Starting phenix.real_space_refine on Sat Jun 21 04:38:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zy5_60556/06_2025/8zy5_60556.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zy5_60556/06_2025/8zy5_60556.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zy5_60556/06_2025/8zy5_60556.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zy5_60556/06_2025/8zy5_60556.map" model { file = "/net/cci-nas-00/data/ceres_data/8zy5_60556/06_2025/8zy5_60556.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zy5_60556/06_2025/8zy5_60556.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 105 5.16 5 C 15558 2.51 5 N 3981 2.21 5 O 4806 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24450 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 7856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1010, 7856 Classifications: {'peptide': 1010} Link IDs: {'PTRANS': 44, 'TRANS': 965} Chain breaks: 6 Chain: "B" Number of atoms: 7856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1010, 7856 Classifications: {'peptide': 1010} Link IDs: {'PTRANS': 44, 'TRANS': 965} Chain breaks: 6 Chain: "C" Number of atoms: 7856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1010, 7856 Classifications: {'peptide': 1010} Link IDs: {'PTRANS': 44, 'TRANS': 965} Chain breaks: 6 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: "A" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "B" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "C" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Time building chain proxies: 13.58, per 1000 atoms: 0.56 Number of scatterers: 24450 At special positions: 0 Unit cell: (129.36, 135.96, 163.68, 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 105 16.00 O 4806 8.00 N 3981 7.00 C 15558 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 122 " - pdb=" SG CYS A 151 " distance=2.03 Simple disulfide: pdb=" SG CYS A 270 " - pdb=" SG CYS A 280 " distance=2.03 Simple disulfide: pdb=" SG CYS A 315 " - pdb=" SG CYS A 340 " distance=2.04 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 411 " distance=2.03 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 485 " distance=2.04 Simple disulfide: pdb=" SG CYS A 498 " - pdb=" SG CYS A 550 " distance=2.04 Simple disulfide: pdb=" SG CYS A 577 " - pdb=" SG CYS A 609 " distance=2.03 Simple disulfide: pdb=" SG CYS A 622 " - pdb=" SG CYS A 631 " distance=2.03 Simple disulfide: pdb=" SG CYS A 692 " - pdb=" SG CYS A 714 " distance=2.03 Simple disulfide: pdb=" SG CYS A 697 " - pdb=" SG CYS A 703 " distance=2.03 Simple disulfide: pdb=" SG CYS A 986 " - pdb=" SG CYS A 997 " distance=2.03 Simple disulfide: pdb=" SG CYS A1036 " - pdb=" SG CYS A1080 " distance=2.03 Simple disulfide: pdb=" SG CYS B 122 " - pdb=" SG CYS B 151 " distance=2.03 Simple disulfide: pdb=" SG CYS B 270 " - pdb=" SG CYS B 280 " distance=2.03 Simple disulfide: pdb=" SG CYS B 315 " - pdb=" SG CYS B 340 " distance=2.04 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 411 " distance=2.03 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 485 " distance=2.04 Simple disulfide: pdb=" SG CYS B 498 " - pdb=" SG CYS B 550 " distance=2.04 Simple disulfide: pdb=" SG CYS B 577 " - pdb=" SG CYS B 609 " distance=2.03 Simple disulfide: pdb=" SG CYS B 622 " - pdb=" SG CYS B 631 " distance=2.03 Simple disulfide: pdb=" SG CYS B 692 " - pdb=" SG CYS B 714 " distance=2.02 Simple disulfide: pdb=" SG CYS B 697 " - pdb=" SG CYS B 703 " distance=2.03 Simple disulfide: pdb=" SG CYS B 986 " - pdb=" SG CYS B 997 " distance=2.03 Simple disulfide: pdb=" SG CYS B1036 " - pdb=" SG CYS B1080 " distance=2.03 Simple disulfide: pdb=" SG CYS C 122 " - pdb=" SG CYS C 151 " distance=2.03 Simple disulfide: pdb=" SG CYS C 270 " - pdb=" SG CYS C 280 " distance=2.03 Simple disulfide: pdb=" SG CYS C 315 " - pdb=" SG CYS C 340 " distance=2.04 Simple disulfide: pdb=" SG CYS C 358 " - pdb=" SG CYS C 411 " distance=2.03 Simple disulfide: pdb=" SG CYS C 370 " - pdb=" SG CYS C 485 " distance=2.04 Simple disulfide: pdb=" SG CYS C 498 " - pdb=" SG CYS C 550 " distance=2.04 Simple disulfide: pdb=" SG CYS C 577 " - pdb=" SG CYS C 609 " distance=2.03 Simple disulfide: pdb=" SG CYS C 622 " - pdb=" SG CYS C 631 " distance=2.03 Simple disulfide: pdb=" SG CYS C 692 " - pdb=" SG CYS C 714 " distance=2.02 Simple disulfide: pdb=" SG CYS C 697 " - pdb=" SG CYS C 703 " distance=2.03 Simple disulfide: pdb=" SG CYS C 986 " - pdb=" SG CYS C 997 " distance=2.03 Simple disulfide: pdb=" SG CYS C1036 " - pdb=" SG CYS C1080 " 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-ASN " NAG A1301 " - " ASN A 113 " " NAG A1302 " - " ASN A 310 " " NAG A1304 " - " ASN A 663 " " NAG A1305 " - " ASN A1052 " " NAG A1306 " - " ASN A 150 " " NAG A1307 " - " ASN A 261 " " NAG A1308 " - " ASN A 322 " " NAG A1309 " - " ASN A 576 " " NAG A1310 " - " ASN A 26 " " NAG A1311 " - " ASN A 57 " " NAG A1312 " - " ASN A 103 " " NAG A1313 " - " ASN A 223 " " NAG A1314 " - " ASN A 617 " " NAG A1315 " - " ASN A1088 " " NAG B1301 " - " ASN B 113 " " NAG B1302 " - " ASN B 310 " " NAG B1304 " - " ASN B 663 " " NAG B1305 " - " ASN B1052 " " NAG B1306 " - " ASN B 150 " " NAG B1307 " - " ASN B 261 " " NAG B1308 " - " ASN B 322 " " NAG B1309 " - " ASN B 576 " " NAG B1310 " - " ASN B 26 " " NAG B1311 " - " ASN B 57 " " NAG B1312 " - " ASN B 103 " " NAG B1313 " - " ASN B 223 " " NAG B1314 " - " ASN B 617 " " NAG B1315 " - " ASN B1088 " " NAG C1301 " - " ASN C 113 " " NAG C1302 " - " ASN C 310 " " NAG C1304 " - " ASN C 663 " " NAG C1305 " - " ASN C1052 " " NAG C1306 " - " ASN C 150 " " NAG C1307 " - " ASN C 261 " " NAG C1308 " - " ASN C 322 " " NAG C1309 " - " ASN C 576 " " NAG C1310 " - " ASN C 26 " " NAG C1311 " - " ASN C 57 " " NAG C1312 " - " ASN C 103 " " NAG C1313 " - " ASN C 223 " " NAG C1314 " - " ASN C 617 " " NAG C1315 " - " ASN C1088 " " NAG D 1 " - " ASN A1028 " " NAG E 1 " - " ASN A 671 " " NAG F 1 " - " ASN A 349 " " NAG G 1 " - " ASN B1028 " " NAG H 1 " - " ASN B 671 " " NAG I 1 " - " ASN B 349 " " NAG J 1 " - " ASN C1028 " " NAG K 1 " - " ASN C 671 " " NAG L 1 " - " ASN C 349 " Time building additional restraints: 5.74 Conformation dependent library (CDL) restraints added in 3.1 seconds 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5712 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 48 sheets defined 23.2% alpha, 27.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.11 Creating SS restraints... Processing helix chain 'A' and resid 273 through 282 Processing helix chain 'A' and resid 317 through 322 Processing helix chain 'A' and resid 345 through 349 removed outlier: 4.024A pdb=" N ASN A 349 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 366 removed outlier: 3.906A pdb=" N LEU A 366 " --> pdb=" O PRO A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 Processing helix chain 'A' and resid 396 through 401 Processing helix chain 'A' and resid 579 through 585 Processing helix chain 'A' and resid 592 through 598 removed outlier: 4.470A pdb=" N TYR A 596 " --> pdb=" O ALA A 592 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE A 598 " --> pdb=" O ARG A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 708 Processing helix chain 'A' and resid 710 through 737 removed outlier: 3.695A pdb=" N CYS A 714 " --> pdb=" O TYR A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 780 Processing helix chain 'A' and resid 820 through 838 Processing helix chain 'A' and resid 851 through 861 Processing helix chain 'A' and resid 873 through 895 Processing helix chain 'A' and resid 899 through 920 removed outlier: 3.713A pdb=" N GLN A 903 " --> pdb=" O LEU A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 938 removed outlier: 4.177A pdb=" N ILE A 934 " --> pdb=" O VAL A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 987 removed outlier: 4.780A pdb=" N VAL A 945 " --> pdb=" O VAL A 941 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLN A 946 " --> pdb=" O GLU A 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 282 Processing helix chain 'B' and resid 317 through 322 Processing helix chain 'B' and resid 345 through 349 removed outlier: 3.660A pdb=" N ASN B 349 " --> pdb=" O VAL B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 366 removed outlier: 3.890A pdb=" N LEU B 366 " --> pdb=" O PRO B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 389 Processing helix chain 'B' and resid 396 through 401 Processing helix chain 'B' and resid 579 through 585 Processing helix chain 'B' and resid 592 