Starting phenix.real_space_refine on Tue Oct 27 19:46:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yvh_73524/10_2026/9yvh_73524.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yvh_73524/10_2026/9yvh_73524.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9yvh_73524/10_2026/9yvh_73524.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yvh_73524/10_2026/9yvh_73524.map" model { file = "/net/cci-nas-00/data/ceres_data/9yvh_73524/10_2026/9yvh_73524.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yvh_73524/10_2026/9yvh_73524.cif" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 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 111 5.16 5 C 15999 2.51 5 N 4143 2.21 5 O 4812 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25065 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 8243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1056, 8243 Classifications: {'peptide': 1056} Link IDs: {'PTRANS': 56, 'TRANS': 999} Chain breaks: 6 Chain: "B" Number of atoms: 8243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1056, 8243 Classifications: {'peptide': 1056} Link IDs: {'PTRANS': 56, 'TRANS': 999} Chain breaks: 6 Chain: "C" Number of atoms: 8243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1056, 8243 Classifications: {'peptide': 1056} Link IDs: {'PTRANS': 56, 'TRANS': 999} 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: "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: "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: "M" 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: "N" 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: "O" 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: "P" 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: "Q" 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: "R" 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: "S" 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: "T" 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: "U" 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 Time building chain proxies: 5.05, per 1000 atoms: 0.20 Number of scatterers: 25065 At special positions: 0 Unit cell: (136.341, 131.915, 174.411, 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 111 16.00 O 4812 8.00 N 4143 7.00 C 15999 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 161 " distance=2.04 Simple disulfide: pdb=" SG CYS A 286 " - pdb=" SG CYS A 296 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 356 " distance=2.03 Simple disulfide: pdb=" SG CYS A 374 " - pdb=" SG CYS A 427 " distance=2.03 Simple disulfide: pdb=" SG CYS A 386 " - pdb=" SG CYS A 520 " distance=2.03 Simple disulfide: pdb=" SG CYS A 475 " - pdb=" SG CYS A 483 " distance=2.03 Simple disulfide: pdb=" SG CYS A 533 " - pdb=" SG CYS A 585 " distance=2.03 Simple disulfide: pdb=" SG CYS A 612 " - pdb=" SG CYS A 644 " distance=2.03 Simple disulfide: pdb=" SG CYS A 657 " - pdb=" SG CYS A 666 " distance=2.03 Simple disulfide: pdb=" SG CYS A 733 " - pdb=" SG CYS A 755 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 744 " distance=2.03 Simple disulfide: pdb=" SG CYS A 835 " - pdb=" SG CYS A 846 " distance=2.03 Simple disulfide: pdb=" SG CYS A1027 " - pdb=" SG CYS A1038 " distance=2.03 Simple disulfide: pdb=" SG CYS A1077 " - pdb=" SG CYS A1121 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 161 " distance=2.03 Simple disulfide: pdb=" SG CYS B 286 " - pdb=" SG CYS B 296 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 356 " distance=2.03 Simple disulfide: pdb=" SG CYS B 374 " - pdb=" SG CYS B 427 " distance=2.03 Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 520 " distance=2.03 Simple disulfide: pdb=" SG CYS B 475 " - pdb=" SG CYS B 483 " distance=2.03 Simple disulfide: pdb=" SG CYS B 533 " - pdb=" SG CYS B 585 " distance=2.03 Simple disulfide: pdb=" SG CYS B 612 " - pdb=" SG CYS B 644 " distance=2.03 Simple disulfide: pdb=" SG CYS B 657 " - pdb=" SG CYS B 666 " distance=2.03 Simple disulfide: pdb=" SG CYS B 733 " - pdb=" SG CYS B 755 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 744 " distance=2.03 Simple disulfide: pdb=" SG CYS B 835 " - pdb=" SG CYS B 846 " distance=2.03 Simple disulfide: pdb=" SG CYS B1027 " - pdb=" SG CYS B1038 " distance=2.03 Simple disulfide: pdb=" SG CYS B1077 " - pdb=" SG CYS B1121 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 161 " distance=2.03 Simple disulfide: pdb=" SG CYS C 286 " - pdb=" SG CYS C 296 " distance=2.03 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 356 " distance=2.03 Simple disulfide: pdb=" SG CYS C 374 " - pdb=" SG CYS C 427 " distance=2.03 Simple disulfide: pdb=" SG CYS C 386 " - pdb=" SG CYS C 520 " distance=2.03 Simple disulfide: pdb=" SG CYS C 475 " - pdb=" SG CYS C 483 " distance=2.03 Simple disulfide: pdb=" SG CYS C 533 " - pdb=" SG CYS C 585 " distance=2.03 Simple disulfide: pdb=" SG CYS C 657 " - pdb=" SG CYS C 666 " distance=2.03 Simple disulfide: pdb=" SG CYS C 733 " - pdb=" SG CYS C 755 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 744 " distance=2.03 Simple disulfide: pdb=" SG CYS C 835 " - pdb=" SG CYS C 846 " distance=2.03 Simple disulfide: pdb=" SG CYS C1027 " - pdb=" SG CYS C1038 " distance=2.03 Simple disulfide: pdb=" SG CYS C1077 " - pdb=" SG CYS C1121 " 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 