Starting phenix.real_space_refine on Sat May 24 02:17:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v0u_42870/05_2025/8v0u_42870.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v0u_42870/05_2025/8v0u_42870.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v0u_42870/05_2025/8v0u_42870.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v0u_42870/05_2025/8v0u_42870.map" model { file = "/net/cci-nas-00/data/ceres_data/8v0u_42870/05_2025/8v0u_42870.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v0u_42870/05_2025/8v0u_42870.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.034 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 114 5.16 5 C 15831 2.51 5 N 4082 2.21 5 O 4784 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 24811 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1036, 8095 Classifications: {'peptide': 1036} Link IDs: {'PTRANS': 51, 'TRANS': 984} Chain breaks: 6 Chain: "B" Number of atoms: 8075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8075 Classifications: {'peptide': 1033} Link IDs: {'PTRANS': 50, 'TRANS': 982} Chain breaks: 6 Chain: "C" Number of atoms: 8095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1036, 8095 Classifications: {'peptide': 1036} Link IDs: {'PTRANS': 51, 'TRANS': 984} Chain breaks: 6 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 15.84, per 1000 atoms: 0.64 Number of scatterers: 24811 At special positions: 0 Unit cell: (136.08, 129.6, 177.12, 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 114 16.00 O 4784 8.00 N 4082 7.00 C 15831 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 343 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A1134 " " NAG A1308 " - " ASN A 282 " " NAG A1309 " - " ASN A 801 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 343 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B1074 " " NAG B1307 " - " ASN B1134 " " NAG B1308 " - " ASN B 282 " " NAG B1309 " - " ASN B 801 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 343 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C1074 " " NAG C1307 " - " ASN C1134 " " NAG C1308 " - " ASN C 282 " " NAG C1309 " - " ASN C 801 " " NAG D 1 " - " ASN A1098 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN B1098 " " NAG G 1 " - " ASN B 717 " " NAG H 1 " - " ASN C1098 " " NAG I 1 " - " ASN C 717 " Time building additional restraints: 7.05 Conformation dependent library (CDL) restraints added in 3.5 seconds 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5826 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 49 sheets defined 26.3% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.81 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 4.043A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.884A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.901A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 752 Processing helix chain 'A' and resid 753 through 757 removed outlier: 4.013A pdb=" N GLY A 757 " --> pdb=" O LEU A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.777A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.592A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 842 Processing helix chain 'A' and resid 848 through 856 removed outlier: 3.681A pdb=" N ASN A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.680A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.600A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.659A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 Processing helix chain 'A' and resid 1140 through 1148 removed outlier: 4.149A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE A1148 " --> pdb=" O GLU A1144 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.514A pdb=" N ASN B 343 " --> pdb=" O HIS B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 366 No H-bonds generated for 'chain 'B' and resid 364 through 366' Processing helix chain 'B' and resid 367 through 372 Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.517A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.637A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.753A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 842 removed outlier: 3.511A pdb=" N GLY B 842 " --> pdb=" O GLY B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 855 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.645A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.746A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.669A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.547A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 Processing helix chain 'B' and resid 1141 through 1148 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.946A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 372 Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.794A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.794A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN C 409 " --> pdb=" O GLU C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.667A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.676A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 836 through 842 removed outlier: 3.522A pdb=" N CYS C 840 " --> pdb=" O GLN C 836 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.321A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.737A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU C 959 " --> pdb=" O ASN C 955 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 