through 598 removed outlier: 4.234A pdb=" N TYR B 596 " --> pdb=" O ALA B 592 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE B 598 " --> pdb=" O ARG B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 708 Processing helix chain 'B' and resid 710 through 737 removed outlier: 3.681A pdb=" N CYS B 714 " --> pdb=" O TYR B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 780 Processing helix chain 'B' and resid 807 through 811 Processing helix chain 'B' and resid 820 through 838 Processing helix chain 'B' and resid 839 through 843 removed outlier: 3.848A pdb=" N PHE B 842 " --> pdb=" O GLY B 839 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLY B 843 " --> pdb=" O TRP B 840 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 839 through 843' Processing helix chain 'B' and resid 851 through 861 Processing helix chain 'B' and resid 873 through 895 Processing helix chain 'B' and resid 899 through 920 removed outlier: 3.696A pdb=" N GLN B 903 " --> pdb=" O LEU B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 930 through 938 removed outlier: 4.193A pdb=" N ILE B 934 " --> pdb=" O VAL B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 987 removed outlier: 4.840A pdb=" N VAL B 945 " --> pdb=" O VAL B 941 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN B 946 " --> pdb=" O GLU B 942 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 282 Processing helix chain 'C' and resid 317 through 322 Processing helix chain 'C' and resid 345 through 349 removed outlier: 4.046A pdb=" N ASN C 349 " --> pdb=" O VAL C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 366 removed outlier: 3.827A pdb=" N LEU C 366 " --> pdb=" O PRO C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 389 Processing helix chain 'C' and resid 579 through 585 Processing helix chain 'C' and resid 592 through 598 removed outlier: 4.305A pdb=" N TYR C 596 " --> pdb=" O ALA C 592 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE C 598 " --> pdb=" O ARG C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 700 through 708 Processing helix chain 'C' and resid 711 through 737 Processing helix chain 'C' and resid 770 through 780 Processing helix chain 'C' and resid 820 through 838 Processing helix chain 'C' and resid 839 through 843 removed outlier: 3.741A pdb=" N PHE C 842 " --> pdb=" O GLY C 839 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY C 843 " --> pdb=" O TRP C 840 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 839 through 843' Processing helix chain 'C' and resid 851 through 861 Processing helix chain 'C' and resid 873 through 895 Processing helix chain 'C' and resid 899 through 920 removed outlier: 3.724A pdb=" N GLN C 903 " --> pdb=" O LEU C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 930 through 938 removed outlier: 4.178A pdb=" N ILE C 934 " --> pdb=" O VAL C 930 " (cutoff:3.500A) Processing helix chain 'C' and resid 939 through 987 removed outlier: 4.870A pdb=" N VAL C 945 " --> pdb=" O VAL C 941 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLN C 946 " --> pdb=" O GLU C 942 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 53 removed outlier: 4.613A pdb=" N LYS A 266 " --> pdb=" O SER A 257 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 75 through 76 removed outlier: 3.743A pdb=" N GLY A 94 " --> pdb=" O VAL A 230 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 213 through 218 removed outlier: 6.154A pdb=" N GLY A 190 " --> pdb=" O PRO A 214 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N TRP A 216 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE A 188 " --> pdb=" O TRP A 216 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 118 through 126 removed outlier: 6.741A pdb=" N ILE A 119 " --> pdb=" O SER A 154 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N SER A 154 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL A 121 " --> pdb=" O THR A 152 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N TYR A 123 " --> pdb=" O ASN A 150 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ASN A 150 " --> pdb=" O TYR A 123 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N GLN A 125 " --> pdb=" O SER A 148 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N SER A 148 " --> pdb=" O GLN A 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 290 through 293 removed outlier: 3.878A pdb=" N GLY A 608 " --> pdb=" O THR A 605 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 304 through 307 removed outlier: 3.866A pdb=" N ASN A 502 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ASP A 534 " --> pdb=" O ILE A 547 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N THR A 533 " --> pdb=" O ASP A 528 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASP A 528 " --> pdb=" O THR A 533 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER A 535 " --> pdb=" O GLY A 526 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 333 through 337 removed outlier: 3.847A pdb=" N VAL A 374 " --> pdb=" O ILE A 337 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER A 373 " --> pdb=" O GLU A 476 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 423 through 428 Processing sheet with id=AA9, first strand: chain 'A' and resid 613 through 615 removed outlier: 5.485A pdb=" N GLU A 614 " --> pdb=" O ALA A 648 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N ALA A 650 " --> pdb=" O GLU A 614 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL A 630 " --> pdb=" O ILE A 626 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE A 626 " --> pdb=" O VAL A 630 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 656 through 657 Processing sheet with id=AB2, first strand: chain 'A' and resid 665 through 682 removed outlier: 6.418A pdb=" N SER A 665 " --> pdb=" O THR A1030 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N THR A1030 " --> pdb=" O SER A 665 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ALA A 667 " --> pdb=" O ASN A1028 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ASN A1028 " --> pdb=" O ALA A 667 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLU A1026 " --> pdb=" O PRO A 669 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ASN A 671 " --> pdb=" O ALA A1024 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N MET A1004 " --> pdb=" O VAL A1019 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 665 through 682 removed outlier: 6.418A pdb=" N SER A 665 " --> pdb=" O THR A1030 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N THR A1030 " --> pdb=" O SER A 665 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ALA A 667 " --> pdb=" O ASN A1028 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ASN A1028 " --> pdb=" O ALA A 667 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLU A1026 " --> pdb=" O PRO A 669 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ASN A 671 " --> pdb=" O ALA A1024 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N THR A1030 " --> pdb=" O SER A1051 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 687 through 689 removed outlier: 4.407A pdb=" N LYS A 687 " --> pdb=" O LEU A 815 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 742 through 743 removed outlier: 5.808A pdb=" N ILE A 742 " --> pdb=" O SER C 657 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 750 through 751 Processing sheet with id=AB7, first strand: chain 'A' and resid 1074 through 1076 Processing sheet with id=AB8, first strand: chain 'B' and resid 46 through 53 removed outlier: 4.692A pdb=" N LYS B 266 " --> pdb=" O SER B 257 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 75 through 76 removed outlier: 3.610A pdb=" N MET B 75 " --> pdb=" O PHE B 227 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE B 227 " --> pdb=" O MET B 75 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY B 94 " --> pdb=" O VAL B 230 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N THR B 232 " --> pdb=" O VAL B 92 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N VAL B 92 " --> pdb=" O THR B 232 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 75 through 76 removed outlier: 3.610A pdb=" N MET B 75 " --> pdb=" O PHE B 227 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE B 227 " --> pdb=" O MET B 75 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE B 132 " --> pdb=" O LEU B 231 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'B' and resid 213 through 218 removed outlier: 6.170A pdb=" N GLY B 190 " --> pdb=" O PRO B 214 