Starting phenix.real_space_refine on Sun Aug 24 23:25:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h11_34421/08_2025/8h11_34421.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h11_34421/08_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_34421/08_2025/8h11_34421.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h11_34421/08_2025/8h11_34421.map" model { file = "/net/cci-nas-00/data/ceres_data/8h11_34421/08_2025/8h11_34421.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h11_34421/08_2025/8h11_34421.cif" } resolution = 2.72 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.51, per 1000 atoms: 0.23 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: 1.69 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.91 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: 5.44 Time building geometry restraints manager: 2.31 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 1312)) selection = (chain 'B' and (resid 31 through 132 or resid 155 through 204 or resid 209 throu \ gh 810 or resid 834 through 1312)) selection = (chain 'C' and (resid 31 through 132 or resid 155 through 204 or resid 209 throu \ gh 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: 2.360 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.260 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.850 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (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 ARG 0.006 0.001 ARG C 758 TYR 0.040 0.002 TYR B 440 PHE 0.043 0.002 PHE B 360 TRP 0.016 0.002 TRP B 868 HIS 0.007 0.001 HIS B1046 Details of bonding type rmsd covalent geometry : bond 0.00592 (24073) covalent geometry : angle 0.83709 (32704) SS BOND : bond 0.00676 ( 40) SS BOND : angle 1.93362 ( 80) hydrogen bonds : bond 0.14293 ( 973) hydrogen bonds : angle 6.87995 ( 2811) link_BETA1-4 : bond 0.00266 ( 1) link_BETA1-4 : angle 4.64780 ( 3) link_NAG-ASN : bond 0.00757 ( 38) link_NAG-ASN : angle 5.94339 ( 114) *********************** 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 : 0.562 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: 0.5948 time to fit residues: 148.7307 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 : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3822 r_free = 0.3822 target = 0.147414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.100742 restraints weight = 29298.409| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.98 r_work: 0.3006 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.0819 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= 0.125 Angle : 0.614 19.599 32901 Z= 0.305 Chirality : 0.046 0.456 3828 Planarity : 0.005 0.076 4163 Dihedral : 6.783 58.258 3972 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.66 % Allowed : 5.36 % Favored : 93.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.15), residues: 2883 helix: 1.13 (0.20), residues: 692 sheet: 0.87 (0.19), residues: 701 loop : -1.69 (0.14), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 758 TYR 0.025 0.001 TYR A 491 PHE 0.022 0.001 PHE A 629 TRP 0.009 0.001 TRP B 423 HIS 0.005 0.001 HIS C1046 Details of bonding type rmsd covalent geometry : bond 0.00278 (24073) covalent geometry : angle 0.54935 (32704) SS BOND : bond 0.00387 ( 40) SS BOND : angle 1.32828 ( 80) hydrogen bonds : bond 0.05789 ( 973) hydrogen bonds : angle 5.36804 ( 2811) link_BETA1-4 : bond 0.00905 ( 1) link_BETA1-4 : angle 2.70320 ( 3) link_NAG-ASN : bond 0.00899 ( 38) link_NAG-ASN : angle 4.56578 ( 114) *********************** 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 199 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 182 time to evaluate : 0.752 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: 0.8471 (m-30) cc_final: 0.8125 (m-30) REVERT: B 768 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.8018 (pttm) REVERT: B 1063 ILE cc_start: 0.8819 (pt) cc_final: 0.8416 (mt) REVERT: A 600 ASP cc_start: 0.7583 (m-30) cc_final: 0.7292 (t0) REVERT: A 793 LYS cc_start: 0.7139 (ttpt) cc_final: 0.6841 (ttpt) REVERT: C 110 LYS cc_start: 0.7893 (ptpt) cc_final: 0.7258 (tptt) REVERT: C 965 ARG cc_start: 0.7971 (ptp-170) cc_final: 0.7667 (ptp-110) outliers start: 17 outliers final: 5 residues processed: 190 average time/residue: 0.4513 time to fit residues: 101.5524 Evaluate side-chains 163 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 157 time to evaluate : 0.732 ------------------------------------------------------------------------------- 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 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 61 optimal weight: 0.5980 chunk 90 optimal weight: 0.5980 chunk 188 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 227 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 290 optimal weight: 3.9990 chunk 240 optimal weight: 6.