Starting phenix.real_space_refine on Fri May 23 03:25:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h11_34421/05_2025/8h11_34421.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h11_34421/05_2025/8h11_34421.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8h11_34421/05_2025/8h11_34421.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h11_34421/05_2025/8h11_34421.map" model { file = "/net/cci-nas-00/data/ceres_data/8h11_34421/05_2025/8h11_34421.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h11_34421/05_2025/8h11_34421.cif" } resolution = 2.72 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 125 5.16 5 C 15022 2.51 5 N 3863 2.21 5 O 4556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 23566 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 7751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 7751 Classifications: {'peptide': 992} Link IDs: {'PTRANS': 44, 'TRANS': 947} Chain breaks: 9 Chain: "A" Number of atoms: 7657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 979, 7657 Classifications: {'peptide': 979} Link IDs: {'PTRANS': 46, 'TRANS': 932} Chain breaks: 10 Chain: "C" Number of atoms: 7612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 974, 7612 Classifications: {'peptide': 974} Link IDs: {'PTRANS': 44, 'TRANS': 929} Chain breaks: 9 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 14.72, per 1000 atoms: 0.62 Number of scatterers: 23566 At special positions: 0 Unit cell: (129.21, 133.59, 163.155, 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 125 16.00 O 4556 8.00 N 3863 7.00 C 15022 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 288 " distance=2.03 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 348 " distance=2.05 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS B 419 " distance=2.03 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS C 967 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 511 " distance=2.03 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 635 " distance=2.03 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.04 Simple disulfide: pdb=" SG CYS B 720 " - pdb=" SG CYS B 742 " distance=2.03 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.04 Simple disulfide: pdb=" SG CYS B 822 " - pdb=" SG CYS B 833 " distance=2.05 Simple disulfide: pdb=" SG CYS B 967 " - pdb=" SG CYS A 370 " distance=2.05 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.03 Simple disulfide: pdb=" SG CYS B1064 " - pdb=" SG CYS B1108 " distance=2.03 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 366 " - pdb=" SG CYS A 419 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 511 " 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=2.03 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.04 Simple disulfide: pdb=" SG CYS A 720 " - pdb=" SG CYS A 742 " distance=2.04 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.04 Simple disulfide: pdb=" SG CYS A 967 " - pdb=" SG CYS C 370 " distance=2.04 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.01 Simple disulfide: pdb=" SG CYS A1064 " - pdb=" SG CYS A1108 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 288 " distance=2.03 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 348 " distance=2.03 Simple disulfide: pdb=" SG CYS C 366 " - pdb=" SG CYS C 419 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 511 " distance=2.03 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.03 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 635 " distance=2.03 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C 657 " distance=2.03 Simple disulfide: pdb=" SG CYS C 720 " - pdb=" SG CYS C 742 " distance=2.03 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.03 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.01 Simple disulfide: pdb=" SG CYS C1064 " - pdb=" SG CYS C1108 " 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-ASN " NAG A1301 " - " ASN A 65 " " NAG A1302 " - " ASN A1080 " " NAG A1303 " - " ASN A 119 " " NAG A1304 " - " ASN A 158 " " NAG A1305 " - " ASN A 227 " " NAG A1306 " - " ASN A 269 " " NAG A1307 " - " ASN A 318 " " NAG A1308 " - " ASN A 602 " " NAG A1309 " - " ASN A 691 " " NAG A1310 " - " ASN A 699 " " NAG A1311 " - " ASN A 783 " " NAG A1312 " - " ASN A1056 " " NAG A1313 " - " ASN A1116 " " NAG B1301 " - " ASN B 65 " " NAG B1302 " - " ASN B1080 " " NAG B1303 " - " ASN B 119 " " NAG B1304 " - " ASN B 158 " " NAG B1305 " - " ASN B 269 " " NAG B1306 " - " ASN B 318 " " NAG B1307 " - " ASN B 602 " " NAG B1308 " - " ASN B 691 " " NAG B1309 " - " ASN B 699 " " NAG B1310 " - " ASN B 783 " " NAG B1311 " - " ASN B1056 " " NAG B1312 " - " ASN B1116 " " NAG C1301 " - " ASN C 65 " " NAG C1302 " - " ASN C1080 " " NAG C1303 " - " ASN C 119 " " NAG C1304 " - " ASN C 227 " " NAG C1305 " - " ASN C 269 " " NAG C1306 " - " ASN C 318 " " NAG C1307 " - " ASN C 602 " " NAG C1308 " - " ASN C 691 " " NAG C1309 " - " ASN C 699 " " NAG C1310 " - " ASN C 783 " " NAG C1311 " - " ASN C1056 " " NAG C1312 " - " ASN C1116 " " NAG D 1 " - " ASN B 227 " Time building additional restraints: 6.12 Conformation dependent library (CDL) restraints added in 3.1 seconds 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5526 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 46 sheets defined 26.0% alpha, 30.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.40 Creating SS restraints... Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 325 through 330 Processing helix chain 'B' and resid 352 through 357 removed outlier: 3.923A pdb=" N TYR B 356 " --> pdb=" O TYR B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 409 Processing helix chain 'B' and resid 602 through 612 Processing helix chain 'B' and resid 719 through 725 Processing helix chain 'B' and resid 729 through 736 Processing helix chain 'B' and resid 737 through 739 No H-bonds generated for 'chain 'B' and resid 737 through 739' Processing helix chain 'B' and resid 741 through 765 removed outlier: 3.802A pdb=" N ASP B 757 " --> pdb=" O ALA B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 788 removed outlier: 3.622A pdb=" N LEU B 788 " --> pdb=" O SER B 785 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 785 through 788' Processing helix chain 'B' and resid 798 through 808 removed outlier: 3.611A pdb=" N VAL B 808 " --> pdb=" O LEU B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 867 removed outlier: 3.526A pdb=" N GLY B 867 " --> pdb=" O THR B 863 " (cutoff:3.500A) Processing helix chain 'B' and resid 868 through 872 removed outlier: 3.629A pdb=" N GLY B 871 " --> pdb=" O TRP B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 891 Processing helix chain 'B' and resid 894 through 900 removed outlier: 4.138A pdb=" N LEU B 898 " --> pdb=" O THR B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 920 removed outlier: 3.548A pdb=" N GLN B 917 " --> pdb=" O ILE B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 927 through 947 removed outlier: 3.787A pdb=" N VAL B 933 " --> pdb=" O LYS B 929 " (cutoff:3.500A) removed outlier: 3.723A 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: 3.685A pdb=" N ILE B 962 " --> pdb=" O VAL B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 1015 removed outlier: 3.745A pdb=" N VAL B 973 " --> pdb=" O VAL B 969 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY B 981 " --> pdb=" O ARG B 977 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU B 999 " --> pdb=" O ILE B 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 325 through 330 Processing helix chain 'A' and resid 352 through 357 removed outlier: 3.881A pdb=" N TYR A 356 " --> pdb=" O TYR A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 376 removed outlier: 4.126A pdb=" N ASN A 375 " --> pdb=" O THR A 372 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP A 376 " --> pdb=" O LYS A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 397 removed outlier: 3.537A pdb=" N ILE A 397 " --> pdb=" O VAL A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 