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N TRP B 216 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE B 188 " --> pdb=" O TRP B 216 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 118 through 126 removed outlier: 6.735A pdb=" N ILE B 119 " --> pdb=" O SER B 154 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N SER B 154 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL B 121 " --> pdb=" O THR B 152 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N TYR B 123 " --> pdb=" O ASN B 150 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ASN B 150 " --> pdb=" O TYR B 123 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N GLN B 125 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N SER B 148 " --> pdb=" O GLN B 125 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 290 through 293 removed outlier: 3.890A pdb=" N GLY B 608 " --> pdb=" O THR B 605 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 304 through 307 removed outlier: 3.826A pdb=" N ASN B 502 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE B 503 " --> pdb=" O LEU B 506 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N ASP B 534 " --> pdb=" O ILE B 547 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N THR B 533 " --> pdb=" O ASP B 528 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ASP B 528 " --> pdb=" O THR B 533 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER B 535 " --> pdb=" O GLY B 526 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 333 through 337 removed outlier: 3.559A pdb=" N GLN B 333 " --> pdb=" O THR B 378 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL B 374 " --> pdb=" O ILE B 337 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER B 373 " --> pdb=" O GLU B 476 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 423 through 428 Processing sheet with id=AC8, first strand: chain 'B' and resid 613 through 615 removed outlier: 5.617A pdb=" N GLU B 614 " --> pdb=" O ALA B 648 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N ALA B 650 " --> pdb=" O GLU B 614 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL B 630 " --> pdb=" O ILE B 626 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE B 626 " --> pdb=" O VAL B 630 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 656 through 657 Processing sheet with id=AD1, first strand: chain 'B' and resid 665 through 682 removed outlier: 6.412A pdb=" N SER B 665 " --> pdb=" O THR B1030 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N THR B1030 " --> pdb=" O SER B 665 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA B 667 " --> pdb=" O ASN B1028 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ASN B1028 " --> pdb=" O ALA B 667 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLU B1026 " --> pdb=" O PRO B 669 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ASN B 671 " --> pdb=" O ALA B1024 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N MET B1004 " --> pdb=" O VAL B1019 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 665 through 682 removed outlier: 6.412A pdb=" N SER B 665 " --> pdb=" O THR B1030 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N THR B1030 " --> pdb=" O SER B 665 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA B 667 " --> pdb=" O ASN B1028 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ASN B1028 " --> pdb=" O ALA B 667 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLU B1026 " --> pdb=" O PRO B 669 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ASN B 671 " --> pdb=" O ALA B1024 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N THR B1030 " --> pdb=" O SER B1051 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 687 through 689 removed outlier: 4.521A pdb=" N LYS B 687 " --> pdb=" O LEU B 815 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 750 through 751 Processing sheet with id=AD5, first strand: chain 'B' and resid 1074 through 1076 Processing sheet with id=AD6, first strand: chain 'C' and resid 46 through 53 removed outlier: 4.652A pdb=" N LYS C 266 " --> pdb=" O SER C 257 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 75 through 76 removed outlier: 3.522A pdb=" N MET C 75 " --> pdb=" O PHE C 227 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE C 227 " --> pdb=" O MET C 75 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY C 94 " --> pdb=" O VAL C 230 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 75 through 76 removed outlier: 3.522A pdb=" N MET C 75 " --> pdb=" O PHE C 227 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE C 227 " --> pdb=" O MET C 75 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE C 132 " --> pdb=" O LEU C 231 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 213 through 218 removed outlier: 6.185A pdb=" N GLY C 190 " --> pdb=" O PRO C 214 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N TRP C 216 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE C 188 " --> pdb=" O TRP C 216 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 118 through 126 removed outlier: 6.736A pdb=" N ILE C 119 " --> pdb=" O SER C 154 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N SER C 154 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL C 121 " --> pdb=" O THR C 152 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N TYR C 123 " --> pdb=" O ASN C 150 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ASN C 150 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N GLN C 125 " --> pdb=" O SER C 148 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N SER C 148 " --> pdb=" O GLN C 125 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 290 through 293 removed outlier: 3.894A pdb=" N GLY C 608 " --> pdb=" O THR C 605 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 304 through 307 removed outlier: 3.724A pdb=" N ASN C 502 " --> pdb=" O VAL C 305 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N ASP C 534 " --> pdb=" O ILE C 547 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N THR C 533 " --> pdb=" O ASP C 528 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASP C 528 " --> pdb=" O THR C 533 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER C 535 " --> pdb=" O GLY C 526 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 333 through 337 removed outlier: 3.519A pdb=" N GLN C 333 " --> pdb=" O THR C 378 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL C 374 " --> pdb=" O ILE C 337 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER C 373 " --> pdb=" O GLU C 476 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 340 through 341 removed outlier: 6.338A pdb=" N CYS C 340 " --> pdb=" O CYS C 485 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'C' and resid 423 through 428 Processing sheet with id=AE7, first strand: chain 'C' and resid 613 through 615 removed outlier: 5.501A pdb=" N GLU C 614 " --> pdb=" O ALA C 648 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N ALA C 650 " --> pdb=" O GLU C 614 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL C 630 " --> pdb=" O ILE C 626 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE C 626 " --> pdb=" O VAL C 630 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 665 through 682 removed outlier: 6.356A pdb=" N SER C 665 " --> pdb=" O THR C1030 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THR C1030 " --> pdb=" O SER C 665 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ALA C 667 " --> pdb=" O ASN C1028 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ASN C1028 " --> pdb=" O ALA C 667 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLU C1026 " --> pdb=" O PRO C 669 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ASN C 671 " --> pdb=" O ALA C1024 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N MET C1004 " --> pdb=" O VAL C1019 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 665 through 682 removed outlier: 6.356A pdb=" N SER C 665 " --> pdb=" O THR C1030 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THR C1030 " --> pdb=" O SER C 665 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ALA C 667 " --> pdb=" O ASN C1028 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ASN C1028 " --> pdb=" O ALA C 667 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLU C1026 " --> pdb=" O PRO C 669 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ASN C 671 " --> pdb=" O ALA C1024 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N THR C1030 " --> pdb=" O SER C1051 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 687 through 689 removed outlier: 4.293A pdb=" N LYS C 687 " --> pdb=" O LEU C 815 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 750 through 751 Processing sheet with id=AF3, first strand: chain 'C' and resid 1074 through 1076 913 hydrogen bonds defined for protein. 