU A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 940 No H-bonds generated for 'chain 'A' and resid 938 through 940' Processing helix chain 'A' and resid 941 through 961 removed outlier: 4.099A pdb=" N VAL A 947 " --> pdb=" O LYS A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 964 No H-bonds generated for 'chain 'A' and resid 962 through 964' Processing helix chain 'A' and resid 972 through 980 Processing helix chain 'A' and resid 981 through 1029 removed outlier: 5.301A pdb=" N VAL A 987 " --> pdb=" O PRO A 983 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN A 988 " --> pdb=" O GLU A 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.034A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 372 Processing helix chain 'B' and resid 383 through 388 removed outlier: 4.300A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 619 through 625 Processing helix chain 'B' and resid 630 through 638 removed outlier: 4.189A pdb=" N TYR B 636 " --> pdb=" O THR B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 739 Processing helix chain 'B' and resid 742 through 751 removed outlier: 3.892A pdb=" N GLN B 751 " --> pdb=" O ASN B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 779 Processing helix chain 'B' and resid 812 through 822 Processing helix chain 'B' and resid 832 through 839 Processing helix chain 'B' and resid 844 through 851 Processing helix chain 'B' and resid 862 through 881 Processing helix chain 'B' and resid 893 through 905 Processing helix chain 'B' and resid 909 through 935 removed outlier: 3.536A pdb=" N TYR B 913 " --> pdb=" O GLN B 909 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N LYS B 917 " --> pdb=" O TYR B 913 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N LEU B 918 " --> pdb=" O GLU B 914 " (cutoff:3.500A) Processing helix chain 'B' and resid 938 through 940 No H-bonds generated for 'chain 'B' and resid 938 through 940' Processing helix chain 'B' and resid 941 through 961 removed outlier: 4.099A pdb=" N VAL B 947 " --> pdb=" O LYS B 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 964 No H-bonds generated for 'chain 'B' and resid 962 through 964' Processing helix chain 'B' and resid 972 through 980 Processing helix chain 'B' and resid 981 through 1029 removed outlier: 5.302A pdb=" N VAL B 987 " --> pdb=" O PRO B 983 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN B 988 " --> pdb=" O GLU B 984 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.034A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 372 Processing helix chain 'C' and resid 383 through 388 removed outlier: 4.301A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 619 through 625 Processing helix chain 'C' and resid 630 through 638 removed outlier: 4.189A pdb=" N TYR C 636 " --> pdb=" O THR C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 739 Processing helix chain 'C' and resid 742 through 751 removed outlier: 3.892A pdb=" N GLN C 751 " --> pdb=" O ASN C 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 754 through 779 Processing helix chain 'C' and resid 812 through 822 Processing helix chain 'C' and resid 832 through 839 Processing helix chain 'C' and resid 844 through 851 Processing helix chain 'C' and resid 862 through 881 Processing helix chain 'C' and resid 893 through 905 Processing helix chain 'C' and resid 909 through 935 removed outlier: 3.536A pdb=" N TYR C 913 " --> pdb=" O GLN C 909 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N LYS C 917 " --> pdb=" O TYR C 913 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N LEU C 918 " --> pdb=" O GLU C 914 " (cutoff:3.500A) Processing helix chain 'C' and resid 938 through 940 No H-bonds generated for 'chain 'C' and resid 938 through 940' Processing helix chain 'C' and resid 941 through 961 removed outlier: 4.099A pdb=" N VAL C 947 " --> pdb=" O LYS C 943 " (cutoff:3.500A) Processing helix chain 'C' and resid 962 through 964 No H-bonds generated for 'chain 'C' and resid 962 through 964' Processing helix chain 'C' and resid 972 through 980 Processing helix chain 'C' and resid 981 through 1029 removed outlier: 5.302A pdb=" N VAL C 987 " --> pdb=" O PRO C 983 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN C 988 " --> pdb=" O GLU C 984 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 7.792A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.281A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.692A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.997A 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: 4.021A 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 removed outlier: 3.655A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 111 through 115 removed outlier: 4.922A pdb=" N PHE A 133 " --> pdb=" O SER A 112 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 315 removed outlier: 4.797A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 4.565A pdb=" N ILE A 584 " --> pdb=" O SER A 555 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.263A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.263A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.180A pdb=" N GLU A 654 " --> pdb=" O ALA A 690 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N THR A 692 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 697 through 698 removed outlier: 6.925A pdb=" N ALA A 697 " --> pdb=" O ILE B 784 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 707 through 724 removed outlier: 6.535A pdb=" N GLN A1067 " --> pdb=" O THR A 712 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N PHE A 714 " --> pdb=" O PRO A1065 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE A 716 " --> pdb=" O TYR A1063 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N TYR A1063 " --> pdb=" O ILE A 716 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL A 718 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL A1061 " --> pdb=" O VAL A 718 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR A 720 " --> pdb=" O LEU A1059 