409 Processing helix chain 'A' and resid 602 through 612 removed outlier: 3.626A pdb=" N ALA A 609 " --> pdb=" O ASP A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 725 Processing helix chain 'A' and resid 728 through 736 Processing helix chain 'A' and resid 737 through 739 No H-bonds generated for 'chain 'A' and resid 737 through 739' Processing helix chain 'A' and resid 741 through 765 removed outlier: 3.796A pdb=" N ASP A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 788 removed outlier: 3.624A pdb=" N LEU A 788 " --> pdb=" O SER A 785 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 785 through 788' Processing helix chain 'A' and resid 798 through 808 removed outlier: 3.715A pdb=" N VAL A 808 " --> pdb=" O LEU A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 867 Processing helix chain 'A' and resid 879 through 891 Processing helix chain 'A' and resid 894 through 901 removed outlier: 4.051A pdb=" N LEU A 898 " --> pdb=" O THR A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 922 Processing helix chain 'A' and resid 927 through 947 removed outlier: 3.716A pdb=" N VAL A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) removed outlier: 3.552A 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: 3.618A pdb=" N ILE A 962 " --> pdb=" O VAL A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 1015 removed outlier: 3.690A pdb=" N GLY A 981 " --> pdb=" O ARG A 977 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU A 999 " --> pdb=" O ILE A 995 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A1015 " --> pdb=" O MET A1011 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 291 Processing helix chain 'C' and resid 324 through 330 removed outlier: 3.758A pdb=" N VAL C 328 " --> pdb=" O PRO C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 340 removed outlier: 4.174A pdb=" N TRP C 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 357 removed outlier: 3.763A pdb=" N TYR C 356 " --> pdb=" O TYR C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 376 removed outlier: 4.021A pdb=" N ASN C 375 " --> pdb=" O THR C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 397 removed outlier: 4.067A pdb=" N VAL C 394 " --> pdb=" O GLY C 391 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ARG C 395 " --> pdb=" O ASP C 392 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE C 397 " --> pdb=" O VAL C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 409 Processing helix chain 'C' and resid 602 through 612 removed outlier: 3.503A pdb=" N VAL C 606 " --> pdb=" O ASN C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 719 through 725 Processing helix chain 'C' and resid 728 through 736 removed outlier: 3.622A pdb=" N ALA C 732 " --> pdb=" O SER C 728 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 739 No H-bonds generated for 'chain 'C' and resid 737 through 739' Processing helix chain 'C' and resid 741 through 765 removed outlier: 3.823A pdb=" N ASP C 757 " --> pdb=" O ALA C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 785 through 788 removed outlier: 3.684A pdb=" N LEU C 788 " --> pdb=" O SER C 785 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 785 through 788' Processing helix chain 'C' and resid 798 through 807 Processing helix chain 'C' and resid 848 through 867 Processing helix chain 'C' and resid 879 through 891 Processing helix chain 'C' and resid 894 through 900 removed outlier: 4.131A pdb=" N LEU C 898 " --> pdb=" O THR C 894 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 920 Processing helix chain 'C' and resid 927 through 947 removed outlier: 4.017A pdb=" N VAL C 933 " --> pdb=" O LYS C 929 " (cutoff:3.500A) removed outlier: 3.733A 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: 3.641A pdb=" N ILE C 962 " --> pdb=" O VAL C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 1015 removed outlier: 3.614A pdb=" N GLY C 981 " --> pdb=" O ARG C 977 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU C 999 " --> pdb=" O ILE C 995 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 32 through 34 removed outlier: 7.814A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA B 251 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE B 220 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N LYS B 198 " --> pdb=" O PRO B 218 " (cutoff:3.500A) removed outlier: 8.833A pdb=" N TYR B 200 " --> pdb=" O LEU B 216 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N LEU B 216 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL B 40 " --> pdb=" O LEU B 216 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 47 removed outlier: 3.509A pdb=" N ARG A 553 " --> pdb=" O PHE B 47 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER A 561 " --> pdb=" O GLY A 552 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ASP A 560 " --> pdb=" O ILE A 573 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 51 through 59 removed outlier: 3.667A pdb=" N THR B 51 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP B 274 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 81 through 82 removed outlier: 6.678A pdb=" N ARG B 232 " --> pdb=" O TRP B 101 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N TRP B 101 " --> pdb=" O ARG B 232 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ILE B 234 " --> pdb=" O ARG B 99 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ARG B 99 " --> pdb=" O ASN B 118 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ASN B 118 " --> pdb=" O ARG B 99 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE B 161 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ASN B 129 " --> pdb=" O CYS B 159 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N CYS B 159 " --> pdb=" O ASN B 129 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 298 through 306 removed outlier: 7.033A pdb=" N VAL B 581 " --> pdb=" O THR B 302 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASN B 304 " --> pdb=" O GLY B 579 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLY B 579 " --> pdb=" O ASN B 304 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLY B 580 " --> pdb=" O GLN B 599 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 312 through 315 removed outlier: 5.488A pdb=" N ASP B 560 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER B 561 " --> pdb=" O GLY B 552 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N PHE B 551 " --> pdb=" O PHE C 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 341 through 345 removed outlier: 4.090A pdb=" N GLU B 341 " --> pdb=" O SER B 386 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER B 386 " --> pdb=" O GLU B 341 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 348 through 349 removed outlier: 6.422A pdb=" N CYS B 348 " --> pdb=" O CYS B 511 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 439 through 441 Processing sheet with id=AB1, first strand: chain 'B' and resid 640 through 641 removed outlier: 6.053A pdb=" N GLU B 640 " --> pdb=" O ALA B 676 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N THR B 678 " --> pdb=" O GLU B 640 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ALA B 658 " --> pdb=" O PRO B 651 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 683 through 685 removed outlier: 7.132A pdb=" N ALA B 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 'B' and resid 693 through 710 removed outlier: 6.431A pdb=" N THR B 693 " --> pdb=" O THR B1058 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THR B1058 " --> pdb=" O THR B 693 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ALA B 695 " --> pdb=" O ASN B1056 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ASN B1056 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLU B1054 " --> pdb=" O PRO B 697 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET B1032 " --> pdb=" O VAL B1047 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TYR B1049 " --> pdb=" O HIS B1030 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N