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.145986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.098919 restraints weight = 29411.059| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.99 r_work: 0.2979 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 24152 Z= 0.151 Angle : 0.619 18.794 32901 Z= 0.309 Chirality : 0.047 0.457 3828 Planarity : 0.004 0.056 4163 Dihedral : 6.298 50.819 3972 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.41 % Allowed : 7.54 % Favored : 91.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.15), residues: 2883 helix: 1.37 (0.20), residues: 695 sheet: 0.93 (0.19), residues: 699 loop : -1.60 (0.14), residues: 1489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1021 TYR 0.019 0.001 TYR C1049 PHE 0.022 0.002 PHE A 629 TRP 0.010 0.001 TRP A 868 HIS 0.006 0.001 HIS C1046 Details of bonding type rmsd covalent geometry : bond 0.00357 (24073) covalent geometry : angle 0.55943 (32704) SS BOND : bond 0.00492 ( 40) SS BOND : angle 1.53024 ( 80) hydrogen bonds : bond 0.06188 ( 973) hydrogen bonds : angle 5.22121 ( 2811) link_BETA1-4 : bond 0.00417 ( 1) link_BETA1-4 : angle 2.40242 ( 3) link_NAG-ASN : bond 0.00776 ( 38) link_NAG-ASN : angle 4.37976 ( 114) *********************** 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 205 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 169 time to evaluate : 0.572 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: 0.8485 (m-30) cc_final: 0.8138 (m-30) REVERT: B 1063 ILE cc_start: 0.8790 (pt) cc_final: 0.8398 (mt) REVERT: A 107 MET cc_start: 0.8449 (mmm) cc_final: 0.8054 (mmm) REVERT: A 600 ASP cc_start: 0.7696 (m-30) cc_final: 0.7376 (OUTLIER) REVERT: A 793 LYS cc_start: 0.6886 (ttpt) cc_final: 0.6668 (ttpt) REVERT: C 58 LEU cc_start: 0.9062 (mt) cc_final: 0.8860 (mp) REVERT: C 110 LYS cc_start: 0.7930 (ptpt) cc_final: 0.7345 (tptt) REVERT: C 214 ASN cc_start: 0.8567 (t0) cc_final: 0.8294 (t0) REVERT: C 932 ASP cc_start: 0.7910 (m-30) cc_final: 0.7548 (m-30) REVERT: C 965 ARG cc_start: 0.7977 (ptp-170) cc_final: 0.7637 (ptp-110) outliers start: 36 outliers final: 12 residues processed: 193 average time/residue: 0.4459 time to fit residues: 102.2310 Evaluate side-chains 169 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 158 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1110 VAL Chi-restraints excluded: chain A residue 224 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 C residue 118 ASN Chi-restraints excluded: chain C residue 551 PHE Chi-restraints excluded: chain C residue 1074 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 133 optimal weight: 9.9990 chunk 149 optimal weight: 5.9990 chunk 279 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 286 optimal weight: 0.0270 chunk 104 optimal weight: 4.9990 chunk 261 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 overall best weight: 2.1844 ------------------------------------------------------------------------------- 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 746 ASN A 108 ASN A 889 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.143485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.096108 restraints weight = 29423.570| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.01 r_work: 0.2939 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 24152 Z= 0.231 Angle : 0.689 18.929 32901 Z= 0.347 Chirality : 0.050 0.468 3828 Planarity : 0.005 0.051 4163 Dihedral : 6.265 46.100 3972 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.02 % Favored : 95.94 % Rotamer: Outliers : 2.11 % Allowed : 9.07 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.15), residues: 