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LEU A1059 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE A 722 " --> pdb=" O VAL A1057 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL A1057 " --> pdb=" O ILE A 722 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N GLY A1055 " --> pdb=" O PRO A 724 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N TYR A1063 " --> pdb=" O HIS A1044 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N HIS A1044 " --> pdb=" O TYR A1063 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 707 through 724 removed outlier: 6.535A pdb=" N GLN A1067 " --> pdb=" O THR A 712 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N PHE A 714 " --> pdb=" O PRO A1065 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE A 716 " --> pdb=" O TYR A1063 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N TYR A1063 " --> pdb=" O ILE A 716 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL A 718 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL A1061 " --> pdb=" O VAL A 718 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR A 720 " --> pdb=" O LEU A1059 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LEU A1059 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE A 722 " --> pdb=" O VAL A1057 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL A1057 " --> pdb=" O ILE A 722 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N GLY A1055 " --> pdb=" O PRO A 724 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 729 through 732 removed outlier: 4.357A pdb=" N LYS A 729 " --> pdb=" O LEU A 857 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 783 through 784 Processing sheet with id=AB7, first strand: chain 'A' and resid 1116 through 1121 removed outlier: 5.074A pdb=" N ALA A1083 " --> pdb=" O SER A1119 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 31 removed outlier: 7.792A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.281A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.693A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.020A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.655A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 111 through 115 removed outlier: 4.922A pdb=" N PHE B 133 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 315 removed outlier: 4.798A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 4.565A pdb=" N ILE B 584 " --> pdb=" O SER B 555 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.264A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.264A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.179A pdb=" N GLU B 654 " --> pdb=" O ALA B 690 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N THR B 692 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 697 through 698 removed outlier: 6.958A pdb=" N ALA B 697 " --> pdb=" O ILE C 784 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 707 through 724 removed outlier: 6.535A pdb=" N GLN B1067 " --> pdb=" O THR B 712 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N PHE B 714 " --> pdb=" O PRO B1065 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE B 716 " --> pdb=" O TYR B1063 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N TYR B1063 " --> pdb=" O ILE B 716 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL B 718 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL B1061 " --> pdb=" O VAL B 718 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR B 720 " --> pdb=" O LEU B1059 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LEU B1059 " --> pdb=" O THR B 720 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE B 722 " --> pdb=" O VAL B1057 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL B1057 " --> pdb=" O ILE B 722 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N GLY B1055 " --> pdb=" O PRO B 724 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N TYR B1063 " --> pdb=" O HIS B1044 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N HIS B1044 " --> pdb=" O TYR B1063 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 707 through 724 removed outlier: 6.535A pdb=" N GLN B1067 " --> pdb=" O THR B 712 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N PHE B 714 " --> pdb=" O PRO B1065 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE B 716 " --> pdb=" O TYR B1063 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N TYR B1063 " --> pdb=" O ILE B 716 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL B 718 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL B1061 " --> pdb=" O VAL B 718 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR B 720 " --> pdb=" O LEU B1059 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LEU B1059 " --> pdb=" O THR B 720 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE B 722 " --> pdb=" O VAL B1057 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL B1057 " --> pdb=" O ILE B 722 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N GLY B1055 " --> pdb=" O PRO B 724 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 729 through 732 removed outlier: 4.357A pdb=" N LYS B 729 " --> pdb=" O LEU B 857 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1116 through 1121 removed outlier: 5.073A pdb=" N ALA B1083 " --> pdb=" O SER B1119 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 27 through 31 removed outlier: 7.792A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.281A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.693A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.021A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.655A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 111 through 115 removed outlier: 4.922A pdb=" N PHE C 133 " --> pdb=" O SER C 112 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 315 removed outlier: 4.797A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 325 through 328 removed outlier: 4.565A pdb=" N ILE C 584 " --> pdb=" O SER C 555 