Starting phenix.real_space_refine on Mon Aug 25 23:01:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y88_39037/08_2025/8y88_39037.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y88_39037/08_2025/8y88_39037.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y88_39037/08_2025/8y88_39037.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y88_39037/08_2025/8y88_39037.map" model { file = "/net/cci-nas-00/data/ceres_data/8y88_39037/08_2025/8y88_39037.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y88_39037/08_2025/8y88_39037.cif" } resolution = 3.03 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= 0.002 sd= 0.032 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 194 5.16 5 C 19941 2.51 5 N 5094 2.21 5 O 6028 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31257 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 9152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1184, 9152 Classifications: {'peptide': 1184} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 3, 'PTRANS': 53, 'TRANS': 1127} Chain breaks: 3 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 2, 'TYR:plan': 1, 'ARG:plan': 3, 'ASP:plan': 3, 'TRP:plan': 1, 'GLU:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 56 Chain: "C" Number of atoms: 9037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1179, 9037 Classifications: {'peptide': 1179} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PCIS': 3, 'PTRANS': 53, 'TRANS': 1122} Chain breaks: 5 Unresolved non-hydrogen bonds: 183 Unresolved non-hydrogen angles: 227 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 6, 'HIS:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 6, 'GLN:plan1': 4, 'PHE:plan': 1, 'TYR:plan': 2, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 128 Chain: "B" Number of atoms: 9239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1194, 9239 Classifications: {'peptide': 1194} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 3, 'PTRANS': 53, 'TRANS': 1137} Chain breaks: 2 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 4, 'TYR:plan': 2, 'ARG:plan': 1, 'GLU:plan': 2, 'ASP:plan': 1, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "T" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1727 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 14, 'TRANS': 222} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 109 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 2, 'PHE:plan': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 80 Chain: "I" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1727 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 14, 'TRANS': 222} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 109 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 2, 'PHE:plan': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 80 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 7.85, per 1000 atoms: 0.25 Number of scatterers: 31257 At special positions: 0 Unit cell: (156.62, 137.76, 240.26, 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 194 16.00 O 6028 8.00 N 5094 7.00 C 19941 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=75, symmetry=0 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS A 156 " distance=2.03 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 163 " - pdb=" SG CYS A 242 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 292 " distance=2.03 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 352 " distance=2.03 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 423 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 603 " distance=2.03 Simple disulfide: pdb=" SG CYS A 466 " - pdb=" SG CYS A 546 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 476 " distance=2.02 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 495 " distance=2.04 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG CYS A 495 " distance=2.04 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 495 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 520 " - pdb=" SG CYS A 533 " distance=2.03 Simple disulfide: pdb=" SG CYS A 556 " - pdb=" SG CYS A 567 " distance=2.03 Simple disulfide: pdb=" SG CYS A 580 " - pdb=" SG CYS A 586 " distance=2.03 Simple disulfide: pdb=" SG CYS A 619 " - pdb=" SG CYS A 672 " distance=2.03 Simple disulfide: pdb=" SG CYS A 697 " - pdb=" SG CYS A 719 " distance=2.03 Simple disulfide: pdb=" SG CYS A 734 " - pdb=" SG CYS A 743 " distance=2.03 Simple disulfide: pdb=" SG CYS A 814 " - pdb=" SG CYS A 836 " distance=2.03 Simple disulfide: pdb=" SG CYS A 819 " - pdb=" SG CYS A 825 " distance=2.03 Simple disulfide: pdb=" SG CYS A 890 " - pdb=" SG CYS A 895 " distance=2.03 Simple disulfide: pdb=" SG CYS A 925 " - pdb=" SG CYS A 936 " distance=2.03 Simple disulfide: pdb=" SG CYS A1113 " - pdb=" SG CYS A1124 " distance=2.03 Simple disulfide: pdb=" SG CYS A1163 " - pdb=" SG CYS A1208 " distance=2.03 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS C 156 " distance=2.03 Simple disulfide: pdb=" SG CYS C 151 " - pdb=" SG CYS C 183 " distance=2.03 Simple disulfide: pdb=" SG CYS C 163 " - pdb=" SG CYS C 242 " distance=2.03 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 292 " distance=2.03 Simple disulfide: pdb=" SG CYS C 327 " - pdb=" SG CYS C 352 " distance=2.03 Simple disulfide: pdb=" SG CYS C 370 " - pdb=" SG CYS C 423 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 603 " distance=2.03 Simple disulfide: pdb=" SG CYS C 466 " - pdb=" SG CYS C 546 " distance=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 495 " distance=2.03 Simple disulfide: pdb=" SG CYS C 476 " - pdb=" SG CYS C 565 " distance=2.03 Simple disulfide: pdb=" SG CYS C 485 " - pdb=" SG CYS C 516 " distance=2.03 Simple disulfide: pdb=" SG CYS C 504 " - pdb=" SG CYS C 518 " distance=2.03 Simple disulfide: pdb=" SG CYS C 520 " - pdb=" SG CYS C 533 " distance=2.03 Simple disulfide: pdb=" SG CYS C 556 " - pdb=" SG CYS C 567 " distance=2.03 Simple disulfide: pdb=" SG CYS C 619 " - pdb=" SG CYS C 672 " distance=2.03 Simple disulfide: pdb=" SG CYS C 697 " - pdb=" SG CYS C 719 " distance=2.03 Simple disulfide: pdb=" SG CYS C 734 " - pdb=" SG CYS C 743 " distance=2.03 Simple disulfide: pdb=" SG CYS C 814 " - pdb=" SG CYS C 836 " distance=2.03 Simple disulfide: pdb=" SG CYS C 819 " - pdb=" SG CYS C 825 " distance=2.03 Simple disulfide: pdb=" SG CYS C 890 " - pdb=" SG CYS C 895 " distance=2.03 Simple disulfide: pdb=" SG CYS C 925 " - pdb=" SG CYS C 936 " distance=2.03 Simple disulfide: pdb=" SG CYS C1113 " - pdb=" SG CYS C1124 " distance=2.03 Simple disulfide: pdb=" SG CYS C1163 " - pdb=" SG CYS C1208 " distance=2.03 Simple disulfide: pdb=" SG CYS B 20 " - pdb=" SG CYS B 156 " distance=2.03 Simple disulfide: pdb=" SG CYS B 151 " - pdb=" SG CYS B 183 " distance=2.03 Simple disulfide: pdb=" SG CYS B 163 " - pdb=" SG CYS B 242 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 292 " distance=2.03 Simple disulfide: pdb=" SG CYS B 327 " - pdb=" SG CYS B 352 " distance=2.03 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 423 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 603 " distance=2.03 Simple disulfide: pdb=" SG CYS B 466 " - pdb=" SG CYS B 546 " distance=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 495 " distance=2.03 Simple disulfide: pdb=" SG CYS B 476 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 485 " - pdb=" SG CYS B 516 " distance=2.03 Simple disulfide: pdb=" SG CYS B 504 " - pdb=" SG CYS B 518 " distance=2.03 Simple disulfide: pdb=" SG CYS B 520 " - pdb=" SG CYS B 533 " distance=2.03 Simple disulfide: pdb=" SG CYS B 556 " - pdb=" SG CYS B 567 " distance=2.03 Simple disulfide: pdb=" SG CYS B 619 " - pdb=" SG CYS B 672 " distance=2.03 Simple disulfide: pdb=" SG CYS B 697 " - pdb=" SG CYS B 719 " distance=2.03 Simple disulfide: pdb=" SG CYS B 734 " - pdb=" SG CYS B 743 " distance=2.03 Simple disulfide: pdb=" SG CYS B 814 " - pdb=" SG CYS B 836 " distance=2.03 Simple disulfide: pdb=" SG CYS B 819 " - pdb=" SG CYS B 825 " distance=2.03 Simple disulfide: pdb=" SG CYS B 890 " - pdb=" SG CYS B 895 " distance=2.03 Simple disulfide: pdb=" SG CYS B 925 " - pdb=" SG CYS B 936 " distance=2.03 Simple disulfide: pdb=" SG CYS B1113 " - pdb=" SG CYS B1124 " distance=2.03 Simple disulfide: pdb=" SG CYS B1163 " - pdb=" SG CYS B1208 " distance=2.03 Simple disulfide: pdb=" SG CYS T 410 " - pdb=" SG CYS T 426 " distance=2.03 Simple disulfide: pdb=" SG CYS T 437 " - pdb=" SG CYS T 465 " distance=2.03 Simple disulfide: pdb=" SG CYS I 410 " - pdb=" SG CYS I 426 " distance=2.03 Simple disulfide: pdb=" SG CYS I 437 " - pdb=" SG CYS I 465 " 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 E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG A1301 " - " ASN A 703 " " NAG A1302 " - " ASN A 335 " " NAG A1303 " - " ASN A 664 " " NAG A1304 " - " ASN A 725 " " NAG A1305 " - " ASN A 793 " " NAG A1306 " - " ASN A1211 " " NAG A1307 " - " ASN A 192 " " NAG A1308 " - " ASN A 58 " " NAG B1301 " - " ASN B 58 " " NAG B1302 " - " ASN B 192 " " NAG B1303 " - " ASN B 725 " " NAG B1304 " - " ASN B1211 " " NAG B1305 " - " ASN B 664 " " NAG C1301 " - " ASN C 58 " " NAG C1302 " - " ASN C 703 " " NAG C1303 " - " ASN C 664 " " NAG C1304 " - " ASN C 793 " " NAG C1305 " - " ASN C 192 " " NAG D 1 " - " ASN A 188 " " NAG E 1 " - " ASN C 132 " " NAG F 1 " - " ASN C 188 " " NAG G 1 " - " ASN B 188 " Time building additional restraints: 2.69 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 715.3 nanoseconds 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7566 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 71 sheets defined 21.7% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'A' and resid 112 through 116 removed outlier: 3.714A pdb=" N ASN A 115 " --> pdb=" O TYR A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 295 removed outlier: 3.536A pdb=" N GLU A 289 " --> pdb=" O SER A 285 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE A 290 " --> pdb=" O PHE A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 344 removed outlier: 3.673A pdb=" N TRP A 344 " --> pdb=" O PRO A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 363 removed outlier: 3.623A pdb=" N LEU A 359 " --> pdb=" O ASN A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 378 Processing helix chain 'A' and resid 397 through 402 removed outlier: 3.832A pdb=" N GLN A 402 " --> pdb=" O ASP A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 443 through 448 removed outlier: 4.067A pdb=" N TYR A 448 " --> pdb=" O TRP A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 704 removed outlier: 4.138A pdb=" N ASN A 702 " --> pdb=" O SER A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 819 removed outlier: 3.640A pdb=" N VAL A 818 " --> pdb=" O CYS A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 830 removed outlier: 3.876A pdb=" N HIS A 826 " --> pdb=" O TYR A 822 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP A 827 " --> pdb=" O ALA A 823 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU A 828 " --> pdb=" O ALA A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 862 removed outlier: 3.575A pdb=" N ILE A 839 " --> pdb=" O PHE A 835 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET A 862 " --> pdb=" O ALA A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 888 Processing helix chain 'A' and resid 901 through 909 removed outlier: 3.813A pdb=" N LEU A 906 " --> pdb=" O PRO A 902 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU A 907 " --> pdb=" O LEU A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 924 removed outlier: 3.916A pdb=" N VAL A 919 " --> pdb=" O ASP A 915 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN A 924 " --> pdb=" O GLU A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 942 removed outlier: 3.555A pdb=" N GLN A 938 " --> pdb=" O LEU A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 951 through 966 removed outlier: 3.615A pdb=" N ALA A 961 " --> pdb=" O GLY A 957 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA A 966 " --> pdb=" O ALA A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 990 removed outlier: 4.178A pdb=" N GLN A 984 " --> pdb=" O PRO A 980 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG A 986 " --> pdb=" O ASN A 982 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 990 " --> pdb=" O ARG A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 998 removed outlier: 3.898A pdb=" N LEU A 997 " --> pdb=" O THR A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1018 Processing helix chain 'A' and resid 1023 through 1045 removed outlier: 3.573A pdb=" N VAL A1032 " --> pdb=" O LYS A1028 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A1033 " --> pdb=" O ILE A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1049 removed outlier: 3.597A pdb=" N ASN A1049 " --> pdb=" O GLN A1046 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1046 through 1049' Processing helix chain 'A' and resid 1057 through 1065 removed outlier: 3.546A pdb=" N ILE A1061 " --> pdb=" O SER A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1113 removed outlier: 3.789A pdb=" N ARG A1076 " --> pdb=" O VAL A1072 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A1077 " --> pdb=" O GLN A1073 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR A1083 " --> pdb=" O ASN A1079 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR A1097 " --> pdb=" O LEU A1093 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU A1098 " --> pdb=" O SER A1094 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG A1105 " --> pdb=" O ALA A1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 91 removed outlier: 3.672A pdb=" N TYR C 90 " --> pdb=" O THR C 87 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS C 91 " --> pdb=" O LEU C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 295 Processing helix chain 'C' and resid 329 through 335 removed outlier: 3.749A pdb=" N LEU C 333 " --> pdb=" O ASP C 330 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN C 335 " --> pdb=" O TRP C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 360 removed outlier: 3.753A pdb=" N LEU C 360 " --> pdb=" O LEU C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 379 removed outlier: 3.565A pdb=" N ILE C 378 " --> pdb=" O ASP C 374 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE C 379 " --> pdb=" O LYS C 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 374 through 379' Processing helix chain 'C' and resid 409 through 413 Processing helix chain 'C' and resid 478 through 483 removed outlier: 3.512A pdb=" N VAL C 482 " --> pdb=" O ASP C 478 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN C 483 " --> pdb=" O PRO C 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 478 through 483' Processing helix chain 'C' and resid 553 through 556 Processing helix chain 'C' and resid 568 through 570 No H-bonds generated for 'chain 'C' and resid 568 through 570' Processing helix chain 'C' and resid 696 through 704 removed outlier: 4.192A pdb=" N ASN C 702 " --> pdb=" O SER C 698 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 831 removed outlier: 3.558A pdb=" N HIS C 826 " --> pdb=" O TYR C 822 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU C 828 " --> pdb=" O ALA C 824 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLU C 831 " --> pdb=" O ASP C 827 " (cutoff:3.500A) Processing helix chain 'C' and resid 834 through 862 removed outlier: 3.579A pdb=" N ILE C 839 " --> pdb=" O PHE C 835 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 888 Processing helix chain 'C' and resid 901 through 909 removed outlier: 3.928A pdb=" N LEU C 906 " --> pdb=" O PRO C 902 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU C 907 " --> pdb=" O LEU C 903 " (cutoff:3.500A) Processing helix chain 'C' and resid 914 through 924 removed outlier: 3.944A pdb=" N VAL C 919 " --> pdb=" O ASP C 915 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN C 924 " --> pdb=" O GLU C 920 " (cutoff:3.500A) Processing helix chain 'C' and resid 935 through 940 Processing helix chain 'C' and resid 953 through 965 removed outlier: 3.643A pdb=" N ALA C 962 " --> pdb=" O TYR C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 989 Processing helix chain 'C' and resid 993 through 1000 removed outlier: 3.830A pdb=" N LEU C 997 " --> pdb=" O THR C 993 " (cutoff:3.500A) Processing helix chain 'C' and resid 1000 through 1018 removed outlier: 3.504A pdb=" N ILE C1004 " --> pdb=" O ASN C1000 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA C1005 " --> pdb=" O GLN C1001 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN C1006 " --> pdb=" O LYS C1002 " (cutoff:3.500A) Processing helix chain 'C' and resid 1023 through 1046 removed outlier: 3.871A pdb=" N VAL C1033 " --> pdb=" O ILE C1029 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN C1036 " --> pdb=" O VAL C1032 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN C1046 " --> pdb=" O SER C1042 " (cutoff:3.500A) Processing helix chain 'C' and resid 1047 through 1049 No H-bonds generated for 'chain 'C' and resid 1047 through 1049' Processing helix chain 'C' and resid 1057 through 1063 Processing helix chain 'C' and resid 1066 through 1114 removed outlier: 3.588A pdb=" N GLN C1071 " --> pdb=" O PRO C1067 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N VAL C1072 " --> pdb=" O PRO C1068 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLN C1073 " --> pdb=" O GLU C1069 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG C1076 " --> pdb=" O VAL C1072 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU C1077 " --> pdb=" O GLN C1073 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER C1094 " --> pdb=" O SER C1090 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N THR C1097 " --> pdb=" O LEU C1093 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU C1098 " --> pdb=" O SER C1094 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.642A pdb=" N ILE B 290 " --> pdb=" O PHE B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 334 removed outlier: 4.053A pdb=" N TRP B 332 " --> pdb=" O ASP B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 363 Processing helix chain 'B' and resid 397 through 402 removed outlier: 3.733A pdb=" N LEU B 401 " --> pdb=" O ARG B 398 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN B 402 " --> pdb=" O ASP B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 413 Processing helix chain 'B' and resid 445 through 449 Processing helix chain 'B' and resid 481 through 485 removed outlier: 3.571A pdb=" N SER B 484 " --> pdb=" O VAL B 481 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N CYS B 485 " --> pdb=" O VAL B 482 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 481 through 485' Processing helix chain 'B' and resid 553 through 556 removed outlier: 3.678A pdb=" N CYS B 556 " --> pdb=" O GLU B 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 553 through 556' Processing helix chain 'B' and resid 568 through 570 No H-bonds generated for 'chain 'B' and resid 568 through 570' Processing helix chain 'B' and resid 699 through 704 Processing helix chain 'B' and resid 822 through 830 removed outlier: 3.623A pdb=" N HIS B 826 " --> pdb=" O TYR B 822 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU B 828 " --> pdb=" O ALA B 824 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 833 No H-bonds generated for 'chain 'B' and resid 831 through 833' Processing helix chain 'B' and resid 836 through 863 Processing helix chain 'B' and resid 884 through 888 Processing helix chain 'B' and resid 901 through 909 removed outlier: 3.740A pdb=" N LEU B 906 " --> pdb=" O PRO B 902 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU B 907 " --> pdb=" O LEU B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 923 removed outlier: 3.881A pdb=" N VAL B 919 " --> pdb=" O ASP B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 933 through 940 removed outlier: 3.699A pdb=" N VAL B 937 " --> pdb=" O ASP B 933 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN B 938 " --> pdb=" O LEU B 934 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE B 940 " --> pdb=" O CYS B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 951 through 964 removed outlier: 3.539A pdb=" N ALA B 961 " --> pdb=" O GLY B 957 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA B 962 " --> pdb=" O TYR B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 968 removed outlier: 3.946A pdb=" N PHE B 968 " --> pdb=" O ALA B 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 965 through 968' Processing helix chain 'B' and resid 978 through 989 Processing helix chain 'B' and resid 993 through 1000 removed outlier: 3.700A pdb=" N LEU B 997 " --> pdb=" O THR B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1000 through 1018 removed outlier: 3.518A pdb=" N ASN B1009 " --> pdb=" O ALA B1005 " (cutoff:3.500A) Processing helix chain 'B' and resid 1023 through 1045 removed outlier: 3.523A pdb=" N VAL B1032 " --> pdb=" O LYS B1028 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL B1033 " --> pdb=" O ILE B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1046 through 1049 removed outlier: 3.654A pdb=" N ASN B1049 " --> pdb=" O GLN B1046 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1046 through 1049' Processing helix chain 'B' and resid 1057 through 1065 removed outlier: 3.556A pdb=" N ILE B1061 " --> pdb=" O SER B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1066 through 1114 removed outlier: 4.361A pdb=" N GLN B1071 " --> pdb=" O PRO B1067 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N VAL B1072 " --> pdb=" O PRO B1068 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLN B1073 " --> pdb=" O GLU B1069 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG B1076 " --> pdb=" O VAL B1072 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU B1077 " --> pdb=" O GLN B1073 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B1093 " --> pdb=" O VAL B1089 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER B1094 " --> pdb=" O SER B1090 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR B1097 " --> pdb=" O LEU B1093 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU B1098 " --> pdb=" O SER B1094 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG B1105 " --> pdb=" O ALA B1101 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL B1114 " --> pdb=" O VAL B1110 " (cutoff:3.500A) Processing helix chain 'T' and resid 299 through 303 Processing helix chain 'T' and resid 406 through 411 Processing helix chain 'T' and resid 480 through 492 Processing helix chain 'I' and resid 299 through 303 Processing helix chain 'I' and resid 406 through 411 Processing helix chain 'I' and resid 480 through 492 removed outlier: 3.842A pdb=" N GLY I 492 " --> pdb=" O MET I 488 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 55 removed outlier: 5.471A pdb=" N VAL A 55 " --> pdb=" O TYR B 649 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU B 648 " --> pdb=" O ILE B 656 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE B 658 " --> pdb=" O TYR B 667 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS B 665 " --> pdb=" O ASP B 660 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 67 removed outlier: 3.686A pdb=" N SER A 262 " --> pdb=" O PHE A 67 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N GLN A 265 " --> pdb=" O ASP A 281 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ASP A 281 " --> pdb=" O GLN A 265 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU A 267 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA A 279 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ASN A 269 " --> pdb=" O THR A 277 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 80 through 81 removed outlier: 6.442A pdb=" N THR A 161 " --> pdb=" O THR A 241 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 96 through 97 removed outlier: 3.772A pdb=" N SER A 96 " --> pdb=" O TYR A 235 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N TYR A 235 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 124 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE A 145 " --> pdb=" O HIS A 142 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHE A 185 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 221 through 226 removed outlier: 5.203A pdb=" N PHE A 222 " --> pdb=" O TYR A 213 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N TYR A 213 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N PHE A 224 " --> pdb=" O ALA A 211 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA A 211 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR A 203 " --> pdb=" O TYR A 210 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 110 through 111 Processing sheet with id=AA7, first strand: chain 'A' and resid 302 through 305 removed outlier: 3.738A pdb=" N TYR A 692 " --> pdb=" O CYS A 719 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N CYS A 719 " --> pdb=" O TYR A 692 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE A 713 " --> pdb=" O VAL A 720 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 316 through 319 removed outlier: 3.795A pdb=" N VAL A 620 " --> pdb=" O GLY A 631 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLY A 631 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR A 622 " --> pdb=" O GLY A 629 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY A 629 " --> pdb=" O TYR A 622 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N THR A 666 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE A 658 " --> pdb=" O TYR A 667 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ILE A 656 " --> pdb=" O ILE A 669 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU A 648 " --> pdb=" O ILE A 656 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 346 through 348 removed outlier: 3.503A pdb=" N ARG A 347 " --> pdb=" O VAL A 388 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL A 388 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N PHE A 383 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE A 597 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLN A 424 " --> pdb=" O PHE A 368 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N PHE A 368 " --> pdb=" O GLN A 424 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N TYR A 426 " --> pdb=" O ASP A 366 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 353 through 354 Processing sheet with id=AB2, first strand: chain 'A' and resid 461 through 463 Processing sheet with id=AB3, first strand: chain 'A' and resid 467 through 468 Processing sheet with id=AB4, first strand: chain 'A' and resid 556 through 557 removed outlier: 4.084A pdb=" N PHE A 566 " --> pdb=" O GLY A 557 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 724 through 731 removed outlier: 6.521A pdb=" N VAL A 724 " --> pdb=" O PHE A 764 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N THR A 766 " --> pdb=" O VAL A 724 " (cutoff:3.500A) removed outlier: 9.990A pdb=" N LEU A 726 " --> pdb=" O THR A 766 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 773 through 775 removed outlier: 6.035A pdb=" N SER A 773 " --> pdb=" O LEU C 867 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 786 through 791 Processing sheet with id=AB8, first strand: chain 'A' and resid 794 through 803 Processing sheet with id=AB9, first strand: chain 'A' and resid 809 through 812 removed outlier: 4.450A pdb=" N LYS A 809 " --> pdb=" O LEU A 946 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS A 944 " --> pdb=" O THR A 811 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 866 through 868 removed outlier: 6.620A pdb=" N LEU A 867 " --> pdb=" O VAL B 775 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 878 through 879 removed outlier: 3.508A pdb=" N VAL A 879 " --> pdb=" O ILE A 882 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1162 through 1163 Processing sheet with id=AC4, first strand: chain 'A' and resid 1169 through 1172 Processing sheet with id=AC5, first strand: chain 'A' and resid 1175 through 1179 Processing sheet with id=AC6, first strand: chain 'C' and resid 60 through 67 removed outlier: 3.697A pdb=" N SER C 262 " --> pdb=" O PHE C 67 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ASN C 278 " --> pdb=" O ASN C 269 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 75 through 76 removed outlier: 3.611A pdb=" N PHE C 224 " --> pdb=" O ALA C 211 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N TYR C 213 " --> pdb=" O PHE C 222 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N PHE C 222 " --> pdb=" O TYR C 213 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 96 through 97 removed outlier: 3.573A pdb=" N SER C 96 " --> pdb=" O TYR C 235 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR C 235 " --> pdb=" O SER C 96 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE C 148 " --> pdb=" O LYS C 187 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 110 through 112 Processing sheet with id=AD1, first strand: chain 'C' and resid 155 through 160 removed outlier: 10.942A pdb=" N TYR C 158 " --> pdb=" O HIS C 175 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N HIS C 175 " --> pdb=" O TYR C 158 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N HIS C 160 " --> pdb=" O SER C 173 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER C 173 " --> pdb=" O HIS C 160 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 302 through 305 removed outlier: 3.713A pdb=" N TYR C 692 " --> pdb=" O CYS C 719 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N CYS C 719 " --> pdb=" O TYR C 692 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE C 713 " --> pdb=" O VAL C 720 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 309 through 310 removed outlier: 3.509A pdb=" N PHE C 309 " --> pdb=" O GLY C 675 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY C 675 " --> pdb=" O PHE C 309 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'C' and resid 337 through 338 Processing sheet with id=AD5, first strand: chain 'C' and resid 346 through 349 removed outlier: 4.026A pdb=" N ARG C 347 " --> pdb=" O VAL C 388 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL C 388 " --> pdb=" O ARG C 347 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER C 385 " --> pdb=" O ASN C 595 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN C 595 " --> pdb=" O SER C 385 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR C 387 " --> pdb=" O ILE C 593 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR C 427 " --> pdb=" O ILE C 588 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE C 592 " --> pdb=" O CYS C 423 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N SER C 428 " --> pdb=" O VAL C 365 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N VAL C 365 " --> pdb=" O SER C 428 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 382 through 383 Processing sheet with id=AD7, first strand: chain 'C' and resid 459 through 463 removed outlier: 3.984A pdb=" N SER C 576 " --> pdb=" O TYR C 462 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 467 through 468 removed outlier: 3.821A pdb=" N LYS C 536 " --> pdb=" O SER C 468 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 504 through 506 Processing sheet with id=AE1, first strand: chain 'C' and resid 550 through 551 removed outlier: 3.523A pdb=" N GLY C 550 " --> pdb=" O LEU C 573 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 619 through 620 removed outlier: 3.947A pdb=" N GLY C 657 " --> pdb=" O LEU C 648 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 724 through 731 removed outlier: 6.230A pdb=" N ASN C 725 " --> pdb=" O TYR C 762 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE C 764 " --> pdb=" O ASN C 725 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N THR C 766 " --> pdb=" O THR C 727 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TYR