HIS B1030 " --> pdb=" O TYR B1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 693 through 710 removed outlier: 6.431A pdb=" N THR B 693 " --> pdb=" O THR B1058 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THR B1058 " --> pdb=" O THR B 693 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ALA B 695 " --> pdb=" O ASN B1056 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ASN B1056 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLU B1054 " --> pdb=" O PRO B 697 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR B1058 " --> pdb=" O PHE B1079 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA B1060 " --> pdb=" O PHE B1077 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N PHE B1077 " --> pdb=" O ALA B1060 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 715 through 718 removed outlier: 4.482A pdb=" N LYS B 715 " --> pdb=" O LEU B 843 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 769 through 771 Processing sheet with id=AB7, first strand: chain 'B' and resid 778 through 779 Processing sheet with id=AB8, first strand: chain 'B' and resid 1102 through 1104 Processing sheet with id=AB9, first strand: chain 'A' and resid 32 through 34 removed outlier: 7.855A pdb=" N ASN A 65 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N TYR A 256 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N LEU A 194 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LYS A 221 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N VAL A 196 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N TYR A 200 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N THR A 215 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL A 40 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 46 through 47 Processing sheet with id=AC2, first strand: chain 'A' and resid 52 through 59 removed outlier: 3.812A pdb=" N ASP A 274 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 81 through 82 removed outlier: 6.821A pdb=" N ASN A 230 " --> pdb=" O PHE A 103 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N PHE A 103 " --> pdb=" O ASN A 230 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ARG A 232 " --> pdb=" O TRP A 101 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N TRP A 101 " --> pdb=" O ARG A 232 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE A 234 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ARG A 99 " --> pdb=" O ASN A 118 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N ASN A 118 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE A 161 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ASN A 129 " --> pdb=" O CYS A 159 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N CYS A 159 " --> pdb=" O ASN A 129 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 298 through 306 removed outlier: 6.917A pdb=" N VAL A 581 " --> pdb=" O THR A 302 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASN A 304 " --> pdb=" O GLY A 579 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLY A 579 " --> pdb=" O ASN A 304 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLY A 580 " --> pdb=" O GLN A 599 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 341 through 345 removed outlier: 3.936A pdb=" N GLU A 341 " --> pdb=" O SER A 386 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER A 386 " --> pdb=" O GLU A 341 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 348 through 349 removed outlier: 6.294A pdb=" N CYS A 348 " --> pdb=" O CYS A 511 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'A' and resid 439 through 441 Processing sheet with id=AC8, first strand: chain 'A' and resid 640 through 641 removed outlier: 6.216A pdb=" N ALA A 658 " --> pdb=" O PRO A 651 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 693 through 710 removed outlier: 6.550A pdb=" N THR A 693 " --> pdb=" O THR A1058 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR A1058 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ALA A 695 " --> pdb=" O ASN A1056 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ASN A1056 " --> pdb=" O ALA A 695 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N GLU A1054 " --> pdb=" O PRO A 697 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET A1032 " --> pdb=" O VAL A1047 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N TYR A1049 " --> pdb=" O HIS A1030 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N HIS A1030 " --> pdb=" O TYR A1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 693 through 710 removed outlier: 6.550A pdb=" N THR A 693 " --> pdb=" O THR A1058 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR A1058 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ALA A 695 " --> pdb=" O ASN A1056 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ASN A1056 " --> pdb=" O ALA A 695 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N GLU A1054 " --> pdb=" O PRO A 697 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR A1058 " --> pdb=" O PHE A1079 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA A1060 " --> pdb=" O PHE A1077 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N PHE A1077 " --> pdb=" O ALA A1060 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 715 through 718 removed outlier: 4.656A pdb=" N LYS A 715 " --> pdb=" O LEU A 843 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 769 through 771 removed outlier: 3.534A pdb=" N SER C 685 " --> pdb=" O MET A 770 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 778 through 779 Processing sheet with id=AD5, first strand: chain 'A' and resid 1102 through 1104 Processing sheet with id=AD6, first strand: chain 'C' and resid 32 through 34 removed outlier: 7.824A pdb=" N ASN C 65 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N TYR C 256 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA C 251 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR C 92 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG C 183 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HIS C 181 " --> pdb=" O GLU C 93 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE C 220 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N LYS C 198 " --> pdb=" O PRO C 218 " (cutoff:3.500A) removed outlier: 8.851A pdb=" N TYR C 200 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N LEU C 216 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL C 40 " --> pdb=" O LEU C 216 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 52 through 59 removed outlier: 3.880A pdb=" N ASP C 274 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 81 through 82 removed outlier: 3.742A pdb=" N GLY C 100 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ARG C 99 " --> pdb=" O ASN C 118 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ASN C 118 " --> pdb=" O ARG C 99 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL C 123 " --> pdb=" O TYR C 163 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N TYR C 163 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ILE C 125 " --> pdb=" O PHE C 161 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N PHE C 161 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N ALA C 127 " --> pdb=" O CYS C 159 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N CYS C 159 " --> pdb=" O ALA C 127 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 298 through 306 removed outlier: 7.048A pdb=" N VAL C 581 " --> pdb=" O THR C 302 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ASN C 304 " --> pdb=" O GLY C 579 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLY C 579 " --> pdb=" O ASN C 304 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLY C 580 " --> pdb=" O GLN C 599 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 312 through 315 Processing sheet with id=AE2, first strand: chain 'C' and resid 341 through 345 removed outlier: 3.974A pdb=" N GLU C 341 " --> pdb=" O SER C 386 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER C 386 " --> pdb=" O