Starting phenix.real_space_refine on Fri Sep 19 08:24:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zy5_60556/09_2025/8zy5_60556.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zy5_60556/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8zy5_60556/09_2025/8zy5_60556.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zy5_60556/09_2025/8zy5_60556.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zy5_60556/09_2025/8zy5_60556.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zy5_60556/09_2025/8zy5_60556.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 5.39, per 1000 atoms: 0.22 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: 1.81 Conformation dependent library (CDL) restraints added in 835.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.01 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: 5.37 Time building geometry restraints manager: 2.34 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: 0.03 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: 1.000 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 21.240 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.370 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG B 527 TYR 0.031 0.002 TYR C 710 PHE 0.045 0.002 PHE B 53 TRP 0.028 0.003 TRP B 66 HIS 0.022 0.002 HIS B 615 Details of bonding type rmsd covalent geometry : bond 0.00519 (24963) covalent geometry : angle 0.89809 (33975) SS BOND : bond 0.00448 ( 36) SS BOND : angle 2.07616 ( 72) hydrogen bonds : bond 0.13115 ( 880) hydrogen bonds : angle 6.83449 ( 2520) link_BETA1-4 : bond 0.01686 ( 9) link_BETA1-4 : angle 5.18971 ( 27) link_NAG-ASN : bond 0.01026 ( 51) link_NAG-ASN : angle 4.87685 ( 153) *********************** 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 : 0.844 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: 0.1402 time to fit residues: 53.2262 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 : 0.672 ------------------------------------------------------------------------------- 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 197 optimal weight: 6.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.0970 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 3.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- 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 = 0.3550 r_free = 0.3550 target = 0.118053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.107253 restraints weight = 46380.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.107856 restraints weight = 35773.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.108540 restraints weight = 31993.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.108765 restraints weight = 28642.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.108850 restraints weight = 25393.515| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 25059 Z= 0.229 Angle : 0.705 11.568 34227 Z= 0.345 Chirality : 0.051 0.446 4104 Planarity : 0.005 0.068 4278 Dihedral : 8.788 104.784 4567 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 1.25 % Allowed : 8.29 % Favored : 90.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.86 (0.14), residues: 2988 helix: 0.65 (0.20), residues: 648 sheet: -0.64 (0.21), residues: 588 loop : -2.32 (0.13), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 769 TYR 0.023 0.002 TYR C 710 PHE 0.033 0.002 PHE A 53 TRP 0.023 0.002 TRP A 62 HIS 0.008 0.001 HIS B 149 Details of bonding type rmsd covalent geometry : bond 0.00534 (24963) covalent geometry : angle 0.64576 (33975) SS BOND : bond 0.00413 ( 36) SS BOND : angle 1.49919 ( 72) hydrogen bonds : bond 0.04532 ( 880) hydrogen bonds : angle 5.51200 ( 2520) link_BETA1-4 : bond 0.00961 ( 9) link_BETA1-4 : angle 3.67646 ( 27) link_NAG-ASN : bond 0.00692 ( 51) link_NAG-ASN : angle 3.87561 ( 153) *********************** 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: 33 poor density : 162 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.6934 (mtm) cc_final: 0.6662 (mtm) REVERT: A 727 GLU cc_start: 0.7277 (tt0) cc_final: 0.6913 (tt0) REVERT: B 296 ASN cc_start: 0.8086 (t0) cc_final: 0.7850 (t0) REVERT: B 476 GLU cc_start: 0.7402 (pm20) cc_final: 0.7177 (pm20) REVERT: B 615 HIS cc_start: 0.7200 (OUTLIER) cc_final: 0.6943 (t-90) REVERT: B 1004 MET cc_start: 0.7075 (ttt) cc_final: 0.6821 (tmm) REVERT: C 31 MET cc_start: 0.6934 (mtm) cc_final: 0.6485 (mtm) REVERT: C 407 ASP cc_start: 0.7041 (OUTLIER) cc_final: 0.6799 (p0) REVERT: C 455 TYR cc_start: 0.8658 (p90) cc_final: 0.8227 (p90) outliers start: 33 outliers final: 26 residues processed: 183 average time/residue: 0.1380 time to fit residues: 41.5888 Evaluate side-chains 174 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 0.609 ------------------------------------------------------------------------------- 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 111 ILE 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 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 28 optimal weight: 0.2980 chunk 272 optimal weight: 0.0970 chunk 69 optimal weight: 0.2980 chunk 175 optimal weight: 1.9990 chunk 163 optimal weight: 5.9990 chunk 280 optimal weight: 5.9990 chunk 135 optimal weight: 0.8980 chunk 149 optimal weight: 6.9990 chunk 262 optimal weight: 6.9990 chunk 155 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 540 GLN ** B 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.121390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.110672 restraints weight = 45779.