2883 helix: 1.23 (0.20), residues: 695 sheet: 0.86 (0.19), residues: 694 loop : -1.63 (0.14), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1021 TYR 0.019 0.002 TYR C1049 PHE 0.024 0.002 PHE A 870 TRP 0.012 0.002 TRP C 868 HIS 0.008 0.001 HIS A1030 Details of bonding type rmsd covalent geometry : bond 0.00571 (24073) covalent geometry : angle 0.63083 (32704) SS BOND : bond 0.00714 ( 40) SS BOND : angle 1.95925 ( 80) hydrogen bonds : bond 0.07444 ( 973) hydrogen bonds : angle 5.35448 ( 2811) link_BETA1-4 : bond 0.00461 ( 1) link_BETA1-4 : angle 2.28059 ( 3) link_NAG-ASN : bond 0.00734 ( 38) link_NAG-ASN : angle 4.49348 ( 114) *********************** 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 220 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 166 time to evaluate : 0.911 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: B 417 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.6823 (tmm) REVERT: B 572 ASP cc_start: 0.8488 (m-30) cc_final: 0.8065 (m-30) REVERT: A 99 ARG cc_start: 0.7339 (pmm-80) cc_final: 0.6972 (pmm-80) REVERT: A 102 VAL cc_start: 0.7861 (OUTLIER) cc_final: 0.7607 (m) REVERT: A 343 LYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7352 (ptpp) REVERT: A 554 ASP cc_start: 0.6253 (OUTLIER) cc_final: 0.6048 (t0) REVERT: A 727 ASP cc_start: 0.7614 (OUTLIER) cc_final: 0.7133 (p0) REVERT: A 793 LYS cc_start: 0.7117 (ttpt) cc_final: 0.6867 (ttpt) REVERT: C 56 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.8469 (tt0) REVERT: C 58 LEU cc_start: 0.9079 (mt) cc_final: 0.8876 (mp) REVERT: C 110 LYS cc_start: 0.8044 (ptpt) cc_final: 0.7465 (tptt) REVERT: C 214 ASN cc_start: 0.8576 (t0) cc_final: 0.8319 (t0) REVERT: C 932 ASP cc_start: 0.8060 (m-30) cc_final: 0.7639 (m-30) outliers start: 54 outliers final: 22 residues processed: 205 average time/residue: 0.4692 time to fit residues: 115.1557 Evaluate side-chains 183 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 ARG Chi-restraints excluded: chain B residue 114 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 877 GLN Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1110 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 343 LYS 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 537 VAL Chi-restraints excluded: chain A residue 554 ASP 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 421 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 173 optimal weight: 0.9990 chunk 20 optimal weight: 0.4980 chunk 28 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 63 optimal weight: 0.5980 chunk 76 optimal weight: 0.5980 chunk 258 optimal weight: 0.6980 chunk 276 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 177 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 C 599 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.147070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.101093 restraints weight = 29160.053| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.04 r_work: 0.2993 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 24152 Z= 0.109 Angle : 0.568 18.765 32901 Z= 0.281 Chirality : 0.045 0.442 3828 Planarity : 0.004 0.048 4163 Dihedral : 5.631 42.336 3972 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.52 % Allowed : 10.59 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.15), residues: 2883 helix: 1.66 (0.20), residues: 689 sheet: 1.00 (0.19), residues: 693 loop : -1.50 (0.14), residues: 1501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 315 TYR 0.018 0.001 TYR B1049 PHE 0.019 0.001 PHE A 629 TRP 0.011 0.001 TRP A 868 HIS 0.004 0.001 HIS C1046 Details of bonding type rmsd covalent geometry : bond 0.00237 (24073) covalent geometry : angle 0.51257 (32704) SS BOND : bond 0.00357 ( 40) SS BOND : angle 1.26327 ( 80) hydrogen bonds : bond 0.05131 ( 973) hydrogen bonds : angle 4.96543 ( 2811) link_BETA1-4 : bond 0.00436 ( 1) link_BETA1-4 : angle 1.94276 ( 3) link_NAG-ASN : bond 0.00727 ( 38) link_NAG-ASN : angle 4.08198 ( 114) *********************** 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 213 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 174 time to evaluate : 0.923 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: symmetry clash