GLU C 341 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 348 through 349 removed outlier: 6.354A pdb=" N CYS C 348 " --> pdb=" O CYS C 511 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 439 through 441 Processing sheet with id=AE5, first strand: chain 'C' and resid 640 through 641 removed outlier: 6.232A pdb=" N ALA C 658 " --> pdb=" O PRO C 651 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 693 through 710 removed outlier: 6.546A pdb=" N THR C 693 " --> pdb=" O THR C1058 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N THR C1058 " --> pdb=" O THR C 693 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ALA C 695 " --> pdb=" O ASN C1056 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ASN C1056 " --> pdb=" O ALA C 695 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N GLU C1054 " --> pdb=" O PRO C 697 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N MET C1032 " --> pdb=" O VAL C1047 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TYR C1049 " --> pdb=" O HIS C1030 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N HIS C1030 " --> pdb=" O TYR C1049 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 693 through 710 removed outlier: 6.546A pdb=" N THR C 693 " --> pdb=" O THR C1058 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N THR C1058 " --> pdb=" O THR C 693 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ALA C 695 " --> pdb=" O ASN C1056 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ASN C1056 " --> pdb=" O ALA C 695 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N GLU C1054 " --> pdb=" O PRO C 697 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N THR C1058 " --> pdb=" O PHE C1079 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA C1060 " --> pdb=" O PHE C1077 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N PHE C1077 " --> pdb=" O ALA C1060 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLN C1088 " --> pdb=" O SER C1093 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N SER C1093 " --> pdb=" O GLN C1088 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 715 through 718 removed outlier: 4.679A pdb=" N LYS C 715 " --> pdb=" O LEU C 843 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 778 through 779 Processing sheet with id=AF1, first strand: chain 'C' and resid 1102 through 1104 1009 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: 10.45 Time building geometry restraints manager: 6.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 4552 1.33 - 1.46: 8168 1.46 - 1.59: 11184 1.59 - 1.72: 2 1.72 - 1.86: 167 Bond restraints: 24073 Sorted by residual: bond pdb=" CG PRO A 202 " pdb=" CD PRO A 202 " ideal model delta sigma weight residual 1.503 1.195 0.308 3.40e-02 8.65e+02 8.21e+01 bond pdb=" CG PRO B 493 " pdb=" CD PRO B 493 " ideal model delta sigma weight residual 1.503 1.196 0.307 3.40e-02 8.65e+02 8.17e+01 bond pdb=" N PRO A 202 " pdb=" CD PRO A 202 " ideal model delta sigma weight residual 1.473 1.539 -0.066 1.40e-02 5.10e+03 2.25e+01 bond pdb=" CB PRO A 202 " pdb=" CG PRO A 202 " ideal model delta sigma weight residual 1.492 1.673 -0.181 5.00e-02 4.00e+02 1.31e+01 bond pdb=" N PRO B 493 " pdb=" CD PRO B 493 " ideal model delta sigma weight residual 1.473 1.516 -0.043 1.40e-02 5.10e+03 9.64e+00 ... (remaining 24068 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.67: 32538 3.67 - 7.35: 140 7.35 - 11.02: 18 11.02 - 14.69: 4 14.69 - 18.37: 4 Bond angle restraints: 32704 Sorted by residual: angle pdb=" N PRO B 493 " pdb=" CD PRO B 493 " pdb=" CG PRO B 493 " ideal model delta sigma weight residual 103.20 84.83 18.37 1.50e+00 4.44e-01 1.50e+02 angle pdb=" N PRO A 202 " pdb=" CD PRO A 202 " pdb=" CG PRO A 202 " ideal model delta sigma weight residual 103.20 85.32 17.88 1.50e+00 4.44e-01 1.42e+02 angle pdb=" CA PRO A 202 " pdb=" N PRO A 202 " pdb=" CD PRO A 202 " ideal model delta sigma weight residual 112.00 96.56 15.44 1.40e+00 5.10e-01 1.22e+02 angle pdb=" CA PRO A 202 " pdb=" CB PRO A 202 " pdb=" CG PRO A 202 " ideal model delta sigma weight residual 104.50 90.33 14.17 1.90e+00 2.77e-01 5.56e+01 angle pdb=" CA PRO B 493 " pdb=" N PRO B 493 " pdb=" CD PRO B 493 " ideal model delta sigma weight residual 112.00 101.81 10.19 1.40e+00 5.10e-01 5.30e+01 ... (remaining 32699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 13682 17.55 - 35.11: 911 35.11 - 52.66: 218 52.66 - 70.21: 38 70.21 - 87.76: 14 Dihedral angle restraints: 14863 sinusoidal: 6289 harmonic: 8574 Sorted by residual: dihedral pdb=" CB CYS C 278 " pdb=" SG CYS C 278 " pdb=" SG CYS C 288 " pdb=" CB CYS C 288 " ideal model delta sinusoidal sigma weight residual -86.00 -173.76 87.76 1 1.00e+01 1.00e-02 9.23e+01 dihedral pdb=" CB CYS A 278 " pdb=" SG CYS A 278 " pdb=" SG CYS A 288 " pdb=" CB CYS A 288 " ideal model delta sinusoidal sigma weight residual -86.00 -173.40 87.40 1 1.00e+01 1.00e-02 9.16e+01 dihedral pdb=" CA VAL B 205 " pdb=" C VAL B 205 " pdb=" N VAL B 206 " pdb=" CA VAL B 206 " ideal model delta harmonic sigma weight residual 180.00 139.26 40.74 0 5.00e+00 4.00e-02 6.64e+01 ... (remaining 14860 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 3681 0.115 - 0.231: 137 0.231 - 0.346: 7 0.346 - 0.461: 1 0.461 - 0.577: 2 Chirality restraints: 3828 Sorted by residual: chirality pdb=" C1 NAG C1306 " pdb=" ND2 ASN C 318 " pdb=" C2 NAG C1306 " pdb=" O5 NAG C1306 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-01 2.50e+01 8.32e+00 chirality pdb=" C1 NAG B1311 " pdb=" ND2 ASN B1056 " pdb=" C2 NAG B1311 " pdb=" O5 NAG B1311 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-01 2.50e+01 8.31e+00 chirality pdb=" C1 NAG A1312 " pdb=" ND2 ASN A1056 " pdb=" C2 NAG A1312 " pdb=" O5 NAG A1312 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.17e+00 ... (remaining 3825 not shown) Planarity restraints: 4201 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 334 " 0.083 5.00e-02 4.00e+02 1.24e-01 2.47e+01 pdb=" N PRO C 335 " -0.215 5.00e-02 4.00e+02 pdb=" CA PRO C 335 " 0.067 5.00e-02 4.00e+02 pdb=" CD PRO C 335 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 227 " -0.004 2.00e-02 2.50e+03 4.25e-02 2.26e+01 pdb=" CG ASN B 227 " 0.043 2.00e-02 2.50e+03 pdb=" OD1 ASN B 227 " -0.048 2.00e-02 2.50e+03 pdb=" ND2 ASN B 227 " 0.054 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 492 " -0.081 5.00e-02 4.00e+02 1.15e-01 2.11e+01 pdb=" N PRO B 493 " 0.198 5.00e-02 4.00e+02 pdb=" CA PRO B 493 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO B 493 " -0.060 5.00e-02 4.00e+02 ... (remaining 4198 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4707 2.78 - 3.31: 19354 3.31 - 3.84: 36409 3.84 - 4.37: 43842 4.37 - 4.90: 77708 Nonbonded interactions: 182020 Sorted by model distance: nonbonded pdb=" O SER B 380 " pdb=" OG1 THR B 509 " model vdw 2.250 3.040 nonbonded pdb=" O SER A 380 " pdb=" OG1 THR A 509 " model vdw 2.263 3.040 nonbonded pdb=" O SER C 380 " pdb=" OG1 THR C 509 " model vdw 2.286 3.040 nonbonded pdb=" OG1 THR A 698 " pdb=" O GLN A1053 " model vdw 2.301 3.040 nonbonded pdb=" OG1 THR C 894 " pdb=" OD1 ASN C 896 " model vdw 2.309 3.040 ... (remaining 182015 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 31 through 455 or resid 477 through 1123 or resid 1301 thr \ ough 1312)) selection = (chain 'B' and (resid 31 through 132 or resid 155 through 204 or resid 209 throu \ gh 810 or resid 834 through 1123 or resid 1301 through 1312)) selection = (chain 'C' and (resid 31 through 132 or resid 155 through 204 or resid 209 throu \ gh 1123 or resid 1301 through 1312)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.860 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 55.820 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 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 : 0.006 0.308 24152 Z= 0.253 Angle : 0.911 24.326 32901 Z= 0.485 Chirality : 0.055 0.577 3828 Planarity : 0.007 0.124 4163 Dihedral : 12.518 87.630 9217 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.04 % Allowed : 0.08 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.14), residues: 2883 helix: -0.07 (0.19), residues: 695 sheet: 0.64 (0.18), residues: 741 loop : -1.97 (0.14), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 868 HIS 0.007 0.001 HIS B1046 PHE 0.043 0.002 PHE B 360 TYR 0.040 0.002 TYR B 440 ARG 0.006 0.001 ARG C 758 Details of bonding type rmsd link_NAG-ASN : bond 0.00757 ( 38) link_NAG-ASN : angle 5.94339 ( 114) link_BETA1-4 : bond 0.00266 ( 1) link_BETA1-4 : angle 4.64780 ( 3) hydrogen bonds : bond 0.14293 ( 973) hydrogen bonds : angle 6.87995 ( 2811) SS BOND : bond 0.00676 ( 40) SS BOND : angle 1.93362 ( 80) covalent geometry : bond 0.00592 (24073) covalent geometry : angle 0.83709 (32704) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 215 time to evaluate : 2.