Starting phenix.real_space_refine on Fri May 23 17:54:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zy5_60556/05_2025/8zy5_60556.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zy5_60556/05_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_60556/05_2025/8zy5_60556.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zy5_60556/05_2025/8zy5_60556.map" model { file = "/net/cci-nas-00/data/ceres_data/8zy5_60556/05_2025/8zy5_60556.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zy5_60556/05_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-5687/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: 14.16, per 1000 atoms: 0.58 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: 6.56 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: 3.44 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: 9.58 Time building geometry restraints manager: 7.53 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: 1.080 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: 0.010 Extract box with map and model: 0.820 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 55.170 Find NCS groups from input model: 0.970 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: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.250 ------------------------------------------------------------------------------- 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 : 2.377 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: 0.3295 time to fit residues: 124.1666 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 : 2.571 ------------------------------------------------------------------------------- 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 = 0.105781 restraints weight = 33625.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.106162 restraints weight = 30141.958| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 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 : 2.594 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: 0.6927 (mtm) REVERT: A 694 MET cc_start: 0.6656 (tmm) cc_final: 0.6242 (ttm) REVERT: A 727 GLU cc_start: 0.7392 (tt0) cc_final: 0.7049 (tt0) REVERT: B 296 ASN cc_start: 0.8347 (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: 0.7315 (pm20) cc_final: 0.7075 (pm20) REVERT: B 615 HIS cc_start: 0.7377 (OUTLIER) cc_final: 0.7106 (t-90) REVERT: B 856 MET cc_start: 0.8428 (tpp) cc_final: 0.8206 (tpp) REVERT: B 1004 MET cc_start: 0.7115 (ttt) cc_final: 0.6879 (tmm) REVERT: C 31 MET cc_start: 0.7089 (mtm) cc_final: 0.6591 (mtm) REVERT: C 407 ASP cc_start: 0.7300 (OUTLIER) cc_final: 0.7070 (p0) REVERT: C 452 LEU cc_start: 0.8075 (mm) cc_final: 0.7716 (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: 0.3362 time to fit residues: 101.5742 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 : 2.385 ------------------------------------------------------------------------------- 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: 0.9990 chunk 82 optimal weight: 5.9990 chunk 222 optimal weight: 2.9990 chunk 210 optimal weight: 4.9990 chunk 283 optimal weight: 0.8980 chunk 220 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 230 optimal weight: 7.9990 chunk 228 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3536 r_free = 0.3536 target = 0.117036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.105131 restraints weight = 46085.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.106525 restraints weight = 35263.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.107452 restraints weight = 26902.497| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25059 Z= 0.149 Angle : 0.625 11.696 34227 Z= 0.304 Chirality : 0.048 0.410 4104 Planarity : 0.004 0.062 4278 Dihedral : 8.217 99.640 4567 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 1.32 % Allowed : 12.75 % Favored : 85.93 % 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: -1.53 (0.15), residues: 2988 helix: 1.26 (0.21), residues: 642 sheet: -0.74 (0.21), residues: 588 loop : -2.11 (0.13), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 66 HIS 0.009 0.001 HIS B 615 PHE 0.019 0.001 PHE A 53 TYR 0.022 0.001 TYR B 710 ARG 0.004 0.000 ARG C 719 Details of bonding type rmsd link_NAG-ASN : bond 0.00679 ( 51) link_NAG-ASN : angle 3.69223 ( 153) link_BETA1-4 : bond 0.01084 ( 9) link_BETA1-4 : angle 3.56835 ( 27) hydrogen bonds : bond 0.03992 ( 880) hydrogen bonds : angle 5.28797 ( 2520) SS BOND : bond 0.00374 ( 36) SS BOND : angle 1.50510 ( 72) covalent geometry : bond 0.00337 (24963) covalent geometry : angle 0.56288 (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 194 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 159 time to evaluate : 2.