Starting phenix.real_space_refine on Sun Jul 5 00:40:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zh1_14717/07_2026/7zh1_14717.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zh1_14717/07_2026/7zh1_14717.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zh1_14717/07_2026/7zh1_14717.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zh1_14717/07_2026/7zh1_14717.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7zh1_14717/07_2026/7zh1_14717.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zh1_14717/07_2026/7zh1_14717.cif" model { file = "/net/cci-nas-00/data/ceres_data/7zh1_14717/07_2026/7zh1_14717.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zh1_14717/07_2026/7zh1_14717.cif" } resolution = 2.48 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= 0.001 sd= 0.013 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 132 5.16 5 C 15651 2.51 5 N 3996 2.21 5 O 4722 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24501 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 7979 Classifications: {'peptide': 1020} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 48, 'TRANS': 971} Chain breaks: 6 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 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 chiralities: 2 Chain: "A" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 160 Unusual residues: {'EIC': 1, 'NAG': 10} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Restraints were copied for chains: B, C, E, F Time building chain proxies: 8.93, per 1000 atoms: 0.36 Number of scatterers: 24501 At special positions: 0 Unit cell: (128.1, 137.55, 169.05, 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 132 16.00 O 4722 8.00 N 3996 7.00 C 15651 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.02 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 288 " distance=2.03 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 348 " distance=2.06 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 511 " distance=2.03 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 474 " distance=2.03 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 635 " distance=2.05 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.03 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS A 822 " - pdb=" SG CYS A 833 " distance=2.04 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 159 " distance=2.02 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 159 " distance=2.02 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 288 " distance=2.03 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 288 " distance=2.04 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 348 " distance=2.06 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 348 " distance=2.06 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 511 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 511 " distance=2.03 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 474 " distance=2.03 Simple disulfide: pdb=" SG CYS C 467 " - pdb=" SG CYS C 474 " distance=2.03 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 635 " distance=2.05 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 635 " distance=2.05 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.03 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C 657 " distance=2.03 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.03 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B 822 " - pdb=" SG CYS B 833 " distance=2.04 Simple disulfide: pdb=" SG CYS C 822 " - pdb=" SG CYS C 833 " distance=2.04 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.03 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1302 " - " ASN A 109 " " NAG A1303 " - " ASN A 119 " " NAG A1304 " - " ASN A 158 " " NAG A1305 " - " ASN A 269 " " NAG A1306 " - " ASN A 318 " " NAG A1307 " - " ASN A 357 " " NAG A1308 " - " ASN A 602 " " NAG A1310 " - " ASN A 783 " " NAG B1302 " - " ASN B 109 " " NAG B1303 " - " ASN B 119 " " NAG B1304 " - " ASN B 158 " " NAG B1305 " - " ASN B 269 " " NAG B1306 " - " ASN B 318 " " NAG B1307 " - " ASN B 357 " " NAG B1308 " - " ASN B 602 " " NAG B1310 " - " ASN B 783 " " NAG C1302 " - " ASN C 109 " " NAG C1303 " - " ASN C 119 " " NAG C1304 " - " ASN C 158 " " NAG C1305 " - " ASN C 269 " " NAG C1306 " - " ASN C 318 " " NAG C1307 " - " ASN C 357 " " NAG C1308 " - " ASN C 602 " " NAG C1310 " - " ASN C 783 " " NAG D 1 " - " ASN A 227 " " NAG E 1 " - " ASN B 227 " " NAG F 1 " - " ASN C 227 " Time building additional restraints: 2.47 Conformation dependent library (CDL) restraints added in 908.0 milliseconds 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5742 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 48 sheets defined 26.1% alpha, 31.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 353 through 358 removed outlier: 3.538A pdb=" N ASN A 357 " --> pdb=" O VAL A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 376 removed outlier: 4.248A pdb=" N ASN A 375 " --> pdb=" O THR A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 397 removed outlier: 4.128A pdb=" N ARG A 395 " --> pdb=" O ASP A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 409 Processing helix chain 'A' and resid 425 through 430 removed outlier: 3.508A pdb=" N ALA A 430 " --> pdb=" O ARG A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 491 Processing helix chain 'A' and resid 719 through 724 Processing helix chain 'A' and resid 728 through 737 removed outlier: 3.510A pdb=" N ALA A 732 " --> pdb=" O SER A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 765 Processing helix chain 'A' and resid 798 through 808 Processing helix chain 'A' and resid 818 through 825 Processing helix chain 'A' and resid 830 through 838 Processing helix chain 'A' and resid 848 through 865 Processing helix chain 'A' and resid 879 through 892 Processing helix chain 'A' and resid 894 through 901 removed outlier: 3.897A pdb=" N LEU A 898 " --> pdb=" O THR A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 922 removed outlier: 3.628A pdb=" N THR A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 947 removed outlier: 6.168A pdb=" N VAL A 934 " --> pdb=" O LEU A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 950 No H-bonds generated for 'chain 'A' and resid 948 through 950' Processing helix chain 'A' and resid 958 through 966 removed outlier: 3.502A pdb=" N ILE A 962 " --> pdb=" O VAL A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 1015 removed outlier: 3.877A pdb=" N VAL A 973 " --> pdb=" O VAL A 969 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLN A 974 " --> pdb=" O GLU A 970 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 324 through 330 Processing helix chain 'B' and resid 353 through 358 removed outlier: 3.538A pdb=" N ASN B 357 " --> pdb=" O VAL B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 376 removed outlier: 4.248A pdb=" N ASN B 375 " --> pdb=" O THR B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 397 removed outlier: 4.128A pdb=" N ARG B 395 " --> pdb=" O ASP B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 409 Processing helix chain 'B' and resid 425 through 430 removed outlier: 3.508A pdb=" N ALA B 430 " --> pdb=" O ARG B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 491 Processing helix chain 'B' and resid 719 through 724 Processing helix chain 'B' and resid 728 through 737 removed outlier: 3.511A pdb=" N ALA B 732 " --> pdb=" O SER B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 765 Processing helix chain 'B' and resid 798 through 808 Processing helix chain 'B' and resid 818 through 825 Processing helix chain 'B' and resid 830 through 838 Processing helix chain 'B' and resid 848 through 865 Processing helix chain 'B' and resid 879 through 892 Processing helix chain 'B' and resid 894 through 901 removed outlier: 3.897A pdb=" N LEU B 898 " --> pdb=" O THR B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 922 removed outlier: 3.627A pdb=" N THR B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 928 through 947 removed outlier: 6.168A pdb=" N VAL B 934 " --> pdb=" O LEU B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 950 No H-bonds generated for 'chain 'B' and resid 948 through 950' Processing helix chain 'B' and resid 958 through 966 removed outlier: 3.503A pdb=" N ILE B 962 " --> pdb=" O VAL B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 1015 removed outlier: 3.878A pdb=" N VAL B 973 " --> pdb=" O VAL B 969 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLN B 974 " --> pdb=" O GLU B 970 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 291 Processing helix chain 'C' and resid 324 through 330 Processing helix chain 'C' and resid 353 through 358 removed outlier: 3.538A pdb=" N ASN C 357 " --> pdb=" O VAL C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 376 removed outlier: 4.248A pdb=" N ASN C 375 " --> pdb=" O THR C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 397 removed outlier: 4.128A pdb=" N ARG C 395 " --> pdb=" O ASP C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 409 Processing helix chain 'C' and resid 425 through 430 removed outlier: 3.508A pdb=" N ALA C 430 " --> pdb=" O ARG C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 491 Processing helix chain 'C' and resid 719 through 724 Processing helix chain 'C' and resid 728 through 737 removed outlier: 3.511A pdb=" N ALA C 732 " --> pdb=" O SER C 728 " (cutoff:3.500A) Processing helix chain 'C' and resid 741 through 765 Processing helix chain 'C' and resid 798 through 808 Processing helix chain 'C' and resid 818 through 825 Processing helix chain 'C' and resid 830 through 838 Processing helix chain 'C' and resid 848 through 865 Processing helix chain 'C' and resid 879 through 892 Processing helix chain 'C' and resid 894 through 901 removed outlier: 3.897A pdb=" N LEU C 898 " --> pdb=" O THR C 894 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 922 removed outlier: 3.628A pdb=" N THR C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 928 through 947 removed outlier: 6.168A pdb=" N VAL C 934 " --> pdb=" O LEU C 930 " (cutoff:3.500A) Processing helix chain 'C' and resid 948 through 950 No H-bonds generated for 'chain 'C' and resid 948 through 950' Processing helix chain 'C' and resid 958 through 966 removed outlier: 3.502A pdb=" N ILE C 962 " --> pdb=" O VAL C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 1015 removed outlier: 3.877A pdb=" N VAL C 973 " --> pdb=" O VAL C 969 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLN C 974 " --> pdb=" O GLU C 970 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 35 removed outlier: 3.716A pdb=" N THR A 31 " --> pdb=" O GLY A 68 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER A 64 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ASN A 65 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N TYR A 256 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE A 220 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LYS A 198 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 9.006A pdb=" N TYR A 200 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N LEU A 216 