Processing helix chain 'C' and resid 1141 through 1148 removed outlier: 3.503A pdb=" N LEU C1145 " --> pdb=" O LEU C1141 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 30 removed outlier: 7.700A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE A 201 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.741A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.849A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.513A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 318 removed outlier: 6.995A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 538 through 540 removed outlier: 5.656A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 660 removed outlier: 5.999A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.649A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 722 Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 722 removed outlier: 6.944A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.624A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AC2, first strand: chain 'B' and resid 25 through 26 removed outlier: 7.474A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.942A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 116 through 120 removed outlier: 3.552A pdb=" N ILE B 119 " --> pdb=" O TRP B 104 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 189 through 190 Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 317 removed outlier: 7.079A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.687A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'B' and resid 538 through 539 Processing sheet with id=AD2, first strand: chain 'B' and resid 565 through 566 removed outlier: 7.212A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.931A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 713 removed outlier: 3.874A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 718 through 722 Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 722 removed outlier: 7.007A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.636A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE1, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AE2, first strand: chain 'C' and resid 25 through 26 removed outlier: 7.960A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER C 94 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.559A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.507A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LYS C 129 " --> pdb=" O LEU C 118 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.986A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.500A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE8, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.844A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 713 removed outlier: 3.604A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.010A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.648A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.505A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 943 hydrogen bonds defined for protein. 2589 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: 11.15 Time building geometry restraints manager: 8.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7904 1.35 - 1.47: 6523 1.47 - 1.60: 10800 1.60 - 1.73: 0 1.73 - 1.85: 141 Bond restraints: 25368 Sorted by residual: bond pdb=" CA ASN C 61 " pdb=" CB ASN C 61 " ideal model delta sigma weight residual 1.525 1.565 -0.041 1.47e-02 4.63e+03 7.63e+00 bond pdb=" C1 NAG A1305 " pdb=" O5 NAG A1305 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.60e+00 bond pdb=" C1 NAG A1309 " pdb=" O5 NAG A1309 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.93e+00 bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.72e+00 bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.61e+00 ... (remaining 25363 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 33480 2.03 - 4.07: 891 4.07 - 6.10: 97 6.10 - 8.13: 22 8.13 - 10.17: 10 Bond angle restraints: 34500 Sorted by residual: angle pdb=" C PHE A 32 " pdb=" N THR A 33 " pdb=" CA THR A 33 " ideal model delta sigma weight residual 121.54 129.74 -8.20 1.91e+00 2.74e-01 1.84e+01 angle pdb=" C PHE B 32 " pdb=" N THR B 33 " pdb=" CA THR B 33 " ideal model delta sigma weight residual 122.46 128.42 -5.96 1.41e+00 5.03e-01 1.79e+01 angle pdb=" C PHE C 32 " pdb=" N THR C 33 " pdb=" CA THR C 33 " ideal model delta sigma weight residual 121.54 129.42 -7.88 1.91e+00 2.74e-01 1.70e+01 angle pdb=" C CYS C 131 " pdb=" N GLU C 132 " pdb=" CA GLU C 132 " ideal model delta sigma weight residual 121.54 128.95 -7.41 1.91e+00 2.74e-01 1.51e+01 angle pdb=" C ILE C 197 " pdb=" N ASP C 198 " pdb=" CA ASP C 198 " ideal model delta sigma weight residual 121.54 128.81 -7.27 1.91e+00 2.74e-01 1.45e+01 ... (remaining 34495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 13906 17.58 - 35.16: 1402 35.16 - 52.74: 240 52.74 - 70.32: 56 70.32 - 87.91: 39 Dihedral angle restraints: 15643 sinusoidal: 6595 harmonic: 9048 Sorted by residual: dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -5.67 -80.33 1 1.00e+01 1.00e-02 7.99e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -15.04 -70.96 1 1.00e+01 1.00e-02 6.47e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -21.34 -64.66 1 1.00e+01 1.00e-02 5.49e+01 ... (remaining 15640 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 3468 0.079 - 0.158: 