2520 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: 10.05 Time building geometry restraints manager: 6.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7390 1.34 - 1.46: 5895 1.46 - 1.58: 11543 1.58 - 1.70: 0 1.70 - 1.83: 135 Bond restraints: 24963 Sorted by residual: bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.518 -0.112 2.00e-02 2.50e+03 3.16e+01 bond pdb=" CA PRO B 816 " pdb=" C PRO B 816 " ideal model delta sigma weight residual 1.517 1.474 0.043 9.30e-03 1.16e+04 2.10e+01 bond pdb=" N VAL C 86 " pdb=" CA VAL C 86 " ideal model delta sigma weight residual 1.456 1.492 -0.035 9.50e-03 1.11e+04 1.38e+01 bond pdb=" C1 NAG C1302 " pdb=" O5 NAG C1302 " ideal model delta sigma weight residual 1.406 1.478 -0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" C1 NAG B1302 " pdb=" O5 NAG B1302 " ideal model delta sigma weight residual 1.406 1.478 -0.072 2.00e-02 2.50e+03 1.29e+01 ... (remaining 24958 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 33020 2.47 - 4.94: 819 4.94 - 7.40: 108 7.40 - 9.87: 20 9.87 - 12.34: 8 Bond angle restraints: 33975 Sorted by residual: angle pdb=" N VAL C 86 " pdb=" CA VAL C 86 " pdb=" C VAL C 86 " ideal model delta sigma weight residual 113.53 101.56 11.97 9.80e-01 1.04e+00 1.49e+02 angle pdb=" N VAL A 396 " pdb=" CA VAL A 396 " pdb=" C VAL A 396 " ideal model delta sigma weight residual 111.67 103.66 8.01 9.50e-01 1.11e+00 7.10e+01 angle pdb=" N VAL B 86 " pdb=" CA VAL B 86 " pdb=" C VAL B 86 " ideal model delta sigma weight residual 113.42 104.04 9.38 1.17e+00 7.31e-01 6.43e+01 angle pdb=" N LYS A 808 " pdb=" CA LYS A 808 " pdb=" C LYS A 808 " ideal model delta sigma weight residual 114.31 104.32 9.99 1.29e+00 6.01e-01 6.00e+01 angle pdb=" N VAL A 86 " pdb=" CA VAL A 86 " pdb=" C VAL A 86 " ideal model delta sigma weight residual 113.39 103.33 10.06 1.47e+00 4.63e-01 4.68e+01 ... (remaining 33970 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.82: 14591 22.82 - 45.64: 945 45.64 - 68.45: 125 68.45 - 91.27: 26 91.27 - 114.09: 3 Dihedral angle restraints: 15690 sinusoidal: 6846 harmonic: 8844 Sorted by residual: dihedral pdb=" CB CYS C 370 " pdb=" SG CYS C 370 " pdb=" SG CYS C 485 " pdb=" CB CYS C 485 " ideal model delta sinusoidal sigma weight residual -86.00 -9.72 -76.28 1 1.00e+01 1.00e-02 7.32e+01 dihedral pdb=" CB CYS A 370 " pdb=" SG CYS A 370 " pdb=" SG CYS A 485 " pdb=" CB CYS A 485 " ideal model delta sinusoidal sigma weight residual -86.00 -10.59 -75.41 1 1.00e+01 1.00e-02 7.18e+01 dihedral pdb=" CB CYS B 370 " pdb=" SG CYS B 370 " pdb=" SG CYS B 485 " pdb=" CB CYS B 485 " ideal model delta sinusoidal sigma weight residual -86.00 -12.39 -73.61 1 1.00e+01 1.00e-02 6.89e+01 ... (remaining 15687 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 3890 0.116 - 0.233: 193 0.233 - 0.349: 11 0.349 - 0.466: 7 0.466 - 0.582: 3 Chirality restraints: 4104 Sorted by residual: chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN C 349 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-01 2.50e+01 8.47e+00 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN B 349 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.56e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 349 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 7.07e+00 ... (remaining 4101 not shown) Planarity restraints: 4329 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 461 " -0.051 5.00e-02 4.00e+02 7.81e-02 9.77e+00 pdb=" N PRO A 462 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO A 462 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 462 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 461 " -0.049 5.00e-02 4.00e+02 7.47e-02 8.92e+00 pdb=" N PRO C 462 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO C 462 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 462 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 397 " 0.014 2.00e-02 2.50e+03 2.88e-02 8.28e+00 pdb=" C ILE C 397 " -0.050 2.00e-02 2.50e+03 pdb=" O ILE C 397 " 0.018 2.00e-02 2.50e+03 pdb=" N ALA C 398 " 0.017 2.00e-02 2.50e+03 ... (remaining 4326 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 6541 2.81 - 3.33: 20652 3.33 - 3.85: 39234 3.85 - 4.38: 44432 4.38 - 4.90: 78736 Nonbonded interactions: 189595 Sorted by model distance: nonbonded pdb=" OG SER A 352 " pdb=" OG SER C 384 " model vdw 2.283 3.040 nonbonded pdb=" O ARG C 55 " pdb=" OG SER C 58 " model vdw 2.290 3.040 nonbonded pdb=" O LEU C 347 " pdb=" OG1 THR C 351 " model vdw 2.306 3.040 nonbonded pdb=" OG SER A 384 " pdb=" OG SER B 352 " model vdw 2.309 3.040 nonbonded pdb=" O LEU B 347 " pdb=" OG1 THR B 351 " model vdw 2.310 3.040 ... (remaining 189590 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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' } 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: 0.920 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: 0.840 Check model and map are aligned: 0.170 Set scattering table: 0.230 Process input model: 54.300 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.120 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 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 : 0.005 0.112 25059 Z= 0.265 Angle : 0.968 15.424 34227 Z= 0.509 Chirality : 0.062 0.582 4104 Planarity : 0.006 0.078 4278 Dihedral : 14.399 114.091 9870 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.66 % Favored : 93.17 % Rotamer: Outliers : 0.23 % Allowed : 0.53 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.14), residues: 2988 helix: -0.61 (0.18), residues: 657 sheet: -0.66 (0.20), residues: 654 loop : -2.49 (0.13), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP B 66 HIS 0.022 0.002 HIS B 615 PHE 0.045 0.002 PHE B 53 TYR 0.031 0.002 TYR C 710 ARG 0.004 0.000 ARG B 527 Details of bonding type rmsd link_NAG-ASN : bond 0.01026 ( 51) link_NAG-ASN : angle 4.87685 ( 153) link_BETA1-4 : bond 0.01686 ( 9) link_BETA1-4 : angle 5.18971 ( 27) hydrogen bonds : bond 0.13115 ( 880) hydrogen bonds : angle 6.83449 ( 2520) SS BOND : bond 0.00448 ( 36) SS BOND : angle 2.07616 ( 72) covalent geometry : bond 0.00519 (24963) covalent geometry : angle 0.89809 (33975) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 226 time to evaluate : 3.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 858 TYR cc_start: 0.7389 (m-80) cc_final: 0.7155 (m-10) REVERT: B 858 TYR cc_start: 0.7625 (m-80) cc_final: 0.7419 (m-80) REVERT: B 983 MET cc_start: 0.8458 (ttm) cc_final: 0.8173 (ttp) REVERT: B 1070 THR cc_start: 0.7896 (m) cc_final: 0.7691 (m) REVERT: C 31 MET cc_start: 0.6428 (mtm) cc_final: 0.6203 (mtm) REVERT: C 397 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.8141 (tt) REVERT: C 455 TYR cc_start: 0.8323 (p90) cc_final: 0.7994 (p90) outliers start: 6 outliers final: 1 residues processed: 231 average time/residue: 0.3774 time to fit residues: 141.8118 Evaluate side-chains 160 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 158 time to evaluate : 3.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 809 PHE Chi-restraints excluded: chain C residue 397 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 255 optimal weight: 6.9990 chunk 229 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 chunk 154 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 237 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 144 optimal weight: 1.9990 chunk 176 optimal weight: 10.0000 chunk 275 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 HIS B 149 HIS ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 615 HIS B1002 HIS B1060 GLN B1062 ASN C 149 HIS C1002 HIS C1060 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.116543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.105121 restraints weight = 46489.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.105786 restraints weight = 33625.