REVERT: A 54 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8349 (mm) REVERT: A 99 ARG cc_start: 0.7315 (pmm-80) cc_final: 0.6941 (pmm-80) REVERT: A 600 ASP cc_start: 0.7787 (m-30) cc_final: 0.7452 (t0) REVERT: A 793 LYS cc_start: 0.6861 (ttpt) cc_final: 0.6607 (ttpt) REVERT: C 110 LYS cc_start: 0.7952 (ptpt) cc_final: 0.7367 (tptt) REVERT: C 214 ASN cc_start: 0.8495 (t0) cc_final: 0.8273 (t0) REVERT: C 321 ASN cc_start: 0.7574 (m-40) cc_final: 0.7127 (p0) REVERT: C 965 ARG cc_start: 0.8003 (ptp-170) cc_final: 0.7659 (ptp-110) outliers start: 39 outliers final: 14 residues processed: 206 average time/residue: 0.4748 time to fit residues: 117.7685 Evaluate side-chains 175 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 160 time to evaluate : 0.927 ------------------------------------------------------------------------------- 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 322 LEU Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain A residue 54 LEU 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 624 THR 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 793 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 251 optimal weight: 6.9990 chunk 243 optimal weight: 3.9990 chunk 233 optimal weight: 8.9990 chunk 143 optimal weight: 0.7980 chunk 190 optimal weight: 0.0030 chunk 22 optimal weight: 0.0570 chunk 54 optimal weight: 4.9990 chunk 197 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 101 optimal weight: 4.9990 overall best weight: 0.9712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 ASN B 112 GLN ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 889 ASN ** A 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.146031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.099398 restraints weight = 29379.799| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.11 r_work: 0.2962 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24152 Z= 0.131 Angle : 0.581 18.680 32901 Z= 0.290 Chirality : 0.046 0.448 3828 Planarity : 0.004 0.048 4163 Dihedral : 5.511 41.885 3972 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.41 % Allowed : 11.34 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.15), residues: 2883 helix: 1.72 (0.20), residues: 695 sheet: 0.98 (0.19), residues: 702 loop : -1.47 (0.14), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1021 TYR 0.024 0.001 TYR C 200 PHE 0.021 0.001 PHE A 629 TRP 0.010 0.001 TRP A 868 HIS 0.004 0.001 HIS C1046 Details of bonding type rmsd covalent geometry : bond 0.00304 (24073) covalent geometry : angle 0.52646 (32704) SS BOND : bond 0.00409 ( 40) SS BOND : angle 1.49978 ( 80) hydrogen bonds : bond 0.05607 ( 973) hydrogen bonds : angle 4.96697 ( 2811) link_BETA1-4 : bond 0.00546 ( 1) link_BETA1-4 : angle 1.83520 ( 3) link_NAG-ASN : bond 0.00697 ( 38) link_NAG-ASN : angle 4.02934 ( 114) *********************** 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 208 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 172 time to evaluate : 0.887 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: symmetry clash REVERT: B 301 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8484 (tp40) REVERT: B 572 ASP cc_start: 0.8422 (m-30) cc_final: 0.8074 (m-30) REVERT: A 54 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8372 (mm) REVERT: A 99 ARG cc_start: 0.7322 (pmm-80) cc_final: 0.7001 (pmm-80) REVERT: A 600 ASP cc_start: 0.7809 (m-30) cc_final: 0.7466 (t0) REVERT: A 727 ASP cc_start: 0.7586 (OUTLIER) cc_final: 0.7060 (p0) REVERT: C 56 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8448 (tt0) REVERT: C 110 LYS cc_start: 0.7969 (ptpt) cc_final: 0.7367 (tptt) REVERT: C 124 VAL cc_start: 0.7665 (OUTLIER) cc_final: 0.7369 (m) REVERT: C 214 ASN cc_start: 0.8524 (t0) cc_final: 0.8293 (t0) REVERT: C 321 ASN cc_start: 0.7668 (m-40) cc_final: 0.7351 (p0) REVERT: C 965 ARG cc_start: 0.7969 (ptp-170) cc_final: 0.7611 (ptp-110) outliers start: 36 outliers final: 22 residues processed: 200 average time/residue: 0.4496 time to fit residues: 108.3657 Evaluate side-chains 187 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 0.751 ------------------------------------------------------------------------------- 