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL A 40 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 59 removed outlier: 4.195A pdb=" N ASP A 274 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 81 through 82 Processing sheet with id=AA4, first strand: chain 'A' and resid 81 through 82 removed outlier: 7.027A pdb=" N ASN A 230 " --> pdb=" O PHE A 103 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N PHE A 103 " --> pdb=" O ASN A 230 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ARG A 232 " --> pdb=" O TRP A 101 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N TRP A 101 " --> pdb=" O ARG A 232 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE A 234 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ARG A 99 " --> pdb=" O ASN A 118 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL A 123 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ILE A 164 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ILE A 125 " --> pdb=" O GLU A 162 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLU A 162 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ALA A 127 " --> pdb=" O THR A 160 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ASN A 129 " --> pdb=" O ASN A 158 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ASN A 158 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N GLU A 131 " --> pdb=" O ALA A 156 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ALA A 156 " --> pdb=" O GLU A 131 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 298 through 302 removed outlier: 4.351A pdb=" N VAL A 581 " --> pdb=" O THR A 302 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 312 through 315 removed outlier: 5.224A pdb=" N ASP A 560 " --> pdb=" O ILE A 573 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 341 through 345 removed outlier: 3.626A pdb=" N GLU A 341 " --> pdb=" O SER A 386 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL A 382 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ASN A 381 " --> pdb=" O GLU A 502 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N GLU A 502 " --> pdb=" O ASN A 381 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 341 through 345 removed outlier: 3.626A pdb=" N GLU A 341 " --> pdb=" O SER A 386 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL A 382 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 510 " --> pdb=" O PHE A 379 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 439 through 441 Processing sheet with id=AB1, first strand: chain 'A' and resid 640 through 641 removed outlier: 6.333A pdb=" N GLU A 640 " --> pdb=" O ALA A 676 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N THR A 678 " --> pdb=" O GLU A 640 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 683 through 685 removed outlier: 6.541A pdb=" N ALA A 683 " --> pdb=" O MET C 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 693 through 710 removed outlier: 6.821A pdb=" N GLN A1053 " --> pdb=" O THR A 698 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N PHE A 700 " --> pdb=" O PRO A1051 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ILE A 702 " --> pdb=" O TYR A1049 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N TYR A1049 " --> pdb=" O ILE A 702 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ILE A 704 " --> pdb=" O VAL A1047 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL A1047 " --> pdb=" O ILE A 704 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N THR A 706 " --> pdb=" O LEU A1045 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU A1045 " --> pdb=" O THR A 706 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL A 708 " --> pdb=" O VAL A1043 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL A1043 " --> pdb=" O VAL A 708 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N GLY A1041 " --> pdb=" O PRO A 710 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET A1032 " --> pdb=" O VAL A1047 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N TYR A1049 " --> pdb=" O HIS A1030 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N HIS A1030 " --> pdb=" O TYR A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 693 through 710 removed outlier: 6.821A pdb=" N GLN A1053 " --> pdb=" O THR A 698 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N PHE A 700 " --> pdb=" O PRO A1051 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ILE A 702 " --> pdb=" O TYR A1049 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N TYR A1049 " --> pdb=" O ILE A 702 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ILE A 704 " --> pdb=" O VAL A1047 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL A1047 " --> pdb=" O ILE A 704 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N THR A 706 " --> pdb=" O LEU A1045 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU A1045 " --> pdb=" O THR A 706 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL A 708 " --> pdb=" O VAL A1043 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL A1043 " --> pdb=" O VAL A 708 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N GLY A1041 " --> pdb=" O PRO A 710 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N THR A1058 " --> pdb=" O PHE A1079 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N PHE A1077 " --> pdb=" O ALA A1060 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 715 through 718 removed outlier: 4.468A pdb=" N LYS A 715 " --> pdb=" O LEU A 843 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 769 through 771 Processing sheet with id=AB7, first strand: chain 'A' and resid 778 through 779 Processing sheet with id=AB8, first strand: chain 'A' and resid 1070 through 1071 Processing sheet with id=AB9, first strand: chain 'B' and resid 31 through 35 removed outlier: 3.716A pdb=" N THR B 31 " --> pdb=" O GLY B 68 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER B 64 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE B 220 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N LYS B 198 " --> pdb=" O PRO B 218 " (cutoff:3.500A) removed outlier: 9.006A pdb=" N TYR B 200 " --> pdb=" O LEU B 216 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N LEU B 216 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL B 40 " --> pdb=" O LEU B 216 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 51 through 59 removed outlier: 4.195A pdb=" N ASP B 274 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 81 through 82 Processing sheet with id=AC3, first strand: chain 'B' and resid 81 through 82 removed outlier: 7.027A pdb=" N ASN B 230 " --> pdb=" O PHE B 103 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N PHE B 103 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ARG B 232 " --> pdb=" O TRP B 101 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N TRP B 101 " --> pdb=" O ARG B 232 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE B 234 " --> pdb=" O ARG B 99 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ARG B 99 " --> pdb=" O ASN B 118 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL B 123 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ILE B 164 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ILE B 125 " --> pdb=" O GLU B 162 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLU B 162 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ALA B 127 " --> pdb=" O THR B 160 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ASN B 129 " --> pdb=" O ASN B 158 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ASN B 158 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N GLU B 131 " --> pdb=" O ALA B 156 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N ALA B 156 " --> pdb=" O GLU B 131 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 298 through 302 removed outlier: 4.351A pdb=" N VAL B 581 " --> pdb=" O THR B 302 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 312 through 315 removed outlier: 5.224A pdb=" N ASP B 560 " --> pdb=" O ILE B 573 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 341 through 345 removed outlier: 3.625A pdb=" N GLU B 341 " --> pdb=" O SER B 386 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL B 382 " --> pdb=" O ILE B 345 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ASN B 381 " --> pdb=" O GLU B 502 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N GLU B 502 " --> pdb=" O ASN B 381 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 341 through 345 removed outlier: 3.625A pdb=" N GLU B 341 " --> pdb=" O SER B 386 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL B 382 " --> pdb=" O ILE B 345 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL B 510 " --> pdb=" O PHE B 379 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 439 through 441 Processing sheet with id=AC9, first strand: chain 'B' and resid 640 through 641 removed outlier: 6.333A pdb=" N GLU B 640 " --> pdb=" O ALA B 676 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N THR B 678 " --> pdb=" O GLU B 640 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE B 656 " --> pdb=" O ILE B 652 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 693 through 710 removed outlier: 6.821A pdb=" N GLN B1053 " --> pdb=" O THR B 698 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N PHE B 700 " --> pdb=" O PRO B1051 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ILE B 702 " --> pdb=" O TYR B1049 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N TYR B1049 " --> pdb=" O ILE B 702 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ILE B 704 " --> pdb=" O VAL B1047 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL B1047 " --> pdb=" O ILE B 704 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N THR B 706 " --> pdb=" O LEU B1045 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU B1045 " --> pdb=" O THR B 706 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL B 708 " --> pdb=" O VAL B1043 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL B1043 " --> pdb=" O VAL B 708 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N GLY B1041 " --> pdb=" O PRO B 710 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET B1032 " --> pdb=" O VAL B1047 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N TYR B1049 " --> pdb=" O HIS B1030 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N HIS B1030 " --> pdb=" O TYR B1049 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 693 through 710 removed outlier: 6.821A pdb=" N GLN B1053 " --> pdb=" O THR B 698 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N PHE B 700 " --> pdb=" O PRO B1051 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ILE B 702 " --> pdb=" O TYR B1049 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N TYR B1049 " --> pdb=" O ILE B 702 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ILE B 704 " --> pdb=" O VAL B1047 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL B1047 " --> pdb=" O ILE B 704 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N THR B 706 " --> pdb=" O LEU B1045 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU B1045 " --> pdb=" O THR B 706 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL B 708 " --> pdb=" O VAL B1043 