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.263A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.263A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.179A pdb=" N GLU C 654 " --> pdb=" O ALA C 690 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N THR C 692 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 707 through 724 removed outlier: 6.534A pdb=" N GLN C1067 " --> pdb=" O THR C 712 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N PHE C 714 " --> pdb=" O PRO C1065 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE C 716 " --> pdb=" O TYR C1063 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N TYR C1063 " --> pdb=" O ILE C 716 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL C 718 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL C1061 " --> pdb=" O VAL C 718 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR C 720 " --> pdb=" O LEU C1059 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LEU C1059 " --> pdb=" O THR C 720 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE C 722 " --> pdb=" O VAL C1057 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL C1057 " --> pdb=" O ILE C 722 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N GLY C1055 " --> pdb=" O PRO C 724 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N TYR C1063 " --> pdb=" O HIS C1044 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N HIS C1044 " --> pdb=" O TYR C1063 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 707 through 724 removed outlier: 6.534A pdb=" N GLN C1067 " --> pdb=" O THR C 712 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N PHE C 714 " --> pdb=" O PRO C1065 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE C 716 " --> pdb=" O TYR C1063 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N TYR C1063 " --> pdb=" O ILE C 716 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL C 718 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL C1061 " --> pdb=" O VAL C 718 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR C 720 " --> pdb=" O LEU C1059 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LEU C1059 " --> pdb=" O THR C 720 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE C 722 " --> pdb=" O VAL C1057 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL C1057 " --> pdb=" O ILE C 722 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N GLY C1055 " --> pdb=" O PRO C 724 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 729 through 732 removed outlier: 4.356A pdb=" N LYS C 729 " --> pdb=" O LEU C 857 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1116 through 1121 removed outlier: 5.074A pdb=" N ALA C1083 " --> pdb=" O SER C1119 " (cutoff:3.500A) 1085 hydrogen bonds defined for protein. 2982 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: 5.83 Time building geometry restraints manager: 2.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4204 1.31 - 1.44: 7458 1.44 - 1.58: 14778 1.58 - 1.71: 0 1.71 - 1.84: 150 Bond restraints: 26590 Sorted by residual: bond pdb=" C4C BLA B1314 " pdb=" NC BLA B1314 " ideal model delta sigma weight residual 1.375 1.542 -0.167 2.00e-02 2.50e+03 6.94e+01 bond pdb=" C4C BLA C1314 " pdb=" NC BLA C1314 " ideal model delta sigma weight residual 1.375 1.541 -0.166 2.00e-02 2.50e+03 6.92e+01 bond pdb=" C4C BLA A1314 " pdb=" NC BLA A1314 " ideal model delta sigma weight residual 1.375 1.541 -0.166 2.00e-02 2.50e+03 6.86e+01 bond pdb=" NB BLA B1314 " pdb=" C4B BLA B1314 " ideal model delta sigma weight residual 1.371 1.534 -0.163 2.00e-02 2.50e+03 6.66e+01 bond pdb=" NB BLA C1314 " pdb=" C4B BLA C1314 " ideal model delta sigma weight residual 1.371 1.534 -0.163 2.00e-02 2.50e+03 6.65e+01 ... (remaining 26585 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 35018 1.85 - 3.70: 920 3.70 - 5.55: 223 5.55 - 7.40: 38 7.40 - 9.25: 13 Bond angle restraints: 36212 Sorted by residual: angle pdb=" CA GLU C1013 " pdb=" CB GLU C1013 " pdb=" CG GLU C1013 " ideal model delta sigma weight residual 114.10 123.03 -8.93 2.00e+00 2.50e-01 2.00e+01 angle pdb=" CA GLU B1013 " pdb=" CB GLU B1013 " pdb=" CG GLU B1013 " ideal model delta sigma weight residual 114.10 123.01 -8.91 2.00e+00 2.50e-01 1.99e+01 angle pdb=" CA GLU A1013 " pdb=" CB GLU A1013 " pdb=" CG GLU A1013 " ideal model delta sigma weight residual 114.10 123.01 -8.91 2.00e+00 2.50e-01 1.98e+01 angle pdb=" CB LYS A 782 " pdb=" CG LYS A 782 " pdb=" CD LYS A 782 " ideal model delta sigma weight residual 111.30 120.09 -8.79 2.30e+00 1.89e-01 1.46e+01 angle pdb=" CB LYS B 782 " pdb=" CG LYS B 782 " pdb=" CD LYS B 782 " ideal model delta sigma weight residual 111.30 120.09 -8.79 2.30e+00 1.89e-01 1.46e+01 ... (remaining 36207 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 15358 17.84 - 35.67: 969 35.67 - 53.51: 228 53.51 - 71.34: 87 71.34 - 89.18: 42 Dihedral angle restraints: 16684 sinusoidal: 7344 harmonic: 9340 Sorted by residual: dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -8.28 -77.72 1 1.00e+01 1.00e-02 7.56e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -8.29 -77.71 1 1.00e+01 1.00e-02 7.56e+01 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -8.30 -77.70 1 1.00e+01 1.00e-02 7.55e+01 ... (remaining 16681 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 3791 0.080 - 0.161: 472 0.161 - 0.241: 12 0.241 - 0.321: 6 0.321 - 0.402: 6 Chirality restraints: 4287 Sorted by residual: chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B 122 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" C1 NAG C1302 " pdb=" ND2 ASN C 122 " pdb=" C2 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 122 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.00e+00 ... (remaining 4284 not shown) Planarity restraints: 4654 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" ND BLA A1314 " -0.053 2.00e-02 2.50e+03 6.71e-02 1.12e+02 pdb=" C1A BLA A1314 " 0.152 2.00e-02 2.50e+03 pdb=" C1D BLA A1314 " -0.014 2.00e-02 2.50e+03 pdb=" C2D BLA A1314 " 0.016 2.00e-02 2.50e+03 pdb=" C3D BLA A1314 " -0.016 2.00e-02 2.50e+03 pdb=" C4D BLA A1314 " -0.056 2.00e-02 2.50e+03 