C 729 " --> pdb=" O THR C 766 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N PHE C 742 " --> pdb=" O MET C 738 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU C 736 " --> pdb=" O ILE C 744 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 773 through 775 removed outlier: 6.080A pdb=" N SER C 773 " --> pdb=" O LEU B 867 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'C' and resid 786 through 803 removed outlier: 7.007A pdb=" N GLU C 787 " --> pdb=" O LEU C1157 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N LEU C1157 " --> pdb=" O GLU C 787 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLN C 789 " --> pdb=" O THR C1155 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR C1155 " --> pdb=" O GLN C 789 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N PHE C1153 " --> pdb=" O PRO C 791 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ASN C 793 " --> pdb=" O THR C1151 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA C1137 " --> pdb=" O GLY C1140 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU C1131 " --> pdb=" O PHE C1146 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TYR C1148 " --> pdb=" O HIS C1129 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N HIS C1129 " --> pdb=" O TYR C1148 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 809 through 811 removed outlier: 4.480A pdb=" N LYS C 809 " --> pdb=" O LEU C 946 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS C 944 " --> pdb=" O THR C 811 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1202 through 1205 removed outlier: 3.532A pdb=" N GLY C1169 " --> pdb=" O MET C1205 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG C1168 " --> pdb=" O LEU C1164 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1175 through 1179 Processing sheet with id=AE9, first strand: chain 'B' and resid 35 through 39 removed outlier: 8.078A pdb=" N SER B 36 " --> pdb=" O ASP B 76 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N ASP B 76 " --> pdb=" O SER B 36 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ASP B 38 " --> pdb=" O PHE B 74 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N PHE B 74 " --> pdb=" O ASP B 38 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N ASN B 73 " --> pdb=" O PRO B 260 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA B 211 " --> pdb=" O PHE B 224 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE B 224 " --> pdb=" O ALA B 211 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N TYR B 213 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N PHE B 222 " --> pdb=" O TYR B 213 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 63 through 67 Processing sheet with id=AF2, first strand: chain 'B' and resid 96 through 97 removed outlier: 3.725A pdb=" N SER B 96 " --> pdb=" O TYR B 235 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR B 235 " --> pdb=" O SER B 96 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N THR B 123 " --> pdb=" O MET B 238 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE B 124 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN B 140 " --> pdb=" O GLU B 147 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N PHE B 185 " --> pdb=" O ALA B 150 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 109 through 113 removed outlier: 3.952A pdb=" N THR B 109 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU B 120 " --> pdb=" O THR B 109 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 161 through 162 removed outlier: 6.701A pdb=" N THR B 161 " --> pdb=" O THR B 241 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'B' and resid 302 through 305 Processing sheet with id=AF6, first strand: chain 'B' and resid 317 through 319 removed outlier: 7.455A pdb=" N VAL B 317 " --> pdb=" O ASP B 623 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY B 631 " --> pdb=" O VAL B 620 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'B' and resid 337 through 339 Processing sheet with id=AF8, first strand: chain 'B' and resid 346 through 350 removed outlier: 3.616A pdb=" N ARG B 347 " --> pdb=" O VAL B 388 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL B 388 " --> pdb=" O ARG B 347 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER B 385 " --> pdb=" O ASN B 595 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR B 427 " --> pdb=" O ILE B 588 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N SER B 422 " --> pdb=" O CYS B 370 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N CYS B 370 " --> pdb=" O SER B 422 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N GLN B 424 " --> pdb=" O PHE B 368 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N PHE B 368 " --> pdb=" O GLN B 424 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N TYR B 426 " --> pdb=" O ASP B 366 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'B' and resid 346 through 350 removed outlier: 3.616A pdb=" N ARG B 347 " --> pdb=" O VAL B 388 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL B 388 " --> pdb=" O ARG B 347 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER B 385 " --> pdb=" O ASN B 595 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'B' and resid 382 through 383 Processing sheet with id=AG2, first strand: chain 'B' and resid 459 through 463 removed outlier: 3.521A pdb=" N TYR B 462 " --> pdb=" O SER B 576 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 467 through 468 removed outlier: 3.785A pdb=" N LYS B 536 " --> pdb=" O SER B 468 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'B' and resid 504 through 506 Processing sheet with id=AG5, first strand: chain 'B' and resid 550 through 551 removed outlier: 3.893A pdb=" N GLY B 550 " --> pdb=" O LEU B 573 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 573 " --> pdb=" O GLY B 550 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'B' and resid 730 through 731 removed outlier: 6.883A pdb=" N PHE B 742 " --> pdb=" O MET B 738 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'B' and resid 786 through 791 removed outlier: 7.219A pdb=" N LEU B1157 " --> pdb=" O LYS B1179 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LYS B1179 " --> pdb=" O LEU B1157 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE B1177 " --> pdb=" O SER B1159 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'B' and resid 794 through 795 Processing sheet with id=AG9, first strand: chain 'B' and resid 798 through 803 removed outlier: 3.544A pdb=" N ALA B1137 " --> pdb=" O GLY B1140 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU B1131 " --> pdb=" O PHE B1146 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'B' and resid 809 through 812 removed outlier: 4.398A pdb=" N LYS B 809 " --> pdb=" O LEU B 946 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'B' and resid 1202 through 1204 Processing sheet with id=AH3, first strand: chain 'T' and resid 260 through 261 removed outlier: 4.276A pdb=" N ASN T 398 " --> pdb=" O GLY T 383 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY T 383 " --> pdb=" O ASN T 398 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LEU T 378 " --> pdb=" O SER T 448 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N SER T 448 " --> pdb=" O LEU T 378 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL T 446 " --> pdb=" O TRP T 380 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N SER T 382 " --> pdb=" O PRO T 444 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N GLY T 457 " --> pdb=" O PRO T 444 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'T' and resid 452 through 453 removed outlier: 3.601A pdb=" N LYS T 449 " --> pdb=" O ILE T 452 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N SER T 382 " --> pdb=" O PRO T 444 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL T 446 " --> pdb=" O TRP T 380 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N SER T 448 " --> pdb=" O LEU T 378 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LEU T 378 " --> pdb=" O SER T 448 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY T 383 " --> pdb=" O ASN T 398 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ASN T 398 " --> pdb=" O GLY T 383 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N CYS T 426 " --> pdb=" O ILE T 405 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE T 425 " --> pdb=" O TYR T 474 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR T 474 " --> pdb=" O ILE T 425 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'T' and resid 278 through 283 removed outlier: 5.034A pdb=" N HIS T 279 " --> pdb=" O VAL T 275 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL T 275 " --> pdb=" O HIS T 279 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N CYS T 281 " --> pdb=" O LEU T 273 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER T 272 " --> pdb=" O PHE T 311 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS T 330 " --> pdb=" O LYS T 350 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'I' and resid 260 through 261 removed outlier: 4.330A pdb=" N ASN I 398 " --> pdb=" O GLY I 383 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY I 383 " --> pdb=" O ASN I 398 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N LEU I 378 " --> pdb=" O SER I 448 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N SER I 448 " --> pdb=" O LEU I 378 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL I 446 " --> pdb=" O TRP I 380 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N SER I 382 " --> pdb=" O PRO I 444 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS I 449 " --> pdb=" O ILE I 452 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'I' and resid 260 through 261 removed outlier: 4.452A pdb=" N CYS I 426 " --> pdb=" O ILE I 405 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N GLY I 457 " --> pdb=" O PRO I 444 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY I 442 " --> pdb=" O THR I 459 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS I 449 " --> pdb=" O ILE I 452 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'I' and resid 278 through 283 removed outlier: 5.053A pdb=" N HIS I 279 " --> pdb=" O VAL I 275 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL I 275 " --> pdb=" O HIS I 279 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N CYS I 281 " --> pdb=" O LEU I 273 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER I 272 " --> pdb=" O PHE I 311 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS I 330 " --> pdb=" O LYS I 350 " (cutoff:3.500A) 948 hydrogen bonds defined for protein. 2586 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: 8.49 Time building geometry restraints manager: 3.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9940 1.34 - 1.46: 7852 1.46 - 1.58: 14004 1.58 - 1.70: 0 1.70 - 1.81: 229 Bond restraints: 32025 Sorted by residual: bond pdb=" C1 BMA E 3 " pdb=" C2 BMA E 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.38e+00 bond pdb=" C1 NAG B1305 " pdb=" O5 NAG B1305 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.04e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 2.02e+00 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 2.01e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 2.01e+00 ... (remaining 32020 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 42792 1.26 - 2.53: 726 2.53 - 3.79: 169 3.79 - 5.06: 16 5.06 - 6.32: 4 Bond angle restraints: 43707 Sorted by residual: angle pdb=" N ILE A 656 " pdb=" CA ILE A 656 " pdb=" C ILE A 656 " ideal model delta sigma weight residual 112.96 108.95 4.01 1.00e+00 1.00e+00 1.61e+01 angle pdb=" C ALA A 392 " pdb=" N ILE A 393 " pdb=" CA ILE A 393 " ideal model delta sigma weight residual 122.13 126.74 -4.61 1.85e+00 2.92e-01 6.20e+00 angle pdb=" CA GLY T 462 " pdb=" C GLY T 462 " pdb=" N SER T 463 " ideal model delta sigma weight residual 114.58 116.71 -2.13 8.60e-01 1.35e+00 6.15e+00 angle pdb=" N VAL B 482 " pdb=" CA VAL B 482 " pdb=" C VAL B 482 " ideal model delta sigma weight residual 113.07 109.79 3.28 1.36e+00 5.41e-01 5.82e+00 angle pdb=" N PRO B1067 " pdb=" CA PRO B1067 " pdb=" C PRO B1067 " ideal model delta sigma weight residual 110.70 113.56 -2.86 1.22e+00 6.72e-01 5.49e+00 ... (remaining 43702 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.80: 18970 21.80 - 43.60: 332 43.60 - 65.40: 37 65.40 - 87.20: 9 87.20 - 109.00: 4 Dihedral angle restraints: 19352 sinusoidal: 7575 harmonic: 11777 Sorted by residual: dihedral pdb=" CB CYS A 476 " pdb=" SG CYS A 476 " pdb=" SG CYS A 495 " pdb=" CB CYS A 495 " ideal model delta sinusoidal sigma weight residual -86.00 -4.56 -81.44 1 1.00e+01 1.00e-02 8.17e+01 dihedral pdb=" CB CYS A 495 " pdb=" SG CYS A 495 " pdb=" SG CYS A 565 " pdb=" CB CYS A 565 " ideal model delta sinusoidal sigma weight residual -86.00 -151.72 65.72 1 1.00e+01 1.00e-02 5.65e+01 dihedral pdb=" CB CYS A 474 " pdb=" SG CYS A 474 " pdb=" SG CYS A 476 " pdb=" CB CYS A 476 " ideal model delta sinusoidal sigma weight residual -86.00 -150.68 64.68 1 1.00e+01 1.00e-02 5.49e+01 ... (remaining 19349 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 4291 0.055 - 0.109: 663 0.109 - 0.164: 81 0.164 - 0.219: 0 0.219 - 0.273: 1 Chirality restraints: 5036 Sorted by residual: chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CB ILE A 393 " pdb=" CA ILE A 393 " pdb=" CG1 ILE A 393 " pdb=" CG2 ILE A 393 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.69e-01 chirality pdb=" C2 BMA E 3 " pdb=" C1 BMA E 3 " pdb=" C3 BMA E 3 " pdb=" O2 BMA E 3 " both_signs ideal model delta sigma weight residual False 2.47 2.61 -0.14 2.00e-01 2.50e+01 4.59e-01 ... (remaining 5033 not shown) Planarity restraints: 5622 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B1067 " 0.045 5.00e-02 4.00e+02 6.67e-02 7.11e+00 pdb=" N PRO B1068 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO B1068 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B1068 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B1066 " -0.024 5.00e-02 4.00e+02 3.58e-02 2.05e+00 pdb=" N PRO B1067 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO B1067 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B1067 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C1066 " -0.023 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO C1067 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO C1067 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C1067 " -0.019 5.00e-02 4.00e+02 ... (remaining 5619 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2709 2.75 - 3.29: 29656 3.29 - 3.82: 47811 3.82 - 4.36: 55404 4.36 - 4.90: 98860 Nonbonded interactions: 234440 Sorted by model distance: nonbonded pdb=" O VAL B 113 " pdb=" OG1 THR B 116 " model vdw 2.210 3.040 nonbonded pdb=" O VAL C 113 " pdb=" OG1 THR C 116 " model vdw 2.222 3.040 nonbonded pdb=" OD1 ASN A 351 " pdb=" OG1 THR A 601 " model vdw 2.251 3.040 nonbonded pdb=" OD2 ASP C 507 " pdb=" OG SER I 463 " model vdw 2.259 3.040 nonbonded pdb=" O TRP C 89 " pdb=" OH TYR C 236 " model vdw 2.265 3.040 ... (remaining 234435 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 or (resid 26 and (name N or name CA or nam \ e C or name O or name CB )) or resid 27 or (resid 28 and (name N or name CA or n \ ame C or name O or name CB )) or resid 29 or (resid 30 through 31 and (name N or \ name CA or name C or name O or name CB )) or resid 32 through 83 or (resid 84 a \ nd (name N or name CA or name C or name O or name CB )) or resid 85 through 242 \ or (resid 243 through 245 and (name N or name CA or name C or name O or name CB \ )) or resid 246 through 359 or (resid 360 through 362 and (name N or name CA or \ name C or name O or name CB )) or resid 363 or (resid 364 and (name N or name CA \ or name C or name O or name CB )) or resid 365 through 370 or (resid 371 throug \ h 375 and (name N or name CA or name C or name O or name CB )) or resid 376 or ( \ resid 377 and (name N or name CA