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL B1043 " --> pdb=" O VAL B 708 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N GLY B1041 " --> pdb=" O PRO B 710 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N THR B1058 " --> pdb=" O PHE B1079 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N PHE B1077 " --> pdb=" O ALA B1060 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 715 through 718 removed outlier: 4.469A pdb=" N LYS B 715 " --> pdb=" O LEU B 843 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 769 through 771 Processing sheet with id=AD5, first strand: chain 'B' and resid 778 through 779 Processing sheet with id=AD6, first strand: chain 'B' and resid 1070 through 1071 Processing sheet with id=AD7, first strand: chain 'C' and resid 31 through 35 removed outlier: 3.715A pdb=" N THR C 31 " --> pdb=" O GLY C 68 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER C 64 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ASN C 65 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N TYR C 256 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE C 220 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N LYS C 198 " --> pdb=" O PRO C 218 " (cutoff:3.500A) removed outlier: 9.006A pdb=" N TYR C 200 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N LEU C 216 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL C 40 " --> pdb=" O LEU C 216 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 51 through 59 removed outlier: 4.194A pdb=" N ASP C 274 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 81 through 82 Processing sheet with id=AE1, first strand: chain 'C' and resid 81 through 82 removed outlier: 7.028A pdb=" N ASN C 230 " --> pdb=" O PHE C 103 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N PHE C 103 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ARG C 232 " --> pdb=" O TRP C 101 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N TRP C 101 " --> pdb=" O ARG C 232 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE C 234 " --> pdb=" O ARG C 99 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ARG C 99 " --> pdb=" O ASN C 118 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL C 123 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ILE C 164 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ILE C 125 " --> pdb=" O GLU C 162 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLU C 162 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ALA C 127 " --> pdb=" O THR C 160 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ASN C 129 " --> pdb=" O ASN C 158 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ASN C 158 " --> pdb=" O ASN C 129 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N GLU C 131 " --> pdb=" O ALA C 156 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ALA C 156 " --> pdb=" O GLU C 131 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 298 through 302 removed outlier: 4.352A pdb=" N VAL C 581 " --> pdb=" O THR C 302 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 312 through 315 removed outlier: 5.224A pdb=" N ASP C 560 " --> pdb=" O ILE C 573 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 341 through 345 removed outlier: 3.626A pdb=" N GLU C 341 " --> pdb=" O SER C 386 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL C 382 " --> pdb=" O ILE C 345 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ASN C 381 " --> pdb=" O GLU C 502 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N GLU C 502 " --> pdb=" O ASN C 381 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 341 through 345 removed outlier: 3.626A pdb=" N GLU C 341 " --> pdb=" O SER C 386 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL C 382 " --> pdb=" O ILE C 345 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL C 510 " --> pdb=" O PHE C 379 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 439 through 441 Processing sheet with id=AE7, first strand: chain 'C' and resid 640 through 641 removed outlier: 6.333A pdb=" N GLU C 640 " --> pdb=" O ALA C 676 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N THR C 678 " --> pdb=" O GLU C 640 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE C 656 " --> pdb=" O ILE C 652 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 693 through 710 removed outlier: 6.822A pdb=" N GLN C1053 " --> pdb=" O THR C 698 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N PHE C 700 " --> pdb=" O PRO C1051 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ILE C 702 " --> pdb=" O TYR C1049 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N TYR C1049 " --> pdb=" O ILE C 702 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ILE C 704 " --> pdb=" O VAL C1047 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL C1047 " --> pdb=" O ILE C 704 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR C 706 " --> pdb=" O LEU C1045 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU C1045 " --> pdb=" O THR C 706 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL C 708 " --> pdb=" O VAL C1043 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL C1043 " --> pdb=" O VAL C 708 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLY C1041 " --> pdb=" O PRO C 710 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET C1032 " --> pdb=" O VAL C1047 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N TYR C1049 " --> pdb=" O HIS C1030 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N HIS C1030 " --> pdb=" O TYR C1049 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 693 through 710 removed outlier: 6.822A pdb=" N GLN C1053 " --> pdb=" O THR C 698 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N PHE C 700 " --> pdb=" O PRO C1051 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ILE C 702 " --> pdb=" O TYR C1049 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N TYR C1049 " --> pdb=" O ILE C 702 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ILE C 704 " --> pdb=" O VAL C1047 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL C1047 " --> pdb=" O ILE C 704 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR C 706 " --> pdb=" O LEU C1045 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU C1045 " --> pdb=" O THR C 706 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL C 708 " --> pdb=" O VAL C1043 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL C1043 " --> pdb=" O VAL C 708 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLY C1041 " --> pdb=" O PRO C 710 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N THR C1058 " --> pdb=" O PHE C1079 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N PHE C1077 " --> pdb=" O ALA C1060 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 715 through 718 removed outlier: 4.468A pdb=" N LYS C 715 " --> pdb=" O LEU C 843 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 778 through 779 Processing sheet with id=AF3, first strand: chain 'C' and resid 1070 through 1071 1021 hydrogen bonds defined for protein. 2811 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.73 Time building geometry restraints manager: 3.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5714 1.33 - 1.46: 6608 1.46 - 1.58: 12557 1.58 - 1.71: 0 1.71 - 1.84: 180 Bond restraints: 25059 Sorted by residual: bond pdb=" N ILE A 428 " pdb=" CA ILE A 428 " ideal model delta sigma weight residual 1.452 1.498 -0.046 1.18e-02 7.18e+03 1.52e+01 bond pdb=" N ILE C 428 " pdb=" CA ILE C 428 " ideal model delta sigma weight residual 1.452 1.498 -0.046 1.18e-02 7.18e+03 1.51e+01 bond pdb=" N ILE B 428 " pdb=" CA ILE B 428 " ideal model delta sigma weight residual 1.452 1.498 -0.046 1.18e-02 7.18e+03 1.51e+01 bond pdb=" N CYS A 159 " pdb=" CA CYS A 159 " ideal model delta sigma weight residual 1.456 1.500 -0.043 1.22e-02 6.72e+03 1.26e+01 bond pdb=" N CYS C 159 " pdb=" CA CYS C 159 " ideal model delta sigma weight residual 1.456 1.500 -0.043 1.22e-02 6.72e+03 1.25e+01 ... (remaining 25054 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 32109 2.45 - 4.90: 1693 4.90 - 7.35: 199 7.35 - 9.80: 37 9.80 - 12.25: 9 Bond angle restraints: 34047 Sorted by residual: angle pdb=" O LYS C 929 " pdb=" C LYS C 929 " pdb=" N LEU C 930 " ideal model delta sigma weight residual 122.07 128.54 -6.47 1.03e+00 9.43e-01 3.95e+01 angle pdb=" O LYS A 929 " pdb=" C LYS A 929 " pdb=" N LEU A 930 " ideal model delta sigma weight residual 122.07 128.51 -6.44 1.03e+00 9.43e-01 3.91e+01 angle pdb=" O LYS B 929 " pdb=" C LYS B 929 " pdb=" N LEU B 930 " ideal model delta sigma weight residual 122.07 128.49 -6.42 1.03e+00 9.43e-01 3.89e+01 angle pdb=" CA LYS B 929 " pdb=" C LYS B 929 " pdb=" N LEU B 930 " ideal model delta sigma weight residual 117.07 110.50 6.57 1.14e+00 7.69e-01 3.32e+01 angle pdb=" CA LYS C 929 " pdb=" C LYS C 929 " pdb=" N LEU C 930 " ideal model delta sigma weight residual 117.07 110.50 6.57 1.14e+00 7.69e-01 3.32e+01 ... (remaining 34042 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 12852 17.74 - 35.48: 1233 35.48 - 53.22: 392 53.22 - 70.95: 88 70.95 - 88.69: 39 Dihedral angle restraints: 14604 sinusoidal: 5679 harmonic: 8925 Sorted by residual: dihedral pdb=" CB CYS C 725 " pdb=" SG CYS C 725 " pdb=" SG CYS C 731 " pdb=" CB CYS C 731 " ideal model delta sinusoidal sigma weight residual -86.00 -55.84 -30.16 1 1.00e+01 1.00e-02 1.30e+01 dihedral pdb=" CB CYS B 725 " pdb=" SG CYS B 725 " pdb=" SG CYS B 731 " pdb=" CB CYS B 731 " ideal model delta sinusoidal sigma weight residual -86.00 -55.85 -30.15 1 1.00e+01 1.00e-02 1.30e+01 dihedral pdb=" CB CYS A 725 " pdb=" SG CYS A 725 " pdb=" SG CYS A 731 " pdb=" CB CYS A 731 " ideal model delta sinusoidal sigma weight residual -86.00 -55.86 -30.14 1 1.00e+01 1.00e-02 1.30e+01 ... (remaining 14601 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.172: 3800 0.172 - 0.344: 105 0.344 - 0.516: 13 0.516 - 0.688: 0 0.688 - 0.860: 3 Chirality restraints: 3921 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.00e+01 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 6.97e+01 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 6.92e+01 ... (remaining 3918 not shown) Planarity restraints: 4386 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1310 " -0.350 2.00e-02 2.50e+03 3.00e-01 1.13e+03 pdb=" C7 NAG C1310 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG C1310 " -0.158 2.00e-02 2.50e+03 pdb=" N2 NAG C1310 " 0.532 2.00e-02 2.50e+03 pdb=" O7 NAG C1310 " -0.110 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1310 " 0.350 2.00e-02 2.50e+03 3.00e-01 1.12e+03 pdb=" C7 NAG B1310 " -0.086 2.00e-02 2.50e+03 pdb=" C8 NAG B1310 " 0.158 2.00e-02 2.50e+03 pdb=" N2 NAG B1310 " -0.532 2.00e-02 2.50e+03 pdb=" O7 NAG B1310 " 0.110 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1310 " -0.350 2.00e-02 2.50e+03 3.00e-01 1.12e+03 pdb=" C7 NAG A1310 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG A1310 " -0.158 2.00e-02 2.50e+03 pdb=" N2 NAG A1310 " 0.532 2.00e-02 2.50e+03 pdb=" O7 NAG A1310 " -0.110 2.00e-02 2.50e+03 ... (remaining 4383 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 441 2.68 - 3.23: 21834 3.23 - 3.79: 35048 3.79 - 4.34: 49877 4.34 - 4.90: 82607 Nonbonded interactions: 189807 Sorted by model distance: nonbonded pdb=" ND2 ASN A 699 " pdb=" C1 NAG A1309 " model vdw 2.120 3.550 nonbonded pdb=" ND2 ASN B 699 " pdb=" C1 NAG B1309 " model vdw 2.120 3.550 nonbonded pdb=" ND2 ASN C 699 " pdb=" C1 NAG C1309 " model vdw 2.121 3.550 nonbonded pdb=" O SER C 740 " pdb=" OG SER C 740 " model vdw 2.159 3.040 nonbonded pdb=" O SER A 740 " pdb=" OG SER A 740 " model vdw 2.160 3.040 ... (remaining 189802 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 26.970 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 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:6.