524 0.158 - 0.237: 33 0.237 - 0.316: 2 0.316 - 0.395: 2 Chirality restraints: 4029 Sorted by residual: chirality pdb=" C1 NAG B1304 " pdb=" ND2 ASN B 616 " pdb=" C2 NAG B1304 " pdb=" O5 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.90e+00 chirality pdb=" C2 NAG F 1 " pdb=" C1 NAG F 1 " pdb=" C3 NAG F 1 " pdb=" N2 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.11 -0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" CB ILE C 101 " pdb=" CA ILE C 101 " pdb=" CG1 ILE C 101 " pdb=" CG2 ILE C 101 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 4026 not shown) Planarity restraints: 4444 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 133 " 0.024 2.00e-02 2.50e+03 2.72e-02 1.30e+01 pdb=" CG PHE A 133 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 PHE A 133 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE A 133 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE A 133 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 133 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 133 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 383 " -0.049 5.00e-02 4.00e+02 7.39e-02 8.74e+00 pdb=" N PRO B 384 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO B 384 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 384 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 520 " 0.042 5.00e-02 4.00e+02 6.27e-02 6.29e+00 pdb=" N PRO C 521 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO C 521 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 521 " 0.035 5.00e-02 4.00e+02 ... (remaining 4441 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 6424 2.80 - 3.33: 19927 3.33 - 3.85: 39540 3.85 - 4.38: 44007 4.38 - 4.90: 80317 Nonbonded interactions: 190215 Sorted by model distance: nonbonded pdb=" O ALA A 879 " pdb=" OG1 THR A 883 " model vdw 2.280 3.040 nonbonded pdb=" OD1 ASN C 360 " pdb=" OG1 THR C 523 " model vdw 2.289 3.040 nonbonded pdb=" O GLY A 880 " pdb=" OG SER A 884 " model vdw 2.295 3.040 nonbonded pdb=" OG1 THR B 108 " pdb=" O ASN B 234 " model vdw 2.304 3.040 nonbonded pdb=" OG SER A 735 " pdb=" OG1 THR A 859 " model vdw 2.305 3.040 ... (remaining 190210 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 24 through 69 or resid 84 through 1148 or resid 1301 throu \ gh 1309)) selection = chain 'B' selection = (chain 'C' and (resid 24 through 69 or resid 84 through 1148 or resid 1301 throu \ gh 1309)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.720 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: 0.030 Extract box with map and model: 1.120 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 60.960 Find NCS groups from input model: 1.250 Set up NCS constraints: 0.110 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 25447 Z= 0.215 Angle : 0.770 10.167 34697 Z= 0.402 Chirality : 0.053 0.395 4029 Planarity : 0.006 0.074 4411 Dihedral : 14.478 87.905 9697 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.73 % Favored : 95.23 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.14), residues: 3063 helix: -0.83 (0.16), residues: 708 sheet: -0.05 (0.19), residues: 728 loop : -1.72 (0.14), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 886 HIS 0.004 0.001 HIS B 519 PHE 0.063 0.002 PHE A 133 TYR 0.029 0.001 TYR B 453 ARG 0.010 0.000 ARG B 646 Details of bonding type rmsd link_NAG-ASN : bond 0.00402 ( 33) link_NAG-ASN : angle 2.25259 ( 99) link_BETA1-4 : bond 0.00623 ( 6) link_BETA1-4 : angle 1.61884 ( 18) hydrogen bonds : bond 0.15981 ( 931) hydrogen bonds : angle 6.65524 ( 2589) SS BOND : bond 0.00540 ( 40) SS BOND : angle 1.53205 ( 80) covalent geometry : bond 0.00454 (25368) covalent geometry : angle 0.75812 (34500) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 2.609 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 305 SER cc_start: 0.8896 (t) cc_final: 0.8665 (t) REVERT: A 571 ASP cc_start: 0.7484 (t0) cc_final: 0.7237 (t0) REVERT: B 1135 ASN cc_start: 0.7590 (t0) cc_final: 0.7258 (t0) REVERT: C 303 LEU cc_start: 0.8124 (mt) cc_final: 0.7878 (mt) REVERT: C 1101 HIS cc_start: 0.7151 (m90) cc_final: 0.6569 (m90) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.3166 time to fit residues: 122.1251 Evaluate side-chains 190 residues out of total 2698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 2.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 260 optimal weight: 0.6980 chunk 234 optimal weight: 0.9990 chunk 129 optimal weight: 9.9990 chunk 80 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 125 optimal weight: 0.5980 chunk 242 optimal weight: 8.9990 chunk 93 optimal weight: 3.9990 chunk 147 optimal weight: 8.9990 chunk 180 optimal weight: 3.9990 chunk 280 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 HIS B 394 ASN B1002 GLN C 556 ASN C1002 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.158964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.123125 restraints weight = 32284.082| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.79 r_work: 0.3043 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.0874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25447 Z= 0.158 Angle : 0.546 9.796 34697 Z= 0.283 Chirality : 0.045 0.300 4029 Planarity : 0.004 0.052 4411 Dihedral : 6.214 57.297 4140 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.56 % Allowed : 6.15 % Favored : 93.