or name C or name O or name CB )) or resid 378 \ through 395 or (resid 396 through 402 and (name N or name CA or name C or name O \ or name CB )) or (resid 408 and (name N or name CA or name C or name O or name \ CB )) or resid 409 or (resid 410 and (name N or name CA or name C or name O or n \ ame CB )) or resid 411 or (resid 412 through 413 and (name N or name CA or name \ C or name O or name CB )) or resid 422 through 430 or (resid 431 through 432 and \ (name N or name CA or name C or name O or name CB )) or resid 433 through 436 o \ r (resid 437 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 38 through 446 or resid 449 through 461 or (resid 462 through 465 and (name N or \ name CA or name C or name O or name CB )) or resid 466 through 491 or (resid 49 \ 2 through 493 and (name N or name CA or name C or name O or name CB )) or resid \ 494 through 557 or resid 563 through 584 or (resid 585 and (name N or name CA or \ name C or name O or name CB )) or resid 586 through 608 or (resid 609 and (name \ N or name CA or name C or name O or name CB )) or resid 610 through 615 or (res \ id 616 and (name N or name CA or name C or name O or name CB )) or resid 617 thr \ ough 619 or (resid 620 and (name N or name CA or name C or name O or name CB )) \ or resid 621 through 629 or (resid 630 and (name N or name CA or name C or name \ O or name CB )) or resid 631 or (resid 632 and (name N or name CA or name C or n \ ame O or name CB )) or resid 633 or (resid 634 and (name N or name CA or name C \ or name O or name CB )) or resid 635 through 651 or (resid 652 and (name N or na \ me CA or name C or name O or name CB )) or resid 653 or (resid 654 and (name N o \ r name CA or name C or name O or name CB )) or resid 655 through 659 or (resid 6 \ 60 and (name N or name CA or name C or name O or name CB )) or resid 661 through \ 708 or (resid 709 and (name N or name CA or name C or name O or name CB )) or r \ esid 710 through 779 or (resid 780 and (name N or name CA or name C or name O or \ name CB )) or resid 781 through 871 or (resid 872 and (name N or name CA or nam \ e C or name O or name CB )) or resid 873 or (resid 874 and (name N or name CA or \ name C or name O or name CB )) or resid 875 or (resid 876 and (name N or name C \ A or name C or name O or name CB )) or resid 877 through 893 or (resid 894 and ( \ name N or name CA or name C or name O or name CB )) or resid 895 through 929 or \ (resid 930 through 932 and (name N or name CA or name C or name O or name CB )) \ or resid 933 through 951 or (resid 952 and (name N or name CA or name C or name \ O or name CB )) or resid 953 through 998 or (resid 999 and (name N or name CA or \ name C or name O or name CB )) or resid 1000 through 1148 or (resid 1149 and (n \ ame N or name CA or name C or name O or name CB )) or resid 1150 through 1199 or \ (resid 1200 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 201 through 1305)) selection = (chain 'B' and (resid 14 through 68 or (resid 69 and (name N or name CA or name \ C or name O or name CB )) or resid 70 through 72 or (resid 73 and (name N or nam \ e CA or name C or name O or name CB )) or resid 74 through 81 or (resid 82 and ( \ name N or name CA or name C or name O or name CB )) or resid 83 through 90 or (r \ esid 91 and (name N or name CA or name C or name O or name CB )) or resid 92 thr \ ough 157 or (resid 158 and (name N or name CA or name C or name O or name CB )) \ or resid 159 through 163 or (resid 164 through 166 and (name N or name CA or nam \ e C or name O or name CB )) or resid 167 through 168 or (resid 169 and (name N o \ r name CA or name C or name O or name CB )) or resid 170 through 205 or (resid 2 \ 06 and (name N or name CA or name C or name O or name CB )) or resid 207 through \ 244 or (resid 245 and (name N or name CA or name C or name O or name CB )) or r \ esid 246 through 359 or (resid 360 through 362 and (name N or name CA or name C \ or name O or name CB )) or resid 363 or (resid 364 and (name N or name CA or nam \ e C or name O or name CB )) or resid 365 through 370 or (resid 371 through 375 a \ nd (name N or name CA or name C or name O or name CB )) or resid 376 or (resid 3 \ 77 and (name N or name CA or name C or name O or name CB )) or resid 378 through \ 395 or (resid 396 through 402 and (name N or name CA or name C or name O or nam \ e CB )) or (resid 408 and (name N or name CA or name C or name O or name CB )) o \ r resid 409 or (resid 410 and (name N or name CA or name C or name O or name CB \ )) or resid 411 or (resid 412 through 413 and (name N or name CA or name C or na \ me O or name CB )) or resid 422 through 430 or (resid 431 through 432 and (name \ N or name CA or name C or name O or name CB )) or resid 433 through 436 or (resi \ d 437 and (name N or name CA or name C or name O or name CB )) or resid 438 thro \ ugh 446 or resid 449 through 461 or (resid 462 through 465 and (name N or name C \ A or name C or name O or name CB )) or resid 466 through 469 or (resid 470 and ( \ name N or name CA or name C or name O or name CB )) or resid 471 or (resid 472 a \ nd (name N or name CA or name C or name O or name CB )) or resid 473 through 501 \ or (resid 502 and (name N or name CA or name C or name O or name CB )) or resid \ 503 or (resid 515 and (name N or name CA or name C or name O or name CB )) or r \ esid 516 through 520 or (resid 521 and (name N or name CA or name C or name O or \ name CB )) or resid 522 or (resid 523 and (name N or name CA or name C or name \ O or name CB )) or resid 524 through 584 or (resid 585 and (name N or name CA or \ name C or name O or name CB )) or resid 586 through 608 or (resid 609 and (name \ N or name CA or name C or name O or name CB )) or resid 610 through 659 or (res \ id 660 and (name N or name CA or name C or name O or name CB )) or resid 661 thr \ ough 705 or (resid 706 and (name N or name CA or name C or name O or name CB )) \ or resid 707 through 708 or (resid 709 and (name N or name CA or name C or name \ O or name CB )) or resid 710 through 779 or (resid 780 and (name N or name CA or \ name C or name O or name CB )) or resid 781 through 871 or (resid 872 and (name \ N or name CA or name C or name O or name CB )) or resid 873 or (resid 874 and ( \ name N or name CA or name C or name O or name CB )) or resid 875 through 893 or \ (resid 894 and (name N or name CA or name C or name O or name CB )) or resid 895 \ through 931 or (resid 932 and (name N or name CA or name C or name O or name CB \ )) or resid 933 through 951 or (resid 952 and (name N or name CA or name C or n \ ame O or name CB )) or resid 953 through 998 or (resid 999 and (name N or name C \ A or name C or name O or name CB )) or resid 1000 through 1199 or (resid 1200 an \ d (name N or name CA or name C or name O or name CB )) or resid 1201 through 130 \ 5)) selection = (chain 'C' and (resid 14 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 or (resid 26 and (name N or name CA or nam \ e C or name O or name CB )) or resid 27 or (resid 28 and (name N or name CA or n \ ame C or name O or name CB )) or resid 29 through 30 or (resid 31 and (name N or \ name CA or name C or name O or name CB )) or resid 32 through 68 or (resid 69 a \ nd (name N or name CA or name C or name O or name CB )) or resid 70 through 72 o \ r (resid 73 and (name N or name CA or name C or name O or name CB )) or resid 74 \ through 81 or (resid 82 and (name N or name CA or name C or name O or name CB ) \ ) or resid 83 or (resid 84 and (name N or name CA or name C or name O or name CB \ )) or resid 85 through 90 or (resid 91 and (name N or name CA or name C or name \ O or name CB )) or resid 92 through 157 or (resid 158 and (name N or name CA or \ name C or name O or name CB )) or resid 159 through 163 or (resid 164 through 1 \ 66 and (name N or name CA or name C or name O or name CB )) or resid 167 through \ 168 or (resid 169 and (name N or name CA or name C or name O or name CB )) or r \ esid 170 through 205 or (resid 206 and (name N or name CA or name C or name O or \ name CB )) or resid 207 through 217 or (resid 218 and (name N or name CA or nam \ e C or name O or name CB )) or resid 219 through 242 or (resid 243 through 245 a \ nd (name N or name CA or name C or name O or name CB )) or resid 246 through 311 \ or (resid 312 and (name N or name CA or name C or name O or name CB )) or resid \ 313 through 469 or (resid 470 and (name N or name CA or name C or name O or nam \ e CB )) or resid 471 or (resid 472 and (name N or name CA or name C or name O or \ name CB )) or resid 473 through 501 or (resid 502 and (name N or name CA or nam \ e C or name O or name CB )) or resid 503 or (resid 515 and (name N or name CA or \ name C or name O or name CB )) or resid 516 through 520 or (resid 521 and (name \ N or name CA or name C or name O or name CB )) or resid 522 or (resid 523 and ( \ name N or name CA or name C or name O or name CB )) or resid 524 through 615 or \ (resid 616 and (name N or name CA or name C or name O or name CB )) or resid 617 \ through 619 or (resid 620 and (name N or name CA or name C or name O or name CB \ )) or resid 621 through 629 or (resid 630 and (name N or name CA or name C or n \ ame O or name CB )) or resid 631 or (resid 632 and (name N or name CA or name C \ or name O or name CB )) or resid 633 through 651 or (resid 652 and (name N or na \ me CA or name C or name O or name CB )) or resid 653 or (resid 654 and (name N o \ r name CA or name C or name O or name CB )) or resid 655 through 705 or (resid 7 \ 06 and (name N or name CA or name C or name O or name CB )) or resid 707 through \ 875 or (resid 876 and (name N or name CA or name C or name O or name CB )) or r \ esid 877 through 930 or (resid 931 through 932 and (name N or name CA or name C \ or name O or name CB )) or resid 933 through 1148 or (resid 1149 and (name N or \ name CA or name C or name O or name CB )) or resid 1150 through 1305)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'I' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 4.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 31.960 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 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 : 0.002 0.046 32127 Z= 0.100 Angle : 0.421 9.220 43938 Z= 0.219 Chirality : 0.041 0.273 5036 Planarity : 0.003 0.067 5600 Dihedral : 7.750 109.005 11561 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.72 % Allowed : 4.05 % Favored : 94.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % 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: -3.28 (0.11), residues: 4001 helix: -3.45 (0.10), residues: 715 sheet: -0.85 (0.18), residues: 757 loop : -2.33 (0.11), residues: 2529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 676 TYR 0.006 0.001 TYR C 649 PHE 0.006 0.001 PHE A 121 TRP 0.012 0.001 TRP C 344 HIS 0.002 0.000 HIS C 826 Details of bonding type rmsd covalent geometry : bond 0.00204 (32025) covalent geometry : angle 0.41354 (43707) SS BOND : bond 0.00158 ( 75) SS BOND : angle 1.26256 ( 150) hydrogen bonds : bond 0.32355 ( 931) hydrogen bonds : angle 9.22147 ( 2586) link_BETA1-4 : bond 0.00349 ( 5) link_BETA1-4 : angle 0.96151 ( 15) link_NAG-ASN : bond 0.00152 ( 22) link_NAG-ASN : angle 0.88555 ( 66) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 867 residues out of total 3583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 808 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8682 (OUTLIER) cc_final: 0.8460 (t) REVERT: A 147 GLU cc_start: 0.6717 (tm-30) cc_final: 0.6461 (tm-30) REVERT: A 160 HIS cc_start: 0.7694 (p90) cc_final: 0.7391 (p90) REVERT: A 266 TYR cc_start: 0.8063 (m-80) cc_final: 0.7811 (m-80) REVERT: A 277 THR cc_start: 0.8784 (m) cc_final: 0.8304 (p) REVERT: A 415 LYS cc_start: 0.8424 (tttm) cc_final: 0.8213 (ttpp) REVERT: A 439 PHE cc_start: 0.8106 (t80) cc_final: 0.7801 (t80) REVERT: A 500 LYS cc_start: 0.7998 (pptt) cc_final: 0.7557 (pptt) REVERT: A 632 ILE cc_start: 0.8355 (mt) cc_final: 0.8025 (mp) REVERT: A 646 ASN cc_start: 0.6949 (p0) cc_final: 0.6644 (p0) REVERT: A 669 ILE cc_start: 0.8530 (mt) cc_final: 0.8325 (mt) REVERT: A 670 LEU cc_start: 0.7773 (mp) cc_final: 0.7495 (mp) REVERT: A 801 GLU cc_start: 0.7019 (tt0) cc_final: 0.6715 (tt0) REVERT: A 884 PHE cc_start: 0.7550 (m-10) cc_final: 0.7024 (m-10) REVERT: A 998 ASN cc_start: 0.7792 (m110) cc_final: 0.7576 (m110) REVERT: A 1010 LYS cc_start: 0.8453 (ttmm) cc_final: 0.8208 (ttmm) REVERT: A 1036 ASN cc_start: 0.8143 (t0) cc_final: 0.7926 (t0) REVERT: A 1095 ASP cc_start: 0.7459 (t0) cc_final: 0.7200 (t0) REVERT: A 1147 SER cc_start: 0.8369 (p) cc_final: 0.8115 (m) REVERT: A 1214 LYS cc_start: 0.7879 (mptp) cc_final: 0.7573 (mptp) REVERT: C 17 ASP cc_start: 0.7277 (m-30) cc_final: 0.7050 (m-30) REVERT: C 66 TYR cc_start: 0.8421 (m-80) cc_final: 0.8209 (m-80) REVERT: C 712 TYR cc_start: 0.8083 (p90) cc_final: 0.7783 (p90) REVERT: C 851 ASP cc_start: 0.7099 (m-30) cc_final: 0.6857 (m-30) REVERT: C 883 ASP cc_start: 0.7868 (t70) cc_final: 0.7582 (t0) REVERT: C 885 LYS cc_start: 0.8384 (ttmm) cc_final: 0.8063 (ttpp) REVERT: C 949 ILE cc_start: 0.8139 (mt) cc_final: 0.7702 (mt) REVERT: C 1156 VAL cc_start: 0.8472 (p) cc_final: 0.8216 (m) REVERT: B 114 ASN cc_start: 0.8157 (t0) cc_final: 0.7928 (t0) REVERT: B 142 HIS cc_start: 0.7386 (m-70) cc_final: 0.7120 (m-70) REVERT: B 146 LEU cc_start: 0.8355 (mt) cc_final: 0.8153 (mt) REVERT: B 161 THR cc_start: 0.7951 (t) cc_final: 0.7660 (m) REVERT: B 186 LYS cc_start: 0.7980 (mtmt) cc_final: 0.7779 (mtmt) REVERT: B 334 ASN cc_start: 0.7632 (t0) cc_final: 0.7245 (t0) REVERT: B 614 ILE cc_start: 0.7145 (pt) cc_final: 0.6643 (pt) REVERT: B 623 ASP cc_start: 0.7957 (t0) cc_final: 0.7697 (t0) REVERT: B 636 VAL cc_start: 0.8546 (p) cc_final: 0.8282 (t) REVERT: B 655 ILE cc_start: 0.8265 (tt) cc_final: 0.7889 (tt) REVERT: B 660 ASP cc_start: 0.7638 (t0) cc_final: 0.7307 (t70) REVERT: B 812 ILE cc_start: 0.8323 (mt) cc_final: 0.8097 (mm) REVERT: B 1028 LYS cc_start: 0.8250 (mttt) cc_final: 0.7980 (mtpp) REVERT: B 1060 GLU cc_start: 0.7533 (tt0) cc_final: 0.7254 (tt0) REVERT: B 1066 ASP cc_start: 0.7321 (OUTLIER) cc_final: 0.6872 (p0) REVERT: B 1114 VAL cc_start: 0.7552 (OUTLIER) cc_final: 0.7343 (m) REVERT: B 1120 ARG cc_start: 0.8454 (mtp180) cc_final: 0.8103 (mtp180) REVERT: B 1170 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8350 (pt) REVERT: B 1198 SER cc_start: 0.8200 (p) cc_final: 0.7744 (m) REVERT: T 405 ILE cc_start: 0.4694 (pt) cc_final: 0.4371 (pt) outliers start: 59 outliers final: 19 residues processed: 850 average time/residue: 0.1986 time to fit residues: 273.8431 Evaluate side-chains 653 residues out of total 3583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 630 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 814 CYS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1114 VAL Chi-restraints excluded: chain B residue 1170 ILE Chi-restraints excluded: chain B residue 1218 ILE Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 387 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 40.0000 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.0070 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.9980 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN A 152 GLN A 175 HIS A 204 GLN A 291 GLN A 353 ASN A 364 HIS ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 ASN A 598 ASN A 605 ASN A 709 GLN A 722 ASN A 840 ASN A 847 ASN A 941 ASN A1135 GLN C 171 ASN C 265 GLN C 440 ASN ** C 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 854 GLN C 954 GLN C 988 ASN C 998 ASN C1038 GLN C1041 ASN C1046 GLN C1071 GLN C1111 ASN C1201 ASN B 19 ASN B 22 ASN B 29 ASN B 160 HIS B 204 GLN B 646 ASN B 840 ASN B 856 GLN B1073 GLN B1092 GLN T 276 GLN T 334 HIS I 276 GLN I 476 ASN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.173351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.129654 restraints weight = 49529.465| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.64 r_work: 0.3429 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 32127 Z= 0.165 Angle : 0.572 20.211 43938 Z= 0.300 Chirality : 0.045 0.280 5036 Planarity : 0.004 0.078 5600 Dihedral : 5.491 67.010 4905 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.65 % Allowed : 9.72 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % 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: -1.92 (0.12), residues: 4001 helix: -0.36 (0.18), residues: 739 sheet: -0.31 (0.18), residues: 814 loop : -2.01 (0.12), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 361 TYR 0.023 0.002 TYR C 212 PHE 0.033 0.002 PHE A 713 TRP 0.020 0.001 TRP C 444 HIS 0.006 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00374 (32025) covalent geometry : angle 0.55313 (43707) SS BOND : bond 0.00677 ( 75) SS BOND : angle 2.39288 ( 150) hydrogen bonds : bond 0.07018 ( 931) hydrogen bonds : angle 5.86085 ( 2586) link_BETA1-4 : bond 0.00400 ( 5) link_BETA1-4 : angle 1.56485 ( 15) link_NAG-ASN : bond 0.00202 ( 22) link_NAG-ASN : angle 1.22526 ( 66) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 3583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 635 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 VAL cc_start: 0.8130 (t) cc_final: 0.7264 (p) REVERT: A 160 HIS cc_start: 0.8305 (p90) cc_final: 0.7835 (p90) REVERT: A 255 GLU cc_start: 0.6966 (mt-10) cc_final: 0.6733 (mt-10) REVERT: A 289 GLU cc_start: 0.8316 (tp30) cc_final: 0.7968 (tp30) REVERT: A 344 TRP cc_start: 0.8768 (p-90) cc_final: 0.8486 (p-90) REVERT: A 365 VAL cc_start: 0.9034 (p) cc_final: 0.8810 (m) REVERT: A 415 LYS cc_start: 0.8820 (tttm) cc_final: 0.8568 (ttpp) REVERT: A 439 PHE cc_start: 0.8537 (t80) cc_final: 0.8248 (t80) REVERT: A 443 SER cc_start: 0.8752 (t) cc_final: 0.8544 (m) REVERT: A 463 SER cc_start: 0.8624 (m) cc_final: 0.8269 (t) REVERT: A 464 ASP cc_start: 0.8115 (t0) cc_final: 0.7885 (t70) REVERT: A 500 LYS cc_start: 0.8295 (pptt) cc_final: 0.7804 (pptt) REVERT: A 632 ILE cc_start: 0.8894 (mt) cc_final: 0.8626 (mp) REVERT: A 646 ASN cc_start: 0.7905 (p0) cc_final: 0.7684 (p0) REVERT: A 670 LEU cc_start: 0.8422 (mp) cc_final: 0.8156 (mt) REVERT: A 838 ASN cc_start: 0.8180 (m110) cc_final: 0.7764 (m110) REVERT: A 884 PHE cc_start: 0.8032 (m-10) cc_final: 0.7791 (m-10) REVERT: A 1010 LYS cc_start: 0.8559 (ttmm) cc_final: 0.8344 (ttmm) REVERT: A 1095 ASP cc_start: 0.8350 (t0) cc_final: 0.8075 (t0) REVERT: C 85 LEU cc_start: 0.8134 (mt) cc_final: 0.7917 (mp) REVERT: C 120 GLU cc_start: 0.8148 (mp0) cc_final: 0.7928 (mp0) REVERT: C 614 ILE cc_start: 0.8524 (mm) cc_final: 0.7960 (mt) REVERT: C 712 TYR cc_start: 0.8626 (p90) cc_final: 0.8404 (p90) REVERT: C 738 MET cc_start: 0.8839 (mmt) cc_final: 0.8622 (mmp) REVERT: C 845 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7202 (mp0) REVERT: C 848 ASP cc_start: 0.8022 (m-30) cc_final: 0.7677 (m-30) REVERT: C 883 ASP cc_start: 0.8273 (t70) cc_final: 0.8060 (t0) REVERT: C 885 LYS cc_start: 0.8487 (ttmm) cc_final: 0.8182 (ttpp) REVERT: C 1031 SER cc_start: 0.8634 (m) cc_final: 0.8303 (p) REVERT: C 1069 GLU cc_start: 0.8168 (tp30) cc_final: 0.7851 (tp30) REVERT: C 1075 ASP cc_start: 0.8161 (t0) cc_final: 0.7649 (t0) REVERT: C 1156 VAL cc_start: 0.8717 (p) cc_final: 0.8345 (m) REVERT: B 114 ASN cc_start: 0.8514 (t0) cc_final: 0.8234 (t0) REVERT: B 142 HIS cc_start: 0.7922 (m-70) cc_final: 0.7666 (m-70) REVERT: B 147 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7790 (pt0) REVERT: B 153 TYR cc_start: 0.8303 (m-80) cc_final: 0.8067 (m-10) REVERT: B 155 MET cc_start: 0.7140 (mmm) cc_final: 0.6812 (mmm) REVERT: B 320 ARG cc_start: 0.8689 (ttm170) cc_final: 0.8382 (ttm-80) REVERT: B 334 ASN cc_start: 0.7994 (t0) cc_final: 0.7578 (t0) REVERT: B 655 ILE cc_start: 0.8625 (tt) cc_final: 0.8392 (tt) REVERT: B 724 VAL cc_start: 0.8997 (m) cc_final: 0.8758 (p) REVERT: B 786 PHE cc_start: 0.8179 (m-80) cc_final: 0.7797 (m-80) REVERT: B 933 ASP cc_start: 0.7869 (t0) cc_final: 0.7609 (t0) REVERT: B 1028 LYS cc_start: 0.8688 (mttt) cc_final: 0.8330 (mtpp) REVERT: B 1066 ASP cc_start: 0.8023 (OUTLIER) cc_final: 0.7643 (p0) REVERT: B 1076 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.8193 (mtt90) REVERT: B 1112 GLU cc_start: 0.8425 (mt-10) cc_final: 0.7725 (mp0) REVERT: B 1131 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8192 (mp) REVERT: B 1170 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8250 (pt) REVERT: T 405 ILE cc_start: 0.5380 (pt) cc_final: 0.5142 (pt) REVERT: I 406 GLU cc_start: 0.7508 (pm20) cc_final: 0.6864 (pp20) outliers start: 91 outliers final: 42 residues processed: 696 average time/residue: 0.1740 time to fit residues: 200.6615 Evaluate side-chains 648 residues out of total 3583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 601 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 746 TYR Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 575 TRP Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 674 SER Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 1152 SER Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 733 SER Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1076 ARG Chi-restraints excluded: chain B residue 1114 VAL Chi-restraints excluded: chain B residue 1131 LEU Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain B residue 1170 ILE Chi-restraints excluded: chain B residue 1218 ILE Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 387 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 227 optimal weight: 0.6980 chunk 220 optimal weight: 2.9990 chunk 295 optimal weight: 2.9990 chunk 184 optimal weight: 0.9990 chunk 308 optimal weight: 0.6980 chunk 244 optimal weight: 0.1980 chunk 311 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 200 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN A 204 GLN A 353 ASN A1111 ASN C 171 ASN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 854 GLN C1041 ASN C1111 ASN C1135 GLN C1201 ASN B 152 GLN B 204 GLN ** B 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 334 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.172650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.128794 restraints weight = 49540.446| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.64 r_work: 0.3422 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 32127 Z= 0.128 Angle : 0.523 12.160 43938 Z= 0.272 Chirality : 0.044 0.203 5036 Planarity : 0.004 0.082 5600 Dihedral : 4.879 57.584 4900 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.79 % Allowed : 11.64 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % 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: -1.35 (0.13), residues: 4001 helix: 0.83 (0.20), residues: 747 sheet: -0.09 (0.18), residues: 810 loop : -1.84 (0.12), residues: 2444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 361 TYR 0.025 0.001 TYR A 462 PHE 0.020 0.001 PHE A 713 TRP 0.023 0.001 TRP C 444 HIS 0.008 0.001 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00295 (32025) covalent geometry : angle 0.50760 (43707) SS BOND : bond 0.00666 ( 75) SS BOND : angle 2.05987 ( 150) hydrogen bonds : bond 0.05580 ( 931) hydrogen bonds : angle 5.25727 ( 2586) link_BETA1-4 : bond 0.00344 ( 5) link_BETA1-4 : angle 1.54196 ( 15) link_NAG-ASN : bond 0.00170 ( 22) link_NAG-ASN : angle 1.14968 ( 66) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 3583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 611 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 VAL cc_start: 0.8271 (t) cc_final: 0.7321 (p) REVERT: A 160 HIS cc_start: 0.8236 (p90) cc_final: 0.7803 (p90) REVERT: A 255 GLU cc_start: 0.6951 (mt-10) cc_final: 0.6664 (mt-10) REVERT: A 289 GLU cc_start: 0.8300 (tp30) cc_final: 0.7976 (tp30) REVERT: A 365 VAL cc_start: 0.9046 (p) cc_final: 0.8816 (m) REVERT: A 439 PHE cc_start: 0.8548 (t80) cc_final: 0.8265 (t80) REVERT: A 463 SER cc_start: 0.8644 (m) cc_final: 0.8268 (t) REVERT: A 464 ASP cc_start: 0.8057 (t0) cc_final: 0.7757 (t70) REVERT: A 500 LYS cc_start: 0.8262 (pptt) cc_final: 0.7767 (pptt) REVERT: A 632 ILE cc_start: 0.8931 (mt) cc_final: 0.8682 (mp) REVERT: A 670 LEU cc_start: 0.8411 (mp) cc_final: 0.8138 (mt) REVERT: A 780 GLU cc_start: 0.8442 (tp30) cc_final: 0.8200 (mp0) REVERT: A 884 PHE cc_start: 0.8001 (m-10) cc_final: 0.7795 (m-10) REVERT: A 1010 LYS cc_start: 0.8609 (ttmm) cc_final: 0.8408 (ttmm) REVERT: A 1095 ASP cc_start: 0.8307 (t0) cc_final: 0.8015 (t0) REVERT: C 85 LEU cc_start: 0.8208 (mt) cc_final: 0.7998 (mp) REVERT: C 120 GLU cc_start: 0.8142 (mp0) cc_final: 0.7939 (mp0) REVERT: C 255 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7418 (mm-30) REVERT: C 309 PHE cc_start: -0.1241 (OUTLIER) cc_final: -0.1967 (p90) REVERT: C 500 LYS cc_start: 0.8059 (tttm) cc_final: 0.7837 (ptmm) REVERT: C 614 ILE cc_start: 0.8626 (mm) cc_final: 0.8063 (mt) REVERT: C 712 TYR cc_start: 0.8677 (p90) cc_final: 0.8473 (p90) REVERT: C 735 ASP cc_start: 0.8330 (m-30) cc_final: 0.8110 (m-30) REVERT: C 812 ILE cc_start: 0.8744 (mm) cc_final: 0.8468 (mm) REVERT: C 845 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7137 (mp0) REVERT: C 848 ASP cc_start: 0.7973 (m-30) cc_final: 0.7689 (m-30) REVERT: C 851 ASP cc_start: 0.7949 (m-30) cc_final: 0.7729 (m-30) REVERT: C 883 ASP cc_start: 0.8255 (t70) cc_final: 0.8053 (t0) REVERT: C 885 LYS cc_start: 0.8533 (ttmm) cc_final: 0.8237 (ttpp) REVERT: C 1031 SER cc_start: 0.8576 (m) cc_final: 0.8298 (p) REVERT: C 1069 GLU cc_start: 0.8137 (tp30) cc_final: 0.7679 (tp30) REVERT: C 1075 ASP cc_start: 0.7962 (t0) cc_final: 0.7606 (t0) REVERT: C 1156 VAL cc_start: 0.8745 (p) cc_final: 0.8351 (m) REVERT: C 1202 VAL cc_start: 0.8699 (m) cc_final: 0.8481 (p) REVERT: B 114 ASN cc_start: 0.8525 (t0) cc_final: 0.8240 (t0) REVERT: B 147 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7751 (mt-10) REVERT: B 152 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.7928 (tt0) REVERT: B 153 TYR cc_start: 0.8316 (m-80) cc_final: 0.7872 (m-10) REVERT: B 155 MET cc_start: 0.7135 (mmm) cc_final: 0.6774 (mmm) REVERT: B 320 ARG cc_start: 0.8691 (ttm170) cc_final: 0.8374 (ttm-80) REVERT: B 334 ASN cc_start: 0.7974 (t0) cc_final: 0.7551 (t0) REVERT: B 623 ASP cc_start: 0.8504 (t0) cc_final: 0.8251 (t0) REVERT: B 655 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8405 (tt) REVERT: B 667 TYR cc_start: 0.8346 (m-80) cc_final: 0.8061 (m-10) REVERT: B 745 ASP cc_start: 0.7638 (t0) cc_final: 0.7368 (t0) REVERT: B 933 ASP cc_start: 0.7830 (t0) cc_final: 0.7628 (t0) REVERT: B 1028 LYS cc_start: 0.8670 (mttt) cc_final: 0.8371 (mtpp) REVERT: B 1069 GLU cc_start: 0.7677 (pm20) cc_final: 0.7191 (pm20) REVERT: B 1076 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.8120 (mtt180) REVERT: B 1131 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8239 (mp) REVERT: B 1170 ILE cc_start: 0.8609 (OUTLIER) cc_final: 0.8306 (pt) REVERT: T 405 ILE cc_start: 0.5388 (pt) cc_final: 0.5140 (pt) REVERT: T 424 MET cc_start: 0.0719 (OUTLIER) cc_final: 0.0088 (tmm) REVERT: I 406 GLU cc_start: 0.7525 (pm20) cc_final: 0.7000 (pp20) outliers start: 96 outliers final: 63 residues processed: 670 average time/residue: 0.1736 time to fit residues: 191.6834 Evaluate side-chains 654 residues out of total 3583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 583 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 630 GLN Chi-restraints excluded: chain A residue 746 TYR Chi-restraints excluded: chain A residue 814 CYS Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1163 CYS Chi-restraints excluded: chain A residue 1218 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 140 GLN Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 309 PHE Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 651 SER Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 674 SER Chi-restraints excluded: chain C residue 728 SER Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 1152 SER Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 674 SER Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1076 ARG Chi-restraints excluded: chain B residue 1114 VAL Chi-restraints excluded: chain B residue 1131 LEU Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain B residue 1170 ILE Chi-restraints excluded: chain B residue 1218 ILE Chi-restraints excluded: chain T residue 424 MET Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 387 THR Chi-restraints excluded: chain I residue 405 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 285 optimal weight: 7.9990 chunk 334 optimal weight: 0.0870 chunk 86 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 354 optimal weight: 8.9990 chunk 262 optimal weight: 0.9990 chunk 133 optimal weight: 0.0270 chunk 75 optimal weight: 0.4980 chunk 54 optimal weight: 1.9990 chunk 175 optimal weight: 0.2980 chunk 391 optimal weight: 40.0000 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN A 204 GLN A 353 ASN ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 ASN A 694 ASN C 171 ASN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 854 GLN C1111 ASN C1201 ASN B 152 GLN ** B 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 ASN B 856 GLN T 334 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.173458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.129731 restraints weight = 49236.928| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.63 r_work: 0.3427 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 32127 Z= 0.100 Angle : 0.504 12.160 43938 Z= 0.260 Chirality : 0.043 0.200 5036 Planarity : 0.004 0.083 5600 Dihedral : 4.583 58.801 4900 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.11 % Allowed : 12.08 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % 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: -1.07 (0.13), residues: 4001 helix: 1.24 (0.21), residues: 752 sheet: 0.07 (0.18), residues: 804 loop : -1.71 (0.12), residues: 2445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 361 TYR 0.022 0.001 TYR B 712 PHE 0.023 0.001 PHE C 24 TRP 0.025 0.001 TRP C 444 HIS 0.005 0.001 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00225 (32025) covalent geometry : angle 0.48896 (43707) SS BOND : bond 0.00581 ( 75) SS BOND : angle 1.99505 ( 150) hydrogen bonds : bond 0.04596 ( 931) hydrogen bonds : angle 4.98738 ( 2586) link_BETA1-4 : bond 0.00339 ( 5) link_BETA1-4 : angle 1.54031 ( 15) link_NAG-ASN : bond 0.00150 ( 22) link_NAG-ASN : angle 1.11789 ( 66) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 3583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 591 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 HIS cc_start: 0.8251 (p90) cc_final: 0.7760 (p90) REVERT: A 255 GLU cc_start: 0.6941 (mt-10) cc_final: 0.6626 (mt-10) REVERT: A 289 GLU cc_start: 0.8317 (tp30) cc_final: 0.7980 (tp30) REVERT: A 359 LEU cc_start: 0.8745 (tp) cc_final: 0.8514 (tp) REVERT: A 365 VAL cc_start: 0.9018 (p) cc_final: 0.8793 (m) REVERT: A 439 PHE cc_start: 0.8558 (t80) cc_final: 0.8213 (t80) REVERT: A 463 SER cc_start: 0.8686 (m) cc_final: 0.8299 (t) REVERT: A 500 LYS cc_start: 0.8224 (pptt) cc_final: 0.7684 (pptt) REVERT: A 780 GLU cc_start: 0.8409 (tp30) cc_final: 0.8161 (mp0) REVERT: A 884 PHE cc_start: 0.8006 (m-10) cc_final: 0.7750 (m-10) REVERT: A 1010 LYS cc_start: 0.8521 (ttmm) cc_final: 0.8316 (ttmm) REVERT: A 1095 ASP cc_start: 0.8262 (t0) cc_final: 0.7991 (t0) REVERT: C 255 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7390 (mm-30) REVERT: C 309 PHE cc_start: -0.1226 (OUTLIER) cc_final: -0.1985 (p90) REVERT: C 500 LYS cc_start: 0.8074 (tttm) cc_final: 0.7857 (ptmm) REVERT: C 614 ILE cc_start: 0.8598 (mm) cc_final: 0.8246 (mm) REVERT: C 812 ILE cc_start: 0.8713 (mm) cc_final: 0.8443 (mm) REVERT: C 845 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7042 (mp0) REVERT: C 848 ASP cc_start: 0.7949 (m-30) cc_final: 0.7646 (m-30) REVERT: C 883 ASP cc_start: 0.8264 (t70) cc_final: 