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 572 ASP cc_start: 0.7945 (m-30) cc_final: 0.7682 (m-30) REVERT: C 110 LYS cc_start: 0.7830 (ptpt) cc_final: 0.7283 (tptt) REVERT: C 793 LYS cc_start: 0.6064 (ttpt) cc_final: 0.5834 (mtmt) REVERT: C 965 ARG cc_start: 0.7798 (ptp-170) cc_final: 0.7558 (ptp-110) outliers start: 1 outliers final: 0 residues processed: 216 average time/residue: 1.1929 time to fit residues: 301.0391 Evaluate side-chains 153 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 2.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 247 optimal weight: 0.8980 chunk 222 optimal weight: 4.9990 chunk 123 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 chunk 118 optimal weight: 0.8980 chunk 229 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 139 optimal weight: 0.6980 chunk 170 optimal weight: 0.7980 chunk 266 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 GLN B 96 ASN B 108 ASN A 599 GLN ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.147316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.100682 restraints weight = 29101.027| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.97 r_work: 0.3006 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.0795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24152 Z= 0.126 Angle : 0.618 19.753 32901 Z= 0.307 Chirality : 0.046 0.457 3828 Planarity : 0.005 0.076 4163 Dihedral : 6.842 58.413 3972 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.70 % Allowed : 5.36 % Favored : 93.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.15), residues: 2883 helix: 1.14 (0.20), residues: 692 sheet: 0.87 (0.19), residues: 701 loop : -1.70 (0.14), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 423 HIS 0.005 0.001 HIS C1046 PHE 0.022 0.001 PHE A 629 TYR 0.027 0.001 TYR A 491 ARG 0.002 0.000 ARG B 315 Details of bonding type rmsd link_NAG-ASN : bond 0.00851 ( 38) link_NAG-ASN : angle 4.57819 ( 114) link_BETA1-4 : bond 0.00443 ( 1) link_BETA1-4 : angle 2.76102 ( 3) hydrogen bonds : bond 0.05842 ( 973) hydrogen bonds : angle 5.37988 ( 2811) SS BOND : bond 0.00415 ( 40) SS BOND : angle 1.35828 ( 80) covalent geometry : bond 0.00281 (24073) covalent geometry : angle 0.55293 (32704) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 177 time to evaluate : 2.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 572 ASP cc_start: 0.8480 (m-30) cc_final: 0.8134 (m-30) REVERT: B 768 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7965 (pttm) REVERT: B 1011 MET cc_start: 0.9134 (OUTLIER) cc_final: 0.8204 (tpp) REVERT: B 1063 ILE cc_start: 0.8832 (pt) cc_final: 0.8417 (mt) REVERT: A 793 LYS cc_start: 0.7140 (ttpt) cc_final: 0.6840 (ttpt) REVERT: C 110 LYS cc_start: 0.7895 (ptpt) cc_final: 0.7259 (tptt) REVERT: C 965 ARG cc_start: 0.7977 (ptp-170) cc_final: 0.7674 (ptp-110) outliers start: 18 outliers final: 5 residues processed: 184 average time/residue: 1.0862 time to fit residues: 238.5859 Evaluate side-chains 158 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 151 time to evaluate : 2.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 768 LYS Chi-restraints excluded: chain B residue 1011 MET Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain C residue 551 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 286 optimal weight: 0.9990 chunk 146 optimal weight: 5.9990 chunk 176 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 287 optimal weight: 0.4980 chunk 107 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 9 optimal weight: 0.0980 chunk 213 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 181 HIS B 744 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.146999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.100222 restraints weight = 29235.060| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.97 r_work: 0.2998 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 24152 Z= 0.128 Angle : 0.593 18.698 32901 Z= 0.295 Chirality : 0.046 0.453 3828 Planarity : 0.004 0.057 4163 Dihedral : 6.168 50.886 3972 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.25 % Allowed : 7.43 % Favored : 91.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.15), residues: 2883 helix: 1.47 (0.20), residues: 694 sheet: 0.96 (0.19), residues: 699 loop : -1.58 (0.14), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 868 HIS 0.005 0.001 HIS C1046 PHE 0.021 0.001 PHE A 629 TYR 0.019 0.001 TYR C1049 ARG 0.003 0.000 ARG B 982 Details of bonding type rmsd link_NAG-ASN : bond 0.00784 ( 38) link_NAG-ASN : angle 4.28883 ( 114) link_BETA1-4 : bond 0.00119 ( 1) link_BETA1-4 : angle 2.36569 ( 3) hydrogen bonds : bond 0.05651 ( 973) hydrogen bonds : angle 5.13814 ( 2811) SS BOND : bond 0.00388 ( 40) SS BOND : angle 1.43644 ( 80) covalent geometry : bond 0.00292 (24073) covalent geometry : angle 0.53308 (32704) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 171 time to evaluate : 2.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 572 ASP cc_start: 0.8466 (m-30) cc_final: 0.8097 (m-30) REVERT: B 1011 MET cc_start: 0.9116 (OUTLIER) cc_final: 0.8173 (tpp) REVERT: B 1063 ILE cc_start: 0.8748 (pt) cc_final: 0.8385 (mt) REVERT: A 107 MET cc_start: 0.8437 (mmm) cc_final: 0.8059 (mmm) REVERT: A 600 ASP cc_start: 0.7696 (m-30) cc_final: 0.7379 (OUTLIER) REVERT: A 793 LYS cc_start: 0.6858 (ttpt) cc_final: 0.6657 (ttpt) REVERT: C 58 LEU cc_start: 0.9050 (mt) cc_final: 0.8842 (mp) REVERT: C 110 LYS cc_start: 0.7913 (ptpt) cc_final: 0.7333 (tptt) REVERT: C 214 ASN cc_start: 0.8552 (t0) cc_final: 0.8287 (t0) REVERT: C 932 ASP cc_start: 0.7909 (m-30) cc_final: 0.7546 (m-30) REVERT: C 965 ARG cc_start: 0.7958 (ptp-170) cc_final: 0.7644 (ptp-110) outliers start: 32 outliers final: 10 residues processed: 195 average time/residue: 1.0062 time to fit residues: 235.4510 Evaluate side-chains 166 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 156 time to evaluate : 2.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 1011 MET Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 551 PHE Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 551 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 189 optimal weight: 4.9990 chunk 182 optimal weight: 2.9990 chunk 255 optimal weight: 4.9990 chunk 264 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 231 optimal weight: 0.1980 chunk 227 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 248 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 ASN B 746 ASN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.144305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.097619 restraints weight = 29383.842| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.09 r_work: 0.2936 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 24152 Z= 0.199 Angle : 0.656 18.786 32901 Z= 0.330 Chirality : 0.049 0.465 3828 Planarity : 0.005 0.050 4163 Dihedral : 6.101 45.390 3972 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.71 % Favored : 96.25 % Rotamer: Outliers : 1.72 % Allowed : 9.15 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.15), residues: 2883 helix: 1.36 (0.20), residues: 694 sheet: 0.92 (0.19), residues: 694 loop : -1.58 (0.14), residues: 1495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 868 HIS 0.007 0.001 HIS A1030 PHE 0.023 0.002 PHE B 870 TYR 0.019 0.002 TYR C1049 ARG 0.005 0.000 ARG A1021 Details of bonding type rmsd link_NAG-ASN : bond 0.00733 ( 38) link_NAG-ASN : angle 4.38344 ( 114) link_BETA1-4 : bond 0.00435 ( 1) link_BETA1-4 : angle 2.18977 ( 3) hydrogen bonds : bond 0.06972 ( 973) hydrogen bonds : angle 5.26529 ( 2811) SS BOND : bond 0.00635 ( 40) SS BOND : angle 1.75863 ( 80) covalent geometry : bond 0.00486 (24073) covalent geometry : angle 0.59800 (32704) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 169 time to evaluate : 2.