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.14), residues: 3063 helix: 0.68 (0.19), residues: 727 sheet: -0.01 (0.19), residues: 721 loop : -1.55 (0.14), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 436 HIS 0.006 0.001 HIS B1048 PHE 0.021 0.001 PHE C 238 TYR 0.025 0.001 TYR B 453 ARG 0.004 0.000 ARG A 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00319 ( 33) link_NAG-ASN : angle 1.69090 ( 99) link_BETA1-4 : bond 0.00249 ( 6) link_BETA1-4 : angle 1.14580 ( 18) hydrogen bonds : bond 0.05053 ( 931) hydrogen bonds : angle 5.09490 ( 2589) SS BOND : bond 0.00417 ( 40) SS BOND : angle 1.39844 ( 80) covalent geometry : bond 0.00380 (25368) covalent geometry : angle 0.53498 (34500) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 204 time to evaluate : 2.596 Fit side-chains REVERT: A 305 SER cc_start: 0.9189 (t) cc_final: 0.8972 (t) REVERT: A 458 LYS cc_start: 0.7568 (mtmt) cc_final: 0.7294 (pttm) REVERT: B 592 PHE cc_start: 0.7862 (p90) cc_final: 0.7610 (p90) REVERT: B 1135 ASN cc_start: 0.7915 (t0) cc_final: 0.7533 (t0) REVERT: C 200 TYR cc_start: 0.7258 (m-80) cc_final: 0.7047 (m-80) REVERT: C 319 ARG cc_start: 0.8351 (ttm-80) cc_final: 0.7863 (ttm110) REVERT: C 556 ASN cc_start: 0.8240 (t0) cc_final: 0.7952 (m-40) REVERT: C 564 GLN cc_start: 0.7458 (OUTLIER) cc_final: 0.6612 (tm-30) REVERT: C 886 TRP cc_start: 0.8459 (p90) cc_final: 0.7830 (p90) REVERT: C 1101 HIS cc_start: 0.7932 (m90) cc_final: 0.7223 (m90) outliers start: 15 outliers final: 11 residues processed: 211 average time/residue: 0.3477 time to fit residues: 120.3721 Evaluate side-chains 200 residues out of total 2698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 188 time to evaluate : 2.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 235 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 305 optimal weight: 2.9990 chunk 230 optimal weight: 0.7980 chunk 155 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 216 optimal weight: 30.0000 chunk 208 optimal weight: 5.9990 chunk 273 optimal weight: 4.9990 chunk 301 optimal weight: 0.1980 chunk 233 optimal weight: 4.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 ASN A 505 HIS A 613 GLN A 644 GLN A 762 GLN B 613 GLN B1002 GLN C 926 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.157768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.122212 restraints weight = 32318.101| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.70 r_work: 0.3078 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25447 Z= 0.166 Angle : 0.543 9.627 34697 Z= 0.280 Chirality : 0.045 0.272 4029 Planarity : 0.004 0.045 4411 Dihedral : 5.749 55.815 4140 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.78 % Allowed : 9.15 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.15), residues: 3063 helix: 1.20 (0.20), residues: 725 sheet: 0.02 (0.19), residues: 694 loop : -1.53 (0.14), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 436 HIS 0.005 0.001 HIS B1048 PHE 0.033 0.001 PHE A 133 TYR 0.024 0.001 TYR B 453 ARG 0.004 0.000 ARG A 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00281 ( 33) link_NAG-ASN : angle 1.68607 ( 99) link_BETA1-4 : bond 0.00370 ( 6) link_BETA1-4 : angle 1.04422 ( 18) hydrogen bonds : bond 0.05068 ( 931) hydrogen bonds : angle 4.85685 ( 2589) SS BOND : bond 0.00373 ( 40) SS BOND : angle 1.40753 ( 80) covalent geometry : bond 0.00403 (25368) covalent geometry : angle 0.53253 (34500) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 197 time to evaluate : 2.597 Fit side-chains REVERT: A 241 LEU cc_start: 0.7305 (tt) cc_final: 0.6993 (mp) REVERT: A 458 LYS cc_start: 0.7774 (mtmt) cc_final: 0.7446 (pttm) REVERT: B 339 HIS cc_start: 0.7243 (t-90) cc_final: 0.7040 (p90) REVERT: B 571 ASP cc_start: 0.7594 (t0) cc_final: 0.6969 (t0) REVERT: B 592 PHE cc_start: 0.7875 (p90) cc_final: 0.7620 (p90) REVERT: B 1135 ASN cc_start: 0.7917 (t0) cc_final: 0.7609 (t0) REVERT: C 200 TYR cc_start: 0.7134 (m-80) cc_final: 0.6825 (m-80) REVERT: C 319 ARG cc_start: 0.8369 (ttm-80) cc_final: 0.7949 (ttm110) REVERT: C 390 LEU cc_start: 0.8554 (pp) cc_final: 0.8259 (pp) REVERT: C 556 ASN cc_start: 0.8342 (t0) cc_final: 0.8092 (m-40) REVERT: C 564 GLN cc_start: 0.7628 (OUTLIER) cc_final: 0.6762 (tm-30) REVERT: C 850 ILE cc_start: 0.7351 (mm) cc_final: 0.6974 (mt) REVERT: C 886 TRP cc_start: 0.8390 (p90) cc_final: 0.7898 (p90) REVERT: C 1101 HIS cc_start: 0.7925 (m90) cc_final: 0.7318 (m90) REVERT: C 1142 GLN cc_start: 0.8351 (tp40) cc_final: 0.8071 (tp-100) outliers start: 21 outliers final: 14 residues processed: 211 average time/residue: 0.3208 time to fit residues: 112.2130 Evaluate side-chains 199 residues out of total 2698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 184 time to evaluate : 2.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 35 optimal weight: 0.9980 chunk 119 optimal weight: 0.0270 chunk 247 optimal weight: 9.9990 chunk 205 optimal weight: 4.9990 chunk 212 optimal weight: 0.2980 chunk 17 optimal weight: 3.9990 chunk 186 optimal weight: 3.9990 chunk 151 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 chunk 271 optimal weight: 0.6980 chunk 208 optimal weight: 7.