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 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 : 0.007 0.084 25122 Z= 0.467 Angle : 1.182 12.254 34203 Z= 0.730 Chirality : 0.074 0.860 3921 Planarity : 0.016 0.300 4359 Dihedral : 16.656 88.692 8763 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.50 % Allowed : 4.31 % Favored : 95.20 % Rotamer: Outliers : 2.38 % Allowed : 18.33 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.14), residues: 3018 helix: 1.35 (0.18), residues: 732 sheet: 1.31 (0.22), residues: 513 loop : -1.27 (0.12), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 758 TYR 0.047 0.003 TYR A1070 PHE 0.086 0.002 PHE B 784 TRP 0.015 0.001 TRP B 868 HIS 0.006 0.002 HIS C1046 Details of bonding type rmsd/Z covalent geometry : bond 0.00717 / 0.46 (25059) covalent geometry : angle 1.14421 / 0.72 (34047) SS BOND : bond 0.01148 / 0.73 ( 33) SS BOND : angle 1.81105 / 1.31 ( 66) hydrogen bonds : bond 0.16134 / 10.52 ( 988) hydrogen bonds : angle 6.75981 / 4.69 ( 2811) link_BETA1-4 : bond 0.00372 / 0.19 ( 3) link_BETA1-4 : angle 5.54798 / 3.42 ( 9) link_NAG-ASN : bond 0.02908 / 1.75 ( 27) link_NAG-ASN : angle 5.81673 / 3.92 ( 81) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 338 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 ILE cc_start: 0.8392 (mm) cc_final: 0.7984 (mm) REVERT: A 504 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8101 (mt) REVERT: A 816 MET cc_start: 0.8335 (ttp) cc_final: 0.8057 (ttp) REVERT: B 96 ASN cc_start: 0.6405 (OUTLIER) cc_final: 0.5799 (p0) REVERT: B 164 ILE cc_start: 0.8557 (mm) cc_final: 0.8188 (mm) REVERT: B 449 ARG cc_start: 0.7807 (mtp180) cc_final: 0.7427 (mtm180) REVERT: B 741 PHE cc_start: 0.6173 (m-80) cc_final: 0.5724 (m-80) REVERT: B 917 GLN cc_start: 0.6781 (OUTLIER) cc_final: 0.6578 (tm-30) REVERT: B 1098 THR cc_start: 0.5697 (m) cc_final: 0.5304 (p) REVERT: C 96 ASN cc_start: 0.6527 (OUTLIER) cc_final: 0.5631 (p0) REVERT: C 99 ARG cc_start: 0.8242 (mmt90) cc_final: 0.8004 (mmt180) REVERT: C 201 GLN cc_start: 0.7023 (tt0) cc_final: 0.6793 (tt0) REVERT: C 741 PHE cc_start: 0.6157 (m-80) cc_final: 0.5577 (m-80) REVERT: C 889 ASN cc_start: 0.7919 (m110) cc_final: 0.7637 (m110) REVERT: C 1085 PHE cc_start: 0.6801 (m-80) cc_final: 0.6415 (m-80) outliers start: 63 outliers final: 18 residues processed: 377 average time/residue: 0.5430 time to fit residues: 237.4558 Evaluate side-chains 292 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 270 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 882 MET Chi-restraints excluded: chain A residue 883 GLN Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 1032 MET Chi-restraints excluded: chain A residue 1064 CYS Chi-restraints excluded: chain B residue 96 ASN Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain B residue 882 MET Chi-restraints excluded: chain B residue 917 GLN Chi-restraints excluded: chain B residue 1064 CYS Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 318 ASN Chi-restraints excluded: chain C residue 334 PHE Chi-restraints excluded: chain C residue 877 GLN Chi-restraints excluded: chain C residue 882 MET Chi-restraints excluded: chain C residue 1064 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.4980 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 0.0570 overall best weight: 2.3102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 122 ASN A 473 ASN A 737 GLN A 877 GLN A 895 GLN A 904 GLN B 122 ASN B 737 GLN B 827 ASN B 877 GLN C 122 ASN C 473 ASN C 737 GLN C 744 GLN C 877 GLN C1040 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.148670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.121092 restraints weight = 25857.316| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.65 r_work: 0.3123 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 25122 Z= 0.170 Angle : 0.679 10.936 34203 Z= 0.361 Chirality : 0.048 0.267 3921 Planarity : 0.005 0.043 4359 Dihedral : 6.719 85.311 3378 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.48 % Favored : 96.32 % Rotamer: Outliers : 2.95 % Allowed : 18.18 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.14), residues: 3018 helix: 1.93 (0.19), residues: 735 sheet: 1.31 (0.19), residues: 636 loop : -1.28 (0.13), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 426 TYR 0.023 0.002 TYR A 367 PHE 0.019 0.002 PHE C 805 TRP 0.013 0.002 TRP B 423 HIS 0.008 0.001 HIS B1046 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.17 (25059) covalent geometry : angle 0.66095 / 0.36 (34047) SS BOND : bond 0.00726 / 0.42 ( 33) SS BOND : angle 2.04338 / 1.37 ( 66) hydrogen bonds : bond 0.07757 / 5.00 ( 988) hydrogen bonds : angle 5.66250 / 3.99 ( 2811) link_BETA1-4 : bond 0.00547 / 0.28 ( 3) link_BETA1-4 : angle 1.95346 / 1.19 ( 9) link_NAG-ASN : bond 0.00453 / 0.27 ( 27) link_NAG-ASN : angle 2.65497 / 1.73 ( 81) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 287 time to evaluate : 0.832 Fit side-chains revert: symmetry clash REVERT: A 164 ILE cc_start: 0.8242 (mm) cc_final: 0.7998 (mm) REVERT: A 201 GLN cc_start: 0.7303 (tt0) cc_final: 0.7076 (tt0) REVERT: A 258 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7911 (mttp) REVERT: A 449 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.8496 (mtp180) REVERT: A 487 THR cc_start: 0.7068 (t) cc_final: 0.6796 (t) REVERT: A 709 MET cc_start: 0.9080 (OUTLIER) cc_final: 0.8858 (mtm) REVERT: A 747 ARG cc_start: 0.8386 (mtm-85) cc_final: 0.8129 (ttm110) REVERT: A 911 LYS cc_start: 0.7759 (OUTLIER) cc_final: 0.7511 (tttt) REVERT: A 917 GLN cc_start: 0.7306 (tm-30) cc_final: 0.6959 (tt0) REVERT: A 959 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8262 (tt) REVERT: A 1055 ARG cc_start: 0.5975 (ttp80) cc_final: 0.5733 (ttp80) REVERT: A 1088 GLN cc_start: 0.7215 (OUTLIER) cc_final: 0.6975 (mt0) REVERT: B 258 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7908 (mmtp) REVERT: B 546 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7814 (mm110) REVERT: B 886 TYR cc_start: 0.7735 (t80) cc_final: 0.7344 (t80) REVERT: B 911 LYS cc_start: 0.7812 (ttmp) cc_final: 0.7451 (tttt) REVERT: B 917 GLN cc_start: 0.7141 (tm-30) cc_final: 0.6929 (tm-30) REVERT: B 959 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8290 (tt) REVERT: B 1098 THR cc_start: 0.5597 (m) cc_final: 0.4971 (p) REVERT: C 417 MET cc_start: 0.9168 (ttm) cc_final: 0.8822 (ttp) REVERT: C 449 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8420 (mtp180) REVERT: C 546 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7971 (mm110) REVERT: C 640 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.6992 (mm-30) REVERT: C 769 GLN cc_start: 0.7750 (tp40) cc_final: 0.7372 (mt0) REVERT: C 877 GLN cc_start: 0.5667 (OUTLIER) cc_final: 0.5374 (tp-100) REVERT: C 904 GLN cc_start: 0.8034 (tt0) cc_final: 0.7801 (tt0) REVERT: C 911 LYS cc_start: 0.7940 (ttmm) cc_final: 0.7594 (tttt) REVERT: C 996 ARG cc_start: 0.8763 (mtt-85) cc_final: 0.8514 (mtt180) REVERT: C 1085 PHE cc_start: 0.7138 (m-80) cc_final: 0.6781 (m-80) REVERT: C 1088 GLN cc_start: 0.7409 (OUTLIER) cc_final: 0.6955 (pt0) REVERT: C 1098 THR cc_start: 0.5955 (m) cc_final: 0.5360 (p) outliers start: 78 outliers final: 26 residues processed: 336 average time/residue: 0.5920 time to fit residues: 228.6924 Evaluate side-chains 301 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 261 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 449 ARG Chi-restraints excluded: chain A residue 568 SER Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain A residue 882 MET Chi-restraints excluded: chain A residue 911 LYS Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1088 GLN Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 546 GLN Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain B residue 882 MET Chi-restraints excluded: chain B residue 883 GLN Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 972 GLU Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 128 CYS Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 546 GLN Chi-restraints excluded: chain C residue 561 SER Chi-restraints excluded: chain C residue 640 GLU Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 877 GLN Chi-restraints excluded: chain C residue 883 GLN Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 1088 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 64 optimal weight: 10.0000 chunk 240 optimal weight: 10.0000 chunk 102 optimal weight: 20.0000 chunk 279 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 chunk 94 optimal weight: 0.6980 chunk 260 optimal weight: 0.7980 chunk 239 optimal weight: 8.9990 chunk 236 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 284 optimal weight: 5.9990 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 280 GLN A 473 ASN A 908 GLN A1040 HIS A1056 ASN B 122 ASN B 181 HIS B 201 GLN B 280 GLN B 473 ASN B 827 ASN B 877 GLN B 908 GLN B1056 ASN B1065 HIS C 201 GLN C 280 GLN C 473 ASN C 917 GLN C1040 HIS C1053 GLN C1056 ASN ** C1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.144016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.116805 restraints weight = 25693.919| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.71 r_work: 0.3058 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 25122 Z= 0.210 Angle : 0.750 16.079 34203 Z= 0.403 Chirality : 0.050 0.204 3921 Planarity : 0.005 0.048 4359 Dihedral : 6.474 84.661 3342 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.24 % Favored : 95.56 % Rotamer: Outliers : 3.85 % Allowed : 16.10 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.14), residues: 3018 helix: 1.45 (0.18), residues: 753 sheet: 1.02 (0.20), residues: 645 loop : -1.57 (0.12), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1055 TYR 0.031 0.002 TYR B 367 PHE 0.022 0.002 PHE B 805 TRP 0.015 0.002 TRP B 423 HIS 0.010 0.002 HIS B1046 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.21 (25059) covalent geometry : angle 0.73416 / 0.40 (34047) SS BOND : bond 0.00848 / 0.51 ( 33) SS BOND : angle 2.55232 / 1.81 ( 66) hydrogen bonds : bond 0.09019 / 5.81 ( 988) hydrogen bonds : angle 5.77491 / 4.06 ( 2811) link_BETA1-4 : bond 0.00285 / 0.14 ( 3) link_BETA1-4 : angle 2.79959 / 1.69 ( 9) link_NAG-ASN : bond 0.00325 / 0.20 ( 27) link_NAG-ASN : angle 2.25695 / 1.52 ( 81) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 275 time to evaluate : 0.829 Fit side-chains REVERT: A 258 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7946 (mttp) REVERT: A 449 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.8542 (mtp180) REVERT: A 546 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7834 (mt0) REVERT: A 911 LYS cc_start: 0.7834 (OUTLIER) cc_final: 0.7560 (tttt) REVERT: A 917 GLN cc_start: 0.7423 (tm-30) cc_final: 0.7061 (tt0) REVERT: A 959 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8325 (tt) REVERT: A 1088 GLN cc_start: 0.7179 (OUTLIER) cc_final: 0.6925 (mt0) REVERT: B 45 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7304 (mp0) REVERT: B 258 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7891 (mmtp) REVERT: B 285 GLU cc_start: 0.7390 (tp30) cc_final: 0.7187 (tp30) REVERT: B 911 LYS cc_start: 0.7875 (ttmp) cc_final: 0.7529 (tttt) REVERT: B 917 GLN cc_start: 0.7174 (tm-30) cc_final: 0.6925 (tm-30) REVERT: B 959 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8496 (tt) REVERT: B 1088 GLN cc_start: 0.7258 (OUTLIER) cc_final: 0.6881 (pt0) REVERT: C 56 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.7864 (tt0) REVERT: C 417 MET cc_start: 0.9145 (ttm) cc_final: 0.8790 (ttp) REVERT: C 449 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.8509 (mtp180) REVERT: C 546 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7843 (mt0) REVERT: C 769 GLN cc_start: 0.7742 (OUTLIER) cc_final: 0.7485 (mt0) REVERT: C 877 GLN cc_start: 0.5982 (OUTLIER) cc_final: 0.5746 (tp-100) REVERT: C 904 GLN cc_start: 0.8227 (tt0) cc_final: 0.7944 (tt0) REVERT: C 996 ARG cc_start: 0.8854 (mtt-85) cc_final: 0.8514 (mtt180) REVERT: C 1020 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.8076 (mmtp) REVERT: C 1085 PHE cc_start: 0.7204 (m-80) cc_final: 0.6900 (m-80) REVERT: C 1088 GLN cc_start: 0.7385 (OUTLIER) cc_final: 0.6925 (pt0) outliers start: 102 outliers final: 37 residues processed: 340 average time/residue: 0.5829 time to fit residues: 227.2317 Evaluate side-chains 309 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 255 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 449 ARG Chi-restraints excluded: chain A residue 546 GLN Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain A residue 882 MET Chi-restraints excluded: chain A residue 911 LYS Chi-restraints excluded: chain A residue 915 GLN Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1088 GLN Chi-restraints excluded: chain A residue 1099 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain B residue 882 MET Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 967 ASP Chi-restraints excluded: chain B residue 972 GLU Chi-restraints excluded: chain B residue 1088 GLN Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 546 GLN Chi-restraints excluded: chain C residue 561 SER Chi-restraints excluded: chain C residue 631 THR Chi-restraints excluded: chain C residue 640 GLU Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 769 GLN Chi-restraints excluded: chain C residue 877 GLN Chi-restraints excluded: chain C residue 883 GLN Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 972 GLU Chi-restraints excluded: chain C residue 1020 LYS Chi-restraints excluded: chain C residue 1088 GLN Chi-restraints excluded: chain C residue 1099 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 279 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 128 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 201 optimal weight: 4.9990 chunk 87 optimal weight: 0.4980 chunk 220 optimal weight: 9.9990 chunk 273 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 889 ASN A 895 GLN A 937 ASN A1053 GLN A1056 ASN B 181 HIS B 473 ASN B 769 GLN B 827 ASN B1040 HIS B1056 ASN C 473 ASN C1040 HIS C1056 ASN ** C1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.144634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.117778 restraints weight = 25659.536| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.64 r_work: 0.3066 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 25122 Z= 0.181 Angle : 0.680 12.397 34203 Z= 0.366 Chirality : 0.048 0.230 3921 Planarity : 0.005 0.050 4359 Dihedral : 6.470 84.466 3342 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.58 % Favored : 96.22 % Rotamer: Outliers : 3.59 % Allowed : 16.10 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.14), residues: 3018 helix: 1.48 (0.19), residues: 735 sheet: 0.80 (0.19), residues: 633 loop : -1.56 (0.13), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 797 TYR 0.027 0.002 TYR A 367 PHE 0.015 0.002 PHE C 578 TRP 0.015 0.002 TRP B 423 HIS 0.010 0.001 HIS C1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.18 (25059) covalent geometry : angle 0.66432 / 0.36 (34047) SS BOND : bond 0.00583 / 0.36 ( 33) SS BOND : angle 2.40428 / 1.71 ( 66) hydrogen bonds : bond 0.08232 / 5.31 ( 988) hydrogen bonds : angle 5.65185 / 3.98 ( 2811) link_BETA1-4 : bond 0.00108 / 0.05 ( 3) link_BETA1-4 : angle 2.21514 / 1.33 ( 9) link_NAG-ASN : bond 0.00305 / 0.20 ( 27) link_NAG-ASN : angle 2.10905 / 1.42 ( 81) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 266 time to evaluate : 1.019 Fit side-chains REVERT: A 56 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.8018 (tm-30) REVERT: A 258 LYS cc_start: 0.8308 (mtpp) cc_final: 0.7949 (mttp) REVERT: A 449 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.8525 (mtp180) REVERT: A 546 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7873 (mt0) REVERT: A 709 MET cc_start: 0.9271 (mtp) cc_final: 0.8974 (mtm) REVERT: A 911 LYS cc_start: 0.7868 (tppp) cc_final: 0.7603 (tttt) REVERT: A 959 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8305 (tt) REVERT: A 1088 GLN cc_start: 0.7110 (OUTLIER) cc_final: 0.6863 (mt0) REVERT: B 155 ASN cc_start: 0.5407 (OUTLIER) cc_final: 0.5105 (t0) REVERT: B 258 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7820 (mmtp) REVERT: B 722 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8350 (ttm) REVERT: B 784 PHE cc_start: 0.8502 (m-80) cc_final: 0.8258 (m-80) REVERT: B 917 GLN cc_start: 0.7212 (tm-30) cc_final: 0.6971 (tm-30) REVERT: B 959 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8480 (tt) REVERT: B 1020 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8105 (mmtp) REVERT: C 56 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.7899 (tm-30) REVERT: C 417 MET cc_start: 0.9138 (ttm) cc_final: 0.8736 (ttp) REVERT: C 449 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.8563 (mtp180) REVERT: C 546 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7876 (mt0) REVERT: C 640 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7185 (mm-30) REVERT: C 643 ASP cc_start: 0.6981 (OUTLIER) cc_final: 0.6636 (t0) REVERT: C 769 GLN cc_start: 0.7764 (tp40) cc_final: 0.7499 (mt0) REVERT: C 877 GLN cc_start: 0.5834 (OUTLIER) cc_final: 0.5612 (tp-100) REVERT: C 904 GLN cc_start: 0.8254 (tt0) cc_final: 0.7968 (tt0) REVERT: C 917 GLN cc_start: 0.7578 (tt0) cc_final: 0.7307 (tt0) REVERT: C 996 ARG cc_start: 0.8794 (mtt-85) cc_final: 0.8538 (mtt180) REVERT: C 1020 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.8058 (mmtp) REVERT: C 1085 PHE cc_start: 0.7227 (m-80) cc_final: 0.6906 (m-80) REVERT: C 1088 GLN cc_start: 0.7323 (OUTLIER) cc_final: 0.6898 (pt0) outliers start: 95 outliers final: 43 residues processed: 328 average time/residue: 0.5934 time to fit residues: 224.2131 Evaluate side-chains 316 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 255 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 449 ARG Chi-restraints excluded: chain A residue 546 GLN Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain A residue 769 GLN Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 882 MET Chi-restraints excluded: chain A residue 915 GLN Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1088 GLN Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 722 MET Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain B residue 882 MET Chi-restraints excluded: chain B residue 883 GLN Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 972 GLU Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1020 LYS Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 546 GLN Chi-restraints excluded: chain C residue 561 SER Chi-restraints excluded: chain C residue 640 GLU Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 792 LEU Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 877 GLN Chi-restraints excluded: chain C residue 883 GLN Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 915 GLN Chi-restraints excluded: chain C residue 1020 LYS Chi-restraints excluded: chain C residue 1088 GLN Chi-restraints excluded: chain C residue 1099 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 199 optimal weight: 9.9990 chunk 177 optimal weight: 0.6980 chunk 135 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 247 optimal weight: 10.0000 chunk 54 optimal weight: 0.0670 chunk 224 optimal weight: 6.9990 chunk 118 optimal weight: 0.9980 chunk 160 optimal weight: 8.9990 chunk 228 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 overall best weight: 1.3522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 129 ASN A 201 GLN A 304 ASN A 877 GLN A 937 ASN A1040 HIS A1056 ASN B 129 ASN B 181 HIS B 473 ASN B 827 ASN C 129 ASN C 304 ASN C 473 ASN C 827 ASN C1040 HIS C1056 ASN C1065 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.147344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.120459 restraints weight = 25778.703| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.62 r_work: 0.3124 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 25122 Z= 0.130 Angle : 0.571 9.756 34203 Z= 0.305 Chirality : 0.044 0.191 3921 Planarity : 0.004 0.047 4359 Dihedral : 6.113 81.984 3342 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.78 % Favored : 96.09 % Rotamer: Outliers : 2.53 % Allowed : 17.12 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.14), residues: 3018 helix: 1.97 (0.19), residues: 717 sheet: 1.02 (0.19), residues: 663 loop : -1.49 (0.13), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1055 TYR 0.019 0.001 TYR C 352 PHE 0.016 0.001 PHE A1092 TRP 0.012 0.001 TRP B 423 HIS 0.007 0.001 HIS C1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.13 (25059) covalent geometry : angle 0.55686 / 0.30 (34047) SS BOND : bond 0.00704 / 0.41 ( 33) SS BOND : angle 2.03937 / 1.44 ( 66) hydrogen bonds : bond 0.06529 / 4.20 ( 988) hydrogen bonds : angle 5.34901 / 3.77 ( 2811) link_BETA1-4 : bond 0.00256 / 0.13 ( 3) link_BETA1-4 : angle 1.57180 / 0.96 ( 9) link_NAG-ASN : bond 0.00183 / 0.11 ( 27) link_NAG-ASN : angle 1.86602 / 1.27 ( 81) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 265 time to evaluate : 0.789 Fit side-chains REVERT: A 164 ILE cc_start: 0.8242 (mm) cc_final: 0.8004 (mm) REVERT: A 258 LYS cc_start: 0.8295 (mtpp) cc_final: 0.7922 (mttp) REVERT: A 333 LYS cc_start: 0.8187 (mtpt) cc_final: 0.7843 (mmmt) REVERT: A 546 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7786 (mt0) REVERT: A 572 ASP cc_start: 0.8402 (m-30) cc_final: 0.8156 (m-30) REVERT: A 709 MET cc_start: 0.9252 (mtp) cc_final: 0.8957 (mtm) REVERT: A 747 ARG cc_start: 0.8287 (mtm-85) cc_final: 0.8020 (ttm110) REVERT: A 911 LYS cc_start: 0.7819 (tppp) cc_final: 0.7590 (ttmm) REVERT: A 959 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8301 (tt) REVERT: A 1020 