pdb=" CAD BLA A1314 " 0.008 2.00e-02 2.50e+03 pdb=" CHA BLA A1314 " -0.101 2.00e-02 2.50e+03 pdb=" CHD BLA A1314 " -0.004 2.00e-02 2.50e+03 pdb=" CMD BLA A1314 " 0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND BLA C1314 " -0.053 2.00e-02 2.50e+03 6.70e-02 1.12e+02 pdb=" C1A BLA C1314 " 0.152 2.00e-02 2.50e+03 pdb=" C1D BLA C1314 " -0.015 2.00e-02 2.50e+03 pdb=" C2D BLA C1314 " 0.016 2.00e-02 2.50e+03 pdb=" C3D BLA C1314 " -0.015 2.00e-02 2.50e+03 pdb=" C4D BLA C1314 " -0.056 2.00e-02 2.50e+03 pdb=" CAD BLA C1314 " 0.008 2.00e-02 2.50e+03 pdb=" CHA BLA C1314 " -0.101 2.00e-02 2.50e+03 pdb=" CHD BLA C1314 " -0.003 2.00e-02 2.50e+03 pdb=" CMD BLA C1314 " 0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND BLA B1314 " -0.053 2.00e-02 2.50e+03 6.70e-02 1.12e+02 pdb=" C1A BLA B1314 " 0.152 2.00e-02 2.50e+03 pdb=" C1D BLA B1314 " -0.015 2.00e-02 2.50e+03 pdb=" C2D BLA B1314 " 0.016 2.00e-02 2.50e+03 pdb=" C3D BLA B1314 " -0.016 2.00e-02 2.50e+03 pdb=" C4D BLA B1314 " -0.056 2.00e-02 2.50e+03 pdb=" CAD BLA B1314 " 0.008 2.00e-02 2.50e+03 pdb=" CHA BLA B1314 " -0.101 2.00e-02 2.50e+03 pdb=" CHD BLA B1314 " -0.004 2.00e-02 2.50e+03 pdb=" CMD BLA B1314 " 0.069 2.00e-02 2.50e+03 ... (remaining 4651 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 335 2.60 - 3.17: 23760 3.17 - 3.75: 39792 3.75 - 4.32: 56564 4.32 - 4.90: 92643 Nonbonded interactions: 213094 Sorted by model distance: nonbonded pdb=" OG1 THR B 323 " pdb=" OE1 GLU B 324 " model vdw 2.025 3.040 nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.025 3.040 nonbonded pdb=" OG1 THR A 323 " pdb=" OE1 GLU A 324 " model vdw 2.025 3.040 nonbonded pdb=" OG SER C 880 " pdb=" O LEU C 890 " model vdw 2.038 3.040 nonbonded pdb=" OG SER A 880 " pdb=" O LEU A 890 " model vdw 2.038 3.040 ... (remaining 213089 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' selection = chain 'B' selection = (chain 'C' and (resid 15 through 176 or resid 185 through 1314)) } 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=0.00 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: 1.010 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: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 24.850 Find NCS groups from input model: 0.610 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: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 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 : 0.009 0.520 26701 Z= 0.445 Angle : 0.851 16.123 36497 Z= 0.418 Chirality : 0.050 0.402 4287 Planarity : 0.005 0.067 4603 Dihedral : 13.204 89.178 10528 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.43 % Allowed : 0.22 % Favored : 99.35 % 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: -0.78 (0.14), residues: 3172 helix: 0.05 (0.18), residues: 783 sheet: -0.03 (0.18), residues: 675 loop : -0.96 (0.15), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 646 TYR 0.011 0.001 TYR C1063 PHE 0.014 0.001 PHE B 592 TRP 0.006 0.001 TRP A 64 HIS 0.002 0.001 HIS A1044 Details of bonding type rmsd covalent geometry : bond 0.00720 (26590) covalent geometry : angle 0.78171 (36212) SS BOND : bond 0.00756 ( 48) SS BOND : angle 2.16535 ( 96) hydrogen bonds : bond 0.13443 ( 1055) hydrogen bonds : angle 7.62980 ( 2982) link_BETA1-4 : bond 0.00453 ( 12) link_BETA1-4 : angle 2.51769 ( 36) link_NAG-ASN : bond 0.12595 ( 51) link_NAG-ASN : angle 4.86853 ( 153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 358 ILE cc_start: 0.9238 (mt) cc_final: 0.8929 (mm) outliers start: 12 outliers final: 8 residues processed: 127 average time/residue: 0.1441 time to fit residues: 31.8429 Evaluate side-chains 91 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 864 GLU Chi-restraints excluded: chain A residue 1013 GLU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 864 GLU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 864 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 0.0170 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 8.9990 overall best weight: 4.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 783 GLN A 909 GLN A 998 GLN B 115 GLN B 783 GLN B 909 GLN B 998 GLN C 115 GLN C 783 GLN C 909 GLN C 998 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.080630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.059599 restraints weight = 91967.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.061843 restraints weight = 43962.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.063276 restraints weight = 28449.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.064162 restraints weight = 22003.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.064716 restraints weight = 18923.883| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 26701 Z= 0.290 Angle : 0.734 10.963 36497 Z= 0.369 Chirality : 0.049 0.351 4287 Planarity : 0.004 0.042 4603 Dihedral : 8.393 95.342 4859 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.54 % Allowed : 5.16 % Favored : 94.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.14), residues: 3172 helix: 0.53 (0.18), residues: 781 sheet: -0.23 (0.18), residues: 726 loop : -0.88 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 901 TYR 0.024 0.002 TYR A 833 PHE 0.017 0.002 PHE C 894 TRP 0.008 0.002 TRP B 64 HIS 0.004 0.001 HIS C1044 Details of bonding type rmsd covalent geometry : bond 0.00644 (26590) covalent geometry : angle 0.69508 (36212) SS BOND : bond 0.00576 ( 48) SS BOND : angle 1.77638 ( 96) hydrogen bonds : bond 0.04732 ( 1055) hydrogen bonds : angle 6.23036 ( 2982) link_BETA1-4 : bond 0.00479 ( 12) link_BETA1-4 : angle 1.88505 ( 36) link_NAG-ASN : bond 0.00370 ( 51) link_NAG-ASN : angle 3.38523 ( 153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 998 GLN cc_start: 0.8640 (tp-100) cc_final: 0.8430 (tp40) REVERT: C 998 GLN cc_start: 0.8634 (tp-100) cc_final: 0.8401 (tp40) outliers start: 15 outliers final: 8 residues processed: 115 average time/residue: 0.1560 time to fit residues: 30.8856 Evaluate side-chains 88 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 863 ASP Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 1073 THR Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 1073 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 312 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 chunk 297 optimal weight: 1.9990 chunk 189 optimal weight: 4.9990 chunk 147 optimal weight: 20.0000 chunk 149 optimal weight: 0.9990 chunk 277 optimal weight: 1.9990 chunk 271 optimal weight: 10.0000 chunk 63 optimal weight: 0.6980 chunk 171 optimal weight: 5.9990 chunk 301 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 628 GLN B 628 GLN ** B 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 GLN C 951 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.082087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.061219 restraints weight = 90749.