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.106123 restraints weight = 30171.178| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 25059 Z= 0.259 Angle : 0.740 10.850 34227 Z= 0.363 Chirality : 0.051 0.453 4104 Planarity : 0.005 0.066 4278 Dihedral : 8.850 104.015 4567 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 1.32 % Allowed : 9.46 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.14), residues: 2988 helix: 0.71 (0.20), residues: 645 sheet: -0.67 (0.22), residues: 525 loop : -2.24 (0.13), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP A 62 HIS 0.009 0.001 HIS B 149 PHE 0.035 0.002 PHE A 53 TYR 0.023 0.002 TYR C 710 ARG 0.006 0.001 ARG B 527 Details of bonding type rmsd link_NAG-ASN : bond 0.00662 ( 51) link_NAG-ASN : angle 3.81666 ( 153) link_BETA1-4 : bond 0.00898 ( 9) link_BETA1-4 : angle 3.67038 ( 27) hydrogen bonds : bond 0.04532 ( 880) hydrogen bonds : angle 5.49778 ( 2520) SS BOND : bond 0.00476 ( 36) SS BOND : angle 1.55236 ( 72) covalent geometry : bond 0.00604 (24963) covalent geometry : angle 0.68555 (33975) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 160 time to evaluate : 2.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.7208 (mtm) cc_final: 0.6928 (mtm) REVERT: A 694 MET cc_start: 0.6648 (tmm) cc_final: 0.6242 (ttm) REVERT: A 727 GLU cc_start: 0.7390 (tt0) cc_final: 0.7051 (tt0) REVERT: B 296 ASN cc_start: 0.8348 (t0) cc_final: 0.8127 (t0) REVERT: B 304 GLU cc_start: 0.5721 (pm20) cc_final: 0.5454 (pm20) REVERT: B 476 GLU cc_start: 0.7317 (pm20) cc_final: 0.7077 (pm20) REVERT: B 615 HIS cc_start: 0.7375 (OUTLIER) cc_final: 0.7105 (t-90) REVERT: B 856 MET cc_start: 0.8427 (tpp) cc_final: 0.8202 (tpp) REVERT: B 1004 MET cc_start: 0.7113 (ttt) cc_final: 0.6877 (tmm) REVERT: C 31 MET cc_start: 0.7092 (mtm) cc_final: 0.6593 (mtm) REVERT: C 407 ASP cc_start: 0.7304 (OUTLIER) cc_final: 0.7076 (p0) REVERT: C 452 LEU cc_start: 0.8072 (mm) cc_final: 0.7713 (pp) REVERT: C 455 TYR cc_start: 0.8770 (p90) cc_final: 0.8318 (p90) outliers start: 35 outliers final: 28 residues processed: 184 average time/residue: 0.3293 time to fit residues: 99.0792 Evaluate side-chains 176 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 146 time to evaluate : 2.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain B residue 63 TYR Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 615 HIS Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 809 PHE Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 126 PHE Chi-restraints excluded: chain C residue 149 HIS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 216 TRP Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 475 PHE Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 1076 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 38 optimal weight: 6.9990 chunk 188 optimal weight: 0.9980 chunk 171 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 222 optimal weight: 2.9990 chunk 210 optimal weight: 4.9990 chunk 283 optimal weight: 3.9990 chunk 220 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 230 optimal weight: 6.9990 chunk 228 optimal weight: 2.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1060 GLN ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.116002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.104316 restraints weight = 46115.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.105447 restraints weight = 34826.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.106037 restraints weight = 27998.261| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 25059 Z= 0.213 Angle : 0.676 11.519 34227 Z= 0.330 Chirality : 0.050 0.429 4104 Planarity : 0.004 0.060 4278 Dihedral : 8.461 99.999 4567 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 1.93 % Allowed : 12.94 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.15), residues: 2988 helix: 1.16 (0.21), residues: 642 sheet: -0.84 (0.20), residues: 606 loop : -2.18 (0.13), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 415 HIS 0.016 0.002 HIS C 149 PHE 0.019 0.002 PHE A 53 TYR 0.022 0.002 TYR B 710 ARG 0.004 0.000 ARG C 719 Details of bonding type rmsd link_NAG-ASN : bond 0.00674 ( 51) link_NAG-ASN : angle 3.78326 ( 153) link_BETA1-4 : bond 0.00968 ( 9) link_BETA1-4 : angle 3.76556 ( 27) hydrogen bonds : bond 0.04312 ( 880) hydrogen bonds : angle 5.39452 ( 2520) SS BOND : bond 0.00477 ( 36) SS BOND : angle 1.54076 ( 72) covalent geometry : bond 0.00494 (24963) covalent geometry : angle 0.61581 (33975) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 156 time to evaluate : 3.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.7317 (mtm) cc_final: 0.7013 (mtm) REVERT: A 694 MET cc_start: 0.6689 (OUTLIER) cc_final: 0.6389 (mtt) REVERT: A 727 GLU cc_start: 0.7486 (tt0) cc_final: 0.7098 (tt0) REVERT: B 476 GLU cc_start: 0.7415 (pm20) cc_final: 0.7108 (pm20) REVERT: B 620 TYR cc_start: 0.8044 (OUTLIER) cc_final: 0.7546 (m-10) REVERT: B 707 LEU cc_start: 0.7467 (tp) cc_final: 0.7229 (tp) REVERT: B 729 ASP cc_start: 0.7168 (m-30) cc_final: 0.6820 (m-30) REVERT: B 856 MET cc_start: 0.8355 (tpp) cc_final: 0.8153 (tpp) REVERT: B 1004 MET cc_start: 0.7095 (ttt) cc_final: 0.6810 (tmm) REVERT: C 407 ASP cc_start: 0.7406 (OUTLIER) cc_final: 0.7148 (p0) REVERT: C 452 LEU cc_start: 0.8046 (mm) cc_final: 0.7695 (pp) REVERT: C 455 TYR cc_start: 0.8593 (p90) cc_final: 0.8143 (p90) REVERT: C 615 HIS cc_start: 0.7141 (t70) cc_final: 0.6634 (t-90) REVERT: C 620 TYR cc_start: 0.8129 (OUTLIER) cc_final: 0.7709 (m-80) outliers start: 51 outliers final: 40 residues processed: 193 average time/residue: 0.3945 time to fit residues: 127.0719 Evaluate side-chains 187 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 143 time to evaluate : 2.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 TYR Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain B residue 63 TYR Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 809 PHE Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 126 PHE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 216 TRP Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 475 PHE Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain C residue 1076 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 55 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 223 optimal weight: 0.0970 chunk 131 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 136 optimal weight: 4.9990 chunk 161 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 269 optimal weight: 0.3980 chunk 183 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 524 GLN A 604 GLN ** B 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.118376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.106442 restraints weight = 46412.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.108154 restraints weight = 35041.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.109089 restraints weight = 26309.833| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 25059 Z= 0.107 Angle : 0.590 11.527 34227 Z= 0.285 Chirality : 0.047 0.387 4104 Planarity : 0.003 0.060 4278 Dihedral : 7.709 92.027 4567 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.70 % Allowed : 14.49 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.15), residues: 2988 helix: 1.50 (0.21), residues: 645 sheet: -0.68 (0.21), residues: 588 loop : -1.99 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 66 HIS 0.008 0.001 HIS B 615 PHE 0.016 0.001 PHE A 53 TYR 0.018 0.001 TYR B 710 ARG 0.002 0.000 ARG C 719 Details of bonding type rmsd link_NAG-ASN : bond 0.00699 ( 51) link_NAG-ASN : angle 3.54824 ( 153) link_BETA1-4 : bond 0.01095 ( 9) link_BETA1-4 : angle 3.42233 ( 27) hydrogen bonds : bond 0.03585 ( 880) hydrogen bonds : angle 5.12802 ( 2520) SS BOND : bond 0.00292 ( 36) SS BOND : angle 1.32176 ( 72) covalent geometry : bond 0.00233 (24963) covalent geometry : angle 0.53060 (33975) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 176 time to evaluate : 3.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.7153 (mtm) cc_final: 0.6817 (mtm) REVERT: A 95 TRP cc_start: 0.8660 (m-90) cc_final: 0.8331 (m-90) REVERT: A 417 THR cc_start: 0.7973 (OUTLIER) cc_final: 0.7605 (t) REVERT: A 620 TYR cc_start: 0.7944 (OUTLIER) cc_final: 0.7583 (m-10) REVERT: A 694 MET cc_start: 0.6610 (tmm) cc_final: 0.5950 (mtt) REVERT: A 727 GLU cc_start: 0.7350 (tt0) cc_final: 0.6993 (tt0) REVERT: B 296 ASN cc_start: 0.7876 (t0) cc_final: 0.7585 (t0) REVERT: B 707 LEU cc_start: 0.7337 (tp) cc_final: 0.7076 (tp) REVERT: C 173 ARG cc_start: 0.3439 (ttt-90) cc_final: 0.3090 (mtp180) REVERT: C 397 ILE cc_start: 0.8565 (OUTLIER) cc_final: 0.8290 (pt) REVERT: C 407 ASP cc_start: 0.7310 (OUTLIER) cc_final: 0.7056 (p0) REVERT: C 452 LEU cc_start: 0.8033 (mm) cc_final: 0.7686 (pp) REVERT: C 455 TYR cc_start: 0.8497 (p90) cc_final: 0.8171 (p90) REVERT: C 615 HIS cc_start: 0.6983 (t70) cc_final: 0.6499 (t-90) REVERT: C 871 TYR cc_start: 0.8206 (m-80) cc_final: 0.7731 (m-80) outliers start: 45 outliers final: 30 residues processed: 207 average time/residue: 0.4223 time to fit residues: 144.4020 Evaluate side-chains 185 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 151 time to evaluate : 2.