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.8155 (mmtp) REVERT: A 1088 GLN cc_start: 0.6865 (OUTLIER) cc_final: 0.5902 (mm-40) REVERT: B 190 LYS cc_start: 0.8166 (mttt) cc_final: 0.7816 (tppt) REVERT: B 258 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7785 (mmtp) REVERT: B 758 ARG cc_start: 0.7985 (ttp80) cc_final: 0.7645 (ttp-170) REVERT: B 911 LYS cc_start: 0.7992 (ttmm) cc_final: 0.7578 (mtpp) REVERT: B 917 GLN cc_start: 0.7244 (tm-30) cc_final: 0.7023 (tm-30) REVERT: B 959 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8433 (tt) REVERT: B 1020 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.8055 (mmtp) REVERT: C 417 MET cc_start: 0.9108 (ttm) cc_final: 0.8746 (ttp) REVERT: C 433 THR cc_start: 0.7430 (p) cc_final: 0.7036 (t) REVERT: C 449 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.8559 (mtp180) REVERT: C 514 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8200 (tttp) REVERT: C 546 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7793 (mt0) REVERT: C 643 ASP cc_start: 0.6789 (OUTLIER) cc_final: 0.6444 (t0) REVERT: C 769 GLN cc_start: 0.7695 (tp40) cc_final: 0.7419 (mt0) REVERT: C 877 GLN cc_start: 0.5755 (OUTLIER) cc_final: 0.5260 (tp-100) REVERT: C 904 GLN cc_start: 0.8194 (tt0) cc_final: 0.7914 (tt0) REVERT: C 917 GLN cc_start: 0.7564 (tt0) cc_final: 0.7335 (tt0) REVERT: C 996 ARG cc_start: 0.8677 (mtt-85) cc_final: 0.8440 (mtt180) REVERT: C 1020 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.8035 (mmtp) REVERT: C 1085 PHE cc_start: 0.7301 (m-80) cc_final: 0.6960 (m-80) REVERT: C 1088 GLN cc_start: 0.7010 (OUTLIER) cc_final: 0.5940 (mm-40) outliers start: 67 outliers final: 26 residues processed: 309 average time/residue: 0.6012 time to fit residues: 212.6242 Evaluate side-chains 297 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 257 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 546 GLN Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 915 GLN Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1020 LYS Chi-restraints excluded: chain A residue 1088 GLN Chi-restraints excluded: chain A residue 1099 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 690 SER Chi-restraints excluded: chain B residue 769 GLN Chi-restraints excluded: chain B residue 883 GLN Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 972 GLU Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1020 LYS Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 514 LYS Chi-restraints excluded: chain C residue 546 GLN Chi-restraints excluded: chain C residue 561 SER Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 877 GLN Chi-restraints excluded: chain C residue 883 GLN Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 915 GLN Chi-restraints excluded: chain C residue 972 GLU Chi-restraints excluded: chain C residue 1020 LYS Chi-restraints excluded: chain C residue 1088 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 305 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 252 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 221 optimal weight: 6.9990 chunk 193 optimal weight: 5.9990 chunk 233 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 78 optimal weight: 9.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 GLN A 304 ASN A 937 ASN A1056 ASN B 129 ASN B 181 HIS B 473 ASN B 827 ASN B1056 ASN C 129 ASN C 304 ASN C 473 ASN C 827 ASN C 895 GLN C 951 ASN C1040 HIS C1056 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.144772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.117661 restraints weight = 25694.329| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.68 r_work: 0.3068 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 25122 Z= 0.171 Angle : 0.653 11.469 34203 Z= 0.350 Chirality : 0.047 0.184 3921 Planarity : 0.005 0.048 4359 Dihedral : 6.287 83.757 3336 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.88 % Favored : 96.02 % Rotamer: Outliers : 2.91 % Allowed : 16.74 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.14), residues: 3018 helix: 1.64 (0.19), residues: 732 sheet: 0.91 (0.20), residues: 618 loop : -1.59 (0.13), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 797 TYR 0.026 0.002 TYR A 367 PHE 0.014 0.002 PHE A 629 TRP 0.013 0.002 TRP B 423 HIS 0.008 0.001 HIS B1046 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.17 (25059) covalent geometry : angle 0.63775 / 0.35 (34047) SS BOND : bond 0.00591 / 0.36 ( 33) SS BOND : angle 2.33946 / 1.65 ( 66) hydrogen bonds : bond 0.07977 / 5.13 ( 988) hydrogen bonds : angle 5.53560 / 3.90 ( 2811) link_BETA1-4 : bond 0.00136 / 0.07 ( 3) link_BETA1-4 : angle 2.19399 / 1.32 ( 9) link_NAG-ASN : bond 0.00255 / 0.16 ( 27) link_NAG-ASN : angle 2.08113 / 1.42 ( 81) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 261 time to evaluate : 0.962 Fit side-chains revert: symmetry clash REVERT: A 56 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.7991 (tm-30) REVERT: A 258 LYS cc_start: 0.8318 (mtpp) cc_final: 0.7894 (mptt) REVERT: A 546 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7831 (mt0) REVERT: A 709 MET cc_start: 0.9275 (mtp) cc_final: 0.8972 (mtm) REVERT: A 911 LYS cc_start: 0.7876 (tppp) cc_final: 0.7637 (ttmm) REVERT: A 959 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8295 (tt) REVERT: A 1020 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.8070 (mmtp) REVERT: A 1088 GLN cc_start: 0.6923 (OUTLIER) cc_final: 0.5937 (mm-40) REVERT: B 190 LYS cc_start: 0.8257 (mttt) cc_final: 0.7913 (tppt) REVERT: B 258 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7809 (mmtp) REVERT: B 722 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8391 (ttm) REVERT: B 758 ARG cc_start: 0.8093 (ttp80) cc_final: 0.7687 (ttp-170) REVERT: B 917 GLN cc_start: 0.7259 (tm-30) cc_final: 0.7036 (tm-30) REVERT: B 959 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8491 (tt) REVERT: C 56 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.7885 (tt0) REVERT: C 417 MET cc_start: 0.9131 (ttm) cc_final: 0.8747 (ttp) REVERT: C 433 THR cc_start: 0.7503 (p) cc_final: 0.7004 (t) REVERT: C 449 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.8577 (mtp180) REVERT: C 514 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8214 (tttp) REVERT: C 546 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7830 (mt0) REVERT: C 640 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7131 (mm-30) REVERT: C 643 ASP cc_start: 0.6976 (OUTLIER) cc_final: 0.6622 (t0) REVERT: C 769 GLN cc_start: 0.7751 (OUTLIER) cc_final: 0.7454 (mt0) REVERT: C 904 GLN cc_start: 0.8221 (tt0) cc_final: 0.7938 (tt0) REVERT: C 917 GLN cc_start: 0.7624 (tt0) cc_final: 0.7337 (tt0) REVERT: C 996 ARG cc_start: 0.8786 (mtt-85) cc_final: 0.8539 (mtt180) REVERT: C 1085 PHE cc_start: 0.7298 (m-80) cc_final: 0.6987 (m-80) REVERT: C 1088 GLN cc_start: 0.7171 (OUTLIER) cc_final: 0.6011 (mm-40) outliers start: 77 outliers final: 44 residues processed: 316 average time/residue: 0.6487 time to fit residues: 234.8414 Evaluate side-chains 314 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 254 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 546 GLN Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 690 SER Chi-restraints excluded: chain A residue 769 GLN Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 882 MET Chi-restraints excluded: chain A residue 915 GLN Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1020 LYS Chi-restraints excluded: chain A residue 1088 GLN Chi-restraints excluded: chain A residue 1099 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 690 SER Chi-restraints excluded: chain B residue 722 MET Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 883 GLN Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 900 GLU Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 967 ASP Chi-restraints excluded: chain B residue 972 GLU Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 514 LYS Chi-restraints excluded: chain C residue 546 GLN Chi-restraints excluded: chain C residue 561 SER Chi-restraints excluded: chain C residue 631 THR Chi-restraints excluded: chain C residue 640 GLU Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 690 SER Chi-restraints excluded: chain C residue 769 GLN Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 883 GLN Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 915 GLN Chi-restraints excluded: chain C residue 972 GLU Chi-restraints excluded: chain C residue 1088 GLN Chi-restraints excluded: chain C residue 1099 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 77 optimal weight: 3.9990 chunk 218 optimal weight: 3.9990 chunk 266 optimal weight: 10.0000 chunk 125 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 188 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 138 optimal weight: 6.9990 chunk 294 optimal weight: 7.9990 chunk 114 optimal weight: 6.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 937 ASN A1040 HIS A1056 ASN A1101 ASN B 129 ASN B 181 HIS B 473 ASN B 827 ASN B 895 GLN B1056 ASN ** C 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 473 ASN C 827 ASN C 877 GLN C1040 HIS C1056 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.143301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.116467 restraints weight = 25693.822| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.63 r_work: 0.3050 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 25122 Z= 0.189 Angle : 0.687 12.834 34203 Z= 0.371 Chirality : 0.048 0.188 3921 Planarity : 0.005 0.051 4359 Dihedral : 6.327 58.959 3333 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.04 % Favored : 95.89 % Rotamer: Outliers : 3.21 % Allowed : 16.86 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.14), residues: 3018 helix: 1.47 (0.19), residues: 732 sheet: 0.90 (0.19), residues: 651 loop : -1.67 (0.13), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B1055 TYR 0.027 0.002 TYR B 367 PHE 0.021 0.002 PHE A1092 TRP 0.014 0.002 TRP B 423 HIS 0.009 0.001 HIS B1046 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.19 (25059) covalent geometry : angle 0.67203 / 0.37 (34047) SS BOND : bond 0.00650 / 0.40 ( 33) SS BOND : angle 2.44175 / 1.72 ( 66) hydrogen bonds : bond 0.08498 / 5.47 ( 988) hydrogen bonds : angle 5.64133 / 3.97 ( 2811) link_BETA1-4 : bond 0.00141 / 0.07 ( 3) link_BETA1-4 : angle 2.03923 / 1.23 ( 9) link_NAG-ASN : bond 0.00277 / 0.18 ( 27) link_NAG-ASN : angle 2.06527 / 1.42 ( 81) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 260 time to evaluate : 0.842 Fit side-chains revert: symmetry clash REVERT: A 56 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.7977 (tm-30) REVERT: A 258 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7839 (mptt) REVERT: A 333 LYS cc_start: 0.7743 (mmpt) cc_final: 0.7380 (mmmt) REVERT: A 546 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.7906 (mt0) REVERT: A 709 MET cc_start: 0.9302 (mtp) cc_final: 0.9002 (mtm) REVERT: A 911 LYS cc_start: 0.7892 (tppp) cc_final: 0.7661 (ttmm) REVERT: A 917 GLN cc_start: 0.7580 (tm-30) cc_final: 0.7129 (tt0) REVERT: A 959 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8297 (tt) REVERT: A 1088 GLN cc_start: 0.6965 (OUTLIER) cc_final: 