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 572 ASP cc_start: 0.8511 (m-30) cc_final: 0.8107 (m-30) REVERT: B 965 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.8025 (ptt180) REVERT: A 99 ARG cc_start: 0.7334 (pmm-80) cc_final: 0.6959 (pmm-80) REVERT: A 600 ASP cc_start: 0.7767 (m-30) cc_final: 0.7432 (t0) REVERT: A 727 ASP cc_start: 0.7586 (OUTLIER) cc_final: 0.7111 (p0) REVERT: A 793 LYS cc_start: 0.7013 (ttpt) cc_final: 0.6772 (ttpt) REVERT: C 56 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8465 (tt0) REVERT: C 58 LEU cc_start: 0.9065 (mt) cc_final: 0.8850 (mp) REVERT: C 110 LYS cc_start: 0.7972 (ptpt) cc_final: 0.7382 (tptt) REVERT: C 214 ASN cc_start: 0.8575 (t0) cc_final: 0.8291 (t0) REVERT: C 321 ASN cc_start: 0.7608 (m-40) cc_final: 0.7121 (p0) REVERT: C 932 ASP cc_start: 0.8041 (m-30) cc_final: 0.7610 (m-30) REVERT: C 965 ARG cc_start: 0.7999 (ptp-170) cc_final: 0.7645 (ptp-110) outliers start: 44 outliers final: 17 residues processed: 200 average time/residue: 1.0271 time to fit residues: 246.1180 Evaluate side-chains 179 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 2.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 877 GLN Chi-restraints excluded: chain B residue 965 ARG Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 727 ASP Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 551 PHE Chi-restraints excluded: chain C residue 1074 GLU Chi-restraints excluded: chain C residue 1109 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 259 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 270 optimal weight: 0.9980 chunk 180 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 chunk 268 optimal weight: 3.9990 chunk 274 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 228 optimal weight: 10.0000 chunk 185 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 ASN B 427 ASN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 889 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.145253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.098246 restraints weight = 29310.621| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.98 r_work: 0.2970 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 24152 Z= 0.154 Angle : 0.611 18.846 32901 Z= 0.305 Chirality : 0.047 0.453 3828 Planarity : 0.004 0.050 4163 Dihedral : 5.801 43.500 3972 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.80 % Allowed : 10.28 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.15), residues: 2883 helix: 1.51 (0.20), residues: 693 sheet: 0.93 (0.19), residues: 705 loop : -1.55 (0.14), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 868 HIS 0.005 0.001 HIS A1030 PHE 0.021 0.002 PHE A 629 TYR 0.018 0.001 TYR C1049 ARG 0.004 0.000 ARG B1021 Details of bonding type rmsd link_NAG-ASN : bond 0.00720 ( 38) link_NAG-ASN : angle 4.20576 ( 114) link_BETA1-4 : bond 0.00686 ( 1) link_BETA1-4 : angle 2.01443 ( 3) hydrogen bonds : bond 0.06165 ( 973) hydrogen bonds : angle 5.12122 ( 2811) SS BOND : bond 0.00516 ( 40) SS BOND : angle 1.50169 ( 80) covalent geometry : bond 0.00368 (24073) covalent geometry : angle 0.55462 (32704) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 168 time to evaluate : 2.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 301 GLN cc_start: 0.8795 (tt0) cc_final: 0.8590 (tp40) REVERT: B 572 ASP cc_start: 0.8478 (m-30) cc_final: 0.8105 (m-30) REVERT: B 965 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7965 (ptt180) REVERT: A 54 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8390 (mm) REVERT: A 99 ARG cc_start: 0.7304 (pmm-80) cc_final: 0.6991 (pmm-80) REVERT: A 102 VAL cc_start: 0.7828 (OUTLIER) cc_final: 0.7585 (m) REVERT: A 600 ASP cc_start: 0.7804 (m-30) cc_final: 0.7473 (t0) REVERT: C 56 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.8448 (tt0) REVERT: C 110 LYS cc_start: 0.7978 (ptpt) cc_final: 0.7371 (tptt) REVERT: C 214 ASN cc_start: 0.8542 (t0) cc_final: 0.8296 (t0) REVERT: C 321 ASN cc_start: 0.7574 (m-40) cc_final: 0.7088 (p0) REVERT: C 965 ARG cc_start: 0.8052 (ptp-170) cc_final: 0.7706 (ptp-110) outliers start: 46 outliers final: 23 residues processed: 204 average time/residue: 0.9794 time to fit residues: 242.7492 Evaluate side-chains 190 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 163 time to evaluate : 2.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 965 ARG Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 551 PHE Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 1032 MET Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 551 PHE Chi-restraints excluded: chain C residue 793 LYS Chi-restraints excluded: chain C residue 898 LEU Chi-restraints excluded: chain C residue 1074 GLU Chi-restraints excluded: chain C residue 1109 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 125 optimal weight: 6.9990 chunk 275 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 chunk 266 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 230 optimal weight: 9.9990 chunk 9 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 168 optimal weight: 6.9990 chunk 141 optimal weight: 4.9990 chunk 182 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 ASN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 889 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.143347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.096095 restraints weight = 29182.973| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.99 r_work: 0.2935 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 24152 Z= 0.232 Angle : 0.680 18.949 32901 Z= 0.343 Chirality : 0.050 0.468 3828 Planarity : 0.005 0.053 4163 Dihedral : 5.936 43.584 3972 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.23 % Favored : 95.73 % Rotamer: Outliers : 2.03 % Allowed : 10.75 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.15), residues: 2883 helix: 1.32 (0.20), residues: 695 sheet: 0.77 (0.19), residues: 716 loop : -1.60 (0.14), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 868 HIS 0.008 0.001 HIS A1030 PHE 0.025 0.002 PHE A 629 TYR 0.023 0.002 TYR C 200 ARG 0.006 0.001 ARG A1021 Details of bonding type rmsd link_NAG-ASN : bond 0.00703 ( 38) link_NAG-ASN : angle 4.30916 ( 114) link_BETA1-4 : bond 0.00496 ( 1) link_BETA1-4 : angle 2.11588 ( 3) hydrogen bonds : bond 0.07357 ( 973) hydrogen bonds : angle 5.28042 ( 2811) SS BOND : bond 0.00675 ( 40) SS BOND : angle 1.97145 ( 80) covalent geometry : bond 0.00573 (24073) covalent geometry : angle 0.62525 (32704) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 163 time to evaluate : 2.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 417 MET cc_start: 0.7707 (OUTLIER) cc_final: 0.6901 (tmm) REVERT: B 572 ASP cc_start: 0.8490 (m-30) cc_final: 0.8036 (m-30) REVERT: B 835 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.8072 (mt0) REVERT: A 99 ARG cc_start: 0.7338 (pmm-80) cc_final: 0.6920 (pmm-80) REVERT: A 102 VAL cc_start: 0.7900 (OUTLIER) cc_final: 0.7628 (m) REVERT: A 600 ASP cc_start: 0.7838 (m-30) cc_final: 0.7479 (t0) REVERT: A 727 ASP cc_start: 0.7582 (OUTLIER) cc_final: 0.7062 (p0) REVERT: C 56 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.8466 (tt0) REVERT: C 110 LYS cc_start: 0.8079 (ptpt) cc_final: 0.7493 (tptt) REVERT: C 124 VAL cc_start: 0.7696 (OUTLIER) cc_final: 0.7365 (m) REVERT: C 214 ASN cc_start: 0.8553 (t0) cc_final: 0.8336 (t0) REVERT: C 321 ASN cc_start: 0.7815 (m-40) cc_final: 0.7405 (p0) REVERT: C 932 ASP cc_start: 0.8141 (m-30) cc_final: 0.7631 (m-30) REVERT: C 965 ARG cc_start: 0.8076 (ptp-170) cc_final: 0.7693 (ptp-110) outliers start: 52 outliers final: 28 residues processed: 204 average time/residue: 0.9428 time to fit residues: 233.7222 Evaluate side-chains 190 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 156 time to evaluate : 2.