0.8049 (t70) REVERT: C 885 LYS cc_start: 0.8480 (ttmm) cc_final: 0.8242 (ttpp) REVERT: C 1031 SER cc_start: 0.8525 (m) cc_final: 0.8254 (p) REVERT: C 1069 GLU cc_start: 0.8143 (tp30) cc_final: 0.7614 (tp30) REVERT: C 1156 VAL cc_start: 0.8741 (p) cc_final: 0.8343 (m) REVERT: C 1202 VAL cc_start: 0.8703 (m) cc_final: 0.8481 (p) REVERT: B 114 ASN cc_start: 0.8596 (t0) cc_final: 0.8262 (t0) REVERT: B 147 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7742 (mt-10) REVERT: B 153 TYR cc_start: 0.8326 (m-80) cc_final: 0.7854 (m-10) REVERT: B 155 MET cc_start: 0.7167 (mmm) cc_final: 0.6788 (mmm) REVERT: B 320 ARG cc_start: 0.8637 (ttm170) cc_final: 0.8301 (ttm-80) REVERT: B 334 ASN cc_start: 0.7934 (t0) cc_final: 0.7496 (t0) REVERT: B 623 ASP cc_start: 0.8484 (t0) cc_final: 0.8210 (t0) REVERT: B 655 ILE cc_start: 0.8619 (tt) cc_final: 0.8368 (tt) REVERT: B 667 TYR cc_start: 0.8351 (m-80) cc_final: 0.8070 (m-10) REVERT: B 744 ILE cc_start: 0.7579 (mm) cc_final: 0.7297 (mm) REVERT: B 1028 LYS cc_start: 0.8612 (mttt) cc_final: 0.8310 (mtpp) REVERT: B 1069 GLU cc_start: 0.7682 (pm20) cc_final: 0.7324 (pm20) REVERT: B 1076 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7978 (mtt180) REVERT: B 1131 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8176 (mp) REVERT: B 1170 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.8301 (pt) REVERT: B 1180 GLN cc_start: 0.8285 (tt0) cc_final: 0.8079 (tt0) REVERT: B 1202 VAL cc_start: 0.8903 (m) cc_final: 0.8685 (p) REVERT: T 405 ILE cc_start: 0.5449 (pt) cc_final: 0.5205 (pt) REVERT: T 424 MET cc_start: 0.0782 (OUTLIER) cc_final: 0.0085 (tmm) outliers start: 107 outliers final: 68 residues processed: 657 average time/residue: 0.1434 time to fit residues: 156.4931 Evaluate side-chains 649 residues out of total 3583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 575 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 630 GLN Chi-restraints excluded: chain A residue 746 TYR Chi-restraints excluded: chain A residue 814 CYS Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain A residue 862 MET Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1163 CYS Chi-restraints excluded: chain A residue 1218 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 140 GLN Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 309 PHE Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 423 CYS Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 651 SER Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 728 SER Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 1105 ARG Chi-restraints excluded: chain C residue 1152 SER Chi-restraints excluded: chain C residue 1163 CYS Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 643 ASN Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1076 ARG Chi-restraints excluded: chain B residue 1114 VAL Chi-restraints excluded: chain B residue 1131 LEU Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain B residue 1170 ILE Chi-restraints excluded: chain B residue 1218 ILE Chi-restraints excluded: chain T residue 424 MET Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 387 THR Chi-restraints excluded: chain I residue 405 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 300 optimal weight: 2.9990 chunk 365 optimal weight: 20.0000 chunk 46 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 377 optimal weight: 3.9990 chunk 347 optimal weight: 1.9990 chunk 386 optimal weight: 40.0000 chunk 338 optimal weight: 3.9990 chunk 344 optimal weight: 0.9990 chunk 154 optimal weight: 10.0000 chunk 299 optimal weight: 0.9980 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN A 204 GLN A 353 ASN ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 545 HIS A 646 ASN C 171 ASN C 265 GLN ** C 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 854 GLN C 954 GLN C1111 ASN C1201 ASN B1045 GLN B1111 ASN T 334 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.169366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.125405 restraints weight = 49279.737| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.59 r_work: 0.3362 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 32127 Z= 0.197 Angle : 0.584 12.668 43938 Z= 0.301 Chirality : 0.046 0.264 5036 Planarity : 0.004 0.082 5600 Dihedral : 4.820 59.751 4900 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.29 % Allowed : 12.75 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -1.08 (0.13), residues: 4001 helix: 1.18 (0.20), residues: 764 sheet: 0.01 (0.18), residues: 800 loop : -1.70 (0.12), residues: 2437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1105 TYR 0.025 0.002 TYR B 712 PHE 0.035 0.002 PHE A 713 TRP 0.025 0.001 TRP C 444 HIS 0.009 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00470 (32025) covalent geometry : angle 0.56714 (43707) SS BOND : bond 0.00665 ( 75) SS BOND : angle 2.16946 ( 150) hydrogen bonds : bond 0.05648 ( 931) hydrogen bonds : angle 4.93058 ( 2586) link_BETA1-4 : bond 0.00327 ( 5) link_BETA1-4 : angle 1.43422 ( 15) link_NAG-ASN : bond 0.00359 ( 22) link_NAG-ASN : angle 1.60064 ( 66) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 724 residues out of total 3583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 611 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 HIS cc_start: 0.8193 (p90) cc_final: 0.7736 (p90) REVERT: A 255 GLU cc_start: 0.7005 (mt-10) cc_final: 0.6633 (mt-10) REVERT: A 289 GLU cc_start: 0.8334 (tp30) cc_final: 0.7998 (tp30) REVERT: A 359 LEU cc_start: 0.8732 (tp) cc_final: 0.8441 (tt) REVERT: A 365 VAL cc_start: 0.9062 (p) cc_final: 0.8846 (m) REVERT: A 500 LYS cc_start: 0.8231 (pptt) cc_final: 0.7680 (pptt) REVERT: A 768 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7761 (mt-10) REVERT: A 780 GLU cc_start: 0.8434 (tp30) cc_final: 0.8186 (mp0) REVERT: A 884 PHE cc_start: 0.8086 (m-10) cc_final: 0.7864 (m-10) REVERT: A 1010 LYS cc_start: 0.8600 (ttmm) cc_final: 0.8392 (ttmm) REVERT: A 1095 ASP cc_start: 0.8320 (t0) cc_final: 0.8065 (t0) REVERT: C 34 ARG cc_start: 0.7582 (ptm160) cc_final: 0.7363 (ptm160) REVERT: C 41 ASP cc_start: 0.8012 (t0) cc_final: 0.7788 (t0) REVERT: C 111 LEU cc_start: 0.7648 (mm) cc_final: 0.7282 (mp) REVERT: C 309 PHE cc_start: -0.1024 (OUTLIER) cc_final: -0.1771 (p90) REVERT: C 614 ILE cc_start: 0.8798 (mm) cc_final: 0.8516 (mm) REVERT: C 711 PHE cc_start: 0.8035 (m-10) cc_final: 0.7820 (m-10) REVERT: C 735 ASP cc_start: 0.8377 (m-30) cc_final: 0.8164 (m-30) REVERT: C 831 GLU cc_start: 0.8424 (pt0) cc_final: 0.8192 (pt0) REVERT: C 845 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7279 (mp0) REVERT: C 883 ASP cc_start: 0.8335 (t70) cc_final: 0.8114 (t70) REVERT: C 885 LYS cc_start: 0.8579 (ttmm) cc_final: 0.8341 (ttpp) REVERT: C 1031 SER cc_start: 0.8588 (m) cc_final: 0.8259 (p) REVERT: C 1069 GLU cc_start: 0.8147 (tp30) cc_final: 0.7622 (tp30) REVERT: C 1075 ASP cc_start: 0.8113 (t0) cc_final: 0.7592 (t0) REVERT: C 1202 VAL cc_start: 0.8745 (m) cc_final: 0.8502 (p) REVERT: C 1203 VAL cc_start: 0.8113 (m) cc_final: 0.7869 (p) REVERT: B 114 ASN cc_start: 0.8460 (t0) cc_final: 0.8148 (t0) REVERT: B 147 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7659 (mt-10) REVERT: B 153 TYR cc_start: 0.8338 (m-80) cc_final: 0.7927 (m-10) REVERT: B 155 MET cc_start: 0.7240 (mmm) cc_final: 0.6879 (mmm) REVERT: B 240 LEU cc_start: 0.6554 (OUTLIER) cc_final: 0.6217 (tt) REVERT: B 320 ARG cc_start: 0.8633 (ttm170) cc_final: 0.8327 (ttm-80) REVERT: B 334 ASN cc_start: 0.8043 (t0) cc_final: 0.7604 (t0) REVERT: B 623 ASP cc_start: 0.8560 (t0) cc_final: 0.8283 (t0) REVERT: B 666 THR cc_start: 0.8539 (p) cc_final: 0.8239 (p) REVERT: B 744 ILE cc_start: 0.7816 (mm) cc_final: 0.7566 (mm) REVERT: B 913 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8543 (mt) REVERT: B 1028 LYS cc_start: 0.8693 (mttt) cc_final: 0.8388 (mtpp) REVERT: B 1066 ASP cc_start: 0.7911 (OUTLIER) cc_final: 0.7390 (p0) REVERT: B 1069 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7475 (pm20) REVERT: B 1131 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8335 (mp) REVERT: B 1167 ASP cc_start: 0.7171 (t70) cc_final: 0.6644 (t70) REVERT: B 1170 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8399 (pt) REVERT: B 1180 GLN cc_start: 0.8440 (tt0) cc_final: 0.8202 (tt0) REVERT: B 1200 LYS cc_start: 0.8658 (ptpp) cc_final: 0.8410 (ptpp) REVERT: T 405 ILE cc_start: 0.5390 (pt) cc_final: 0.5134 (pt) REVERT: T 424 MET cc_start: 0.0788 (OUTLIER) cc_final: 0.0003 (tmm) REVERT: I 406 GLU cc_start: 0.7750 (pm20) cc_final: 0.7142 (pp20) outliers start: 113 outliers final: 71 residues processed: 677 average time/residue: 0.1544 time to fit residues: 174.2179 Evaluate side-chains 666 residues out of total 3583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 586 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 630 GLN Chi-restraints excluded: chain A residue 646 ASN Chi-restraints excluded: chain A residue 746 TYR Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain A residue 862 MET Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1163 CYS Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 140 GLN Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 309 PHE Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 423 CYS Chi-restraints excluded: chain C residue 577 PHE Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 651 SER Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 728 SER Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1152 SER Chi-restraints excluded: chain C residue 1163 CYS Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 643 ASN Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 863 GLN Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 943 ILE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1069 GLU Chi-restraints excluded: chain B residue 1114 VAL Chi-restraints excluded: chain B residue 1131 LEU Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain B residue 1170 ILE Chi-restraints excluded: chain T residue 424 MET Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 387 THR Chi-restraints excluded: chain I residue 405 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 396 optimal weight: 40.0000 chunk 334 optimal weight: 1.9990 chunk 397 optimal weight: 40.0000 chunk 164 optimal weight: 20.0000 chunk 18 optimal weight: 1.9990 chunk 351 optimal weight: 0.0470 chunk 34 optimal weight: 0.9980 chunk 242 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 158 optimal weight: 4.9990 chunk 301 optimal weight: 2.9990 overall best weight: 1.1882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN A 343 ASN A 353 ASN ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 HIS C 265 GLN ** C 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 854 GLN B 642 ASN B1045 GLN T 334 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.169477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.125481 restraints weight = 49068.974| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.60 r_work: 0.3362 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 32127 Z= 0.173 Angle : 0.575 14.082 43938 Z= 0.296 Chirality : 0.046 0.265 5036 Planarity : 0.004 0.083 5600 Dihedral : 4.864 58.319 4898 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.77 % Favored : 94.20 % Rotamer: Outliers : 3.52 % Allowed : 13.60 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -1.05 (0.13), residues: 4001 helix: 1.28 (0.20), residues: 761 sheet: 0.00 (0.18), residues: 777 loop : -1.68 (0.12), residues: 2463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 361 TYR 0.033 0.002 TYR A 236 PHE 0.033 0.002 PHE B 224 TRP 0.019 0.001 TRP C 444 HIS 0.007 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00411 (32025) covalent geometry : angle 0.55368 (43707) SS BOND : bond 0.00599 ( 75) SS BOND : angle 2.48829 ( 150) hydrogen bonds : bond 0.05211 ( 931) hydrogen bonds : angle 4.85785 ( 2586) link_BETA1-4 : bond 0.00308 ( 5) link_BETA1-4 : angle 1.35917 ( 15) link_NAG-ASN : bond 0.00252 ( 22) link_NAG-ASN : angle 1.62477 ( 66) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 3583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 586 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 PHE cc_start: 0.8803 (m-80) cc_final: 0.8358 (m-80) REVERT: A 160 HIS cc_start: 0.8200 (p90) cc_final: 0.7723 (p90) REVERT: A 255 GLU cc_start: 0.7021 (mt-10) cc_final: 0.6652 (mt-10) REVERT: A 289 GLU cc_start: 0.8349 (tp30) cc_final: 0.8010 (tp30) REVERT: A 359 LEU cc_start: 0.8701 (tp) cc_final: 0.8418 (tt) REVERT: A 365 VAL cc_start: 0.9058 (p) cc_final: 0.8846 (m) REVERT: A 464 ASP cc_start: 0.8000 (t0) cc_final: 0.7713 (t70) REVERT: A 500 LYS cc_start: 0.8173 (pptt) cc_final: 0.7612 (pptt) REVERT: A 768 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7814 (mt-10) REVERT: A 780 GLU cc_start: 0.8458 (tp30) cc_final: 0.8225 (mp0) REVERT: A 884 PHE cc_start: 0.8076 (m-10) cc_final: 0.7862 (m-10) REVERT: A 1064 ARG cc_start: 0.8529 (mtm110) cc_final: 0.8164 (ttm-80) REVERT: A 1095 ASP cc_start: 0.8262 (t0) cc_final: 0.7999 (t0) REVERT: C 34 ARG cc_start: 0.7587 (ptm160) cc_final: 0.7357 (ptm160) REVERT: C 41 ASP cc_start: 0.8054 (t0) cc_final: 0.7770 (t0) REVERT: C 111 LEU cc_start: 0.7654 (mm) cc_final: 0.7308 (mp) REVERT: C 309 PHE cc_start: -0.1010 (OUTLIER) cc_final: -0.1810 (p90) REVERT: C 614 ILE cc_start: 0.8801 (mm) cc_final: 0.8566 (mm) REVERT: C 711 PHE cc_start: 0.8008 (m-10) cc_final: 0.7792 (m-10) REVERT: C 831 GLU cc_start: 0.8405 (pt0) cc_final: 0.8192 (pt0) REVERT: C 845 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7163 (mp0) REVERT: C 883 ASP cc_start: 0.8334 (t70) cc_final: 0.8120 (t70) REVERT: C 885 LYS cc_start: 0.8577 (ttmm) cc_final: 0.8340 (ttpp) REVERT: C 1031 SER cc_start: 0.8574 (m) cc_final: 0.8258 (p) REVERT: C 1069 GLU cc_start: 0.8130 (tp30) cc_final: 0.7590 (tp30) REVERT: C 1075 ASP cc_start: 0.8095 (t0) cc_final: 0.7565 (t0) REVERT: B 114 ASN cc_start: 0.8477 (t0) cc_final: 0.8156 (t0) REVERT: B 147 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7683 (mt-10) REVERT: B 153 TYR cc_start: 0.8330 (m-80) cc_final: 0.8103 (m-10) REVERT: B 155 MET cc_start: 0.7221 (mmm) cc_final: 0.6832 (mmm) REVERT: B 240 LEU cc_start: 0.6502 (OUTLIER) cc_final: 0.6149 (tt) REVERT: B 320 ARG cc_start: 0.8682 (ttm170) cc_final: 0.8383 (ttm-80) REVERT: B 334 ASN cc_start: 0.7960 (t0) cc_final: 0.7530 (t0) REVERT: B 623 ASP cc_start: 0.8552 (t0) cc_final: 0.8259 (t0) REVERT: B 744 ILE cc_start: 0.7822 (mm) cc_final: 0.7583 (mm) REVERT: B 933 ASP cc_start: 0.7544 (t0) cc_final: 0.7338 (t0) REVERT: B 1028 LYS cc_start: 0.8679 (mttt) cc_final: 0.8378 (mtpp) REVERT: B 1066 ASP cc_start: 0.7884 (OUTLIER) cc_final: 0.7312 (p0) REVERT: B 1069 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7376 (pm20) REVERT: B 1076 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.8172 (mtt180) REVERT: B 1131 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8326 (mp) REVERT: B 1167 ASP cc_start: 0.7209 (t70) cc_final: 0.6666 (t70) REVERT: B 1180 GLN cc_start: 0.8454 (tt0) cc_final: 0.8208 (tt0) REVERT: B 1200 LYS cc_start: 0.8626 (ptpp) cc_final: 0.8363 (ptpp) REVERT: T 405 ILE cc_start: 0.5378 (pt) cc_final: 0.5119 (pt) REVERT: T 424 MET cc_start: 0.0804 (OUTLIER) cc_final: 0.0033 (tmm) REVERT: I 406 GLU cc_start: 0.7583 (pm20) cc_final: 0.7012 (pp20) outliers start: 121 outliers final: 79 residues processed: 656 average time/residue: 0.1644 time to fit residues: 177.7067 Evaluate side-chains 672 residues out of total 3583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 585 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 630 GLN Chi-restraints excluded: chain A residue 646 ASN Chi-restraints excluded: chain A residue 746 TYR Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 862 MET Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1163 CYS Chi-restraints excluded: chain A residue 1214 LYS Chi-restraints excluded: chain A