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.7177 (mtm) cc_final: 0.6861 (mtm) REVERT: A 694 MET cc_start: 0.6624 (tmm) cc_final: 0.6345 (mtt) REVERT: A 727 GLU cc_start: 0.7411 (tt0) cc_final: 0.7081 (tt0) REVERT: B 476 GLU cc_start: 0.7365 (pm20) cc_final: 0.7056 (pm20) REVERT: B 615 HIS cc_start: 0.7288 (OUTLIER) cc_final: 0.7029 (t-170) REVERT: C 407 ASP cc_start: 0.7313 (OUTLIER) cc_final: 0.7083 (p0) REVERT: C 452 LEU cc_start: 0.8036 (mm) cc_final: 0.7698 (pp) REVERT: C 455 TYR cc_start: 0.8622 (p90) cc_final: 0.8287 (p90) REVERT: C 615 HIS cc_start: 0.7204 (t70) cc_final: 0.6649 (t-90) REVERT: C 620 TYR cc_start: 0.8107 (OUTLIER) cc_final: 0.7593 (m-10) outliers start: 35 outliers final: 26 residues processed: 181 average time/residue: 0.3312 time to fit residues: 99.5398 Evaluate side-chains 171 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 142 time to evaluate : 2.876 ------------------------------------------------------------------------------- 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 351 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 670 THR 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 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 1076 VAL Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 126 PHE 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: 0.9990 chunk 105 optimal weight: 4.9990 chunk 223 optimal weight: 0.0570 chunk 131 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 chunk 136 optimal weight: 0.0020 chunk 161 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 269 optimal weight: 0.9980 chunk 183 optimal weight: 6.9990 overall best weight: 0.8110 ------------------------------------------------------------------------------- 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 540 GLN ** B 615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.120231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.108860 restraints weight = 45937.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.109490 restraints weight = 37072.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.110262 restraints weight = 32618.410| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 25059 Z= 0.103 Angle : 0.574 11.362 34227 Z= 0.276 Chirality : 0.047 0.383 4104 Planarity : 0.003 0.060 4278 Dihedral : 7.502 93.155 4567 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.66 % Allowed : 13.85 % Favored : 84.49 % 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: -1.28 (0.15), residues: 2988 helix: 1.54 (0.22), residues: 648 sheet: -0.58 (0.21), residues: 582 loop : -1.99 (0.13), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 66 HIS 0.004 0.001 HIS B1002 PHE 0.016 0.001 PHE A 53 TYR 0.017 0.001 TYR B 710 ARG 0.002 0.000 ARG A 769 Details of bonding type rmsd link_NAG-ASN : bond 0.00696 ( 51) link_NAG-ASN : angle 3.47539 ( 153) link_BETA1-4 : bond 0.01132 ( 9) link_BETA1-4 : angle 3.36376 ( 27) hydrogen bonds : bond 0.03493 ( 880) hydrogen bonds : angle 5.03773 ( 2520) SS BOND : bond 0.00311 ( 36) SS BOND : angle 1.15666 ( 72) covalent geometry : bond 0.00220 (24963) covalent geometry : angle 0.51554 (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 217 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 173 time to evaluate : 2.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.7063 (mtm) cc_final: 0.6749 (mtm) REVERT: A 95 TRP cc_start: 0.8647 (m-90) cc_final: 0.8370 (m-90) REVERT: A 417 THR cc_start: 0.7995 (OUTLIER) cc_final: 0.7649 (t) REVERT: A 694 MET cc_start: 0.6642 (OUTLIER) cc_final: 0.6077 (mtt) REVERT: A 727 GLU cc_start: 0.7146 (tt0) cc_final: 0.6814 (tt0) REVERT: B 296 ASN cc_start: 0.7946 (t0) cc_final: 0.7647 (t0) REVERT: C 76 GLU cc_start: 0.7172 (mm-30) cc_final: 0.6970 (mm-30) REVERT: C 173 ARG cc_start: 0.3606 (ttt-90) cc_final: 0.3273 (mtp180) REVERT: C 397 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8325 (pt) REVERT: C 452 LEU cc_start: 0.8048 (mm) cc_final: 0.7689 (pp) REVERT: C 455 TYR cc_start: 0.8639 (p90) cc_final: 0.8296 (p90) REVERT: C 615 HIS cc_start: 0.7103 (t70) cc_final: 0.6571 (t-90) outliers start: 44 outliers final: 30 residues processed: 202 average time/residue: 0.3119 time to fit residues: 103.9818 Evaluate side-chains 186 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 153 time to evaluate : 2.418 ------------------------------------------------------------------------------- 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 253 THR Chi-restraints excluded: chain A residue 315 CYS 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 694 MET Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain B residue 63 TYR 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 351 THR Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 670 THR 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 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 1076 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 174 optimal weight: 0.0970 chunk 169 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 294 optimal weight: 1.9990 chunk 274 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 216 optimal weight: 4.9990 chunk 47 optimal weight: 0.0170 chunk 204 optimal weight: 4.9990 overall best weight: 1.8222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 615 HIS ** 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 = 0.3558 r_free = 0.3558 target = 0.118392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.107709 restraints weight = 46352.