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 301 GLN Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 877 GLN Chi-restraints excluded: chain B residue 999 GLU Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain A residue 54 LEU 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 537 VAL 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 27 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 254 optimal weight: 0.0060 chunk 168 optimal weight: 7.9990 chunk 145 optimal weight: 4.9990 chunk 206 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 13 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.3000 ------------------------------------------------------------------------------- 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 = 0.3799 r_free = 0.3799 target = 0.145387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.098595 restraints weight = 29252.248| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.14 r_work: 0.2950 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24152 Z= 0.154 Angle : 0.606 18.690 32901 Z= 0.302 Chirality : 0.047 0.452 3828 Planarity : 0.004 0.048 4163 Dihedral : 5.514 43.567 3972 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.92 % Allowed : 11.45 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.15), residues: 2883 helix: 1.64 (0.20), residues: 697 sheet: 0.93 (0.19), residues: 717 loop : -1.49 (0.14), residues: 1469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 982 TYR 0.020 0.001 TYR C 200 PHE 0.022 0.002 PHE A 629 TRP 0.010 0.001 TRP A 868 HIS 0.006 0.001 HIS C1046 Details of bonding type rmsd covalent geometry : bond 0.00369 (24073) covalent geometry : angle 0.55290 (32704) SS BOND : bond 0.00471 ( 40) SS BOND : angle 1.61000 ( 80) hydrogen bonds : bond 0.06068 ( 973) hydrogen bonds : angle 5.03210 ( 2811) link_BETA1-4 : bond 0.00492 ( 1) link_BETA1-4 : angle 1.83542 ( 3) link_NAG-ASN : bond 0.00708 ( 38) link_NAG-ASN : angle 4.04819 ( 114) *********************** 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 215 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 166 time to evaluate : 0.867 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: 0.8750 (OUTLIER) cc_final: 0.8522 (tp40) REVERT: B 572 ASP cc_start: 0.8495 (m-30) cc_final: 0.8230 (m-30) REVERT: A 54 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8412 (mm) REVERT: A 99 ARG cc_start: 0.7345 (pmm-80) cc_final: 0.7056 (pmm-80) REVERT: A 102 VAL cc_start: 0.7850 (OUTLIER) cc_final: 0.7620 (m) REVERT: A 117 ILE cc_start: 0.7727 (OUTLIER) cc_final: 0.7472 (mp) REVERT: A 600 ASP cc_start: 0.7878 (m-30) cc_final: 0.7489 (t0) REVERT: A 727 ASP cc_start: 0.7621 (OUTLIER) cc_final: 0.7103 (p0) REVERT: C 56 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.8477 (tt0) REVERT: C 110 LYS cc_start: 0.7974 (ptpt) cc_final: 0.7357 (tptt) REVERT: C 124 VAL cc_start: 0.7684 (OUTLIER) cc_final: 0.7381 (m) REVERT: C 214 ASN cc_start: 0.8543 (t0) cc_final: 0.8315 (t0) REVERT: C 321 ASN cc_start: 0.7619 (m-40) cc_final: 0.7300 (p0) REVERT: C 932 ASP cc_start: 0.8086 (m-30) cc_final: 0.7704 (m-30) REVERT: C 965 ARG cc_start: 0.8004 (ptp-170) cc_final: 0.7664 (ptp-110) outliers start: 49 outliers final: 28 residues processed: 207 average time/residue: 0.4054 time to fit residues: 102.2027 Evaluate side-chains 195 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 160 time to evaluate : 0.878 ------------------------------------------------------------------------------- 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 301 GLN Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 877 GLN Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1110 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 117 ILE 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 537 VAL 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 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 1099 THR Chi-restraints excluded: chain C residue 1109 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 221 optimal weight: 7.9990 chunk 167 optimal weight: 0.6980 chunk 240 optimal weight: 6.9990 chunk 182 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 164 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 250 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 212 optimal weight: 8.