residue 1218 ILE Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 140 GLN Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 309 PHE Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 423 CYS Chi-restraints excluded: chain C residue 577 PHE Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 674 SER Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1152 SER Chi-restraints excluded: chain C residue 1163 CYS Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 643 ASN Chi-restraints excluded: chain B residue 674 SER Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 863 GLN Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 943 ILE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1069 GLU Chi-restraints excluded: chain B residue 1076 ARG Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1114 VAL Chi-restraints excluded: chain B residue 1131 LEU Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain B residue 1170 ILE Chi-restraints excluded: chain B residue 1218 ILE Chi-restraints excluded: chain T residue 424 MET Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 387 THR Chi-restraints excluded: chain I residue 405 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 158 optimal weight: 3.9990 chunk 287 optimal weight: 30.0000 chunk 388 optimal weight: 0.0570 chunk 60 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 120 optimal weight: 0.0980 chunk 30 optimal weight: 0.9990 chunk 157 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 156 optimal weight: 0.0050 chunk 87 optimal weight: 1.9990 overall best weight: 0.3712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN A 152 GLN A 353 ASN ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 ASN C 160 HIS C 234 HIS ** C 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 854 GLN C 954 GLN C1016 GLN B 646 ASN B1045 GLN T 334 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.171403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.127632 restraints weight = 49589.238| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.62 r_work: 0.3403 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 32127 Z= 0.102 Angle : 0.532 18.316 43938 Z= 0.273 Chirality : 0.044 0.260 5036 Planarity : 0.004 0.083 5600 Dihedral : 4.678 59.967 4898 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.85 % Allowed : 14.00 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -0.86 (0.13), residues: 4001 helix: 1.55 (0.21), residues: 759 sheet: 0.11 (0.19), residues: 756 loop : -1.57 (0.12), residues: 2486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 361 TYR 0.029 0.001 TYR C 712 PHE 0.028 0.001 PHE B 224 TRP 0.020 0.001 TRP C 444 HIS 0.005 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00227 (32025) covalent geometry : angle 0.51352 (43707) SS BOND : bond 0.00545 ( 75) SS BOND : angle 2.24709 ( 150) hydrogen bonds : bond 0.04226 ( 931) hydrogen bonds : angle 4.68314 ( 2586) link_BETA1-4 : bond 0.00380 ( 5) link_BETA1-4 : angle 1.26447 ( 15) link_NAG-ASN : bond 0.00167 ( 22) link_NAG-ASN : angle 1.37015 ( 66) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 3583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 582 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 PHE cc_start: 0.8794 (m-80) cc_final: 0.8329 (m-80) REVERT: A 160 HIS cc_start: 0.8197 (p90) cc_final: 0.7712 (p90) REVERT: A 255 GLU cc_start: 0.7007 (mt-10) cc_final: 0.6596 (mt-10) REVERT: A 289 GLU cc_start: 0.8350 (tp30) cc_final: 0.8014 (tp30) REVERT: A 359 LEU cc_start: 0.8658 (tp) cc_final: 0.8429 (tp) REVERT: A 365 VAL cc_start: 0.9032 (p) cc_final: 0.8831 (m) REVERT: A 500 LYS cc_start: 0.8100 (pptt) cc_final: 0.7549 (pptt) REVERT: A 555 LYS cc_start: 0.8094 (mtpp) cc_final: 0.7787 (ttmm) REVERT: A 635 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7767 (tm-30) REVERT: A 768 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7727 (mt-10) REVERT: A 780 GLU cc_start: 0.8429 (tp30) cc_final: 0.8193 (mp0) REVERT: A 884 PHE cc_start: 0.7973 (m-10) cc_final: 0.7754 (m-10) REVERT: A 1064 ARG cc_start: 0.8490 (mtm110) cc_final: 0.8158 (ttm-80) REVERT: A 1095 ASP cc_start: 0.8254 (t0) cc_final: 0.7989 (t0) REVERT: C 34 ARG cc_start: 0.7430 (ptm160) cc_final: 0.7220 (ptm160) REVERT: C 111 LEU cc_start: 0.7628 (mm) cc_final: 0.7326 (mp) REVERT: C 309 PHE cc_start: -0.1077 (OUTLIER) cc_final: -0.1918 (p90) REVERT: C 614 ILE cc_start: 0.8790 (mm) cc_final: 0.8552 (mm) REVERT: C 711 PHE cc_start: 0.8014 (m-10) cc_final: 0.7791 (m-10) REVERT: C 831 GLU cc_start: 0.8420 (pt0) cc_final: 0.8204 (pt0) REVERT: C 845 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7088 (mp0) REVERT: C 883 ASP cc_start: 0.8306 (t70) cc_final: 0.8086 (t70) REVERT: C 885 LYS cc_start: 0.8413 (ttmm) cc_final: 0.8201 (ttpp) REVERT: C 1031 SER cc_start: 0.8537 (m) cc_final: 0.8266 (p) REVERT: C 1069 GLU cc_start: 0.8124 (tp30) cc_final: 0.7668 (tp30) REVERT: C 1202 VAL cc_start: 0.8748 (m) cc_final: 0.8516 (p) REVERT: B 114 ASN cc_start: 0.8521 (t0) cc_final: 0.8170 (t0) REVERT: B 147 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7702 (mt-10) REVERT: B 153 TYR cc_start: 0.8302 (m-80) cc_final: 0.8033 (m-10) REVERT: B 155 MET cc_start: 0.7189 (mmm) cc_final: 0.6787 (mmm) REVERT: B 240 LEU cc_start: 0.6522 (OUTLIER) cc_final: 0.6163 (tt) REVERT: B 320 ARG cc_start: 0.8630 (ttm170) cc_final: 0.8321 (ttm-80) REVERT: B 334 ASN cc_start: 0.7954 (t0) cc_final: 0.7526 (t0) REVERT: B 623 ASP cc_start: 0.8487 (t0) cc_final: 0.8204 (t0) REVERT: B 744 ILE cc_start: 0.7766 (mm) cc_final: 0.7388 (mm) REVERT: B 933 ASP cc_start: 0.7535 (t0) cc_final: 0.7292 (t0) REVERT: B 1028 LYS cc_start: 0.8647 (mttt) cc_final: 0.8353 (mtpp) REVERT: B 1066 ASP cc_start: 0.7851 (OUTLIER) cc_final: 0.7482 (p0) REVERT: B 1076 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7997 (mtt90) REVERT: B 1131 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8272 (mp) REVERT: B 1167 ASP cc_start: 0.7122 (t70) cc_final: 0.6583 (t70) REVERT: B 1180 GLN cc_start: 0.8424 (tt0) cc_final: 0.8190 (tt0) REVERT: B 1200 LYS cc_start: 0.8595 (ptpp) cc_final: 0.8333 (ptpp) REVERT: T 424 MET cc_start: 0.0751 (OUTLIER) cc_final: -0.0078 (tmm) REVERT: I 406 GLU cc_start: 0.7647 (pm20) cc_final: 0.6975 (pp20) outliers start: 98 outliers final: 71 residues processed: 637 average time/residue: 0.1761 time to fit residues: 184.1283 Evaluate side-chains 642 residues out of total 3583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 564 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 646 ASN Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 746 TYR Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 862 MET Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1163 CYS Chi-restraints excluded: chain A residue 1214 LYS Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 140 GLN Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 309 PHE Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 423 CYS Chi-restraints excluded: chain C residue 577 PHE Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 728 SER Chi-restraints excluded: chain C residue 820 SER Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1105 ARG Chi-restraints excluded: chain C residue 1152 SER Chi-restraints excluded: chain C residue 1163 CYS Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 674 SER Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 863 GLN Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1076 ARG Chi-restraints excluded: chain B residue 1114 VAL Chi-restraints excluded: chain B residue 1131 LEU Chi-restraints excluded: chain B residue 1218 ILE Chi-restraints excluded: chain T residue 424 MET Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 387 THR Chi-restraints excluded: chain I residue 405 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 336 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 291 optimal weight: 10.0000 chunk 391 optimal weight: 50.0000 chunk 217 optimal weight: 2.9990 chunk 282 optimal weight: 40.0000 chunk 27 optimal weight: 1.9990 chunk 334 optimal weight: 2.9990 chunk 196 optimal weight: 0.0570 chunk 218 optimal weight: 1.9990 chunk 276 optimal weight: 10.0000 overall best weight: 1.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN A 152 GLN A 343 ASN A 353 ASN ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 GLN ** C 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 854 GLN ** C 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1016 GLN C1201 ASN B 152 GLN ** B1045 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 334 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.168499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.124471 restraints weight = 49040.296| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.59 r_work: 0.3347 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 32127 Z= 0.222 Angle : 0.599 15.383 43938 Z= 0.308 Chirality : 0.047 0.282 5036 Planarity : 0.004 0.083 5600 Dihedral : 4.777 56.772 4894 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.15 % Favored : 93.83 % Rotamer: Outliers : 3.46 % Allowed : 14.00 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -0.96 (0.13), residues: 4001 helix: 1.38 (0.20), residues: 761 sheet: 0.06 (0.18), residues: 782 loop : -1.62 (0.12), residues: 2458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 361 TYR 0.033 0.002 TYR C 712 PHE 0.026 0.002 PHE B 224 TRP 0.015 0.001 TRP B 344 HIS 0.010 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00533 (32025) covalent geometry : angle 0.57964 (43707) SS BOND : bond 0.00519 ( 75) SS BOND : angle 2.40219 ( 150) hydrogen bonds : bond 0.05444 ( 931) hydrogen bonds : angle 4.80242 ( 2586) link_BETA1-4 : bond 0.00341 ( 5) link_BETA1-4 : angle 1.34712 ( 15) link_NAG-ASN : bond 0.00373 ( 22) link_NAG-ASN : angle 1.72071 ( 66) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 3583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 597 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.6880 (OUTLIER) cc_final: 0.6610 (p90) REVERT: A 130 PHE cc_start: 0.8832 (m-80) cc_final: 0.8395 (m-80) REVERT: A 151 CYS cc_start: 0.5770 (OUTLIER) cc_final: 0.5396 (m) REVERT: A 160 HIS cc_start: 0.8192 (p90) cc_final: 0.7724 (p90) REVERT: A 255 GLU cc_start: 0.7038 (mt-10) cc_final: 0.6616 (mt-10) REVERT: A 289 GLU cc_start: 0.8357 (tp30) cc_final: 0.8017 (tp30) REVERT: A 359 LEU cc_start: 0.8701 (tp) cc_final: 0.8480 (tp) REVERT: A 365 VAL cc_start: 0.9072 (p) cc_final: 0.8861 (m) REVERT: A 500 LYS cc_start: 0.8168 (pptt) cc_final: 0.7625 (pptt) REVERT: A 555 LYS cc_start: 0.8310 (mtpp) cc_final: 0.7982 (ttmm) REVERT: A 768 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7771 (mt-10) REVERT: A 780 GLU cc_start: 0.8450 (tp30) cc_final: 0.8225 (mp0) REVERT: A 862 MET cc_start: 0.8852 (OUTLIER) cc_final: 0.8566 (mtp) REVERT: A 884 PHE cc_start: 0.8087 (m-10) cc_final: 0.7862 (m-10) REVERT: A 1013 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8217 (mp) REVERT: A 1064 ARG cc_start: 0.8524 (mtm110) cc_final: 0.8170 (ttm-80) REVERT: A 1095 ASP cc_start: 0.8284 (t0) cc_final: 0.8043 (t0) REVERT: C 34 ARG cc_start: 0.7600 (ptm160) cc_final: 0.7367 (ptm160) REVERT: C 41 ASP cc_start: 0.8096 (t0) cc_final: 0.7815 (t0) REVERT: C 111 LEU cc_start: 0.7676 (mm) cc_final: 0.7336 (mp) REVERT: C 309 PHE cc_start: -0.0965 (OUTLIER) cc_final: -0.1800 (p90) REVERT: C 614 ILE cc_start: 0.8889 (mm) cc_final: 0.8656 (mm) REVERT: C 711 PHE cc_start: 0.8027 (m-10) cc_final: 0.7824 (m-10) REVERT: C 831 GLU cc_start: 0.8481 (pt0) cc_final: 0.8267 (pt0) REVERT: C 845 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7257 (mp0) REVERT: C 883 ASP cc_start: 0.8342 (t70) cc_final: 0.8121 (t70) REVERT: C 885 LYS cc_start: 0.8542 (ttmm) cc_final: 0.8327 (ttpp) REVERT: C 1031 SER cc_start: 0.8573 (m) cc_final: 0.8244 (p) REVERT: C 1069 GLU cc_start: 0.8135 (tp30) cc_final: 0.7598 (tp30) REVERT: C 1075 ASP cc_start: 0.8095 (t0) cc_final: 0.7546 (t0) REVERT: C 1202 VAL cc_start: 0.8762 (m) cc_final: 0.8509 (p) REVERT: B 114 ASN cc_start: 0.8548 (t0) cc_final: 0.8219 (t0) REVERT: B 147 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7670 (mt-10) REVERT: B 149 THR cc_start: 0.7802 (OUTLIER) cc_final: 0.7386 (p) REVERT: B 153 TYR cc_start: 0.8339 (m-80) cc_final: 0.7968 (m-10) REVERT: B 155 MET cc_start: 0.7263 (mmm) cc_final: 0.6876 (mmm) REVERT: B 240 LEU cc_start: 0.6559 (OUTLIER) cc_final: 0.6203 (tt) REVERT: B 320 ARG cc_start: 0.8660 (ttm170) cc_final: 0.8361 (ttm-80) REVERT: B 334 ASN cc_start: 0.8033 (t0) cc_final: 0.7602 (t0) REVERT: B 623 ASP cc_start: 0.8613 (t0) cc_final: 0.8412 (t0) REVERT: B 744 ILE cc_start: 0.7839 (mm) cc_final: 0.7601 (mm) REVERT: B 821 ASN cc_start: 0.8413 (t0) cc_final: 0.7959 (t0) REVERT: B 933 ASP cc_start: 0.7620 (t0) cc_final: 0.7373 (t0) REVERT: B 1028 LYS cc_start: 0.8682 (mttt) cc_final: 0.8338 (mtpp) REVERT: B 1066 ASP cc_start: 0.7799 (OUTLIER) cc_final: 0.7185 (p0) REVERT: B 1069 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7393 (pm20) REVERT: B 1076 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.8203 (mtt180) REVERT: B 1131 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8357 (mp) REVERT: B 1167 ASP cc_start: 0.7309 (t70) cc_final: 0.6777 (t70) REVERT: B 1180 GLN cc_start: 0.8512 (tt0) cc_final: 0.8250 (tt0) REVERT: B 1200 LYS cc_start: 0.8630 (ptpp) cc_final: 0.8367 (ptpp) REVERT: T 424 MET cc_start: 0.0720 (OUTLIER) cc_final: -0.0105 (tmm) REVERT: I 406 GLU cc_start: 0.7631 (pm20) cc_final: 0.6968 (pp20) outliers start: 119 outliers final: 81 residues processed: 663 average time/residue: 0.1729 time to fit residues: 188.5263 Evaluate side-chains 684 residues out of total 3583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 590 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 630 GLN Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 746 TYR Chi-restraints excluded: chain A residue 862 MET Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 885 LYS Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1163 CYS Chi-restraints excluded: chain A residue 1218 ILE Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 140 GLN Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 309 PHE Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 423 CYS Chi-restraints excluded: chain C residue 577 PHE Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 674 SER Chi-restraints excluded: chain C residue 728 SER Chi-restraints excluded: chain C residue 820 SER Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1105 ARG Chi-restraints excluded: chain C residue 1152 SER Chi-restraints excluded: chain C residue 1163 CYS Chi-restraints excluded: chain C residue 1164 LEU Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 674 SER Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 863 GLN Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 943 ILE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1069 GLU Chi-restraints excluded: chain B residue 1076 ARG Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1114 VAL Chi-restraints excluded: chain B residue 1131 LEU Chi-restraints excluded: chain B residue 1218 ILE Chi-restraints excluded: chain T residue 424 MET Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 387 THR Chi-restraints excluded: chain I residue 405 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 309 optimal weight: 1.9990 chunk 296 optimal weight: 1.9990 chunk 239 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 163 optimal weight: 0.6980 chunk 167 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 207 optimal weight: 0.0670 overall best weight: 1.1524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN A 152 GLN ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 ASN ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 GLN C 265 GLN ** C 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 854 GLN C 954 GLN ** C 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1016 