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 TYR Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain B residue 63 TYR Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 1002 HIS Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 126 PHE Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 475 PHE Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 863 ILE Chi-restraints excluded: chain C residue 1076 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 174 optimal weight: 0.8980 chunk 169 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 294 optimal weight: 6.9990 chunk 274 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 216 optimal weight: 5.9990 chunk 47 optimal weight: 0.6980 chunk 204 optimal weight: 7.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 615 HIS ** B 728 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 = 0.3551 r_free = 0.3551 target = 0.117919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.107014 restraints weight = 46323.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.107411 restraints weight = 36958.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.107903 restraints weight = 32260.562| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 25059 Z= 0.147 Angle : 0.614 11.585 34227 Z= 0.297 Chirality : 0.048 0.399 4104 Planarity : 0.003 0.057 4278 Dihedral : 7.509 81.593 4565 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.57 % Allowed : 14.79 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.15), residues: 2988 helix: 1.51 (0.21), residues: 648 sheet: -0.69 (0.21), residues: 591 loop : -1.96 (0.14), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 66 HIS 0.008 0.001 HIS C1002 PHE 0.013 0.001 PHE A 53 TYR 0.017 0.001 TYR B 710 ARG 0.003 0.000 ARG B 527 Details of bonding type rmsd link_NAG-ASN : bond 0.00665 ( 51) link_NAG-ASN : angle 3.51602 ( 153) link_BETA1-4 : bond 0.01073 ( 9) link_BETA1-4 : angle 3.64725 ( 27) hydrogen bonds : bond 0.03762 ( 880) hydrogen bonds : angle 5.08219 ( 2520) SS BOND : bond 0.00326 ( 36) SS BOND : angle 1.53107 ( 72) covalent geometry : bond 0.00339 (24963) covalent geometry : angle 0.55540 (33975) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 161 time to evaluate : 4.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.7257 (mtm) cc_final: 0.6956 (mtm) REVERT: A 417 THR cc_start: 0.8202 (OUTLIER) cc_final: 0.7858 (t) REVERT: A 620 TYR cc_start: 0.7860 (OUTLIER) cc_final: 0.7441 (m-10) REVERT: A 694 MET cc_start: 0.6722 (OUTLIER) cc_final: 0.6105 (mtt) REVERT: A 727 GLU cc_start: 0.7471 (tt0) cc_final: 0.7233 (tt0) REVERT: B 296 ASN cc_start: 0.8052 (t0) cc_final: 0.7748 (t0) REVERT: B 615 HIS cc_start: 0.7587 (OUTLIER) cc_final: 0.7338 (t-90) REVERT: B 620 TYR cc_start: 0.8054 (OUTLIER) cc_final: 0.7554 (m-10) REVERT: B 707 LEU cc_start: 0.7220 (tp) cc_final: 0.6987 (tp) REVERT: C 397 ILE cc_start: 0.8607 (OUTLIER) cc_final: 0.8394 (pt) REVERT: C 452 LEU cc_start: 0.8060 (mm) cc_final: 0.7703 (pp) REVERT: C 455 TYR cc_start: 0.8598 (p90) cc_final: 0.8282 (p90) REVERT: C 615 HIS cc_start: 0.7222 (t70) cc_final: 0.6683 (t-90) REVERT: C 620 TYR cc_start: 0.8111 (OUTLIER) cc_final: 0.7690 (m-80) outliers start: 68 outliers final: 47 residues processed: 212 average time/residue: 0.3473 time to fit residues: 123.6871 Evaluate side-chains 205 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 151 time to evaluate : 2.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain B residue 63 TYR Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 615 HIS Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain B residue 1002 HIS Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 126 PHE Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 475 PHE Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain C residue 863 ILE Chi-restraints excluded: chain C residue 1076 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 187 optimal weight: 4.9990 chunk 224 optimal weight: 0.7980 chunk 135 optimal weight: 3.9990 chunk 210 optimal weight: 7.9990 chunk 162 optimal weight: 1.9990 chunk 179 optimal weight: 4.9990 chunk 63 optimal weight: 8.9990 chunk 8 optimal weight: 10.0000 chunk 251 optimal weight: 20.0000 chunk 98 optimal weight: 8.9990 chunk 186 optimal weight: 6.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 728 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 = 0.3509 r_free = 0.3509 target = 0.115080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.104205 restraints weight = 46526.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.104615 restraints weight = 36575.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.105265 restraints weight = 31150.717| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 25059 Z= 0.221 Angle : 0.678 11.697 34227 Z= 0.331 Chirality : 0.050 0.415 4104 Planarity : 0.004 0.052 4278 Dihedral : 7.595 59.811 4565 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 3.33 % Allowed : 15.25 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.15), residues: 2988 helix: 1.42 (0.21), residues: 648 sheet: -0.84 (0.20), residues: 594 loop : -2.02 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 415 HIS 0.031 0.002 HIS B 615 PHE 0.017 0.002 PHE B 77 TYR 0.019 0.002 TYR C1064 ARG 0.004 0.001 ARG B 527 Details of bonding type rmsd link_NAG-ASN : bond 0.00669 ( 51) link_NAG-ASN : angle 3.62345 ( 153) link_BETA1-4 : bond 0.00855 ( 9) link_BETA1-4 : angle 3.91983 ( 27) hydrogen bonds : bond 0.04178 ( 880) hydrogen bonds : angle 5.24253 ( 2520) SS BOND : bond 0.00388 ( 36) SS BOND : angle 1.83483 ( 72) covalent geometry : bond 0.00519 (24963) covalent geometry : angle 0.61999 (33975) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 154 time to evaluate : 4.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.7413 (mtm) cc_final: 0.7096 (mtm) REVERT: A 283 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7623 (tppt) REVERT: A 417 THR cc_start: 0.8261 (OUTLIER) cc_final: 0.7922 (t) REVERT: A 476 GLU cc_start: 0.7652 (pm20) cc_final: 0.7376 (pm20) REVERT: A 620 TYR cc_start: 0.8054 (OUTLIER) cc_final: 0.7742 (m-80) REVERT: A 694 MET cc_start: 0.6572 (OUTLIER) cc_final: 0.5943 (mtm) REVERT: A 809 PHE cc_start: 0.5339 (OUTLIER) cc_final: 0.4151 (m-80) REVERT: B 296 ASN cc_start: 0.8173 (t0) cc_final: 0.7872 (t0) REVERT: B 620 TYR cc_start: 0.8029 (OUTLIER) cc_final: 0.7653 (m-10) REVERT: B 863 ILE cc_start: 0.7895 (OUTLIER) cc_final: 0.7568 (tp) REVERT: C 452 LEU cc_start: 0.8090 (mm) cc_final: 0.7738 (pp) REVERT: C 455 TYR cc_start: 0.8620 (p90) cc_final: 0.8412 (p90) REVERT: C 615 HIS cc_start: 0.7301 (t70) cc_final: 0.6778 (t-90) REVERT: C 620 TYR cc_start: 0.8132 (OUTLIER) cc_final: 0.7761 (m-80) outliers start: 88 outliers final: 66 residues processed: 224 average time/residue: 0.4065 time to fit residues: 151.4456 Evaluate side-chains 215 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 141 time to evaluate : 2.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 TYR Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 126 PHE Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 809 PHE Chi-restraints excluded: chain A residue 854 MET Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 1058 VAL Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain B residue 63 TYR Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 315 CYS Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain B residue 1002 HIS Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 95 TRP Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 126 PHE Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 216 TRP Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 475 PHE Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 863 ILE Chi-restraints excluded: chain C residue 1076 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 238 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 chunk 251 optimal weight: 0.4980 chunk 257 optimal weight: 3.9990 chunk 196 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 540 GLN ** B 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 728 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 = 0.3549 r_free = 0.3549 target = 0.117673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.106426 restraints weight = 46131.