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.111438 restraints weight = 34656.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.112247 restraints weight = 28236.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.112610 restraints weight = 25627.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.112840 restraints weight = 22573.615| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 25059 Z= 0.102 Angle : 0.587 11.830 34227 Z= 0.285 Chirality : 0.047 0.393 4104 Planarity : 0.004 0.063 4278 Dihedral : 8.000 100.691 4567 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.14 % Allowed : 11.09 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.43 (0.15), residues: 2988 helix: 1.25 (0.21), residues: 648 sheet: -0.59 (0.21), residues: 582 loop : -2.04 (0.13), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 719 TYR 0.016 0.001 TYR B 455 PHE 0.020 0.001 PHE A 53 TRP 0.011 0.001 TRP A 66 HIS 0.013 0.001 HIS B 615 Details of bonding type rmsd covalent geometry : bond 0.00211 (24963) covalent geometry : angle 0.52537 (33975) SS BOND : bond 0.00317 ( 36) SS BOND : angle 1.32214 ( 72) hydrogen bonds : bond 0.03670 ( 880) hydrogen bonds : angle 5.20192 ( 2520) link_BETA1-4 : bond 0.01201 ( 9) link_BETA1-4 : angle 3.32399 ( 27) link_NAG-ASN : bond 0.00695 ( 51) link_NAG-ASN : angle 3.61416 ( 153) *********************** 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 190 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 160 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.6969 (mtm) cc_final: 0.6685 (mtm) REVERT: A 727 GLU cc_start: 0.7330 (tt0) cc_final: 0.6970 (tt0) REVERT: B 296 ASN cc_start: 0.8107 (t0) cc_final: 0.7780 (t0) REVERT: B 476 GLU cc_start: 0.7300 (pm20) cc_final: 0.6989 (pm20) REVERT: C 31 MET cc_start: 0.6957 (mtm) cc_final: 0.6713 (mtp) REVERT: C 173 ARG cc_start: 0.3466 (ttt-90) cc_final: 0.3153 (mtp180) REVERT: C 407 ASP cc_start: 0.7266 (OUTLIER) cc_final: 0.7027 (p0) REVERT: C 452 LEU cc_start: 0.8009 (mm) cc_final: 0.7697 (pp) REVERT: C 455 TYR cc_start: 0.8573 (p90) cc_final: 0.8240 (p90) outliers start: 30 outliers final: 22 residues processed: 179 average time/residue: 0.1432 time to fit residues: 42.1774 Evaluate side-chains 171 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 0.879 ------------------------------------------------------------------------------- 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 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 231 LEU Chi-restraints excluded: chain B residue 246 VAL 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 75 MET 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 246 VAL Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 407 ASP 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 246 optimal weight: 0.3980 chunk 152 optimal weight: 0.0570 chunk 302 optimal weight: 10.0000 chunk 21 optimal weight: 0.0670 chunk 171 optimal weight: 2.9990 chunk 275 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 214 optimal weight: 9.9990 chunk 184 optimal weight: 0.4980 chunk 72 optimal weight: 5.9990 chunk 218 optimal weight: 0.9990 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 GLN ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 615 HIS ** B 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.122573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.111683 restraints weight = 45832.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.112701 restraints weight = 36765.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.113709 restraints weight = 30463.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.113909 restraints weight = 23950.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.113957 restraints weight = 22887.849| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 25059 Z= 0.092 Angle : 0.555 11.415 34227 Z= 0.268 Chirality : 0.046 0.375 4104 Planarity : 0.003 0.063 4278 Dihedral : 7.343 97.532 4567 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.40 % Allowed : 12.45 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.15), residues: 2988 helix: 1.58 (0.21), residues: 648 sheet: -0.46 (0.21), residues: 603 loop : -1.93 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 769 TYR 0.016 0.001 TYR B 455 PHE 0.017 0.001 PHE A 53 TRP 0.010 0.001 TRP A 66 HIS 0.006 0.001 HIS B 615 Details of bonding type rmsd covalent geometry : bond 0.00192 (24963) covalent geometry : angle 0.49704 (33975) SS BOND : bond 