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.108119 restraints weight = 35708.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.108627 restraints weight = 30331.995| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 25059 Z= 0.142 Angle : 0.604 11.009 34227 Z= 0.292 Chirality : 0.048 0.394 4104 Planarity : 0.003 0.056 4278 Dihedral : 7.395 86.564 4565 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.27 % Allowed : 14.34 % Favored : 83.39 % 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: 1.57 (0.21), residues: 648 sheet: -0.62 (0.21), residues: 591 loop : -1.93 (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 0.016 0.001 TYR B 710 ARG 0.003 0.000 ARG B 527 Details of bonding type rmsd link_NAG-ASN : bond 0.00662 ( 51) link_NAG-ASN : angle 3.46336 ( 153) link_BETA1-4 : bond 0.01082 ( 9) link_BETA1-4 : angle 3.57107 ( 27) hydrogen bonds : bond 0.03696 ( 880) hydrogen bonds : angle 5.01390 ( 2520) SS BOND : bond 0.00340 ( 36) SS BOND : angle 1.59462 ( 72) covalent geometry : bond 0.00327 (24963) covalent geometry : angle 0.54622 (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 221 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 161 time to evaluate : 2.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.7182 (mtm) cc_final: 0.6858 (mtm) REVERT: A 417 THR cc_start: 0.8124 (OUTLIER) cc_final: 0.7784 (t) REVERT: A 620 TYR cc_start: 0.7914 (OUTLIER) cc_final: 0.7578 (m-10) REVERT: A 694 MET cc_start: 0.6713 (OUTLIER) cc_final: 0.6103 (mtt) REVERT: A 727 GLU cc_start: 0.7354 (tt0) cc_final: 0.7022 (tt0) REVERT: B 296 ASN cc_start: 0.8062 (t0) cc_final: 0.7752 (t0) REVERT: B 620 TYR cc_start: 0.8043 (OUTLIER) cc_final: 0.7528 (m-10) REVERT: C 397 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8402 (pt) REVERT: C 452 LEU cc_start: 0.8056 (mm) cc_final: 0.7705 (pp) REVERT: C 455 TYR cc_start: 0.8517 (p90) cc_final: 0.8186 (p90) REVERT: C 615 HIS cc_start: 0.7098 (t70) cc_final: 0.6662 (t-90) REVERT: C 620 TYR cc_start: 0.8105 (OUTLIER) cc_final: 0.7590 (m-10) outliers start: 60 outliers final: 44 residues processed: 202 average time/residue: 0.3350 time to fit residues: 113.3295 Evaluate side-chains 200 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 150 time to evaluate : 2.465 ------------------------------------------------------------------------------- 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 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 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 683 VAL 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 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 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 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 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: 5.9990 chunk 224 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 210 optimal weight: 4.9990 chunk 162 optimal weight: 5.9990 chunk 179 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 chunk 8 optimal weight: 10.0000 chunk 251 optimal weight: 20.0000 chunk 98 optimal weight: 6.9990 chunk 186 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN ** B 615 HIS ** 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 = 0.3489 r_free = 0.3489 target = 0.113782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.102448 restraints weight = 46562.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.103285 restraints weight = 38124.