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.107483 restraints weight = 37417.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.108033 restraints weight = 29838.036| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25059 Z= 0.119 Angle : 0.597 11.578 34227 Z= 0.289 Chirality : 0.047 0.381 4104 Planarity : 0.003 0.051 4278 Dihedral : 6.907 57.282 4563 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.84 % Allowed : 16.23 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.15), residues: 2988 helix: 1.70 (0.22), residues: 627 sheet: -0.71 (0.21), residues: 591 loop : -1.91 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 66 HIS 0.005 0.001 HIS C1002 PHE 0.014 0.001 PHE A 842 TYR 0.016 0.001 TYR A 455 ARG 0.002 0.000 ARG B 527 Details of bonding type rmsd link_NAG-ASN : bond 0.00704 ( 51) link_NAG-ASN : angle 3.52402 ( 153) link_BETA1-4 : bond 0.00982 ( 9) link_BETA1-4 : angle 3.28401 ( 27) hydrogen bonds : bond 0.03592 ( 880) hydrogen bonds : angle 5.08345 ( 2520) SS BOND : bond 0.00302 ( 36) SS BOND : angle 1.51810 ( 72) covalent geometry : bond 0.00267 (24963) covalent geometry : angle 0.53782 (33975) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 162 time to evaluate : 2.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.7170 (mtm) cc_final: 0.6850 (mtm) REVERT: A 417 THR cc_start: 0.7942 (OUTLIER) cc_final: 0.7588 (t) REVERT: A 620 TYR cc_start: 0.7943 (OUTLIER) cc_final: 0.7508 (m-10) REVERT: A 694 MET cc_start: 0.6543 (OUTLIER) cc_final: 0.5824 (mtm) REVERT: A 809 PHE cc_start: 0.5206 (OUTLIER) cc_final: 0.4116 (m-80) REVERT: B 296 ASN cc_start: 0.8086 (t0) cc_final: 0.7760 (t0) REVERT: C 173 ARG cc_start: 0.3515 (ttt-90) cc_final: 0.3306 (ttt-90) REVERT: C 452 LEU cc_start: 0.8066 (mm) cc_final: 0.7726 (pp) REVERT: C 615 HIS cc_start: 0.7339 (t70) cc_final: 0.6812 (t-90) REVERT: C 620 TYR cc_start: 0.8068 (OUTLIER) cc_final: 0.7622 (m-80) REVERT: C 813 THR cc_start: 0.8647 (OUTLIER) cc_final: 0.8255 (p) outliers start: 75 outliers final: 51 residues processed: 219 average time/residue: 0.3283 time to fit residues: 118.6178 Evaluate side-chains 212 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 155 time to evaluate : 2.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 TYR Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 809 PHE Chi-restraints excluded: chain A residue 854 MET Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain B residue 63 TYR Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 315 CYS Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 708 LEU Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 1002 HIS Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1058 VAL Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 126 PHE Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 216 TRP Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 475 PHE Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 863 ILE Chi-restraints excluded: chain C residue 1076 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 296 optimal weight: 4.9990 chunk 234 optimal weight: 1.9990 chunk 225 optimal weight: 0.7980 chunk 206 optimal weight: 0.6980 chunk 282 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 276 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 60 optimal weight: 10.0000 chunk 9 optimal weight: 8.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 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 = 0.3541 r_free = 0.3541 target = 0.117233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.106193 restraints weight = 46407.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.106890 restraints weight = 36704.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.107916 restraints weight = 32622.490| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25059 Z= 0.136 Angle : 0.605 11.610 34227 Z= 0.292 Chirality : 0.048 0.425 4104 Planarity : 0.003 0.051 4278 Dihedral : 6.747 58.336 4563 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 3.03 % Allowed : 16.12 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.15), residues: 2988 helix: 1.72 (0.22), residues: 627 sheet: -0.68 (0.21), residues: 591 loop : -1.89 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 66 HIS 0.007 0.001 HIS C1002 PHE 0.016 0.001 PHE C 842 TYR 0.016 0.001 TYR A 455 ARG 0.003 0.000 ARG B 527 Details of bonding type rmsd link_NAG-ASN : bond 0.00707 ( 51) link_NAG-ASN : angle 3.50617 ( 153) link_BETA1-4 : bond 0.00922 ( 9) link_BETA1-4 : angle 3.24565 ( 27) hydrogen bonds : bond 0.03651 ( 880) hydrogen bonds : angle 5.04802 ( 2520) SS BOND : bond 0.00314 ( 36) SS BOND : angle 1.47151 ( 72) covalent geometry : bond 0.00314 (24963) covalent geometry : angle 0.54784 (33975) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 158 time to evaluate : 2.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.7194 (mtm) cc_final: 0.6874 (mtm) REVERT: A 173 ARG cc_start: 0.3341 (mtp180) cc_final: 0.3046 (mtp180) REVERT: A 283 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7558 (tppt) REVERT: A 417 THR cc_start: 0.8066 (OUTLIER) cc_final: 0.7716 (t) REVERT: A 476 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7322 (pm20) REVERT: A 620 TYR cc_start: 0.7896 (OUTLIER) cc_final: 0.7549 (m-10) REVERT: A 694 MET cc_start: 0.6561 (OUTLIER) cc_final: 0.6231 (tmm) REVERT: A 809 PHE cc_start: 0.5270 (OUTLIER) cc_final: 0.4336 (m-80) REVERT: B 283 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.7554 (tttt) REVERT: B 296 ASN cc_start: 0.8081 (t0) cc_final: 0.7729 (t0) REVERT: B 620 TYR cc_start: 0.8006 (OUTLIER) cc_final: 0.7549 (m-10) REVERT: C 615 HIS cc_start: 0.7245 (t70) cc_final: 0.6732 (t-90) REVERT: C 620 TYR cc_start: 0.8090 (OUTLIER) cc_final: 0.7693 (m-80) REVERT: C 813 THR cc_start: 0.8650 (OUTLIER) cc_final: 0.8259 (p) outliers start: 80 outliers final: 63 residues processed: 219 average time/residue: 0.4194 time to fit residues: 154.9472 Evaluate side-chains 228 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 155 time to evaluate : 4.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 TYR Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 809 PHE Chi-restraints excluded: chain A residue 854 MET Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 1058 VAL Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain B residue 63 TYR Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 283 LYS Chi-restraints excluded: chain B residue 315 CYS Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 708 LEU Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain B residue 1002 HIS Chi-restraints excluded: chain B residue 1004 MET Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1058 VAL Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 126 PHE Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 216 TRP Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 475 PHE Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 863 ILE Chi-restraints excluded: chain C residue 1076 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 83 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 150 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 chunk 301 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 251 optimal weight: 3.9990 chunk 222 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1062 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.115499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.104051 restraints weight = 46228.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.105556 restraints weight = 33392.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.106600 restraints weight = 26175.337| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 25059 Z= 0.171 Angle : 0.637 11.833 34227 Z= 0.309 Chirality : 0.049 0.392 4104 Planarity : 0.003 0.050 4278 Dihedral : 6.897 59.877 4563 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 3.06 % Allowed : 16.12 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.15), residues: 2988 helix: 1.65 (0.22), residues: 627 sheet: -0.72 (0.21), residues: 591 loop : -1.91 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 66 HIS 0.009 0.001 HIS C1002 PHE 0.013 0.001 PHE A 842 TYR 0.016 0.001 TYR A 455 ARG 0.003 0.000 ARG B 527 Details of bonding type rmsd link_NAG-ASN : bond 0.00678 ( 51) link_NAG-ASN : angle 3.56212 ( 153) link_BETA1-4 : bond 0.00881 ( 9) link_BETA1-4 : angle 3.34832 ( 27) hydrogen bonds : bond 0.03855 ( 880) hydrogen bonds : angle 5.12114 ( 2520) SS BOND : bond 0.00348 ( 36) SS BOND : angle 1.55402 ( 72) covalent geometry : bond 0.00399 (24963) covalent geometry : angle 0.58084 (33975) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 153 time to evaluate : 2.