0.6012 (mm-40) REVERT: B 190 LYS cc_start: 0.8267 (mttt) cc_final: 0.7937 (tppt) REVERT: B 226 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8213 (pt) REVERT: B 258 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7814 (mmtp) REVERT: B 722 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.8414 (ttm) REVERT: B 959 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8488 (tt) REVERT: C 56 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.7891 (tt0) REVERT: C 101 TRP cc_start: 0.9012 (OUTLIER) cc_final: 0.8077 (m-90) REVERT: C 232 ARG cc_start: 0.8891 (ttm170) cc_final: 0.8503 (ttt180) REVERT: C 248 SER cc_start: 0.6525 (OUTLIER) cc_final: 0.6135 (m) REVERT: C 417 MET cc_start: 0.9139 (ttm) cc_final: 0.8771 (ttp) REVERT: C 433 THR cc_start: 0.7528 (p) cc_final: 0.7035 (t) REVERT: C 449 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.8563 (mtp180) REVERT: C 514 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8216 (tttp) REVERT: C 546 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.7881 (mt0) REVERT: C 640 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7209 (mm-30) REVERT: C 643 ASP cc_start: 0.6986 (OUTLIER) cc_final: 0.6627 (t0) REVERT: C 769 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.7511 (mt0) REVERT: C 877 GLN cc_start: 0.5679 (tp40) cc_final: 0.5411 (tp-100) REVERT: C 904 GLN cc_start: 0.8295 (tt0) cc_final: 0.8002 (tt0) REVERT: C 917 GLN cc_start: 0.7595 (tt0) cc_final: 0.7357 (tt0) REVERT: C 996 ARG cc_start: 0.8842 (mtt-85) cc_final: 0.8580 (mtt180) REVERT: C 1020 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.8123 (mmtp) REVERT: C 1085 PHE cc_start: 0.7292 (m-80) cc_final: 0.7001 (m-80) REVERT: C 1088 GLN cc_start: 0.7226 (OUTLIER) cc_final: 0.6799 (pt0) outliers start: 85 outliers final: 48 residues processed: 319 average time/residue: 0.6038 time to fit residues: 221.1591 Evaluate side-chains 318 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 250 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 546 GLN Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 690 SER Chi-restraints excluded: chain A residue 769 GLN Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 882 MET Chi-restraints excluded: chain A residue 915 GLN Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1088 GLN Chi-restraints excluded: chain A residue 1099 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 690 SER Chi-restraints excluded: chain B residue 722 MET Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 883 GLN Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 900 GLU Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 967 ASP Chi-restraints excluded: chain B residue 972 GLU Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 101 TRP Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 514 LYS Chi-restraints excluded: chain C residue 546 GLN Chi-restraints excluded: chain C residue 561 SER Chi-restraints excluded: chain C residue 631 THR Chi-restraints excluded: chain C residue 640 GLU Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 690 SER Chi-restraints excluded: chain C residue 769 GLN Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 883 GLN Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 915 GLN Chi-restraints excluded: chain C residue 972 GLU Chi-restraints excluded: chain C residue 1020 LYS Chi-restraints excluded: chain C residue 1088 GLN Chi-restraints excluded: chain C residue 1099 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 192 optimal weight: 7.9990 chunk 116 optimal weight: 6.9990 chunk 233 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 108 optimal weight: 9.9990 chunk 242 optimal weight: 0.7980 chunk 136 optimal weight: 0.6980 chunk 113 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 196 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 877 GLN A 937 ASN A1101 ASN B 129 ASN B 181 HIS B 473 ASN B 827 ASN B1056 ASN C 32 GLN ** C 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 473 ASN C 827 ASN C1040 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.145867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.119240 restraints weight = 25790.098| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.62 r_work: 0.3094 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 25122 Z= 0.140 Angle : 0.592 12.159 34203 Z= 0.318 Chirality : 0.045 0.194 3921 Planarity : 0.004 0.049 4359 Dihedral : 6.012 59.682 3333 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.91 % Favored : 96.06 % Rotamer: Outliers : 2.42 % Allowed : 17.50 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.14), residues: 3018 helix: 1.70 (0.19), residues: 732 sheet: 0.95 (0.19), residues: 663 loop : -1.65 (0.13), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1055 TYR 0.021 0.001 TYR A 367 PHE 0.018 0.001 PHE A1092 TRP 0.012 0.001 TRP B 423 HIS 0.005 0.001 HIS B1046 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.14 (25059) covalent geometry : angle 0.57809 / 0.31 (34047) SS BOND : bond 0.00520 / 0.31 ( 33) SS BOND : angle 2.16723 / 1.53 ( 66) hydrogen bonds : bond 0.06972 / 4.48 ( 988) hydrogen bonds : angle 5.40724 / 3.81 ( 2811) link_BETA1-4 : bond 0.00246 / 0.13 ( 3) link_BETA1-4 : angle 1.73572 / 1.06 ( 9) link_NAG-ASN : bond 0.00184 / 0.11 ( 27) link_NAG-ASN : angle 1.84993 / 1.26 ( 81) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 258 time to evaluate : 0.890 Fit side-chains REVERT: A 122 ASN cc_start: 0.7651 (m110) cc_final: 0.7375 (m-40) REVERT: A 258 LYS cc_start: 0.8320 (mtpp) cc_final: 0.7861 (mptt) REVERT: A 333 LYS cc_start: 0.7784 (mmpt) cc_final: 0.7388 (mmmt) REVERT: A 546 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7845 (mt0) REVERT: A 709 MET cc_start: 0.9285 (mtp) cc_final: 0.8979 (mtm) REVERT: A 911 LYS cc_start: 0.7862 (tppp) cc_final: 0.7636 (ttmm) REVERT: A 959 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8317 (tt) REVERT: A 1088 GLN cc_start: 0.6835 (OUTLIER) cc_final: 0.5902 (mm-40) REVERT: B 190 LYS cc_start: 0.8075 (mttt) cc_final: 0.7803 (tppt) REVERT: B 258 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7832 (mmtp) REVERT: B 722 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.8363 (ttm) REVERT: B 911 LYS cc_start: 0.7971 (ttmm) cc_final: 0.7636 (mtpp) REVERT: B 959 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8465 (tt) REVERT: C 232 ARG cc_start: 0.8915 (ttm170) cc_final: 0.8546 (ttt180) REVERT: C 417 MET cc_start: 0.9125 (ttm) cc_final: 0.8780 (ttp) REVERT: C 433 THR cc_start: 0.7495 (p) cc_final: 0.7008 (t) REVERT: C 449 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.8571 (mtp180) REVERT: C 514 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.8198 (tttp) REVERT: C 546 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7866 (mt0) REVERT: C 640 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7115 (mm-30) REVERT: C 643 ASP cc_start: 0.6991 (OUTLIER) cc_final: 0.6624 (t0) REVERT: C 769 GLN cc_start: 0.7715 (tp40) cc_final: 0.7449 (mt0) REVERT: C 797 ARG cc_start: 0.7284 (mtm180) cc_final: 0.6647 (mtp-110) REVERT: C 877 GLN cc_start: 0.5565 (tp40) cc_final: 0.5196 (tp-100) REVERT: C 904 GLN cc_start: 0.8212 (tt0) cc_final: 0.7919 (tt0) REVERT: C 917 GLN cc_start: 0.7623 (tt0) cc_final: 0.7379 (tt0) REVERT: C 984 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.8254 (tt0) REVERT: C 996 ARG cc_start: 0.8739 (mtt-85) cc_final: 0.8494 (mtt180) REVERT: C 1020 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.8119 (mmtp) REVERT: C 1085 PHE cc_start: 0.7354 (m-80) cc_final: 0.7037 (m-80) REVERT: C 1088 GLN cc_start: 0.7021 (OUTLIER) cc_final: 0.5974 (mm-40) outliers start: 64 outliers final: 37 residues processed: 304 average time/residue: 0.6393 time to fit residues: 222.5618 Evaluate side-chains 308 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 257 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 546 GLN Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 690 SER Chi-restraints excluded: chain A residue 769 GLN Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 882 MET Chi-restraints excluded: chain A residue 915 GLN Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1088 GLN Chi-restraints excluded: chain A residue 1099 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 690 SER Chi-restraints excluded: chain B residue 722 MET Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 883 GLN Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 972 GLU Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 514 LYS Chi-restraints excluded: chain C residue 546 GLN Chi-restraints excluded: chain C residue 561 SER Chi-restraints excluded: chain C residue 631 THR Chi-restraints excluded: chain C residue 640 GLU Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 690 SER Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 883 GLN Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 915 GLN Chi-restraints excluded: chain C residue 984 GLN Chi-restraints excluded: chain C residue 1020 LYS Chi-restraints excluded: chain C residue 1088 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 187 optimal weight: 6.9990 chunk 281 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 172 optimal weight: 0.3980 chunk 212 optimal weight: 5.9990 chunk 163 optimal weight: 0.9990 chunk 145 optimal weight: 10.0000 chunk 300 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 146 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 937 ASN B 129 ASN B 181 HIS B 473 ASN B 827 ASN B1056 ASN ** C 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 473 ASN C 827 ASN C1040 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.143947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.117319 restraints weight = 25745.355| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.64 r_work: 0.3060 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 25122 Z= 0.173 Angle : 0.654 13.141 34203 Z= 0.353 Chirality : 0.047 0.241 3921 Planarity : 0.005 0.050 4359 Dihedral : 6.112 58.371 3333 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.04 % Favored : 95.92 % Rotamer: Outliers : 2.49 % Allowed : 17.46 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.14), residues: 3018 helix: 1.56 (0.19), residues: 732 sheet: 0.77 (0.20), residues: 633 loop : -1.61 (0.13), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B1055 TYR 0.026 0.002 TYR A 367 PHE 0.019 0.002 PHE A1092 TRP 0.013 0.002 TRP B 423 HIS 0.008 0.001 HIS B1046 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 (25059) covalent geometry : angle 0.63945 / 0.35 (34047) SS BOND : bond 0.00621 / 0.38 ( 33) SS BOND : angle 2.31402 / 1.63 ( 66) hydrogen bonds : bond 0.08043 / 5.17 ( 988) hydrogen bonds : angle 5.54522 / 3.91 ( 2811) link_BETA1-4 : bond 0.00170 / 0.09 ( 3) link_BETA1-4 : angle 1.96710 / 1.19 ( 9) link_NAG-ASN : bond 0.00229 / 0.14 ( 27) link_NAG-ASN : angle 1.95114 / 1.34 ( 81) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 259 time to evaluate : 1.076 Fit side-chains REVERT: A 122 ASN cc_start: 0.7692 (m110) cc_final: 0.7396 (m-40) REVERT: A 258 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7854 (mptt) REVERT: A 333 LYS cc_start: 