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.104073 restraints weight = 31467.167| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 25059 Z= 0.275 Angle : 0.746 11.845 34227 Z= 0.366 Chirality : 0.052 0.431 4104 Planarity : 0.004 0.050 4278 Dihedral : 7.948 59.961 4565 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 3.37 % Allowed : 14.95 % Favored : 81.69 % 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: -1.55 (0.15), residues: 2988 helix: 1.29 (0.21), residues: 645 sheet: -0.91 (0.20), residues: 615 loop : -2.09 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 415 HIS 0.013 0.002 HIS A1002 PHE 0.021 0.002 PHE A 77 TYR 0.021 0.002 TYR A 455 ARG 0.006 0.001 ARG B 527 Details of bonding type rmsd link_NAG-ASN : bond 0.00666 ( 51) link_NAG-ASN : angle 3.71052 ( 153) link_BETA1-4 : bond 0.00901 ( 9) link_BETA1-4 : angle 4.21837 ( 27) hydrogen bonds : bond 0.04541 ( 880) hydrogen bonds : angle 5.37871 ( 2520) SS BOND : bond 0.00464 ( 36) SS BOND : angle 1.89028 ( 72) covalent geometry : bond 0.00649 (24963) covalent geometry : angle 0.69093 (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 243 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 154 time to evaluate : 2.575 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: 0.7514 (mtm) cc_final: 0.7202 (mtm) REVERT: A 283 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.7868 (tppt) REVERT: A 417 THR cc_start: 0.8396 (OUTLIER) cc_final: 0.8059 (t) REVERT: A 620 TYR cc_start: 0.8115 (OUTLIER) cc_final: 0.7819 (m-80) REVERT: A 694 MET cc_start: 0.6619 (OUTLIER) cc_final: 0.5946 (mtm) REVERT: A 809 PHE cc_start: 0.5347 (OUTLIER) cc_final: 0.4201 (m-80) REVERT: B 620 TYR cc_start: 0.8068 (OUTLIER) cc_final: 0.7760 (m-80) REVERT: B 863 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7702 (tp) REVERT: C 452 LEU cc_start: 0.8077 (mm) cc_final: 0.7723 (pp) REVERT: C 615 HIS cc_start: 0.7360 (t70) cc_final: 0.6837 (t-90) REVERT: C 620 TYR cc_start: 0.8197 (OUTLIER) cc_final: 0.7912 (m-80) outliers start: 89 outliers final: 63 residues processed: 229 average time/residue: 0.3165 time to fit residues: 120.4027 Evaluate side-chains 209 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 138 time to evaluate : 2.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 107 SER 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 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 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 231 LEU 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 494 VAL Chi-restraints excluded: chain B residue 580 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 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 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 152 THR Chi-restraints excluded: chain C residue 216 TRP Chi-restraints excluded: chain C residue 231 LEU 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 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 647 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 238 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 chunk 251 optimal weight: 0.9980 chunk 257 optimal weight: 1.9990 chunk 196 optimal weight: 5.9990 chunk 168 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 447 ASN ** B 615 HIS ** 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 = 0.3546 r_free = 0.3546 target = 0.117617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.106323 restraints weight = 46099.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.107354 restraints weight = 36958.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.109118 restraints weight = 29226.820| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25059 Z= 0.128 Angle : 0.617 11.788 34227 Z= 0.300 Chirality : 0.048 0.385 4104 Planarity : 0.003 0.050 4278 Dihedral : 7.120 57.678 4563 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.88 % Allowed : 15.82 % Favored : 81.31 % 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: -1.29 (0.15), residues: 2988 helix: 1.69 (0.22), residues: 621 sheet: -0.75 (0.21), residues: 591 loop : -1.95 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 95 HIS 0.006 0.001 HIS C1002 PHE 0.011 0.001 PHE A 53 TYR 0.018 0.001 TYR A 710 ARG 0.004 0.000 ARG B 173 Details of bonding type rmsd link_NAG-ASN : bond 0.00710 ( 51) link_NAG-ASN : angle 3.57273 ( 153) link_BETA1-4 : bond 0.00946 ( 9) link_BETA1-4 : angle 3.30614 ( 27) hydrogen bonds : bond 0.03708 ( 880) hydrogen bonds : angle 5.16508 ( 2520) SS BOND : bond 0.00359 ( 36) SS BOND : angle 1.49189 ( 72) covalent geometry : bond 0.00289 (24963) covalent geometry : angle 0.55911 (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 238 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 162 time to evaluate : 2.454 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: 0.7294 (mtm) cc_final: 0.6977 (mtm) REVERT: A 417 THR cc_start: 0.8019 (OUTLIER) cc_final: 0.7644 (t) REVERT: A 620 TYR cc_start: 0.8072 (OUTLIER) cc_final: 0.7745 (m-10) REVERT: A 694 MET cc_start: 0.6519 (OUTLIER) cc_final: 0.5808 (mtm) REVERT: A 809 PHE cc_start: 0.5302 (OUTLIER) cc_final: 0.4143 (m-80) REVERT: B 620 TYR cc_start: 0.7977 (OUTLIER) cc_final: 0.7598 (m-10) REVERT: B 716 GLN cc_start: 0.8087 (tt0) cc_final: 0.7864 (tt0) REVERT: C 173 ARG cc_start: 0.3451 (ttt-90) cc_final: 0.2944 (mtp180) REVERT: C 452 LEU