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 417 MET Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 835 GLN Chi-restraints excluded: chain B residue 877 GLN Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 551 PHE Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 727 ASP Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 551 PHE Chi-restraints excluded: chain C residue 793 LYS Chi-restraints excluded: chain C residue 898 LEU Chi-restraints excluded: chain C residue 1074 GLU Chi-restraints excluded: chain C residue 1109 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 53 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 150 optimal weight: 4.9990 chunk 231 optimal weight: 10.0000 chunk 163 optimal weight: 0.0020 chunk 93 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 35 optimal weight: 10.0000 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 ASN ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 ASN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 889 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.145629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.098815 restraints weight = 29271.885| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.98 r_work: 0.2978 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24152 Z= 0.131 Angle : 0.596 18.781 32901 Z= 0.296 Chirality : 0.046 0.444 3828 Planarity : 0.004 0.048 4163 Dihedral : 5.569 41.651 3972 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.49 % Allowed : 11.77 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.15), residues: 2883 helix: 1.60 (0.20), residues: 692 sheet: 0.90 (0.19), residues: 717 loop : -1.51 (0.14), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 868 HIS 0.006 0.001 HIS C1046 PHE 0.021 0.001 PHE A 629 TYR 0.022 0.001 TYR A1120 ARG 0.003 0.000 ARG A 315 Details of bonding type rmsd link_NAG-ASN : bond 0.00744 ( 38) link_NAG-ASN : angle 4.06238 ( 114) link_BETA1-4 : bond 0.00485 ( 1) link_BETA1-4 : angle 1.93091 ( 3) hydrogen bonds : bond 0.05741 ( 973) hydrogen bonds : angle 5.03264 ( 2811) SS BOND : bond 0.00412 ( 40) SS BOND : angle 1.53423 ( 80) covalent geometry : bond 0.00300 (24073) covalent geometry : angle 0.54251 (32704) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 165 time to evaluate : 2.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 572 ASP cc_start: 0.8461 (m-30) cc_final: 0.8062 (m-30) REVERT: A 54 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8388 (mm) REVERT: A 99 ARG cc_start: 0.7308 (pmm-80) cc_final: 0.6861 (pmm-80) REVERT: A 102 VAL cc_start: 0.7781 (OUTLIER) cc_final: 0.7556 (m) REVERT: A 600 ASP cc_start: 0.7818 (m-30) cc_final: 0.7476 (t0) REVERT: C 56 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8443 (tt0) REVERT: C 110 LYS cc_start: 0.7988 (ptpt) cc_final: 0.7392 (tptt) REVERT: C 124 VAL cc_start: 0.7652 (OUTLIER) cc_final: 0.7355 (m) REVERT: C 214 ASN cc_start: 0.8510 (t0) cc_final: 0.8300 (t0) REVERT: C 321 ASN cc_start: 0.7726 (m-40) cc_final: 0.7362 (p0) REVERT: C 932 ASP cc_start: 0.8046 (m-30) cc_final: 0.7666 (m-30) REVERT: C 965 ARG cc_start: 0.7971 (ptp-170) cc_final: 0.7649 (ptp-110) outliers start: 38 outliers final: 23 residues processed: 195 average time/residue: 0.9534 time to fit residues: 227.1007 Evaluate side-chains 185 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 2.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 877 GLN Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 1032 MET Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 551 PHE Chi-restraints excluded: chain C residue 793 LYS Chi-restraints excluded: chain C residue 1074 GLU Chi-restraints excluded: chain C residue 1099 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 183 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 148 optimal weight: 0.0870 chunk 70 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 179 optimal weight: 0.0670 chunk 225 optimal weight: 4.9990 chunk 192 optimal weight: 1.9990 chunk 168 optimal weight: 7.9990 chunk 257 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.2302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 ASN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.145118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.098038 restraints weight = 29267.866| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.12 r_work: 0.2953 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 24152 Z= 0.150 Angle : 0.603 18.735 32901 Z= 0.302 Chirality : 0.047 0.446 3828 Planarity : 0.004 0.048 4163 Dihedral : 5.523 41.591 3972 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.72 % Allowed : 12.12 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.15), residues: 2883 helix: 1.62 (0.20), residues: 694 sheet: 0.91 (0.19), residues: 718 loop : -1.49 (0.14), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 868 HIS 0.005 0.001 HIS B1046 PHE 0.024 0.002 PHE A 629 TYR 0.021 0.001 TYR A1120 ARG 0.003 0.000 ARG B 982 Details of bonding type rmsd link_NAG-ASN : bond 0.00728 ( 38) link_NAG-ASN : angle 4.04823 ( 114) link_BETA1-4 : bond 0.00506 ( 1) link_BETA1-4 : angle 1.86773 ( 3) hydrogen bonds : bond 0.06058 ( 973) hydrogen bonds : angle 5.04401 ( 2811) SS BOND : bond 0.00461 ( 40) SS BOND : angle 1.54882 ( 80) covalent geometry : bond 0.00356 (24073) covalent geometry : angle 0.55022 (32704) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 165 time to evaluate : 2.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 572 ASP cc_start: 0.8482 (m-30) cc_final: 0.8054 (m-30) REVERT: B 745 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7635 (tt) REVERT: B 965 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7989 (ptt180) REVERT: A 54 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8397 (mm) REVERT: A 99 ARG cc_start: 0.7355 (pmm-80) cc_final: 0.7070 (pmm-80) REVERT: A 102 VAL cc_start: 0.7807 (OUTLIER) cc_final: 0.7576 (m) REVERT: A 600 ASP cc_start: 0.7861 (m-30) cc_final: 0.7425 (t0) REVERT: A 727 ASP cc_start: 0.7575 (OUTLIER) cc_final: 0.7030 (p0) REVERT: C 56 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.8456 (tt0) REVERT: C 110 LYS cc_start: 0.8002 (ptpt) cc_final: 0.7392 (tptt) REVERT: C 124 VAL cc_start: 0.7677 (OUTLIER) cc_final: 0.7376 (m) REVERT: C 214 ASN cc_start: 0.8523 (t0) cc_final: 0.8304 (t0) REVERT: C 321 ASN cc_start: 0.7619 (m-40) cc_final: 0.7313 (p0) REVERT: C 932 ASP cc_start: 0.8102 (m-30) cc_final: 0.7727 (m-30) REVERT: C 965 ARG cc_start: 0.7999 (ptp-170) cc_final: 0.7603 (ptp-110) outliers start: 44 outliers final: 29 residues processed: 202 average time/residue: 0.9561 time to fit residues: 234.2963 Evaluate side-chains 193 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 157 time to evaluate : 2.