0.00252 ( 36) SS BOND : angle 1.05841 ( 72) hydrogen bonds : bond 0.03380 ( 880) hydrogen bonds : angle 4.97490 ( 2520) link_BETA1-4 : bond 0.01135 ( 9) link_BETA1-4 : angle 3.20168 ( 27) link_NAG-ASN : bond 0.00695 ( 51) link_NAG-ASN : angle 3.43453 ( 153) *********************** 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 211 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 174 time to evaluate : 0.928 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: 0.6870 (mtm) cc_final: 0.6609 (mtm) REVERT: A 95 TRP cc_start: 0.8550 (m-90) cc_final: 0.8285 (m-90) REVERT: A 399 ASP cc_start: 0.7999 (m-30) cc_final: 0.7759 (m-30) REVERT: A 727 GLU cc_start: 0.7323 (tt0) cc_final: 0.7013 (tt0) REVERT: B 296 ASN cc_start: 0.8029 (t0) cc_final: 0.7664 (t0) REVERT: B 476 GLU cc_start: 0.7197 (pm20) cc_final: 0.6709 (pm20) REVERT: C 31 MET cc_start: 0.6858 (mtm) cc_final: 0.6458 (mtm) REVERT: C 173 ARG cc_start: 0.3664 (ttt-90) cc_final: 0.3429 (mtp180) REVERT: C 314 PHE cc_start: 0.7637 (OUTLIER) cc_final: 0.7084 (t80) REVERT: C 407 ASP cc_start: 0.7307 (OUTLIER) cc_final: 0.6981 (p0) REVERT: C 455 TYR cc_start: 0.8435 (p90) cc_final: 0.8182 (p90) outliers start: 37 outliers final: 29 residues processed: 197 average time/residue: 0.1381 time to fit residues: 45.3032 Evaluate side-chains 186 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 155 time to evaluate : 0.907 ------------------------------------------------------------------------------- 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 314 PHE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 854 MET 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 231 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 1002 HIS Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain C residue 39 ASP 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 149 HIS Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 314 PHE Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 407 ASP 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 1076 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 301 optimal weight: 0.9980 chunk 137 optimal weight: 9.9990 chunk 295 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 211 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 chunk 129 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 232 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 169 optimal weight: 3.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 524 GLN ** B 615 HIS ** 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 = 0.3557 r_free = 0.3557 target = 0.118296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.107268 restraints weight = 46179.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.107577 restraints weight = 36908.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.108361 restraints weight = 33402.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.108694 restraints weight = 29211.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.109146 restraints weight = 26012.621| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 25059 Z= 0.183 Angle : 0.628 10.894 34227 Z= 0.306 Chirality : 0.049 0.402 4104 Planarity : 0.004 0.057 4278 Dihedral : 7.477 96.069 4565 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 2.04 % Allowed : 13.20 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.15), residues: 2988 helix: 1.52 (0.21), residues: 651 sheet: -0.53 (0.21), residues: 585 loop : -1.97 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 527 TYR 0.019 0.001 TYR A 455 PHE 0.015 0.002 PHE B 842 TRP 0.009 0.002 TRP A 840 HIS 0.022 0.002 HIS C 149 Details of bonding type rmsd covalent geometry : bond 0.00426 (24963) covalent geometry : angle 0.57351 (33975) SS BOND : bond 0.00344 ( 36) SS BOND : angle 1.36302 ( 72) hydrogen bonds : bond 0.03901 ( 880) hydrogen bonds : angle 5.05631 ( 2520) link_BETA1-4 : bond 0.00958 ( 9) link_BETA1-4 : angle 3.56591 ( 27) link_NAG-ASN : bond 0.00647 ( 51) link_NAG-ASN : angle 3.48743 ( 153) *********************** 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 214 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 160 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.7106 (mtm) cc_final: 0.6802 (mtm) REVERT: C 397 ILE cc_start: 0.8666 (OUTLIER) cc_final: 0.8428 (pt) REVERT: C 455 TYR cc_start: 0.8655 (p90) cc_final: 0.8283 (p90) REVERT: C 615 HIS cc_start: 0.7193 (t70) cc_final: 0.6563 (t-90) REVERT: C 620 TYR cc_start: 0.8073 (OUTLIER) cc_final: 0.7637 (m-80) outliers start: 54 outliers final: 39 residues processed: 199 average time/residue: 0.1319 time to fit residues: 43.6355 Evaluate side-chains 188 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 147 time to evaluate : 0.709 ------------------------------------------------------------------------------- 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 144 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 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 