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.063538 restraints weight = 43548.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.065013 restraints weight = 28189.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.065952 restraints weight = 21723.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.066489 restraints weight = 18591.492| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26701 Z= 0.134 Angle : 0.586 9.373 36497 Z= 0.299 Chirality : 0.046 0.337 4287 Planarity : 0.004 0.050 4603 Dihedral : 7.289 59.529 4847 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.90 % Allowed : 6.13 % Favored : 92.97 % 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: -0.27 (0.14), residues: 3172 helix: 0.98 (0.19), residues: 790 sheet: -0.11 (0.17), residues: 768 loop : -0.75 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 214 TYR 0.013 0.001 TYR A 833 PHE 0.011 0.001 PHE C1117 TRP 0.006 0.001 TRP B 104 HIS 0.002 0.001 HIS A1044 Details of bonding type rmsd covalent geometry : bond 0.00285 (26590) covalent geometry : angle 0.54765 (36212) SS BOND : bond 0.00376 ( 48) SS BOND : angle 1.36761 ( 96) hydrogen bonds : bond 0.03901 ( 1055) hydrogen bonds : angle 5.81269 ( 2982) link_BETA1-4 : bond 0.00448 ( 12) link_BETA1-4 : angle 1.99911 ( 36) link_NAG-ASN : bond 0.00404 ( 51) link_NAG-ASN : angle 2.98437 ( 153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 865 MET cc_start: 0.9227 (mtp) cc_final: 0.8987 (mtm) REVERT: A 1013 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7866 (tp30) REVERT: B 769 GLU cc_start: 0.8165 (tt0) cc_final: 0.7905 (tt0) outliers start: 25 outliers final: 11 residues processed: 116 average time/residue: 0.1404 time to fit residues: 28.8553 Evaluate side-chains 94 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 1062 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 1062 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 331 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 5 optimal weight: 0.9980 chunk 186 optimal weight: 6.9990 chunk 263 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 chunk 284 optimal weight: 8.9990 chunk 162 optimal weight: 0.4980 chunk 289 optimal weight: 30.0000 chunk 151 optimal weight: 9.9990 chunk 36 optimal weight: 0.9980 chunk 83 optimal weight: 8.9990 chunk 122 optimal weight: 10.0000 overall best weight: 2.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 998 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 = 0.3616 r_free = 0.3616 target = 0.081417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.060468 restraints weight = 90199.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.062748 restraints weight = 43696.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.064173 restraints weight = 28374.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.065115 restraints weight = 22007.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.065653 restraints weight = 18875.822| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26701 Z= 0.153 Angle : 0.576 8.268 36497 Z= 0.293 Chirality : 0.046 0.319 4287 Planarity : 0.004 0.053 4603 Dihedral : 6.846 57.425 4846 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.22 % Allowed : 7.89 % Favored : 90.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.15), residues: 3172 helix: 1.09 (0.19), residues: 786 sheet: 0.10 (0.18), residues: 750 loop : -0.67 (0.15), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 214 TYR 0.016 0.001 TYR C 833 PHE 0.012 0.001 PHE A 377 TRP 0.006 0.001 TRP B 64 HIS 0.003 0.001 HIS C1044 Details of bonding type rmsd covalent geometry : bond 0.00339 (26590) covalent geometry : angle 0.53990 (36212) SS BOND : bond 0.00347 ( 48) SS BOND : angle 1.41247 ( 96) hydrogen bonds : bond 0.03751 ( 1055) hydrogen bonds : angle 5.65088 ( 2982) link_BETA1-4 : bond 0.00401 ( 12) link_BETA1-4 : angle 1.87087 ( 36) link_NAG-ASN : bond 0.00332 ( 51) link_NAG-ASN : angle 2.82782 ( 153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 93 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1013 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7929 (tm-30) REVERT: B 769 GLU cc_start: 0.8202 (tt0) cc_final: 0.7859 (tt0) REVERT: B 1109 GLN cc_start: 0.8248 (mp10) cc_final: 0.7959 (mp10) outliers start: 34 outliers final: 25 residues processed: 124 average time/residue: 0.1466 time to fit residues: 32.3392 Evaluate side-chains 111 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 1062 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 1062 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 712 THR Chi-restraints excluded: chain C residue 1062 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 297 optimal weight: 5.9990 chunk 310 optimal weight: 0.9980 chunk 103 optimal weight: 9.9990 chunk 67 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 226 optimal weight: 30.0000 chunk 312 optimal weight: 6.9990 chunk 2 optimal weight: 8.9990 chunk 279 optimal weight: 2.9990 chunk 122 optimal weight: 0.0670 chunk 62 optimal weight: 0.8980 overall best weight: 1.3922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 998 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 = 0.3628 r_free = 0.3628 target = 0.082035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.060997 restraints weight = 89813.