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- 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 = 0.3796 r_free = 0.3796 target = 0.145167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.098138 restraints weight = 29078.805| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.98 r_work: 0.2964 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 24152 Z= 0.157 Angle : 0.604 18.692 32901 Z= 0.302 Chirality : 0.047 0.450 3828 Planarity : 0.004 0.048 4163 Dihedral : 5.486 41.247 3972 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.99 % Allowed : 11.96 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.15), residues: 2883 helix: 1.65 (0.20), residues: 693 sheet: 0.95 (0.19), residues: 710 loop : -1.46 (0.14), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 982 TYR 0.023 0.001 TYR A1120 PHE 0.023 0.002 PHE A 629 TRP 0.011 0.001 TRP A 868 HIS 0.005 0.001 HIS C1046 Details of bonding type rmsd covalent geometry : bond 0.00376 (24073) covalent geometry : angle 0.55084 (32704) SS BOND : bond 0.00483 ( 40) SS BOND : angle 1.55534 ( 80) hydrogen bonds : bond 0.06123 ( 973) hydrogen bonds : angle 5.04039 ( 2811) link_BETA1-4 : bond 0.00546 ( 1) link_BETA1-4 : angle 1.84860 ( 3) link_NAG-ASN : bond 0.00718 ( 38) link_NAG-ASN : angle 4.05680 ( 114) *********************** 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 217 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 166 time to evaluate : 0.945 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: B 301 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8528 (tp40) REVERT: B 745 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7605 (tt) REVERT: A 54 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8437 (mm) REVERT: A 99 ARG cc_start: 0.7407 (pmm-80) cc_final: 0.7003 (pmm-80) REVERT: A 102 VAL cc_start: 0.7915 (OUTLIER) cc_final: 0.7671 (m) REVERT: A 117 ILE cc_start: 0.7764 (OUTLIER) cc_final: 0.7508 (mp) REVERT: A 600 ASP cc_start: 0.7865 (m-30) cc_final: 0.7523 (t0) REVERT: A 727 ASP cc_start: 0.7595 (OUTLIER) cc_final: 0.7057 (p0) REVERT: A 984 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.8464 (mp10) REVERT: C 56 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.8457 (tt0) REVERT: C 110 LYS cc_start: 0.7974 (ptpt) cc_final: 0.7401 (tptt) REVERT: C 124 VAL cc_start: 0.7721 (OUTLIER) cc_final: 0.7415 (m) REVERT: C 321 ASN cc_start: 0.7697 (m-40) cc_final: 0.7491 (p0) REVERT: C 932 ASP cc_start: 0.8111 (m-30) cc_final: 0.7745 (m-30) REVERT: C 965 ARG cc_start: 0.8040 (ptp-170) cc_final: 0.7719 (ptp-110) REVERT: C 972 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7321 (mp0) outliers start: 51 outliers final: 29 residues processed: 205 average time/residue: 0.4207 time to fit residues: 104.5048 Evaluate side-chains 197 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 159 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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 301 GLN 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 B residue 1110 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 117 ILE 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 537 VAL Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 727 ASP Chi-restraints excluded: chain A residue 984 GLN 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 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 Chi-restraints excluded: chain C residue 1109 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 221 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 223 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 230 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 226 optimal weight: 9.9990 chunk 15 optimal weight: 0.0050 chunk 217 optimal weight: 3.9990 chunk 166 optimal weight: 3.9990 overall best weight: 1.2798 ------------------------------------------------------------------------------- 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 427 ASN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 889 ASN C 409 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.145378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.098301 restraints weight = 29239.982| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.99 r_work: 0.2965 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1423 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= 0.154 Angle : 0.605 18.721 32901 Z= 0.303 Chirality : 0.047 0.450 3828 Planarity : 0.004 0.048 4163 Dihedral : 5.468 41.198 3972 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.80 % Allowed : 12.43 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.15), residues: 2883 helix: 1.66 (0.20), residues: 693 sheet: 0.92 (0.19), residues: 712 loop : -1.45 (0.14), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1021 TYR 0.022 0.001 TYR A1120 PHE 0.024 0.002 PHE A 629 TRP 0.011 0.001 TRP A 868 HIS 0.006 0.001 HIS C1046 Details of bonding type rmsd covalent geometry : bond 0.00365 (24073) covalent geometry : angle 0.55239 (32704) SS BOND : bond 0.00514 ( 40) SS BOND : angle 1.52065 ( 80) hydrogen bonds : bond 0.06066 ( 973) hydrogen bonds : angle 5.02548 ( 2811) link_BETA1-4 : bond 0.00484 ( 1) link_BETA1-4 : angle 1.81474 ( 3) link_NAG-ASN : bond 0.00710 ( 38) link_NAG-ASN : angle 4.03655 ( 114) *********************** 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 207 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 161 time to evaluate : 0.706 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: B 301 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8530 (tp40) REVERT: B 745 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7603 (tt) REVERT: B 965 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.8109 (ptt180) REVERT: A 54 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8459 (mm) REVERT: A 99 ARG cc_start: 0.7392 (pmm-80) cc_final: 0.7038 (pmm-80) REVERT: A 102 VAL cc_start: 0.7924 (OUTLIER) cc_final: 0.7682 (m) REVERT: A 117 ILE cc_start: 0.7770 (OUTLIER) cc_final: 0.7513 (mp) REVERT: A 600 ASP cc_start: 0.7874 (m-30) cc_final: 0.7482 (t0) REVERT: A 727 ASP cc_start: 0.7609 (OUTLIER) cc_final: 0.7050 (p0) REVERT: A 984 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.8463 (mp10) REVERT: C 56 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.8453 (tt0) REVERT: C 110 LYS cc_start: 0.7972 (ptpt) cc_final: 0.7400 (tptt) REVERT: C 124 VAL cc_start: 0.7726 (OUTLIER) cc_final: 0.7420 (m) REVERT: C 932 ASP cc_start: 0.8107 (m-30) cc_final: 0.7751 (m-30) REVERT: C 965 ARG cc_start: 0.8045 (ptp-170) cc_final: 0.7656 (ptp-110) outliers start: 46 outliers final: 30 residues processed: 198 average time/residue: 0.4337 time to fit residues: 103.5616 Evaluate side-chains 194 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 154 time to evaluate : 0.837 ------------------------------------------------------------------------------- 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 301 GLN 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 B residue 1110 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 117 ILE 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 537 VAL Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 727 ASP Chi-restraints excluded: chain A residue 984 GLN 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 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 Chi-restraints excluded: chain C residue 1109 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 94 optimal weight: 0.6980 chunk 169 optimal weight: 0.0040 chunk 29 optimal weight: 0.7980 chunk 214 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 184 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 66 optimal weight: 0.4980 chunk 281 optimal weight: 1.9990 chunk 60 optimal weight: 0.1980 chunk 238 optimal weight: 5.9990 overall best weight: 0.4392 ------------------------------------------------------------------------------- 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 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3831 r_free = 0.3831 target = 0.148142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.103018 restraints weight = 29306.244| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.08 r_work: 0.3002 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24152 Z= 0.100 Angle : 0.554 18.460 32901 Z= 0.275 Chirality : 0.045 0.428 3828 Planarity : 0.004 0.045 4163 Dihedral : 