111 ILE Chi-restraints excluded: chain B residue 246 VAL 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 463 LEU 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 314 PHE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 374 VAL 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 1076 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 81 optimal weight: 0.4980 chunk 7 optimal weight: 4.9990 chunk 64 optimal weight: 8.9990 chunk 268 optimal weight: 0.6980 chunk 69 optimal weight: 0.0970 chunk 130 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 chunk 252 optimal weight: 0.0870 chunk 6 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 186 optimal weight: 8.9990 overall best weight: 1.0758 ------------------------------------------------------------------------------- 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 = 0.3583 r_free = 0.3583 target = 0.120133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.109224 restraints weight = 45657.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.109959 restraints weight = 35809.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.110362 restraints weight = 30717.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.110949 restraints weight = 27671.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.111093 restraints weight = 24357.319| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 25059 Z= 0.112 Angle : 0.590 11.076 34227 Z= 0.284 Chirality : 0.047 0.377 4104 Planarity : 0.003 0.056 4278 Dihedral : 7.109 87.991 4565 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.70 % Allowed : 14.34 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.15), residues: 2988 helix: 1.72 (0.21), residues: 648 sheet: -0.46 (0.21), residues: 582 loop : -1.88 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 173 TYR 0.017 0.001 TYR A 455 PHE 0.018 0.001 PHE B 842 TRP 0.010 0.001 TRP A 66 HIS 0.005 0.001 HIS C1002 Details of bonding type rmsd covalent geometry : bond 0.00248 (24963) covalent geometry : angle 0.53252 (33975) SS BOND : bond 0.00376 ( 36) SS BOND : angle 1.65176 ( 72) hydrogen bonds : bond 0.03494 ( 880) hydrogen bonds : angle 4.98650 ( 2520) link_BETA1-4 : bond 0.01078 ( 9) link_BETA1-4 : angle 3.40949 ( 27) link_NAG-ASN : bond 0.00672 ( 51) link_NAG-ASN : angle 3.40084 ( 153) *********************** 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 211 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 166 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.7080 (mtm) cc_final: 0.6762 (mtm) REVERT: A 620 TYR cc_start: 0.7811 (OUTLIER) cc_final: 0.7439 (m-10) REVERT: B 173 ARG cc_start: 0.3655 (ttt-90) cc_final: 0.3074 (mtp180) REVERT: C 397 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8398 (pt) REVERT: C 455 TYR cc_start: 0.8621 (p90) cc_final: 0.8295 (p90) REVERT: C 615 HIS cc_start: 0.7301 (t70) cc_final: 0.6660 (t-90) REVERT: C 741 GLN cc_start: 0.8416 (mp10) cc_final: 0.8079 (mm-40) outliers start: 45 outliers final: 35 residues processed: 196 average time/residue: 0.1375 time to fit residues: 44.9595 Evaluate side-chains 191 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 154 time to evaluate : 0.810 ------------------------------------------------------------------------------- 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 246 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain A residue 670 THR 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 231 LEU Chi-restraints excluded: chain B residue 246 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 1002 HIS Chi-restraints excluded: chain B residue 1051 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 231 LEU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 314 PHE 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 568 VAL Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 863 ILE Chi-restraints excluded: chain C residue 1076 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 270 optimal weight: 7.9990 chunk 42 optimal weight: 7.9990 chunk 221 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 102 optimal weight: 0.4980 chunk 109 optimal weight: 7.9990 chunk 58 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 23 optimal weight: 0.0670 chunk 44 optimal weight: 3.9990 chunk 189 optimal weight: 1.9990 overall best weight: 2.9124 ------------------------------------------------------------------------------- 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 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 = 0.3530 r_free = 0.3530 target = 0.116497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.105540 restraints weight = 46269.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.105910 restraints weight = 36975.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.106842 restraints weight = 32908.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.107128 restraints weight = 28440.