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.063292 restraints weight = 43662.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.064747 restraints weight = 28458.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.065659 restraints weight = 22147.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.066220 restraints weight = 19068.192| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26701 Z= 0.120 Angle : 0.545 7.656 36497 Z= 0.278 Chirality : 0.045 0.324 4287 Planarity : 0.004 0.049 4603 Dihedral : 6.452 54.990 4846 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.11 % Allowed : 8.49 % Favored : 90.39 % 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: -0.05 (0.15), residues: 3172 helix: 1.07 (0.19), residues: 803 sheet: 0.13 (0.18), residues: 754 loop : -0.63 (0.15), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 901 TYR 0.023 0.001 TYR A 833 PHE 0.010 0.001 PHE C1117 TRP 0.006 0.001 TRP B 64 HIS 0.002 0.001 HIS C1060 Details of bonding type rmsd covalent geometry : bond 0.00265 (26590) covalent geometry : angle 0.51063 (36212) SS BOND : bond 0.00538 ( 48) SS BOND : angle 1.25039 ( 96) hydrogen bonds : bond 0.03539 ( 1055) hydrogen bonds : angle 5.48481 ( 2982) link_BETA1-4 : bond 0.00445 ( 12) link_BETA1-4 : angle 1.87765 ( 36) link_NAG-ASN : bond 0.00354 ( 51) link_NAG-ASN : angle 2.71789 ( 153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1013 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7924 (tm-30) outliers start: 31 outliers final: 21 residues processed: 128 average time/residue: 0.1522 time to fit residues: 33.2844 Evaluate side-chains 105 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 1062 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 896 MET Chi-restraints excluded: chain C residue 1062 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 200 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 137 optimal weight: 10.0000 chunk 267 optimal weight: 9.9990 chunk 233 optimal weight: 6.9990 chunk 238 optimal weight: 7.9990 chunk 148 optimal weight: 20.0000 chunk 183 optimal weight: 10.0000 chunk 272 optimal weight: 1.9990 chunk 201 optimal weight: 5.9990 chunk 292 optimal weight: 1.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 951 ASN ** C 998 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 = 0.3601 r_free = 0.3601 target = 0.080773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.059645 restraints weight = 90592.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.061870 restraints weight = 44091.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.063315 restraints weight = 28818.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.064233 restraints weight = 22313.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.064774 restraints weight = 19193.098| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 26701 Z= 0.181 Angle : 0.580 8.982 36497 Z= 0.294 Chirality : 0.045 0.314 4287 Planarity : 0.004 0.042 4603 Dihedral : 6.330 54.525 4846 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.51 % Allowed : 8.96 % Favored : 89.53 % 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: -0.08 (0.15), residues: 3172 helix: 1.00 (0.19), residues: 803 sheet: 0.12 (0.18), residues: 795 loop : -0.65 (0.15), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 979 TYR 0.015 0.001 TYR C 833 PHE 0.012 0.001 PHE A 377 TRP 0.007 0.001 TRP B 64 HIS 0.003 0.001 HIS C1060 Details of bonding type rmsd covalent geometry : bond 0.00405 (26590) covalent geometry : angle 0.54457 (36212) SS BOND : bond 0.00385 ( 48) SS BOND : angle 1.70880 ( 96) hydrogen bonds : bond 0.03719 ( 1055) hydrogen bonds : angle 5.48323 ( 2982) link_BETA1-4 : bond 0.00346 ( 12) link_BETA1-4 : angle 1.79105 ( 36) link_NAG-ASN : bond 0.00325 ( 51) link_NAG-ASN : angle 2.72284 ( 153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 87 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 36 residues processed: 125 average time/residue: 0.1407 time to fit residues: 31.4369 Evaluate side-chains 119 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 83 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 693 MET Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 1062 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 1062 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 693 MET Chi-restraints excluded: chain C residue 712 THR Chi-restraints excluded: chain C residue 896 MET Chi-restraints excluded: chain C residue 1062 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 269 optimal weight: 0.9980 chunk 263 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 46 optimal weight: 20.0000 chunk 72 optimal weight: 0.6980 chunk 32 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 287 optimal weight: 9.9990 chunk 101 optimal weight: 9.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 998 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 = 0.3585 r_free = 0.3585 target = 0.080003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.058800 restraints weight = 90902.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.061013 restraints weight = 44437.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.062429 restraints weight = 29201.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.063326 restraints weight = 22773.