5.172 40.036 3972 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.17 % Allowed : 13.21 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.15), residues: 2883 helix: 1.88 (0.20), residues: 690 sheet: 1.03 (0.19), residues: 704 loop : -1.34 (0.15), residues: 1489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 965 TYR 0.021 0.001 TYR A1120 PHE 0.021 0.001 PHE A 629 TRP 0.010 0.001 TRP A 868 HIS 0.003 0.000 HIS C1046 Details of bonding type rmsd covalent geometry : bond 0.00214 (24073) covalent geometry : angle 0.49774 (32704) SS BOND : bond 0.00399 ( 40) SS BOND : angle 2.04781 ( 80) hydrogen bonds : bond 0.04640 ( 973) hydrogen bonds : angle 4.75031 ( 2811) link_BETA1-4 : bond 0.00515 ( 1) link_BETA1-4 : angle 1.67239 ( 3) link_NAG-ASN : bond 0.00704 ( 38) link_NAG-ASN : angle 3.81273 ( 114) ********************** 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 201 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 171 time to evaluate : 0.768 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: B 110 LYS cc_start: 0.7424 (ptpp) cc_final: 0.6959 (ptpp) REVERT: B 965 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.8058 (ptt180) REVERT: A 54 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8388 (mm) REVERT: A 99 ARG cc_start: 0.7297 (pmm-80) cc_final: 0.7087 (pmm-80) REVERT: A 600 ASP cc_start: 0.7772 (m-30) cc_final: 0.7399 (t0) REVERT: A 984 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8425 (mp10) REVERT: C 110 LYS cc_start: 0.7954 (ptpt) cc_final: 0.7347 (tptt) REVERT: C 124 VAL cc_start: 0.7602 (OUTLIER) cc_final: 0.7319 (m) REVERT: C 911 LYS cc_start: 0.8637 (tttp) cc_final: 0.8377 (tttm) REVERT: C 932 ASP cc_start: 0.8057 (m-30) cc_final: 0.7682 (m-30) REVERT: C 965 ARG cc_start: 0.7997 (ptp-170) cc_final: 0.7719 (ptp-110) outliers start: 30 outliers final: 18 residues processed: 194 average time/residue: 0.4020 time to fit residues: 94.1547 Evaluate side-chains 183 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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 215 THR Chi-restraints excluded: chain B residue 965 ARG Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1110 VAL Chi-restraints excluded: chain A residue 54 LEU 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 389 VAL Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 984 GLN 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 161 optimal weight: 0.6980 chunk 197 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 177 optimal weight: 3.9990 chunk 187 optimal weight: 0.5980 chunk 96 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 276 optimal weight: 4.9990 chunk 245 optimal weight: 1.9990 chunk 242 optimal weight: 1.9990 chunk 284 optimal weight: 2.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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** ** 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 = 0.3810 r_free = 0.3810 target = 0.146352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.099402 restraints weight = 29155.079| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.99 r_work: 0.2983 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24152 Z= 0.136 Angle : 0.582 18.506 32901 Z= 0.291 Chirality : 0.046 0.439 3828 Planarity : 0.004 0.046 4163 Dihedral : 5.241 40.782 3972 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.33 % Allowed : 13.21 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.15), residues: 2883 helix: 1.76 (0.20), residues: 703 sheet: 1.01 (0.19), residues: 713 loop : -1.39 (0.15), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 544 TYR 0.022 0.001 TYR A1120 PHE 0.027 0.002 PHE A 629 TRP 0.009 0.001 TRP A 868 HIS 0.005 0.001 HIS A1030 Details of bonding type rmsd covalent geometry : bond 0.00319 (24073) covalent geometry : angle 0.53167 (32704) SS BOND : bond 0.00456 ( 40) SS BOND : angle 1.48939 ( 80) hydrogen bonds : bond 0.05610 ( 973) hydrogen bonds : angle 4.86488 ( 2811) link_BETA1-4 : bond 0.00446 ( 1) link_BETA1-4 : angle 1.74185 ( 3) link_NAG-ASN : bond 0.00688 ( 38) link_NAG-ASN : angle 3.89252 ( 114) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7886.59 seconds wall clock time: 134 minutes 44.14 seconds (8084.14 seconds total)