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 HIS B1002 GLN C 762 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.159658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.121099 restraints weight = 32884.293| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.85 r_work: 0.3133 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 25447 Z= 0.095 Angle : 0.474 9.642 34697 Z= 0.244 Chirality : 0.043 0.255 4029 Planarity : 0.003 0.040 4411 Dihedral : 5.279 55.853 4140 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.48 % Allowed : 10.86 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.15), residues: 3063 helix: 1.51 (0.20), residues: 734 sheet: 0.12 (0.19), residues: 715 loop : -1.39 (0.14), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.003 0.000 HIS B1101 PHE 0.030 0.001 PHE A 133 TYR 0.025 0.001 TYR B 453 ARG 0.002 0.000 ARG C 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00327 ( 33) link_NAG-ASN : angle 1.47887 ( 99) link_BETA1-4 : bond 0.00379 ( 6) link_BETA1-4 : angle 1.01593 ( 18) hydrogen bonds : bond 0.04084 ( 931) hydrogen bonds : angle 4.64331 ( 2589) SS BOND : bond 0.00333 ( 40) SS BOND : angle 1.32251 ( 80) covalent geometry : bond 0.00214 (25368) covalent geometry : angle 0.46372 (34500) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 198 time to evaluate : 2.743 Fit side-chains REVERT: A 241 LEU cc_start: 0.7401 (tt) cc_final: 0.7068 (mp) REVERT: A 458 LYS cc_start: 0.7667 (mtmt) cc_final: 0.7313 (pttm) REVERT: A 571 ASP cc_start: 0.7870 (t0) cc_final: 0.7546 (t0) REVERT: A 902 MET cc_start: 0.8796 (tpt) cc_final: 0.8450 (tpt) REVERT: B 190 ARG cc_start: 0.8145 (mmm160) cc_final: 0.7877 (mmm160) REVERT: B 339 HIS cc_start: 0.7146 (t-90) cc_final: 0.6856 (p90) REVERT: B 374 PHE cc_start: 0.8661 (p90) cc_final: 0.8369 (p90) REVERT: B 571 ASP cc_start: 0.7637 (t0) cc_final: 0.6974 (t0) REVERT: B 859 THR cc_start: 0.8734 (m) cc_final: 0.8142 (p) REVERT: B 1135 ASN cc_start: 0.7988 (t0) cc_final: 0.7527 (t0) REVERT: C 52 GLN cc_start: 0.8845 (tm-30) cc_final: 0.8567 (tm-30) REVERT: C 200 TYR cc_start: 0.7137 (m-80) cc_final: 0.6792 (m-80) REVERT: C 319 ARG cc_start: 0.8312 (ttm-80) cc_final: 0.7772 (ttm110) REVERT: C 390 LEU cc_start: 0.8514 (pp) cc_final: 0.8265 (pp) REVERT: C 556 ASN cc_start: 0.8243 (t0) cc_final: 0.8010 (m-40) REVERT: C 564 GLN cc_start: 0.7829 (mm-40) cc_final: 0.7142 (tp40) REVERT: C 565 PHE cc_start: 0.7044 (m-80) cc_final: 0.6762 (m-80) REVERT: C 886 TRP cc_start: 0.8226 (p90) cc_final: 0.7760 (p90) REVERT: C 1101 HIS cc_start: 0.7745 (m90) cc_final: 0.6866 (m90) REVERT: C 1142 GLN cc_start: 0.8262 (tp40) cc_final: 0.7619 (tm-30) outliers start: 13 outliers final: 9 residues processed: 206 average time/residue: 0.3186 time to fit residues: 109.3233 Evaluate side-chains 199 residues out of total 2698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 190 time to evaluate : 2.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 255 optimal weight: 6.9990 chunk 241 optimal weight: 6.9990 chunk 221 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 104 optimal weight: 0.0670 chunk 57 optimal weight: 5.9990 chunk 225 optimal weight: 5.9990 chunk 106 optimal weight: 0.7980 chunk 222 optimal weight: 5.9990 chunk 185 optimal weight: 0.8980 chunk 149 optimal weight: 10.0000 overall best weight: 1.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1002 GLN C 644 GLN C 762 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.156174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.120443 restraints weight = 32711.993| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.75 r_work: 0.3074 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 25447 Z= 0.192 Angle : 0.546 9.685 34697 Z= 0.281 Chirality : 0.045 0.248 4029 Planarity : 0.004 0.040 4411 Dihedral : 5.431 56.050 4140 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.00 % Allowed : 11.64 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.15), residues: 3063 helix: 1.53 (0.20), residues: 721 sheet: -0.03 (0.19), residues: 708 loop : -1.42 (0.14), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 436 HIS 0.004 0.001 HIS B1048 PHE 0.032 0.001 PHE A 133 TYR 0.022 0.001 TYR B 453 ARG 0.004 0.000 ARG A 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00250 ( 33) link_NAG-ASN : angle 1.69162 ( 99) link_BETA1-4 : bond 0.00325 ( 6) link_BETA1-4 : angle 1.00902 ( 18) hydrogen bonds : bond 0.04990 ( 931) hydrogen bonds : angle 4.74704 ( 2589) SS BOND : bond 0.00366 ( 40) SS BOND : angle 1.51741 ( 80) covalent geometry : bond 0.00472 (25368) covalent geometry : angle 0.53441 (34500) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 193 time to evaluate : 2.603 Fit side-chains REVERT: A 241 LEU cc_start: 0.7473 (tt) cc_final: 0.7272 (mp) REVERT: A 571 ASP cc_start: 0.7985 (t0) cc_final: 0.7746 (t0) REVERT: B 190 ARG cc_start: 0.8385 (mmm160) cc_final: 0.8148 (mmm160) REVERT: B 339 HIS cc_start: 0.7361 (t-90) cc_final: 0.7072 (p90) REVERT: B 571 ASP cc_start: 0.7857 (t0) cc_final: 0.7172 (t0) REVERT: B 1002 GLN cc_start: 0.8105 (tt0) cc_final: 0.7653 (tp-100) REVERT: B 1135 ASN cc_start: 0.7917 (t0) cc_final: 0.7626 (t0) REVERT: C 319 ARG cc_start: 0.8400 (ttm-80) cc_final: 0.7952 (ttm110) REVERT: C 556 ASN cc_start: 0.8319 (t0) cc_final: 0.8081 (m-40) REVERT: C 564 GLN cc_start: 0.7702 (mm-40) cc_final: 0.7092 (tp40) REVERT: C 850 ILE cc_start: 0.7494 (mm) cc_final: 0.7078 (mt) REVERT: C 886 TRP cc_start: 0.8445 (p90) cc_final: 0.8137 (p90) REVERT: C 1101 HIS cc_start: 0.7944 (m90) cc_final: 0.7353 (m90) REVERT: C 1142 GLN cc_start: 0.8291 (tp40) cc_final: 0.7718 (tm-30) outliers start: 27 outliers final: 19 residues processed: 211 average time/residue: 0.3223 time to fit residues: 111.8469 Evaluate side-chains 208 residues out of total 2698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 189 time to evaluate : 2.