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.063789 restraints weight = 19631.553| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 26701 Z= 0.197 Angle : 0.593 12.374 36497 Z= 0.301 Chirality : 0.046 0.318 4287 Planarity : 0.004 0.038 4603 Dihedral : 6.174 53.796 4846 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.72 % Allowed : 9.32 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.15), residues: 3172 helix: 0.99 (0.19), residues: 803 sheet: 0.20 (0.18), residues: 767 loop : -0.66 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 979 TYR 0.011 0.001 TYR B 833 PHE 0.012 0.001 PHE B1117 TRP 0.007 0.001 TRP B 64 HIS 0.003 0.001 HIS C1044 Details of bonding type rmsd covalent geometry : bond 0.00439 (26590) covalent geometry : angle 0.55819 (36212) SS BOND : bond 0.00413 ( 48) SS BOND : angle 1.70546 ( 96) hydrogen bonds : bond 0.03801 ( 1055) hydrogen bonds : angle 5.49320 ( 2982) link_BETA1-4 : bond 0.00346 ( 12) link_BETA1-4 : angle 1.76426 ( 36) link_NAG-ASN : bond 0.00332 ( 51) link_NAG-ASN : angle 2.73871 ( 153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 90 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1013 GLU cc_start: 0.8396 (tp30) cc_final: 0.8037 (tp30) outliers start: 48 outliers final: 44 residues processed: 135 average time/residue: 0.1337 time to fit residues: 32.1807 Evaluate side-chains 128 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 84 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 1062 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 1062 THR Chi-restraints excluded: chain B residue 1073 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 712 THR Chi-restraints excluded: chain C residue 896 MET Chi-restraints excluded: chain C residue 1030 LEU Chi-restraints excluded: chain C residue 1062 THR Chi-restraints excluded: chain C residue 1073 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 133 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 138 optimal weight: 0.9980 chunk 301 optimal weight: 4.9990 chunk 249 optimal weight: 6.9990 chunk 231 optimal weight: 3.9990 chunk 247 optimal weight: 0.9990 chunk 290 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 chunk 152 optimal weight: 8.9990 chunk 171 optimal weight: 0.7980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 897 GLN ** A 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 998 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 = 0.3612 r_free = 0.3612 target = 0.081311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.060230 restraints weight = 90387.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.062501 restraints weight = 43949.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.063944 restraints weight = 28746.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.064846 restraints weight = 22346.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.065405 restraints weight = 19260.538| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26701 Z= 0.115 Angle : 0.543 7.308 36497 Z= 0.278 Chirality : 0.045 0.316 4287 Planarity : 0.003 0.038 4603 Dihedral : 5.910 54.435 4846 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.54 % Allowed : 9.78 % Favored : 88.67 % 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: 0.01 (0.15), residues: 3172 helix: 1.08 (0.19), residues: 803 sheet: 0.23 (0.18), residues: 765 loop : -0.61 (0.15), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 979 TYR 0.009 0.001 TYR B 737 PHE 0.010 0.001 PHE C1117 TRP 0.007 0.001 TRP B 64 HIS 0.002 0.000 HIS C1044 Details of bonding type rmsd covalent geometry : bond 0.00255 (26590) covalent geometry : angle 0.51037 (36212) SS BOND : bond 0.00330 ( 48) SS BOND : angle 1.42824 ( 96) hydrogen bonds : bond 0.03483 ( 1055) hydrogen bonds : angle 5.33489 ( 2982) link_BETA1-4 : bond 0.00417 ( 12) link_BETA1-4 : angle 1.81609 ( 36) link_NAG-ASN : bond 0.00335 ( 51) link_NAG-ASN : angle 2.57487 ( 153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 100 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1013 GLU cc_start: 0.8349 (tp30) cc_final: 0.8041 (tp30) outliers start: 43 outliers final: 40 residues processed: 135 average time/residue: 0.1483 time to fit residues: 34.8225 Evaluate side-chains 132 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 92 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 693 MET Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 1062 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 693 MET Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 693 MET Chi-restraints excluded: chain C residue 712 THR Chi-restraints excluded: chain C residue 896 MET Chi-restraints excluded: chain C residue 1062 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 142 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 219 optimal weight: 40.0000 chunk 274 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 297 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 chunk 256 optimal weight: 9.9990 chunk 195 optimal weight: 2.9990 chunk 213 optimal weight: 0.0870 chunk 179 optimal weight: 3.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 897 GLN ** A 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1102 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 897 GLN ** C 998 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 = 0.3596 r_free = 0.3596 target = 0.080530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.059379 restraints weight = 90606.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.061613 restraints weight = 44370.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.063047 restraints weight = 29139.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.063943 restraints weight = 22718.