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.7302 (mtm) cc_final: 0.6973 (mtm) REVERT: A 173 ARG cc_start: 0.3462 (mtp180) cc_final: 0.3188 (mtp180) REVERT: A 283 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7622 (tppt) REVERT: A 417 THR cc_start: 0.8080 (OUTLIER) cc_final: 0.7721 (t) REVERT: A 476 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7458 (pm20) REVERT: A 620 TYR cc_start: 0.7923 (OUTLIER) cc_final: 0.7635 (m-80) REVERT: A 694 MET cc_start: 0.6597 (OUTLIER) cc_final: 0.6250 (tmm) REVERT: A 809 PHE cc_start: 0.5394 (OUTLIER) cc_final: 0.4411 (m-80) REVERT: B 283 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.7613 (tttt) REVERT: B 296 ASN cc_start: 0.8209 (t0) cc_final: 0.7879 (t0) REVERT: B 620 TYR cc_start: 0.8015 (OUTLIER) cc_final: 0.7622 (m-10) REVERT: B 863 ILE cc_start: 0.7686 (OUTLIER) cc_final: 0.7235 (tp) REVERT: C 615 HIS cc_start: 0.7285 (t70) cc_final: 0.6791 (t-90) REVERT: C 620 TYR cc_start: 0.8140 (OUTLIER) cc_final: 0.7777 (m-80) outliers start: 81 outliers final: 68 residues processed: 219 average time/residue: 0.3598 time to fit residues: 129.3768 Evaluate side-chains 228 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 150 time to evaluate : 2.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 TYR Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 809 PHE Chi-restraints excluded: chain A residue 854 MET Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 1058 VAL Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 283 LYS Chi-restraints excluded: chain B residue 315 CYS Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 708 LEU Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain B residue 1002 HIS Chi-restraints excluded: chain B residue 1004 MET Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1058 VAL Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 126 PHE Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 216 TRP Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 475 PHE Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 863 ILE Chi-restraints excluded: chain C residue 1076 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 92 optimal weight: 3.9990 chunk 210 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 112 optimal weight: 3.9990 chunk 72 optimal weight: 8.9990 chunk 94 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 84 optimal weight: 6.9990 chunk 256 optimal weight: 8.9990 chunk 2 optimal weight: 0.8980 chunk 102 optimal weight: 0.0070 overall best weight: 2.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 524 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.115884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.104817 restraints weight = 46318.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.105403 restraints weight = 36775.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.106901 restraints weight = 30793.105| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 25059 Z= 0.170 Angle : 0.641 11.949 34227 Z= 0.311 Chirality : 0.049 0.389 4104 Planarity : 0.003 0.050 4278 Dihedral : 6.894 59.725 4563 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 3.18 % Allowed : 16.23 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.15), residues: 2988 helix: 1.65 (0.22), residues: 627 sheet: -0.72 (0.21), residues: 588 loop : -1.92 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 62 HIS 0.009 0.001 HIS A1002 PHE 0.019 0.001 PHE C 842 TYR 0.017 0.001 TYR A 455 ARG 0.003 0.000 ARG B 527 Details of bonding type rmsd link_NAG-ASN : bond 0.00697 ( 51) link_NAG-ASN : angle 3.60370 ( 153) link_BETA1-4 : bond 0.00925 ( 9) link_BETA1-4 : angle 3.34653 ( 27) hydrogen bonds : bond 0.03850 ( 880) hydrogen bonds : angle 5.14472 ( 2520) SS BOND : bond 0.00374 ( 36) SS BOND : angle 1.67060 ( 72) covalent geometry : bond 0.00398 (24963) covalent geometry : angle 0.58380 (33975) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 153 time to evaluate : 3.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.7256 (mtm) cc_final: 0.6947 (mtm) REVERT: A 173 ARG cc_start: 0.3534 (mtp180) cc_final: 0.3271 (mtp180) REVERT: A 283 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.7823 (tppt) REVERT: A 407 ASP cc_start: 0.7385 (p0) cc_final: 0.7135 (p0) REVERT: A 417 THR cc_start: 0.8119 (OUTLIER) cc_final: 0.7758 (t) REVERT: A 476 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7486 (pm20) REVERT: A 620 TYR cc_start: 0.8020 (OUTLIER) cc_final: 0.7697 (m-10) REVERT: A 809 PHE cc_start: 0.5340 (OUTLIER) cc_final: 0.4412 (m-80) REVERT: B 283 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.7617 (tttt) REVERT: B 620 TYR cc_start: 0.8011 (OUTLIER) cc_final: 0.7517 (m-10) REVERT: B 863 ILE cc_start: 0.7634 (OUTLIER) cc_final: 0.7098 (tp) REVERT: C 173 ARG cc_start: 0.3719 (ttt-90) cc_final: 0.3089 (mtp-110) REVERT: C 615 HIS cc_start: 0.7346 (t70) cc_final: 0.6909 (t-90) REVERT: C 620 TYR cc_start: 0.8155 (OUTLIER) cc_final: 0.7724 (m-80) outliers start: 84 outliers final: 73 residues processed: 221 average time/residue: 0.3799 time to fit residues: 139.4955 Evaluate side-chains 228 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 146 time to evaluate : 2.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 TYR Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 126 PHE Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 809 PHE Chi-restraints excluded: chain A residue 854 MET Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 1058 VAL Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 283 LYS Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 315 CYS Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 708 LEU Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain B residue 1002 HIS Chi-restraints excluded: chain B residue 1004 MET Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1058 VAL Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 126 PHE Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 216 TRP Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 454 THR Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 475 PHE Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 863 ILE Chi-restraints excluded: chain C residue 1076 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 71 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 188 optimal weight: 4.9990 chunk 84 optimal weight: 8.9990 chunk 286 optimal weight: 5.9990 chunk 193 optimal weight: 0.0370 chunk 297 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 overall best weight: 2.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 728 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 = 0.3523 r_free = 0.3523 target = 0.116120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.105181 restraints weight = 46356.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.105992 restraints weight = 36057.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.106784 restraints weight = 30054.533| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25059 Z= 0.163 Angle : 0.639 11.997 34227 Z= 0.309 Chirality : 0.049 0.387 4104 Planarity : 0.003 0.050 4278 Dihedral : 6.879 59.574 4563 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 3.33 % Allowed : 16.27 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.15), residues: 2988 helix: 1.66 (0.22), residues: 627 sheet: -0.72 (0.21), residues: 588 loop : -1.89 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 66 HIS 0.009 0.001 HIS A1002 PHE 0.015 0.001 PHE A 842 TYR 0.016 0.001 TYR A 455 ARG 0.003 0.000 ARG B 527 Details of bonding type rmsd link_NAG-ASN : bond 0.00690 ( 51) link_NAG-ASN : angle 3.60570 ( 153) link_BETA1-4 : bond 0.00914 ( 9) link_BETA1-4 : angle 3.32187 ( 27) hydrogen bonds : bond 0.03833 ( 880) hydrogen bonds : angle 5.13597 ( 2520) SS BOND : bond 0.00380 ( 36) SS BOND : angle 1.60822 ( 72) covalent geometry : bond 0.00380 (24963) covalent geometry : angle 0.58146 (33975) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6773.20 seconds wall clock time: 126 minutes 13.46 seconds (7573.46 seconds total)