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 197 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 199 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 221 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 286 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.155075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.119358 restraints weight = 32540.837| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.66 r_work: 0.3063 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 25447 Z= 0.194 Angle : 0.559 9.732 34697 Z= 0.286 Chirality : 0.046 0.253 4029 Planarity : 0.004 0.041 4411 Dihedral : 5.533 55.956 4140 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.22 % Allowed : 12.27 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.15), residues: 3063 helix: 1.47 (0.19), residues: 722 sheet: -0.06 (0.19), residues: 724 loop : -1.47 (0.14), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 436 HIS 0.005 0.001 HIS B1048 PHE 0.034 0.002 PHE A 133 TYR 0.027 0.001 TYR B 453 ARG 0.003 0.000 ARG C 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00254 ( 33) link_NAG-ASN : angle 1.73993 ( 99) link_BETA1-4 : bond 0.00321 ( 6) link_BETA1-4 : angle 1.01261 ( 18) hydrogen bonds : bond 0.05130 ( 931) hydrogen bonds : angle 4.78527 ( 2589) SS BOND : bond 0.00384 ( 40) SS BOND : angle 1.57663 ( 80) covalent geometry : bond 0.00479 (25368) covalent geometry : angle 0.54702 (34500) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 191 time to evaluate : 3.046 Fit side-chains revert: symmetry clash REVERT: A 571 ASP cc_start: 0.8019 (t0) cc_final: 0.7629 (t0) REVERT: B 191 GLU cc_start: 0.8080 (mp0) cc_final: 0.7834 (mp0) REVERT: B 339 HIS cc_start: 0.7395 (t-90) cc_final: 0.7074 (p90) REVERT: B 571 ASP cc_start: 0.7998 (t0) cc_final: 0.7336 (t0) REVERT: B 1002 GLN cc_start: 0.8016 (tt0) cc_final: 0.7559 (tp-100) REVERT: B 1135 ASN cc_start: 0.7892 (t0) cc_final: 0.7626 (t0) REVERT: C 319 ARG cc_start: 0.8377 (ttm-80) cc_final: 0.7945 (ttm110) REVERT: C 556 ASN cc_start: 0.8369 (t0) cc_final: 0.8116 (m-40) REVERT: C 564 GLN cc_start: 0.7772 (mm-40) cc_final: 0.7073 (tp40) REVERT: C 886 TRP cc_start: 0.8274 (p90) cc_final: 0.8056 (p90) REVERT: C 1101 HIS cc_start: 0.7938 (m90) cc_final: 0.7344 (m90) outliers start: 33 outliers final: 27 residues processed: 212 average time/residue: 0.3314 time to fit residues: 117.3131 Evaluate side-chains 214 residues out of total 2698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 187 time to evaluate : 2.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 129 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 265 optimal weight: 2.9990 chunk 271 optimal weight: 0.8980 chunk 209 optimal weight: 3.9990 chunk 291 optimal weight: 0.7980 chunk 205 optimal weight: 4.9990 chunk 150 optimal weight: 5.9990 chunk 224 optimal weight: 6.9990 chunk 266 optimal weight: 0.7980 chunk 211 optimal weight: 0.9980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 HIS C1142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.156384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.120686 restraints weight = 32488.413| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.60 r_work: 0.3086 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25447 Z= 0.140 Angle : 0.517 9.709 34697 Z= 0.264 Chirality : 0.044 0.248 4029 Planarity : 0.003 0.041 4411 Dihedral : 5.342 55.424 4140 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.04 % Allowed : 13.23 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.15), residues: 3063 helix: 1.66 (0.20), residues: 722 sheet: -0.04 (0.19), residues: 721 loop : -1.40 (0.14), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.003 0.001 HIS B1048 PHE 0.035 0.001 PHE A 133 TYR 0.026 0.001 TYR B 453 ARG 0.003 0.000 ARG C 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00269 ( 33) link_NAG-ASN : angle 1.61425 ( 99) link_BETA1-4 : bond 0.00330 ( 6) link_BETA1-4 : angle 0.98585 ( 18) hydrogen bonds : bond 0.04602 ( 931) hydrogen bonds : angle 4.66836 ( 2589) SS BOND : bond 0.00377 ( 40) SS BOND : angle 1.42657 ( 80) covalent geometry : bond 0.00338 (25368) covalent geometry : angle 0.50603 (34500) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 190 time to evaluate : 2.713 Fit side-chains REVERT: A 237 ARG cc_start: 0.7123 (ttm-80) cc_final: 0.6881 (ttm-80) REVERT: A 571 ASP cc_start: 0.7922 (t0) cc_final: 0.7516 (t0) REVERT: A 902 MET cc_start: 0.8852 (tpt) cc_final: 0.8558 (tpt) REVERT: B 191 GLU cc_start: 0.8041 (mp0) cc_final: 0.7763 (mp0) REVERT: B 339 HIS cc_start: 0.7350 (t-90) cc_final: 0.7015 (p90) REVERT: B 374 PHE cc_start: 0.8639 (p90) cc_final: 0.8360 (p90) REVERT: B 571 ASP cc_start: 0.7981 (t0) cc_final: 0.7300 (t0) REVERT: B 859 THR cc_start: 0.8905 (m) cc_final: 0.8400 (p) REVERT: B 1135 ASN cc_start: 0.7916 (t0) cc_final: 0.7664 (t0) REVERT: C 200 TYR cc_start: 0.7253 (m-80) cc_final: 0.7016 (m-80) REVERT: C 319 ARG cc_start: 0.8373 (ttm-80) cc_final: 0.7938 (ttm110) REVERT: C 556 ASN cc_start: 0.8267 (t0) cc_final: 0.8042 (m-40) REVERT: C 564 GLN cc_start: 0.7876 (mm-40) cc_final: 0.7193 (tp40) REVERT: C 1101 HIS cc_start: 0.7915 (m90) cc_final: 0.7314 (m90) REVERT: C 1142 GLN cc_start: 0.8089 (tp40) cc_final: 0.7506 (tm-30) outliers start: 28 outliers final: 22 residues processed: 211 average time/residue: 0.3368 time to fit residues: 118.2136 Evaluate side-chains 204 residues out of total 2698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 182 time to evaluate : 2.