cc_start: 0.8041 (mm) cc_final: 0.7778 (pp) REVERT: C 615 HIS cc_start: 0.7346 (t70) cc_final: 0.6824 (t-90) REVERT: C 620 TYR cc_start: 0.8077 (OUTLIER) cc_final: 0.7659 (m-80) outliers start: 76 outliers final: 53 residues processed: 222 average time/residue: 0.3158 time to fit residues: 115.1435 Evaluate side-chains 214 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 155 time to evaluate : 2.610 ------------------------------------------------------------------------------- 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 85 THR Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 417 THR 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 863 ILE Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain B residue 63 TYR 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 253 THR 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 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 1002 HIS Chi-restraints excluded: chain B residue 1004 MET 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 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 152 THR Chi-restraints excluded: chain C residue 216 TRP Chi-restraints excluded: chain C residue 231 LEU 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 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: 5.9990 chunk 234 optimal weight: 2.9990 chunk 225 optimal weight: 0.9990 chunk 206 optimal weight: 2.9990 chunk 282 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 276 optimal weight: 6.9990 chunk 111 optimal weight: 0.1980 chunk 103 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- 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 615 HIS ** 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 = 0.3525 r_free = 0.3525 target = 0.116146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.104396 restraints weight = 46542.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.105966 restraints weight = 33445.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.107064 restraints weight = 26120.023| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25059 Z= 0.138 Angle : 0.614 11.676 34227 Z= 0.297 Chirality : 0.048 0.387 4104 Planarity : 0.003 0.050 4278 Dihedral : 6.895 58.323 4563 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 3.06 % Allowed : 16.08 % 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: -1.26 (0.15), residues: 2988 helix: 1.68 (0.22), residues: 627 sheet: -0.73 (0.21), residues: 588 loop : -1.92 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 66 HIS 0.007 0.001 HIS C1002 PHE 0.015 0.001 PHE C 842 TYR 0.018 0.001 TYR C1064 ARG 0.003 0.000 ARG B 173 Details of bonding type rmsd link_NAG-ASN : bond 0.00692 ( 51) link_NAG-ASN : angle 3.53757 ( 153) link_BETA1-4 : bond 0.00940 ( 9) link_BETA1-4 : angle 3.26767 ( 27) hydrogen bonds : bond 0.03708 ( 880) hydrogen bonds : angle 5.09673 ( 2520) SS BOND : bond 0.00381 ( 36) SS BOND : angle 1.70613 ( 72) covalent geometry : bond 0.00317 (24963) covalent geometry : angle 0.55561 (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 239 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 158 time to evaluate : 2.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.7252 (mtm) cc_final: 0.6933 (mtm) REVERT: A 173 ARG cc_start: 0.3321 (mtp180) cc_final: 0.3027 (mtp180) REVERT: A 417 THR cc_start: 0.8027 (OUTLIER) cc_final: 0.7665 (t) REVERT: A 620 TYR cc_start: 0.8102 (OUTLIER) cc_final: 0.7794 (m-10) REVERT: A 694 MET cc_start: 0.6570 (OUTLIER) cc_final: 0.6226 (tmm) REVERT: A 809 PHE cc_start: 0.5274 (OUTLIER) cc_final: 0.4344 (m-80) REVERT: B 283 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.7575 (tttt) REVERT: B 620 TYR cc_start: 0.7997 (OUTLIER) cc_final: 0.7603 (m-10) REVERT: C 173 ARG cc_start: 0.3457 (ttt-90) cc_final: 0.2894 (mtp-110) REVERT: C 452 LEU cc_start: 0.8066 (mm) cc_final: 0.7805 (pp) REVERT: C 615 HIS cc_start: 0.7244 (t70) cc_final: 0.6727 (t-90) REVERT: C 620 TYR cc_start: 0.8077 (OUTLIER) cc_final: 0.7643 (m-80) outliers start: 81 outliers final: 64 residues processed: 220 average time/residue: 0.3254 time to fit residues: 117.6407 Evaluate side-chains 223 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 152 time to evaluate : 2.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 246 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 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 929 SER 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 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 929 SER 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 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 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: 2.9990 chunk 150 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 chunk 137 optimal weight: 8.9990 chunk 121 optimal weight: 4.9990 chunk 301 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 chunk 251 optimal weight: 9.9990 chunk 222 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 716 GLN ** B 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1062 ASN C 524 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.113969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.102941 restraints weight = 46495.