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.107168 restraints weight = 25836.638| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 25059 Z= 0.203 Angle : 0.669 11.851 34227 Z= 0.325 Chirality : 0.050 0.404 4104 Planarity : 0.004 0.050 4278 Dihedral : 7.315 67.054 4565 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 2.16 % Allowed : 14.45 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.15), residues: 2988 helix: 1.55 (0.21), residues: 648 sheet: -0.65 (0.21), residues: 594 loop : -1.94 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 527 TYR 0.020 0.002 TYR A 455 PHE 0.020 0.002 PHE B 842 TRP 0.012 0.002 TRP A 415 HIS 0.011 0.001 HIS C1002 Details of bonding type rmsd covalent geometry : bond 0.00478 (24963) covalent geometry : angle 0.61502 (33975) SS BOND : bond 0.00380 ( 36) SS BOND : angle 1.73857 ( 72) hydrogen bonds : bond 0.04020 ( 880) hydrogen bonds : angle 5.13592 ( 2520) link_BETA1-4 : bond 0.00913 ( 9) link_BETA1-4 : angle 3.84845 ( 27) link_NAG-ASN : bond 0.00658 ( 51) link_NAG-ASN : angle 3.49322 ( 153) *********************** 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 209 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 152 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.7229 (mtm) cc_final: 0.6904 (mtm) REVERT: A 620 TYR cc_start: 0.7879 (OUTLIER) cc_final: 0.7571 (m-10) REVERT: B 620 TYR cc_start: 0.7988 (OUTLIER) cc_final: 0.7589 (m-10) REVERT: C 455 TYR cc_start: 0.8498 (p90) cc_final: 0.8230 (p90) REVERT: C 615 HIS cc_start: 0.7267 (t70) cc_final: 0.6729 (t-90) REVERT: C 620 TYR cc_start: 0.8103 (OUTLIER) cc_final: 0.7731 (m-80) outliers start: 57 outliers final: 46 residues processed: 195 average time/residue: 0.1310 time to fit residues: 42.6159 Evaluate side-chains 194 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 145 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 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 854 MET Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain B residue 63 TYR Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 111 ILE 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 580 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 1051 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 216 TRP Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 314 PHE 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 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 214 optimal weight: 0.8980 chunk 213 optimal weight: 8.9990 chunk 270 optimal weight: 6.9990 chunk 217 optimal weight: 6.9990 chunk 169 optimal weight: 0.9980 chunk 207 optimal weight: 0.7980 chunk 101 optimal weight: 10.0000 chunk 127 optimal weight: 3.9990 chunk 116 optimal weight: 0.4980 chunk 24 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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 615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.118492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.106498 restraints weight = 46126.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.108369 restraints weight = 34846.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.109824 restraints weight = 26196.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.110242 restraints weight = 20712.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.110830 restraints weight = 17993.890| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2052 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= 0.118 Angle : 0.595 11.112 34227 Z= 0.289 Chirality : 0.047 0.377 4104 Planarity : 0.003 0.049 4278 Dihedral : 6.687 57.489 4563 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.27 % Allowed : 14.95 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.15), residues: 2988 helix: 1.75 (0.22), residues: 627 sheet: -0.57 (0.21), residues: 588 loop : -1.86 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 173 TYR 0.018 0.001 TYR A 455 PHE 0.012 0.001 PHE A 53 TRP 0.013 0.001 TRP A 62 HIS 0.005 0.001 HIS C1002 Details of bonding type rmsd covalent geometry : bond 0.00267 (24963) covalent geometry : angle 0.53905 (33975) SS BOND : bond 0.00371 ( 36) SS BOND : angle 1.61115 ( 72) hydrogen bonds : bond 0.03562 ( 880) hydrogen bonds : angle 5.03928 ( 2520) link_BETA1-4 : bond 0.00917 ( 9) link_BETA1-4 : angle 3.10171 ( 27) link_NAG-ASN : bond 0.00685 ( 51) link_NAG-ASN : angle 3.41570 ( 153) *********************** 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 228 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 168 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.7234 (mtm) cc_final: 0.6907 (mtm) REVERT: A 620 TYR cc_start: 0.7909 (OUTLIER) cc_final: 0.7428 (m-10) REVERT: B 173 ARG cc_start: 0.3497 (ttt-90) cc_final: 0.3111 (mtp180) REVERT: B 620 TYR cc_start: 0.7968 (OUTLIER) cc_final: 0.7574 (m-10) REVERT: C 455 TYR cc_start: 0.8459 (p90) cc_final: 0.8229 (p90) REVERT: C 615 HIS cc_start: 0.7351 (t70) cc_final: 0.6785 (t-90) REVERT: C 620 TYR cc_start: 0.8076 (OUTLIER) cc_final: 0.7545 (m-10) REVERT: C 741 GLN cc_start: 0.8462 (mp10) cc_final: 0.8123 (mm-40) outliers start: 60 outliers final: 48 residues processed: 211 average time/residue: 0.1352 time to fit residues: 47.1628 Evaluate side-chains 212 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 161 time to evaluate : 0.836 ------------------------------------------------------------------------------- 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 246 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 351 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 580 VAL Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 854 MET Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain B residue 63 TYR Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 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 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 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 314 PHE 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 189 optimal weight: 0.9980 chunk 76 optimal weight: 7.9990 chunk 83 optimal weight: 8.9990 chunk 268 optimal weight: 0.9980 chunk 269 optimal weight: 0.0670 chunk 81 optimal weight: 0.1980 chunk 58 optimal weight: 0.1980 chunk 33 optimal weight: 0.6980 chunk 123 optimal weight: 0.6980 chunk 125 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 overall best weight: 0.3718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 604 GLN B 604 GLN ** B 615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 716 GLN B 728 GLN B1062 ASN C 604 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.121400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.109761 restraints weight = 45775.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.111418 restraints weight = 32367.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.112582 restraints weight = 24901.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.113285 restraints weight = 20433.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.113987 restraints weight = 17757.704| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 25059 Z= 0.096 Angle : 0.563 10.683 34227 Z= 0.273 Chirality : 0.047 0.360 4104 Planarity : 0.003 0.050 4278 Dihedral : 6.069 55.806 4563 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 1.93 % Allowed : 15.47 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.15), residues: 2988 helix: 1.94 (0.22), residues: 627 sheet: -0.28 (0.22), residues: 579 loop : -1.74 (0.14), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 173 TYR 0.015 0.001 TYR A 455 PHE 0.018 0.001 PHE A 842 TRP 0.015 0.001 TRP A 66 HIS 0.006 0.001 HIS B1002 Details of bonding type rmsd covalent geometry : bond 0.00206 (24963) covalent geometry : angle 0.51083 (33975) SS BOND : bond 0.00271 ( 36) SS BOND : angle 1.23874 ( 72) hydrogen bonds : bond 0.03218 ( 880) hydrogen bonds : angle 4.88754 ( 2520) link_BETA1-4 : bond 0.01008 ( 9) link_BETA1-4 : angle 2.88368 ( 27) link_NAG-ASN : bond 0.00682 ( 51) link_NAG-ASN : angle 3.29568 ( 153) *********************** 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 232 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 181 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.6957 (mtm) cc_final: 0.6639 (mtm) REVERT: A 173 ARG cc_start: 0.3311 (mtp180) cc_final: 0.3001 (mtp180) REVERT: A 809 PHE cc_start: 0.5005 (OUTLIER) cc_final: 0.4162 (m-80) REVERT: B 173 ARG cc_start: 0.3555 (ttt-90) cc_final: 0.3167 (mtp180) REVERT: C 31 MET cc_start: 0.6952 (mtm) cc_final: 0.6502 (mtm) REVERT: C 455 TYR cc_start: 0.8417 (p90) cc_final: 0.8161 (p90) REVERT: C 582 THR cc_start: 0.8277 (m) cc_final: 0.7645 (p) REVERT: C 615 HIS cc_start: 0.7314 (t70) cc_final: 0.6724 (t-90) REVERT: C 741 GLN cc_start: 0.8467 (mp10) cc_final: 0.8105 (mm-40) outliers start: 51 outliers final: 41 residues processed: 216 average time/residue: 0.1324 time to fit residues: 47.3276 Evaluate side-chains 203 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 161 time to evaluate : 0.625 ------------------------------------------------------------------------------- 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 246 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 351 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 809 PHE Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain B residue 63 TYR Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 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 494 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 117 VAL Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 216 TRP Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 314 PHE 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 1076 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 240 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 167 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 231 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 188 optimal weight: 7.