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 250 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 229 optimal weight: 4.9990 chunk 249 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 114 optimal weight: 0.0000 chunk 262 optimal weight: 1.9990 chunk 227 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 126 optimal weight: 0.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.157338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.121567 restraints weight = 32357.366| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.56 r_work: 0.3108 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25447 Z= 0.117 Angle : 0.498 9.764 34697 Z= 0.254 Chirality : 0.044 0.250 4029 Planarity : 0.003 0.041 4411 Dihedral : 5.170 55.605 4140 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.11 % Allowed : 13.60 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.15), residues: 3063 helix: 1.80 (0.20), residues: 723 sheet: -0.01 (0.19), residues: 723 loop : -1.35 (0.14), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.002 0.000 HIS B1048 PHE 0.034 0.001 PHE A 133 TYR 0.026 0.001 TYR B 453 ARG 0.002 0.000 ARG C 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00282 ( 33) link_NAG-ASN : angle 1.54184 ( 99) link_BETA1-4 : bond 0.00344 ( 6) link_BETA1-4 : angle 0.96863 ( 18) hydrogen bonds : bond 0.04268 ( 931) hydrogen bonds : angle 4.58516 ( 2589) SS BOND : bond 0.00364 ( 40) SS BOND : angle 1.30225 ( 80) covalent geometry : bond 0.00278 (25368) covalent geometry : angle 0.48852 (34500) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 183 time to evaluate : 2.651 Fit side-chains REVERT: A 237 ARG cc_start: 0.7140 (ttm-80) cc_final: 0.6901 (mtt-85) REVERT: A 571 ASP cc_start: 0.7899 (t0) cc_final: 0.7518 (t0) REVERT: A 902 MET cc_start: 0.8825 (tpt) cc_final: 0.8535 (tpt) REVERT: B 339 HIS cc_start: 0.7360 (t-90) cc_final: 0.7022 (p90) REVERT: B 374 PHE cc_start: 0.8635 (p90) cc_final: 0.8402 (p90) REVERT: B 471 GLU cc_start: 0.7494 (tp30) cc_final: 0.6983 (tm-30) REVERT: B 571 ASP cc_start: 0.7973 (t0) cc_final: 0.7335 (t0) REVERT: B 859 THR cc_start: 0.8896 (m) cc_final: 0.8410 (p) REVERT: B 1135 ASN cc_start: 0.7878 (t0) cc_final: 0.7645 (t0) REVERT: C 200 TYR cc_start: 0.7220 (m-80) cc_final: 0.6928 (m-80) REVERT: C 319 ARG cc_start: 0.8337 (ttm-80) cc_final: 0.7919 (ttm110) REVERT: C 556 ASN cc_start: 0.8187 (t0) cc_final: 0.7939 (m-40) REVERT: C 564 GLN cc_start: 0.7859 (mm-40) cc_final: 0.7220 (tp40) REVERT: C 1101 HIS cc_start: 0.7905 (m90) cc_final: 0.7324 (m90) REVERT: C 1142 GLN cc_start: 0.8093 (tp40) cc_final: 0.7591 (tm-30) outliers start: 30 outliers final: 24 residues processed: 207 average time/residue: 0.3302 time to fit residues: 113.0888 Evaluate side-chains 207 residues out of total 2698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 183 time to evaluate : 2.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 141 optimal weight: 0.7980 chunk 138 optimal weight: 10.0000 chunk 66 optimal weight: 0.7980 chunk 143 optimal weight: 6.9990 chunk 298 optimal weight: 0.5980 chunk 302 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 199 optimal weight: 0.4980 chunk 76 optimal weight: 0.7980 chunk 155 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 HIS A 505 HIS C 762 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.158532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.122777 restraints weight = 32605.709| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.60 r_work: 0.3130 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 25447 Z= 0.100 Angle : 0.478 9.727 34697 Z= 0.244 Chirality : 0.043 0.249 4029 Planarity : 0.003 0.042 4411 Dihedral : 4.966 55.593 4140 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.04 % Allowed : 13.57 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.15), residues: 3063 helix: 1.84 (0.20), residues: 735 sheet: 0.05 (0.19), residues: 721 loop : -1.31 (0.15), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.002 0.000 HIS A 207 PHE 0.036 0.001 PHE A 133 TYR 0.028 0.001 TYR B 453 ARG 0.003 0.000 ARG B 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00298 ( 33) link_NAG-ASN : angle 1.45498 ( 99) link_BETA1-4 : bond 0.00391 ( 6) link_BETA1-4 : angle 0.97694 ( 18) hydrogen bonds : bond 0.03930 ( 931) hydrogen bonds : angle 4.46589 ( 2589) SS BOND : bond 0.00351 ( 40) SS BOND : angle 1.15761 ( 80) covalent geometry : bond 0.00232 (25368) covalent geometry : angle 0.46895 (34500) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 193 time to evaluate : 2.615 Fit side-chains REVERT: A 237 ARG cc_start: 0.6941 (ttm-80) cc_final: 0.6281 (mtp-110) REVERT: A 571 ASP cc_start: 0.7751 (t0) cc_final: 0.7397 (t0) REVERT: A 902 MET cc_start: 0.8833 (tpt) cc_final: 0.8527 (tpt) REVERT: B 374 PHE cc_start: 0.8642 (p90) cc_final: 0.8406 (p90) REVERT: B 571 ASP cc_start: 0.7957 (t0) cc_final: 0.7304 (t0) REVERT: B 859 THR cc_start: 0.8839 (m) cc_final: 0.8315 (p) REVERT: B 1135 ASN cc_start: 0.7957 (t0) cc_final: 0.7657 (t0) REVERT: C 200 TYR cc_start: 0.7221 (m-80) cc_final: 0.6917 (m-80) REVERT: C 319 ARG cc_start: 0.8332 (ttm-80) cc_final: 0.7870 (ttm110) REVERT: C 556 ASN cc_start: 0.8123 (t0) cc_final: 0.7865 (m-40) REVERT: C 564 GLN cc_start: 0.7963 (mm-40) cc_final: 0.7600 (tp40) REVERT: C 1101 HIS cc_start: 0.7861 (m90) cc_final: 0.7172 (m90) REVERT: C 1142 GLN cc_start: 0.8055 (tp40) cc_final: 0.7567 (tm-30) outliers start: 28 outliers final: 26 residues processed: 211 average time/residue: 0.3134 time to fit residues: 110.2558 Evaluate side-chains 213 residues out of total 2698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 187 time to evaluate : 2.