0.7765 (mmpt) cc_final: 0.7370 (mmmt) REVERT: A 546 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.7879 (mt0) REVERT: A 709 MET cc_start: 0.9296 (mtp) cc_final: 0.8985 (mtm) REVERT: A 911 LYS cc_start: 0.7882 (tppp) cc_final: 0.7655 (ttmm) REVERT: A 917 GLN cc_start: 0.7585 (tm-30) cc_final: 0.7187 (tt0) REVERT: A 932 ASP cc_start: 0.8141 (m-30) cc_final: 0.7913 (m-30) REVERT: A 959 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8288 (tt) REVERT: A 1088 GLN cc_start: 0.6892 (OUTLIER) cc_final: 0.5940 (mm-40) REVERT: B 190 LYS cc_start: 0.8126 (mttt) cc_final: 0.7865 (tppt) REVERT: B 258 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7821 (mmtp) REVERT: B 722 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8364 (ttm) REVERT: B 784 PHE cc_start: 0.8510 (m-80) cc_final: 0.8252 (m-80) REVERT: B 959 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8487 (tt) REVERT: C 56 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.7892 (tt0) REVERT: C 232 ARG cc_start: 0.8900 (ttm170) cc_final: 0.8527 (ttt180) REVERT: C 248 SER cc_start: 0.6564 (OUTLIER) cc_final: 0.6206 (m) REVERT: C 417 MET cc_start: 0.9141 (ttm) cc_final: 0.8740 (ttp) REVERT: C 433 THR cc_start: 0.7513 (p) cc_final: 0.7014 (t) REVERT: C 449 ARG cc_start: 0.8838 (OUTLIER) cc_final: 0.8590 (mtp180) REVERT: C 514 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8202 (tttp) REVERT: C 546 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.7845 (mt0) REVERT: C 640 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7205 (mm-30) REVERT: C 643 ASP cc_start: 0.7063 (OUTLIER) cc_final: 0.6710 (t0) REVERT: C 769 GLN cc_start: 0.7765 (OUTLIER) cc_final: 0.7481 (mt0) REVERT: C 917 GLN cc_start: 0.7674 (tt0) cc_final: 0.7428 (tt0) REVERT: C 984 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.8293 (tt0) REVERT: C 996 ARG cc_start: 0.8802 (mtt-85) cc_final: 0.8541 (mtt180) REVERT: C 1020 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8023 (UNCLASSIFIED) REVERT: C 1085 PHE cc_start: 0.7344 (m-80) cc_final: 0.7048 (m-80) REVERT: C 1088 GLN cc_start: 0.7138 (OUTLIER) cc_final: 0.5980 (mm-40) outliers start: 66 outliers final: 41 residues processed: 308 average time/residue: 0.7010 time to fit residues: 247.3922 Evaluate side-chains 314 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 255 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain A residue 546 GLN Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 690 SER Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 882 MET Chi-restraints excluded: chain A residue 915 GLN Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1088 GLN Chi-restraints excluded: chain A residue 1099 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 690 SER Chi-restraints excluded: chain B residue 722 MET Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain B residue 883 GLN Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 967 ASP Chi-restraints excluded: chain B residue 972 GLU Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 514 LYS Chi-restraints excluded: chain C residue 546 GLN Chi-restraints excluded: chain C residue 561 SER Chi-restraints excluded: chain C residue 631 THR Chi-restraints excluded: chain C residue 640 GLU Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 690 SER Chi-restraints excluded: chain C residue 769 GLN Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 883 GLN Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 915 GLN Chi-restraints excluded: chain C residue 972 GLU Chi-restraints excluded: chain C residue 984 GLN Chi-restraints excluded: chain C residue 1020 LYS Chi-restraints excluded: chain C residue 1088 GLN Chi-restraints excluded: chain C residue 1099 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 13 optimal weight: 6.9990 chunk 131 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 255 optimal weight: 10.0000 chunk 111 optimal weight: 5.9990 chunk 213 optimal weight: 5.9990 chunk 269 optimal weight: 7.9990 chunk 242 optimal weight: 8.9990 chunk 150 optimal weight: 8.9990 chunk 143 optimal weight: 4.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 937 ASN B 129 ASN B 181 HIS B 473 ASN B 827 ASN B 895 GLN B1056 ASN ** C 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 473 ASN C 827 ASN C1040 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.142124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.115238 restraints weight = 25636.498| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.69 r_work: 0.3028 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 25122 Z= 0.235 Angle : 0.767 14.156 34203 Z= 0.416 Chirality : 0.052 0.221 3921 Planarity : 0.006 0.054 4359 Dihedral : 6.417 58.102 3333 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.54 % Favored : 95.43 % Rotamer: Outliers : 2.57 % Allowed : 17.38 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.14), residues: 3018 helix: 1.21 (0.19), residues: 735 sheet: 0.88 (0.20), residues: 660 loop : -1.77 (0.13), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 829 TYR 0.030 0.003 TYR B 367 PHE 0.020 0.003 PHE A1092 TRP 0.014 0.002 TRP B 423 HIS 0.012 0.002 HIS B1046 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.23 (25059) covalent geometry : angle 0.75194 / 0.41 (34047) SS BOND : bond 0.00795 / 0.49 ( 33) SS BOND : angle 2.60956 / 1.83 ( 66) hydrogen bonds : bond 0.09572 / 6.17 ( 988) hydrogen bonds : angle 5.82542 / 4.10 ( 2811) link_BETA1-4 : bond 0.00133 / 0.07 ( 3) link_BETA1-4 : angle 2.26335 / 1.39 ( 9) link_NAG-ASN : bond 0.00337 / 0.20 ( 27) link_NAG-ASN : angle 2.21721 / 1.51 ( 81) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 251 time to evaluate : 0.991 Fit side-chains REVERT: A 56 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.7963 (tm-30) REVERT: A 122 ASN cc_start: 0.7706 (m110) cc_final: 0.7409 (m-40) REVERT: A 258 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7833 (mptt) REVERT: A 333 LYS cc_start: 0.7670 (mmpt) cc_final: 0.7311 (mmmt) REVERT: A 546 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.7998 (mt0) REVERT: A 709 MET cc_start: 0.9306 (mtp) cc_final: 0.8976 (mtm) REVERT: A 917 GLN cc_start: 0.7523 (tm-30) cc_final: 0.7138 (tt0) REVERT: A 959 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8339 (tt) REVERT: A 1088 GLN cc_start: 0.6967 (OUTLIER) cc_final: 0.6616 (pt0) REVERT: B 190 LYS cc_start: 0.8270 (mttt) cc_final: 0.7976 (tppt) REVERT: B 226 ILE cc_start: 0.8574 (OUTLIER) cc_final: 0.8269 (pt) REVERT: B 258 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7868 (mmtp) REVERT: B 722 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.8414 (ttm) REVERT: B 784 PHE cc_start: 0.8523 (m-80) cc_final: 0.8259 (m-80) REVERT: B 959 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8502 (tt) REVERT: C 56 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.7864 (tt0) REVERT: C 232 ARG cc_start: 0.8867 (ttm170) cc_final: 0.8491 (ttt180) REVERT: C 433 THR cc_start: 0.7487 (p) cc_final: 0.6965 (t) REVERT: C 449 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8540 (mtp180) REVERT: C 514 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8199 (tttp) REVERT: C 546 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7922 (mt0) REVERT: C 640 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7243 (mm-30) REVERT: C 643 ASP cc_start: 0.7035 (OUTLIER) cc_final: 0.6693 (t0) REVERT: C 917 GLN cc_start: 0.7653 (tt0) cc_final: 0.7370 (tt0) REVERT: C 984 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.8331 (tt0) REVERT: C 1020 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.8087 (mmtp) REVERT: C 1085 PHE cc_start: 0.7258 (m-80) cc_final: 0.6989 (m-80) REVERT: C 1088 GLN cc_start: 0.7298 (OUTLIER) cc_final: 0.6848 (pt0) outliers start: 68 outliers final: 43 residues processed: 303 average time/residue: 0.6823 time to fit residues: 237.6756 Evaluate side-chains 310 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 249 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 546 GLN Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 690 SER Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 882 MET Chi-restraints excluded: chain A residue 915 GLN Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1088 GLN Chi-restraints excluded: chain A residue 1099 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 690 SER Chi-restraints excluded: chain B residue 722 MET Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 972 GLU Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 514 LYS Chi-restraints excluded: chain C residue 546 GLN Chi-restraints excluded: chain C residue 561 SER Chi-restraints excluded: chain C residue 631 THR Chi-restraints excluded: chain C residue 640 GLU Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 690 SER Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 883 GLN Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 915 GLN Chi-restraints excluded: chain C residue 972 GLU Chi-restraints excluded: chain C residue 984 GLN Chi-restraints excluded: chain C residue 1020 LYS Chi-restraints excluded: chain C residue 1088 GLN Chi-restraints excluded: chain C residue 1099 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 38 optimal weight: 9.9990 chunk 171 optimal weight: 0.0060 chunk 44 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 229 optimal weight: 0.8980 chunk 158 optimal weight: 0.6980 chunk 192 optimal weight: 6.9990 chunk 71 optimal weight: 0.0470 chunk 81 optimal weight: 7.9990 chunk 96 optimal weight: 10.0000 chunk 189 optimal weight: 4.9990 overall best weight: 1.1296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 937 ASN B 181 HIS B 473 ASN B 827 ASN ** C 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 473 ASN C 769 GLN C 827 ASN C 877 GLN C1040 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.147060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.120492 restraints weight = 25926.819| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.57 r_work: 0.3111 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 25122 Z= 0.130 Angle : 0.573 11.944 34203 Z= 0.309 Chirality : 0.045 0.241 3921 Planarity : 0.004 0.049 4359 Dihedral : 5.837 59.174 3333 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.04 % Allowed : 17.84 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.14), residues: 3018 helix: 1.94 (0.19), residues: 696 sheet: 0.95 (0.19), residues: 663 loop : -1.61 (0.13), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1055 TYR 0.020 0.001 TYR C 352 PHE 0.020 0.001 PHE B 741 TRP 0.011 0.001 TRP B 423 HIS 0.005 0.001 HIS B1046 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.13 (25059) covalent geometry : angle 0.56022 / 0.31 (34047) SS BOND : bond 0.00464 / 0.28 ( 33) SS BOND : angle 1.96784 / 1.39 ( 66) hydrogen bonds : bond 0.06570 / 4.23 ( 988) hydrogen bonds : angle 5.38564 / 3.79 ( 2811) link_BETA1-4 : bond 0.00335 / 0.17 ( 3) link_BETA1-4 : angle 1.68712 / 1.04 ( 9) link_NAG-ASN : bond 0.00148 / 0.09 ( 27) link_NAG-ASN : angle 1.81301 / 1.23 ( 81) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9020.02 seconds wall clock time: 154 minutes 5.75 seconds (9245.75 seconds total)