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 877 GLN Chi-restraints excluded: chain B residue 965 ARG Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 727 ASP Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 551 PHE Chi-restraints excluded: chain C residue 793 LYS Chi-restraints excluded: chain C residue 898 LEU Chi-restraints excluded: chain C residue 1074 GLU Chi-restraints excluded: chain C residue 1099 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 63 optimal weight: 0.6980 chunk 291 optimal weight: 0.7980 chunk 279 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 196 optimal weight: 10.0000 chunk 146 optimal weight: 2.9990 chunk 270 optimal weight: 1.9990 chunk 205 optimal weight: 9.9990 chunk 122 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 91 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 ASN ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 ASN B 769 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.145827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.098933 restraints weight = 29238.199| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.99 r_work: 0.2978 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24152 Z= 0.132 Angle : 0.593 18.707 32901 Z= 0.294 Chirality : 0.046 0.440 3828 Planarity : 0.004 0.046 4163 Dihedral : 5.408 41.072 3972 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.72 % Allowed : 12.24 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.15), residues: 2883 helix: 1.70 (0.20), residues: 693 sheet: 0.96 (0.19), residues: 706 loop : -1.43 (0.14), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 868 HIS 0.005 0.001 HIS C1046 PHE 0.023 0.001 PHE A 629 TYR 0.020 0.001 TYR A1120 ARG 0.003 0.000 ARG A1021 Details of bonding type rmsd link_NAG-ASN : bond 0.00721 ( 38) link_NAG-ASN : angle 4.03427 ( 114) link_BETA1-4 : bond 0.00479 ( 1) link_BETA1-4 : angle 1.82520 ( 3) hydrogen bonds : bond 0.05666 ( 973) hydrogen bonds : angle 4.97360 ( 2811) SS BOND : bond 0.00469 ( 40) SS BOND : angle 1.43092 ( 80) covalent geometry : bond 0.00305 (24073) covalent geometry : angle 0.54023 (32704) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 169 time to evaluate : 2.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 745 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7542 (tt) REVERT: A 54 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8477 (mm) REVERT: A 99 ARG cc_start: 0.7384 (pmm-80) cc_final: 0.7031 (pmm-80) REVERT: A 102 VAL cc_start: 0.7822 (OUTLIER) cc_final: 0.7598 (m) REVERT: A 600 ASP cc_start: 0.7864 (m-30) cc_final: 0.7476 (t0) REVERT: A 727 ASP cc_start: 0.7739 (OUTLIER) cc_final: 0.7222 (p0) REVERT: C 56 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.8450 (tt0) REVERT: C 110 LYS cc_start: 0.7981 (ptpt) cc_final: 0.7400 (tptt) REVERT: C 124 VAL cc_start: 0.7701 (OUTLIER) cc_final: 0.7407 (m) REVERT: C 932 ASP cc_start: 0.8084 (m-30) cc_final: 0.7733 (m-30) REVERT: C 965 ARG cc_start: 0.8009 (ptp-170) cc_final: 0.7633 (ptp-110) outliers start: 44 outliers final: 28 residues processed: 203 average time/residue: 0.9059 time to fit residues: 224.2334 Evaluate side-chains 191 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 157 time to evaluate : 2.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 877 GLN Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 727 ASP Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 1032 MET Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 551 PHE Chi-restraints excluded: chain C residue 793 LYS Chi-restraints excluded: chain C residue 1099 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 9 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 136 optimal weight: 10.0000 chunk 163 optimal weight: 0.6980 chunk 60 optimal weight: 0.0870 chunk 289 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 154 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 140 optimal weight: 0.9990 chunk 37 optimal weight: 8.9990 overall best weight: 0.9564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 ASN B 108 ASN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.146011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.099431 restraints weight = 29317.873| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.11 r_work: 0.2969 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24152 Z= 0.131 Angle : 0.588 18.618 32901 Z= 0.293 Chirality : 0.046 0.438 3828 Planarity : 0.004 0.047 4163 Dihedral : 5.359 41.140 3972 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.64 % Allowed : 12.55 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.15), residues: 2883 helix: 1.72 (0.20), residues: 695 sheet: 0.96 (0.19), residues: 711 loop : -1.42 (0.14), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 868 HIS 0.005 0.001 HIS C1046 PHE 0.024 0.001 PHE A 629 TYR 0.020 0.001 TYR A1120 ARG 0.005 0.000 ARG A 965 Details of bonding type rmsd link_NAG-ASN : bond 0.00703 ( 38) link_NAG-ASN : angle 3.93800 ( 114) link_BETA1-4 : bond 0.00392 ( 1) link_BETA1-4 : angle 1.78723 ( 3) hydrogen bonds : bond 0.05606 ( 973) hydrogen bonds : angle 4.92025 ( 2811) SS BOND : bond 0.00405 ( 40) SS BOND : angle 1.60451 ( 80) covalent geometry : bond 0.00301 (24073) covalent geometry : angle 0.53593 (32704) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5766 Ramachandran restraints generated. 2883 Oldfield, 0 Emsley, 2883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 160 time to evaluate : 2.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 572 ASP cc_start: 0.8412 (m-30) cc_final: 0.8120 (m-30) REVERT: B 745 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7553 (tt) REVERT: A 99 ARG cc_start: 0.7332 (pmm-80) cc_final: 0.6940 (pmm-80) REVERT: A 102 VAL cc_start: 0.7834 (OUTLIER) cc_final: 0.7596 (m) REVERT: A 600 ASP cc_start: 0.7873 (m-30) cc_final: 0.7436 (t0) REVERT: A 727 ASP cc_start: 0.7726 (OUTLIER) cc_final: 0.7184 (p0) REVERT: C 56 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.8440 (tt0) REVERT: C 110 LYS cc_start: 0.8010 (ptpt) cc_final: 0.7389 (tptt) REVERT: C 124 VAL cc_start: 0.7677 (OUTLIER) cc_final: 0.7386 (m) REVERT: C 932 ASP cc_start: 0.8094 (m-30) cc_final: 0.7713 (m-30) REVERT: C 965 ARG cc_start: 0.7964 (ptp-170) cc_final: 0.7566 (ptp-110) outliers start: 42 outliers final: 28 residues processed: 193 average time/residue: 0.9766 time to fit residues: 228.4542 Evaluate side-chains 189 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 156 time to evaluate : 2.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 877 GLN Chi-restraints excluded: chain B residue 1025 CYS Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 727 ASP Chi-restraints excluded: chain A residue 1032 MET Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 551 PHE Chi-restraints excluded: chain C residue 793 LYS Chi-restraints excluded: chain C residue 1099 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 135 optimal weight: 0.0470 chunk 106 optimal weight: 9.9990 chunk 186 optimal weight: 0.9990 chunk 240 optimal weight: 3.9990 chunk 267 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 102 optimal weight: 0.0070 chunk 62 optimal weight: 0.9980 chunk 245 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 208 optimal weight: 3.9990 overall best weight: 1.2100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 ASN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 889 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.144481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.098642 restraints weight = 29126.750| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.01 r_work: 0.2961 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24152 Z= 0.149 Angle : 0.608 18.670 32901 Z= 0.302 Chirality : 0.047 0.443 3828 Planarity : 0.004 0.047 4163 Dihedral : 5.364 41.172 3972 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.60 % Allowed : 12.78 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.15), residues: 2883 helix: 1.64 (0.20), residues: 701 sheet: 0.97 (0.19), residues: 711 loop : -1.46 (0.14), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 868 HIS 0.005 0.001 HIS C1046 PHE 0.027 0.002 PHE A 629 TYR 0.020 0.001 TYR A1120 ARG 0.003 0.000 ARG B 982 Details of bonding type rmsd link_NAG-ASN : bond 0.00694 ( 38) link_NAG-ASN : angle 3.93572 ( 114) link_BETA1-4 : bond 0.00453 ( 1) link_BETA1-4 : angle 1.81158 ( 3) hydrogen bonds : bond 0.05944 ( 973) hydrogen bonds : angle 4.97271 ( 2811) SS BOND : bond 0.00516 ( 40) SS BOND : angle 1.57697 ( 80) covalent geometry : bond 0.00352 (24073) covalent geometry : angle 0.55759 (32704) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16565.76 seconds wall clock time: 285 minutes 52.13 seconds (17152.13 seconds total)