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 728 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 615 HIS ** 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 = 0.3522 r_free = 0.3522 target = 0.115970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.104268 restraints weight = 46428.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.105820 restraints weight = 34615.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.106714 restraints weight = 27172.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.107213 restraints weight = 22256.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.107379 restraints weight = 20379.342| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 25059 Z= 0.190 Angle : 0.650 11.158 34227 Z= 0.317 Chirality : 0.049 0.390 4104 Planarity : 0.003 0.047 4278 Dihedral : 6.643 59.928 4563 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 1.89 % Allowed : 15.93 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.15), residues: 2988 helix: 1.75 (0.22), residues: 627 sheet: -0.53 (0.21), residues: 588 loop : -1.83 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 527 TYR 0.020 0.001 TYR A 455 PHE 0.025 0.002 PHE A 603 TRP 0.012 0.002 TRP A 415 HIS 0.013 0.001 HIS A1002 Details of bonding type rmsd covalent geometry : bond 0.00444 (24963) covalent geometry : angle 0.59818 (33975) SS BOND : bond 0.00374 ( 36) SS BOND : angle 1.74286 ( 72) hydrogen bonds : bond 0.03869 ( 880) hydrogen bonds : angle 5.05511 ( 2520) link_BETA1-4 : bond 0.00896 ( 9) link_BETA1-4 : angle 3.36400 ( 27) link_NAG-ASN : bond 0.00666 ( 51) link_NAG-ASN : angle 3.40334 ( 153) ********************** 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 203 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 153 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.7300 (mtm) cc_final: 0.6981 (mtm) REVERT: A 173 ARG cc_start: 0.3309 (mtp180) cc_final: 0.2953 (mtp180) REVERT: A 407 ASP cc_start: 0.7350 (p0) cc_final: 0.7097 (p0) REVERT: A 620 TYR cc_start: 0.7875 (OUTLIER) cc_final: 0.7378 (m-10) REVERT: B 173 ARG cc_start: 0.3604 (ttt-90) cc_final: 0.3192 (mtp-110) REVERT: B 620 TYR cc_start: 0.8014 (OUTLIER) cc_final: 0.7548 (m-10) REVERT: C 582 THR cc_start: 0.8325 (m) cc_final: 0.7689 (p) REVERT: C 615 HIS cc_start: 0.7341 (t70) cc_final: 0.6727 (t-90) outliers start: 50 outliers final: 44 residues processed: 192 average time/residue: 0.1370 time to fit residues: 43.8528 Evaluate side-chains 196 residues out of total 2643 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 150 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain A residue 854 MET Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 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 1051 SER Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 216 TRP Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 314 PHE 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 568 VAL Chi-restraints excluded: chain C residue 586 LEU 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 201 optimal weight: 8.9990 chunk 258 optimal weight: 0.3980 chunk 287 optimal weight: 9.9990 chunk 70 optimal weight: 0.0370 chunk 257 optimal weight: 7.9990 chunk 129 optimal weight: 5.9990 chunk 186 optimal weight: 3.9990 chunk 293 optimal weight: 3.9990 chunk 241 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 231 optimal weight: 0.0270 overall best weight: 1.6920 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.117160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.105668 restraints weight = 46389.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.107148 restraints weight = 33791.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.108177 restraints weight = 25484.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.108590 restraints weight = 21478.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.108747 restraints weight = 19239.221| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25059 Z= 0.138 Angle : 0.617 11.179 34227 Z= 0.300 Chirality : 0.048 0.370 4104 Planarity : 0.003 0.048 4278 Dihedral : 6.510 58.654 4563 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 1.93 % Allowed : 16.12 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.15), residues: 2988 helix: 1.81 (0.22), residues: 627 sheet: -0.55 (0.21), residues: 588 loop : -1.79 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 173 TYR 0.019 0.001 TYR A 455 PHE 0.022 0.001 PHE A 603 TRP 0.013 0.001 TRP A 66 HIS 0.008 0.001 HIS C1002 Details of bonding type rmsd covalent geometry : bond 0.00317 (24963) covalent geometry : angle 0.56404 (33975) SS BOND : bond 0.00373 ( 36) SS BOND : angle 1.60771 ( 72) hydrogen bonds : bond 0.03608 ( 880) hydrogen bonds : angle 5.03043 ( 2520) link_BETA1-4 : bond 0.00971 ( 9) link_BETA1-4 : angle 3.18528 ( 27) link_NAG-ASN : bond 0.00668 ( 51) link_NAG-ASN : angle 3.40782 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2552.69 seconds wall clock time: 45 minutes 32.55 seconds (2732.55 seconds total)