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.064500 restraints weight = 19565.099| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 26701 Z= 0.162 Angle : 0.563 7.125 36497 Z= 0.286 Chirality : 0.045 0.311 4287 Planarity : 0.004 0.065 4603 Dihedral : 5.893 53.947 4846 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.86 % Allowed : 9.78 % Favored : 88.35 % 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: -0.00 (0.15), residues: 3172 helix: 1.06 (0.19), residues: 803 sheet: 0.17 (0.18), residues: 785 loop : -0.59 (0.16), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 214 TYR 0.009 0.001 TYR B 737 PHE 0.011 0.001 PHE A 377 TRP 0.007 0.001 TRP B 64 HIS 0.011 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00364 (26590) covalent geometry : angle 0.53105 (36212) SS BOND : bond 0.00365 ( 48) SS BOND : angle 1.47612 ( 96) hydrogen bonds : bond 0.03584 ( 1055) hydrogen bonds : angle 5.32121 ( 2982) link_BETA1-4 : bond 0.00346 ( 12) link_BETA1-4 : angle 1.75205 ( 36) link_NAG-ASN : bond 0.00313 ( 51) link_NAG-ASN : angle 2.60216 ( 153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 91 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1013 GLU cc_start: 0.8344 (tp30) cc_final: 0.8023 (tp30) outliers start: 52 outliers final: 50 residues processed: 136 average time/residue: 0.1390 time to fit residues: 33.8583 Evaluate side-chains 139 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 89 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 693 MET Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1062 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 693 MET Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 1073 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 693 MET Chi-restraints excluded: chain C residue 712 THR Chi-restraints excluded: chain C residue 896 MET Chi-restraints excluded: chain C residue 1062 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 99 optimal weight: 0.8980 chunk 30 optimal weight: 6.9990 chunk 245 optimal weight: 7.9990 chunk 289 optimal weight: 40.0000 chunk 10 optimal weight: 9.9990 chunk 211 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 20 optimal weight: 20.0000 chunk 273 optimal weight: 6.9990 chunk 197 optimal weight: 2.9990 chunk 233 optimal weight: 0.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 998 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 = 0.3581 r_free = 0.3581 target = 0.079880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.058602 restraints weight = 90338.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.060822 restraints weight = 44087.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.062260 restraints weight = 28882.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.063146 restraints weight = 22443.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.063625 restraints weight = 19379.656| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 26701 Z= 0.180 Angle : 0.577 7.252 36497 Z= 0.293 Chirality : 0.045 0.308 4287 Planarity : 0.004 0.046 4603 Dihedral : 5.888 53.216 4846 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.79 % Allowed : 9.96 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.15), residues: 3172 helix: 1.02 (0.19), residues: 805 sheet: 0.25 (0.18), residues: 759 loop : -0.56 (0.16), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 214 TYR 0.011 0.001 TYR B 737 PHE 0.011 0.001 PHE A 377 TRP 0.007 0.001 TRP B 64 HIS 0.007 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00404 (26590) covalent geometry : angle 0.54509 (36212) SS BOND : bond 0.00395 ( 48) SS BOND : angle 1.58740 ( 96) hydrogen bonds : bond 0.03708 ( 1055) hydrogen bonds : angle 5.36149 ( 2982) link_BETA1-4 : bond 0.00324 ( 12) link_BETA1-4 : angle 1.69375 ( 36) link_NAG-ASN : bond 0.00312 ( 51) link_NAG-ASN : angle 2.60793 ( 153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 95 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 896 MET cc_start: 0.8273 (mpp) cc_final: 0.7954 (ptp) REVERT: C 1013 GLU cc_start: 0.8356 (tp30) cc_final: 0.8064 (tp30) outliers start: 50 outliers final: 48 residues processed: 136 average time/residue: 0.1437 time to fit residues: 34.7655 Evaluate side-chains 139 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 91 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1062 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 693 MET Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 865 MET Chi-restraints excluded: chain B residue 1073 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 693 MET Chi-restraints excluded: chain C residue 712 THR Chi-restraints excluded: chain C residue 896 MET Chi-restraints excluded: chain C residue 1062 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 130 optimal weight: 7.9990 chunk 180 optimal weight: 0.0570 chunk 7 optimal weight: 30.0000 chunk 213 optimal weight: 0.0070 chunk 294 optimal weight: 0.8980 chunk 14 optimal weight: 10.0000 chunk 297 optimal weight: 4.9990 chunk 153 optimal weight: 5.9990 chunk 211 optimal weight: 10.0000 chunk 174 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 overall best weight: 1.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 998 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 = 0.3598 r_free = 0.3598 target = 0.080666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.059573 restraints weight = 90313.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.061794 restraints weight = 44673.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.063217 restraints weight = 29447.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.064111 restraints weight = 23042.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.064665 restraints weight = 19891.402| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26701 Z= 0.137 Angle : 0.554 7.247 36497 Z= 0.282 Chirality : 0.045 0.311 4287 Planarity : 0.004 0.048 4603 Dihedral : 5.750 53.585 4846 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.83 % Allowed : 9.89 % Favored : 88.28 % 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: 0.06 (0.15), residues: 3172 helix: 1.08 (0.19), residues: 805 sheet: 0.27 (0.18), residues: 745 loop : -0.56 (0.16), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 214 TYR 0.009 0.001 TYR B 737 PHE 0.010 0.001 PHE A 377 TRP 0.007 0.001 TRP A 64 HIS 0.003 0.001 HIS C1060 Details of bonding type rmsd covalent geometry : bond 0.00308 (26590) covalent geometry : angle 0.52270 (36212) SS BOND : bond 0.00331 ( 48) SS BOND : angle 1.42761 ( 96) hydrogen bonds : bond 0.03509 ( 1055) hydrogen bonds : angle 5.26417 ( 2982) link_BETA1-4 : bond 0.00395 ( 12) link_BETA1-4 : angle 1.73658 ( 36) link_NAG-ASN : bond 0.00319 ( 51) link_NAG-ASN : angle 2.53679 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3933.81 seconds wall clock time: 69 minutes 15.72 seconds (4155.72 seconds total)