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 37 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 307 optimal weight: 7.9990 chunk 198 optimal weight: 0.8980 chunk 164 optimal weight: 1.9990 chunk 304 optimal weight: 0.0470 chunk 167 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 21 optimal weight: 0.2980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN A 505 HIS B 49 HIS C 762 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.158749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.120038 restraints weight = 32680.832| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.74 r_work: 0.3116 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 25447 Z= 0.095 Angle : 0.474 9.759 34697 Z= 0.242 Chirality : 0.043 0.248 4029 Planarity : 0.003 0.042 4411 Dihedral : 4.865 55.612 4140 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.00 % Allowed : 13.79 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.15), residues: 3063 helix: 1.96 (0.20), residues: 729 sheet: 0.10 (0.19), residues: 720 loop : -1.26 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.002 0.000 HIS A 207 PHE 0.036 0.001 PHE A 133 TYR 0.028 0.001 TYR B 453 ARG 0.002 0.000 ARG C 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00300 ( 33) link_NAG-ASN : angle 1.42247 ( 99) link_BETA1-4 : bond 0.00364 ( 6) link_BETA1-4 : angle 0.95373 ( 18) hydrogen bonds : bond 0.03812 ( 931) hydrogen bonds : angle 4.42399 ( 2589) SS BOND : bond 0.00316 ( 40) SS BOND : angle 1.09885 ( 80) covalent geometry : bond 0.00218 (25368) covalent geometry : angle 0.46587 (34500) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6126 Ramachandran restraints generated. 3063 Oldfield, 0 Emsley, 3063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 191 time to evaluate : 2.529 Fit side-chains REVERT: A 237 ARG cc_start: 0.6576 (ttm-80) cc_final: 0.5991 (mtp-110) REVERT: A 377 PHE cc_start: 0.8016 (t80) cc_final: 0.7592 (t80) REVERT: A 465 GLU cc_start: 0.7696 (pt0) cc_final: 0.7380 (pt0) REVERT: A 571 ASP cc_start: 0.7661 (t0) cc_final: 0.7297 (t0) REVERT: A 902 MET cc_start: 0.8822 (tpt) cc_final: 0.8485 (tpt) REVERT: B 339 HIS cc_start: 0.7279 (t-90) cc_final: 0.6819 (p90) REVERT: B 374 PHE cc_start: 0.8559 (p90) cc_final: 0.8229 (p90) REVERT: B 471 GLU cc_start: 0.7441 (tp30) cc_final: 0.6845 (tm-30) REVERT: B 571 ASP cc_start: 0.7922 (t0) cc_final: 0.7201 (t0) REVERT: B 859 THR cc_start: 0.8679 (m) cc_final: 0.8088 (p) REVERT: B 1135 ASN cc_start: 0.8108 (t0) cc_final: 0.7643 (t0) REVERT: C 200 TYR cc_start: 0.7164 (m-80) cc_final: 0.6802 (m-80) REVERT: C 319 ARG cc_start: 0.8305 (ttm-80) cc_final: 0.7806 (ttm110) REVERT: C 556 ASN cc_start: 0.8217 (t0) cc_final: 0.7928 (m-40) REVERT: C 1101 HIS cc_start: 0.7712 (m90) cc_final: 0.6828 (m90) REVERT: C 1142 GLN cc_start: 0.7983 (tp40) cc_final: 0.7530 (tm-30) outliers start: 27 outliers final: 25 residues processed: 209 average time/residue: 0.3337 time to fit residues: 116.0768 Evaluate side-chains 215 residues out of total 2698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 190 time to evaluate : 2.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 35 optimal weight: 3.9990 chunk 232 optimal weight: 5.9990 chunk 241 optimal weight: 2.9990 chunk 265 optimal weight: 0.0980 chunk 13 optimal weight: 3.9990 chunk 217 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 195 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 169 optimal weight: 2.9990 chunk 55 optimal weight: 0.3980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.155177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.119459 restraints weight = 32584.956| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.59 r_work: 0.3022 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 25447 Z= 0.190 Angle : 0.553 9.807 34697 Z= 0.283 Chirality : 0.045 0.250 4029 Planarity : 0.004 0.040 4411 Dihedral : 5.224 55.859 4140 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.96 % Allowed : 13.86 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.15), residues: 3063 helix: 1.61 (0.20), residues: 734 sheet: -0.04 (0.19), residues: 708 loop : -1.35 (0.14), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 886 HIS 0.005 0.001 HIS B1048 PHE 0.032 0.002 PHE A 133 TYR 0.027 0.001 TYR B 453 ARG 0.003 0.000 ARG B 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00264 ( 33) link_NAG-ASN : angle 1.65967 ( 99) link_BETA1-4 : bond 0.00259 ( 6) link_BETA1-4 : angle 0.97125 ( 18) hydrogen bonds : bond 0.04890 ( 931) hydrogen bonds : angle 4.64071 ( 2589) SS BOND : bond 0.00371 ( 40) SS BOND : angle 1.56452 ( 80) covalent geometry : bond 0.00472 (25368) covalent geometry : angle 0.54180 (34500) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12513.53 seconds wall clock time: 217 minutes 8.56 seconds (13028.56 seconds total)