GLN C1180 GLN B 646 ASN B1045 GLN T 334 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.169112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.125018 restraints weight = 49181.945| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.62 r_work: 0.3359 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 32127 Z= 0.171 Angle : 0.610 22.092 43938 Z= 0.311 Chirality : 0.046 0.325 5036 Planarity : 0.004 0.083 5600 Dihedral : 4.802 55.854 4894 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 3.06 % Allowed : 14.82 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -0.96 (0.13), residues: 4001 helix: 1.42 (0.20), residues: 759 sheet: 0.06 (0.19), residues: 766 loop : -1.63 (0.12), residues: 2476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 361 TYR 0.032 0.002 TYR C 712 PHE 0.026 0.002 PHE C 24 TRP 0.016 0.001 TRP C 575 HIS 0.007 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00412 (32025) covalent geometry : angle 0.58378 (43707) SS BOND : bond 0.00571 ( 75) SS BOND : angle 2.85473 ( 150) hydrogen bonds : bond 0.05013 ( 931) hydrogen bonds : angle 4.80470 ( 2586) link_BETA1-4 : bond 0.00386 ( 5) link_BETA1-4 : angle 1.32573 ( 15) link_NAG-ASN : bond 0.00228 ( 22) link_NAG-ASN : angle 1.76279 ( 66) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 3583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 592 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.6888 (OUTLIER) cc_final: 0.6618 (p90) REVERT: A 130 PHE cc_start: 0.8832 (m-80) cc_final: 0.8393 (m-80) REVERT: A 160 HIS cc_start: 0.8166 (p90) cc_final: 0.7675 (p90) REVERT: A 255 GLU cc_start: 0.7029 (mt-10) cc_final: 0.6613 (mt-10) REVERT: A 289 GLU cc_start: 0.8359 (tp30) cc_final: 0.8017 (tp30) REVERT: A 359 LEU cc_start: 0.8697 (tp) cc_final: 0.8483 (tp) REVERT: A 365 VAL cc_start: 0.9067 (p) cc_final: 0.8852 (m) REVERT: A 431 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8511 (mt) REVERT: A 500 LYS cc_start: 0.8132 (pptt) cc_final: 0.7648 (pptt) REVERT: A 726 LEU cc_start: 0.8388 (tp) cc_final: 0.8124 (mp) REVERT: A 768 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7802 (mt-10) REVERT: A 780 GLU cc_start: 0.8441 (tp30) cc_final: 0.8231 (mp0) REVERT: A 831 GLU cc_start: 0.7286 (mp0) cc_final: 0.7035 (mp0) REVERT: A 884 PHE cc_start: 0.8060 (m-10) cc_final: 0.7837 (m-10) REVERT: A 1064 ARG cc_start: 0.8505 (mtm110) cc_final: 0.8168 (ttm-80) REVERT: A 1069 GLU cc_start: 0.8156 (pm20) cc_final: 0.7918 (pm20) REVERT: A 1095 ASP cc_start: 0.8287 (t0) cc_final: 0.8042 (t0) REVERT: C 34 ARG cc_start: 0.7556 (ptm160) cc_final: 0.7330 (ptm160) REVERT: C 41 ASP cc_start: 0.8093 (t0) cc_final: 0.7814 (t0) REVERT: C 91 LYS cc_start: 0.8647 (mttp) cc_final: 0.8395 (mttp) REVERT: C 111 LEU cc_start: 0.7651 (mm) cc_final: 0.7331 (mp) REVERT: C 309 PHE cc_start: -0.0941 (OUTLIER) cc_final: -0.1803 (p90) REVERT: C 614 ILE cc_start: 0.8897 (mm) cc_final: 0.8690 (mm) REVERT: C 711 PHE cc_start: 0.8017 (m-10) cc_final: 0.7802 (m-10) REVERT: C 831 GLU cc_start: 0.8480 (pt0) cc_final: 0.8244 (pt0) REVERT: C 845 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7189 (mp0) REVERT: C 879 VAL cc_start: 0.8368 (p) cc_final: 0.8074 (m) REVERT: C 883 ASP cc_start: 0.8322 (t70) cc_final: 0.8102 (t70) REVERT: C 1031 SER cc_start: 0.8587 (m) cc_final: 0.8264 (p) REVERT: C 1069 GLU cc_start: 0.8096 (tp30) cc_final: 0.7574 (tp30) REVERT: C 1075 ASP cc_start: 0.8060 (t0) cc_final: 0.7497 (t0) REVERT: C 1202 VAL cc_start: 0.8773 (m) cc_final: 0.8527 (p) REVERT: B 114 ASN cc_start: 0.8587 (t0) cc_final: 0.8249 (t0) REVERT: B 147 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7686 (mt-10) REVERT: B 149 THR cc_start: 0.7783 (OUTLIER) cc_final: 0.7345 (p) REVERT: B 153 TYR cc_start: 0.8313 (m-80) cc_final: 0.7934 (m-10) REVERT: B 155 MET cc_start: 0.7268 (mmm) cc_final: 0.6873 (mmm) REVERT: B 240 LEU cc_start: 0.6530 (OUTLIER) cc_final: 0.6163 (tt) REVERT: B 320 ARG cc_start: 0.8661 (ttm170) cc_final: 0.8363 (ttm-80) REVERT: B 334 ASN cc_start: 0.7959 (t0) cc_final: 0.7536 (t0) REVERT: B 623 ASP cc_start: 0.8567 (t0) cc_final: 0.8259 (t0) REVERT: B 744 ILE cc_start: 0.7825 (mm) cc_final: 0.7592 (mm) REVERT: B 821 ASN cc_start: 0.8431 (t0) cc_final: 0.7998 (t0) REVERT: B 933 ASP cc_start: 0.7574 (t0) cc_final: 0.7314 (t0) REVERT: B 1028 LYS cc_start: 0.8684 (mttt) cc_final: 0.8383 (mtpp) REVERT: B 1066 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7222 (p0) REVERT: B 1069 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7363 (pm20) REVERT: B 1076 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.8182 (mtt180) REVERT: B 1131 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8339 (mp) REVERT: B 1167 ASP cc_start: 0.7289 (t70) cc_final: 0.6760 (t70) REVERT: B 1180 GLN cc_start: 0.8500 (tt0) cc_final: 0.8229 (tt0) REVERT: B 1200 LYS cc_start: 0.8613 (ptpp) cc_final: 0.8352 (ptpp) REVERT: T 371 MET cc_start: -0.3445 (mmm) cc_final: -0.4116 (mmm) REVERT: T 424 MET cc_start: 0.0693 (OUTLIER) cc_final: -0.0181 (tmm) REVERT: I 406 GLU cc_start: 0.7646 (pm20) cc_final: 0.6996 (pp20) outliers start: 105 outliers final: 84 residues processed: 649 average time/residue: 0.1761 time to fit residues: 187.3136 Evaluate side-chains 682 residues out of total 3583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 587 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 630 GLN Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain A residue 862 MET Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1163 CYS Chi-restraints excluded: chain A residue 1218 ILE Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 309 PHE Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 423 CYS Chi-restraints excluded: chain C residue 577 PHE Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 674 SER Chi-restraints excluded: chain C residue 728 SER Chi-restraints excluded: chain C residue 820 SER Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1105 ARG Chi-restraints excluded: chain C residue 1163 CYS Chi-restraints excluded: chain C residue 1164 LEU Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 674 SER Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 863 GLN Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 943 ILE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1069 GLU Chi-restraints excluded: chain B residue 1076 ARG Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1114 VAL Chi-restraints excluded: chain B residue 1131 LEU Chi-restraints excluded: chain B residue 1173 LYS Chi-restraints excluded: chain B residue 1218 ILE Chi-restraints excluded: chain T residue 424 MET Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 387 THR Chi-restraints excluded: chain I residue 405 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 357 optimal weight: 40.0000 chunk 386 optimal weight: 0.0670 chunk 310 optimal weight: 2.9990 chunk 383 optimal weight: 50.0000 chunk 87 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 316 optimal weight: 1.9990 chunk 308 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN A 152 GLN A 353 ASN ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 ASN C 334 ASN ** C 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 954 GLN C1180 GLN ** B1045 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 334 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.168529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.124465 restraints weight = 49100.538| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.59 r_work: 0.3348 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 32127 Z= 0.201 Angle : 0.622 19.621 43938 Z= 0.318 Chirality : 0.047 0.299 5036 Planarity : 0.004 0.083 5600 Dihedral : 4.891 56.424 4894 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.37 % Favored : 93.60 % Rotamer: Outliers : 2.94 % Allowed : 14.85 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -0.99 (0.13), residues: 4001 helix: 1.40 (0.20), residues: 759 sheet: 0.02 (0.18), residues: 767 loop : -1.64 (0.12), residues: 2475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 361 TYR 0.031 0.002 TYR C 712 PHE 0.026 0.002 PHE C 24 TRP 0.016 0.001 TRP C 575 HIS 0.008 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00482 (32025) covalent geometry : angle 0.59679 (43707) SS BOND : bond 0.00540 ( 75) SS BOND : angle 2.77367 ( 150) hydrogen bonds : bond 0.05258 ( 931) hydrogen bonds : angle 4.79940 ( 2586) link_BETA1-4 : bond 0.00399 ( 5) link_BETA1-4 : angle 1.33245 ( 15) link_NAG-ASN : bond 0.00311 ( 22) link_NAG-ASN : angle 1.84434 ( 66) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8002 Ramachandran restraints generated. 4001 Oldfield, 0 Emsley, 4001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 3583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 595 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.6897 (OUTLIER) cc_final: 0.6648 (p90) REVERT: A 130 PHE cc_start: 0.8835 (m-80) cc_final: 0.8395 (m-80) REVERT: A 151 CYS cc_start: 0.5825 (OUTLIER) cc_final: 0.5442 (m) REVERT: A 160 HIS cc_start: 0.8151 (p90) cc_final: 0.7646 (p90) REVERT: A 255 GLU cc_start: 0.7060 (mt-10) cc_final: 0.6631 (mt-10) REVERT: A 289 GLU cc_start: 0.8332 (tp30) cc_final: 0.7979 (tp30) REVERT: A 365 VAL cc_start: 0.9078 (p) cc_final: 0.8861 (m) REVERT: A 431 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8533 (mt) REVERT: A 500 LYS cc_start: 0.8178 (pptt) cc_final: 0.7634 (pptt) REVERT: A 555 LYS cc_start: 0.8358 (mtpp) cc_final: 0.7862 (ttmm) REVERT: A 726 LEU cc_start: 0.8371 (tp) cc_final: 0.8109 (mp) REVERT: A 768 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7803 (mt-10) REVERT: A 780 GLU cc_start: 0.8506 (tp30) cc_final: 0.8275 (mp0) REVERT: A 831 GLU cc_start: 0.7364 (mp0) cc_final: 0.7092 (mp0) REVERT: A 884 PHE cc_start: 0.8096 (m-10) cc_final: 0.7852 (m-10) REVERT: A 1064 ARG cc_start: 0.8489 (mtm110) cc_final: 0.8139 (ttm-80) REVERT: A 1095 ASP cc_start: 0.8248 (t0) cc_final: 0.8002 (t0) REVERT: C 34 ARG cc_start: 0.7601 (ptm160) cc_final: 0.7349 (ptm160) REVERT: C 41 ASP cc_start: 0.8089 (t0) cc_final: 0.7804 (t0) REVERT: C 91 LYS cc_start: 0.8655 (mttp) cc_final: 0.8361 (mttp) REVERT: C 111 LEU cc_start: 0.7589 (mm) cc_final: 0.7262 (mp) REVERT: C 309 PHE cc_start: -0.0932 (OUTLIER) cc_final: -0.1788 (p90) REVERT: C 614 ILE cc_start: 0.8900 (mm) cc_final: 0.8687 (mm) REVERT: C 711 PHE cc_start: 0.8000 (m-10) cc_final: 0.7787 (m-10) REVERT: C 831 GLU cc_start: 0.8489 (pt0) cc_final: 0.8248 (pt0) REVERT: C 845 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7146 (mp0) REVERT: C 954 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.7646 (mt0) REVERT: C 1031 SER cc_start: 0.8567 (m) cc_final: 0.8221 (p) REVERT: C 1069 GLU cc_start: 0.8097 (tp30) cc_final: 0.7512 (tp30) REVERT: C 1075 ASP cc_start: 0.8090 (t0) cc_final: 0.7601 (t0) REVERT: C 1202 VAL cc_start: 0.8802 (m) cc_final: 0.8540 (p) REVERT: B 114 ASN cc_start: 0.8571 (t0) cc_final: 0.8230 (t0) REVERT: B 147 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7669 (mt-10) REVERT: B 149 THR cc_start: 0.7778 (OUTLIER) cc_final: 0.7333 (p) REVERT: B 153 TYR cc_start: 0.8314 (m-80) cc_final: 0.7917 (m-10) REVERT: B 155 MET cc_start: 0.7210 (mmm) cc_final: 0.6827 (mmm) REVERT: B 240 LEU cc_start: 0.6551 (OUTLIER) cc_final: 0.6173 (tt) REVERT: B 320 ARG cc_start: 0.8643 (ttm170) cc_final: 0.8341 (ttm-80) REVERT: B 334 ASN cc_start: 0.7971 (t0) cc_final: 0.7560 (t0) REVERT: B 744 ILE cc_start: 0.7789 (mm) cc_final: 0.7560 (mm) REVERT: B 821 ASN cc_start: 0.8474 (t0) cc_final: 0.8061 (t0) REVERT: B 933 ASP cc_start: 0.7589 (t0) cc_final: 0.7322 (t0) REVERT: B 1028 LYS cc_start: 0.8652 (mttt) cc_final: 0.8304 (mtpp) REVERT: B 1066 ASP cc_start: 0.7721 (OUTLIER) cc_final: 0.7013 (p0) REVERT: B 1069 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7173 (pm20) REVERT: B 1076 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.8181 (mtt180) REVERT: B 1131 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8322 (mp) REVERT: B 1167 ASP cc_start: 0.7358 (t70) cc_final: 0.6811 (t70) REVERT: B 1180 GLN cc_start: 0.8497 (tt0) cc_final: 0.8244 (tt0) REVERT: B 1200 LYS cc_start: 0.8613 (ptpp) cc_final: 0.8348 (ptpp) REVERT: T 424 MET cc_start: 0.0657 (OUTLIER) cc_final: -0.0211 (tmm) REVERT: I 406 GLU cc_start: 0.7664 (pm20) cc_final: 0.6984 (pp20) outliers start: 101 outliers final: 81 residues processed: 651 average time/residue: 0.1724 time to fit residues: 183.2832 Evaluate side-chains 686 residues out of total 3583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 592 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 630 GLN Chi-restraints excluded: chain A residue 746 TYR Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain A residue 862 MET Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1163 CYS Chi-restraints excluded: chain A residue 1218 ILE Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 309 PHE Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 423 CYS Chi-restraints excluded: chain C residue 577 PHE Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 674 SER Chi-restraints excluded: chain C residue 728 SER Chi-restraints excluded: chain C residue 820 SER Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1163 CYS Chi-restraints excluded: chain C residue 1164 LEU Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 863 GLN Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 943 ILE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1069 GLU Chi-restraints excluded: chain B residue 1076 ARG Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1114 VAL Chi-restraints excluded: chain B residue 1131 LEU Chi-restraints excluded: chain B residue 1173 LYS Chi-restraints excluded: chain B residue 1218 ILE Chi-restraints excluded: chain T residue 424 MET Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 387 THR Chi-restraints excluded: chain I residue 405 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 276 optimal weight: 5.9990 chunk 363 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 195 optimal weight: 0.3980 chunk 141 optimal weight: 9.9990 chunk 314 optimal weight: 0.6980 chunk 178 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 374 optimal weight: 20.0000 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN A 152 GLN A 353 ASN ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 854 GLN C 954 GLN C1180 GLN B 642 ASN B 646 ASN ** B1045 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 334 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.168538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.124093 restraints weight = 49077.723| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.57 r_work: 0.3346 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 32127 Z= 0.200 Angle : 0.622 17.615 43938 Z= 0.318 Chirality : 0.047 0.288 5036 Planarity : 0.004 0.079 5600 Dihedral : 4.936 56.516 4894 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.45 % Favored : 93.53 % Rotamer: Outliers : 2.88 % Allowed : 15.20 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.05 % 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: -1.00 (0.13), residues: 4001 helix: 1.35 (0.20), residues: 766 sheet: 0.02 (0.18), residues: 766 loop : -1.65 (0.12), residues: 2469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 361 TYR 0.031 0.002 TYR C 712 PHE 0.027 0.002 PHE C 24 TRP 0.021 0.001 TRP C 575 HIS 0.008 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00480 (32025) covalent geometry : angle 0.59885 (43707) SS BOND : bond 0.00527 ( 75) SS BOND : angle 2.68356 ( 150) hydrogen bonds : bond 0.05271 ( 931) hydrogen bonds : angle 4.78375 ( 2586) link_BETA1-4 : bond 0.00393 ( 5) link_BETA1-4 : angle 1.31770 ( 15) link_NAG-ASN : bond 0.00293 ( 22) link_NAG-ASN : angle 1.84520 ( 66) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12062.54 seconds wall clock time: 205 minutes 39.53 seconds (12339.53 seconds total)