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.103839 restraints weight = 35654.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.104597 restraints weight = 29581.103| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 25059 Z= 0.236 Angle : 0.708 12.140 34227 Z= 0.345 Chirality : 0.051 0.412 4104 Planarity : 0.004 0.046 4278 Dihedral : 7.327 59.385 4563 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 3.06 % Allowed : 16.23 % Favored : 80.70 % 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: 1.53 (0.22), residues: 621 sheet: -0.81 (0.20), residues: 603 loop : -2.04 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 66 HIS 0.014 0.002 HIS C1002 PHE 0.017 0.002 PHE A 77 TYR 0.019 0.002 TYR C1064 ARG 0.005 0.001 ARG B 527 Details of bonding type rmsd link_NAG-ASN : bond 0.00686 ( 51) link_NAG-ASN : angle 3.68129 ( 153) link_BETA1-4 : bond 0.00821 ( 9) link_BETA1-4 : angle 3.59895 ( 27) hydrogen bonds : bond 0.04261 ( 880) hydrogen bonds : angle 5.29953 ( 2520) SS BOND : bond 0.00476 ( 36) SS BOND : angle 1.94531 ( 72) covalent geometry : bond 0.00554 (24963) covalent geometry : angle 0.65262 (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 229 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 148 time to evaluate : 2.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.7384 (mtm) cc_final: 0.7065 (mtm) REVERT: A 173 ARG cc_start: 0.3627 (mtp180) cc_final: 0.3371 (mtp180) REVERT: A 283 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.7900 (tppt) REVERT: A 407 ASP cc_start: 0.7400 (p0) cc_final: 0.7160 (p0) REVERT: A 417 THR cc_start: 0.8300 (OUTLIER) cc_final: 0.7964 (t) REVERT: A 620 TYR cc_start: 0.8151 (OUTLIER) cc_final: 0.7874 (m-80) REVERT: A 694 MET cc_start: 0.6589 (OUTLIER) cc_final: 0.5931 (mtm) REVERT: A 809 PHE cc_start: 0.5298 (OUTLIER) cc_final: 0.4142 (m-80) REVERT: B 283 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.7861 (tttt) REVERT: B 620 TYR cc_start: 0.8036 (OUTLIER) cc_final: 0.7725 (m-80) REVERT: B 863 ILE cc_start: 0.7856 (OUTLIER) cc_final: 0.7303 (tp) REVERT: C 455 TYR cc_start: 0.8578 (OUTLIER) cc_final: 0.8299 (p90) REVERT: C 615 HIS cc_start: 0.7357 (t70) cc_final: 0.6903 (t-90) REVERT: C 620 TYR cc_start: 0.8099 (OUTLIER) cc_final: 0.7744 (m-80) outliers start: 81 outliers final: 67 residues processed: 217 average time/residue: 0.3259 time to fit residues: 116.0045 Evaluate side-chains 218 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 141 time to evaluate : 2.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 144 VAL Chi-restraints excluded: chain A residue 152 THR 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 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 929 SER 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 126 PHE Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 231 LEU 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 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 929 SER 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 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 455 TYR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 92 optimal weight: 1.9990 chunk 210 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 112 optimal weight: 20.0000 chunk 72 optimal weight: 9.9990 chunk 94 optimal weight: 8.9990 chunk 75 optimal weight: 9.9990 chunk 84 optimal weight: 3.9990 chunk 256 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 102 optimal weight: 0.5980 overall best weight: 2.7188 ------------------------------------------------------------------------------- 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** ** B 615 HIS ** 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 = 0.3513 r_free = 0.3513 target = 0.115407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.104564 restraints weight = 46475.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.105049 restraints weight = 36613.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.105628 restraints weight = 30893.289| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25059 Z= 0.191 Angle : 0.672 12.239 34227 Z= 0.326 Chirality : 0.050 0.398 4104 Planarity : 0.004 0.044 4278 Dihedral : 7.198 59.982 4563 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 3.22 % Allowed : 16.08 % Favored : 80.70 % 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: -1.40 (0.15), residues: 2988 helix: 1.55 (0.22), residues: 624 sheet: -0.83 (0.21), residues: 588 loop : -1.99 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 95 HIS 0.012 0.001 HIS C1002 PHE 0.015 0.002 PHE C 842 TYR 0.021 0.001 TYR C1064 ARG 0.003 0.000 ARG B 527 Details of bonding type rmsd link_NAG-ASN : bond 0.00687 ( 51) link_NAG-ASN : angle 3.69042 ( 153) link_BETA1-4 : bond 0.00888 ( 9) link_BETA1-4 : angle 3.47201 ( 27) hydrogen bonds : bond 0.04062 ( 880) hydrogen bonds : angle 5.28470 ( 2520) SS BOND : bond 0.00480 ( 36) SS BOND : angle 1.80361 ( 72) covalent geometry : bond 0.00448 (24963) covalent geometry : angle 0.61416 (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 233 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 148 time to evaluate : 2.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.7327 (mtm) cc_final: 0.7013 (mtm) REVERT: A 173 ARG cc_start: 0.3631 (mtp180) cc_final: 0.3374 (mtp180) REVERT: A 407 ASP cc_start: 0.7383 (p0) cc_final: 0.7149 (p0) REVERT: A 417 THR cc_start: 0.8253 (OUTLIER) cc_final: 0.7915 (t) REVERT: A 620 TYR cc_start: 0.8129 (OUTLIER) cc_final: 0.7865 (m-80) REVERT: A 694 MET cc_start: 0.6551 (OUTLIER) cc_final: 0.6210 (tmm) REVERT: A 809 PHE cc_start: 0.5299 (OUTLIER) cc_final: 0.4336 (m-80) REVERT: B 283 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.7847 (tttt) REVERT: B 348 TYR cc_start: 0.8131 (m-10) cc_final: 0.7898 (m-10) REVERT: B 620 TYR cc_start: 0.8010 (OUTLIER) cc_final: 0.7711 (m-80) REVERT: B 863 ILE cc_start: 0.7829 (OUTLIER) cc_final: 0.7157 (tp) REVERT: C 455 TYR cc_start: 0.8581 (OUTLIER) cc_final: 0.8288 (p90) REVERT: C 615 HIS cc_start: 0.7381 (t70) cc_final: 0.6939 (t-90) REVERT: C 620 TYR cc_start: 0.8096 (OUTLIER) cc_final: 0.7730 (m-80) REVERT: C 741 GLN cc_start: 0.8470 (mp10) cc_final: 0.8239 (mp10) outliers start: 85 outliers final: 69 residues processed: 216 average time/residue: 0.3285 time to fit residues: 116.8864 Evaluate side-chains 224 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 146 time to evaluate : 2.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 85 THR 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 152 THR 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 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 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 929 SER Chi-restraints excluded: chain A residue 1058 VAL Chi-restraints excluded: chain A residue 1076 VAL 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 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 380 LEU 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 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 929 SER 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 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 455 TYR 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 1076 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 71 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 188 optimal weight: 3.9990 chunk 84 optimal weight: 0.0970 chunk 286 optimal weight: 4.9990 chunk 193 optimal weight: 0.9990 chunk 297 optimal weight: 20.0000 chunk 135 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 615 HIS ** 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 = 0.3538 r_free = 0.3538 target = 0.117047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.105937 restraints weight = 46292.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.107312 restraints weight = 34295.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.108298 restraints weight = 27421.948| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25059 Z= 0.142 Angle : 0.631 12.146 34227 Z= 0.305 Chirality : 0.049 0.486 4104 Planarity : 0.003 0.046 4278 Dihedral : 6.856 58.442 4563 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 2.95 % Allowed : 16.53 % Favored : 80.51 % 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: 1.66 (0.22), residues: 627 sheet: -0.76 (0.21), residues: 588 loop : -1.91 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 95 HIS 0.007 0.001 HIS C1002 PHE 0.011 0.001 PHE A 227 TYR 0.018 0.001 TYR C1064 ARG 0.003 0.000 ARG B 173 Details of bonding type rmsd link_NAG-ASN : bond 0.00712 ( 51) link_NAG-ASN : angle 3.63707 ( 153) link_BETA1-4 : bond 0.00954 ( 9) link_BETA1-4 : angle 3.27742 ( 27) hydrogen bonds : bond 0.03765 ( 880) hydrogen bonds : angle 5.17629 ( 2520) SS BOND : bond 0.00424 ( 36) SS BOND : angle 1.64553 ( 72) covalent geometry : bond 0.00328 (24963) covalent geometry : angle 0.57171 (33975) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5519.06 seconds wall clock time: 99 minutes 6.14 seconds (5946.14 seconds total)