G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG D 1 " - " ASN A 712 " " NAG G 1 " - " ASN A 796 " " NAG I 1 " - " ASN A1093 " " NAG M 1 " - " ASN A1129 " " NAG N 1 " - " ASN B 712 " " NAG O 1 " - " ASN B 796 " " NAG P 1 " - " ASN B1093 " " NAG Q 1 " - " ASN B1129 " " NAG R 1 " - " ASN C 712 " " NAG S 1 " - " ASN C 796 " " NAG T 1 " - " ASN C1093 " " NAG U 1 " - " ASN C1129 " Time building additional restraints: 1.98 Conformation dependent library (CDL) restraints added in 990.0 milliseconds 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5934 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 45 sheets defined 27.7% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 289 through 299 Processing helix chain 'A' and resid 333 through 338 Processing helix chain 'A' and resid 344 through 348 removed outlier: 3.808A pdb=" N TRP A 348 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 removed outlier: 4.057A pdb=" N TYR A 364 " --> pdb=" O SER A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 384 removed outlier: 4.162A pdb=" N ASN A 383 " --> pdb=" O THR A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 402 removed outlier: 3.548A pdb=" N VAL A 402 " --> pdb=" O GLY A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 417 Processing helix chain 'A' and resid 433 through 438 removed outlier: 3.576A pdb=" N SER A 438 " --> pdb=" O ASN A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 501 Processing helix chain 'A' and resid 732 through 739 Processing helix chain 'A' and resid 741 through 749 Processing helix chain 'A' and resid 750 through 752 No H-bonds generated for 'chain 'A' and resid 750 through 752' Processing helix chain 'A' and resid 753 through 778 Processing helix chain 'A' and resid 811 through 821 Processing helix chain 'A' and resid 831 through 837 removed outlier: 3.790A pdb=" N CYS A 835 " --> pdb=" O GLN A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 851 Processing helix chain 'A' and resid 861 through 880 Processing helix chain 'A' and resid 881 through 885 Processing helix chain 'A' and resid 892 through 904 Processing helix chain 'A' and resid 907 through 914 removed outlier: 4.262A pdb=" N LEU A 911 " --> pdb=" O THR A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 936 Processing helix chain 'A' and resid 940 through 960 removed outlier: 3.740A pdb=" N GLN A 944 " --> pdb=" O LEU A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 963 No H-bonds generated for 'chain 'A' and resid 961 through 963' Processing helix chain 'A' and resid 971 through 979 Processing helix chain 'A' and resid 980 through 1028 removed outlier: 4.757A pdb=" N VAL A 986 " --> pdb=" O PRO A 982 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLN A 987 " --> pdb=" O GLU A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 1135 through 1142 removed outlier: 4.092A pdb=" N GLU A1139 " --> pdb=" O PRO A1135 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 299 Processing helix chain 'B' and resid 333 through 338 Processing helix chain 'B' and resid 344 through 348 removed outlier: 3.844A pdb=" N TRP B 348 " --> pdb=" O VAL B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 367 removed outlier: 3.997A pdb=" N TYR B 364 " --> pdb=" O SER B 361 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA B 367 " --> pdb=" O TYR B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 385 removed outlier: 4.311A pdb=" N ASN B 383 " --> pdb=" O THR B 380 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU B 385 " --> pdb=" O LEU B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 405 removed outlier: 4.303A pdb=" N SER B 403 " --> pdb=" O ASN B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 417 Processing helix chain 'B' and resid 433 through 438 removed outlier: 3.588A pdb=" N SER B 438 " --> pdb=" O ASN B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 500 Processing helix chain 'B' and resid 732 through 739 Processing helix chain 'B' and resid 741 through 749 Processing helix chain 'B' and resid 750 through 752 No H-bonds generated for 'chain 'B' and resid 750 through 752' Processing helix chain 'B' and resid 753 through 778 Processing helix chain 'B' and resid 811 through 821 Processing helix chain 'B' and resid 831 through 837 removed outlier: 3.802A pdb=" N CYS B 835 " --> pdb=" O GLN B 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 851 Processing helix chain 'B' and resid 861 through 880 Processing helix chain 'B' and resid 881 through 885 Processing helix chain 'B' and resid 892 through 904 Processing helix chain 'B' and resid 907 through 914 removed outlier: 4.241A pdb=" N LEU B 911 " --> pdb=" O THR B 907 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 936 removed outlier: 3.793A pdb=" N GLN B 930 " --> pdb=" O ILE B 926 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP B 931 " --> pdb=" O GLY B 927 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 960 removed outlier: 4.104A pdb=" N VAL B 946 " --> pdb=" O LYS B 942 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL B 947 " --> pdb=" O LEU B 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 963 No H-bonds generated for 'chain 'B' and resid 961 through 963' Processing helix chain 'B' and resid 971 through 979 Processing helix chain 'B' and resid 980 through 1028 removed outlier: 4.718A pdb=" N VAL B 986 " --> pdb=" O PRO B 982 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN B 987 " --> pdb=" O GLU B 983 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL B1028 " --> pdb=" O MET B1024 " (cutoff:3.500A) Processing helix chain 'B' and resid 1135 through 1142 removed outlier: 4.109A pdb=" N GLU B1139 " --> pdb=" O PRO B1135 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 299 Processing helix chain 'C' and resid 333 through 338 Processing helix chain 'C' and resid 344 through 348 removed outlier: 3.723A pdb=" N TRP C 348 " --> pdb=" O VAL C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 removed outlier: 4.176A pdb=" N TYR C 364 " --> pdb=" O SER C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 384 removed outlier: 4.280A pdb=" N ASN C 383 " --> pdb=" O THR C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 405 removed outlier: 4.380A pdb=" N SER C 403 " --> pdb=" O ASN C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 417 Processing helix chain 'C' and resid 433 through 438 removed outlier: 3.689A pdb=" N SER C 438 " --> pdb=" O ASN C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 500 Processing helix chain 'C' and resid 732 through 739 Processing helix chain 'C' and resid 741 through 749 Processing helix chain 'C' and resid 750 through 752 No H-bonds generated for 'chain 'C' and resid 750 through 752' Processing helix chain 'C' and resid 753 through 778 Processing helix chain 'C' and resid 811 through 821 Processing helix chain 'C' and resid 831 through 837 removed outlier: 3.765A pdb=" N CYS C 835 " --> pdb=" O GLN C 831 " (cutoff:3.500A) Processing helix chain 'C' and resid 842 through 851 Processing helix chain 'C' and resid 861 through 880 Processing helix chain 'C' and resid 881 through 885 Processing helix chain 'C' and resid 892 through 904 Processing helix chain 'C' and resid 907 through 914 removed outlier: 4.305A pdb=" N LEU C 911 " --> pdb=" O THR C 907 " (cutoff:3.500A) Processing helix chain 'C' and resid 914 through 936 removed outlier: 3.601A pdb=" N SER C 934 " --> pdb=" O GLN C 930 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 960 Processing helix chain 'C' and resid 961 through 963 No H-bonds generated for 'chain 'C' and resid 961 through 963' Processing helix chain 'C' and resid 971 through 979 Processing helix chain 'C' and resid 980 through 1028 removed outlier: 4.688A pdb=" N VAL C 986 " --> pdb=" O PRO C 982 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLN C 987 " --> pdb=" O GLU C 983 " (cutoff:3.500A) Processing helix chain 'C' and resid 1135 through 1142 removed outlier: 4.141A pdb=" N GLU C1139 " --> pdb=" O PRO C1135 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 27 removed outlier: 7.469A pdb=" N ASN A 58 " --> pdb=" O TYR A 264 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N TYR A 264 " --> pdb=" O ASN A 58 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ALA A 259 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N THR A 90 " --> pdb=" O ALA A 259 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N SER A 200 " --> pdb=" O PRO A 220 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 40 removed outlier: 5.892A pdb=" N ASP B 569 " --> pdb=" O ILE B 582 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLU B 319 " --> pdb=" O CYS B 533 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 44 through 52 removed outlier: 7.573A pdb=" N THR A 269 " --> pdb=" O ASP A 285 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N ASP A 285 " --> pdb=" O THR A 269 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU A 271 " --> pdb=" O ALA A 283 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ALA A 283 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LYS A 273 " --> pdb=" O THR A 281 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 79 through 80 removed outlier: 6.466A pdb=" N ARG A 97 " --> pdb=" O ASN A 116 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASN A 116 " --> pdb=" O ARG A 97 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 306 through 314 removed outlier: 6.948A pdb=" N VAL A 590 " --> pdb=" O THR A 310 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ASN A 312 " --> pdb=" O GLY A 588 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLY A 588 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLY A 589 " --> pdb=" O GLN A 608 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 320 through 323 removed outlier: 5.799A pdb=" N ASP A 569 " --> pdb=" O ILE A 582 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N PHE A 560 " --> pdb=" O PHE C 40 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 349 through 353 Processing sheet with id=AA8, first strand: chain 'A' and resid 356 through 357 removed outlier: 6.580A pdb=" N CYS A 356 " --> pdb=" O CYS A 520 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 447 through 449 Processing sheet with id=AB1, first strand: chain 'A' and resid 468 through 469 Processing sheet with id=AB2, first strand: chain 'A' and resid 649 through 650 removed outlier: 6.052A pdb=" N GLU A 649 " --> pdb=" O ALA A 689 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N THR A 691 " --> pdb=" O GLU A 649 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ALA A 667 " --> pdb=" O PRO A 660 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 696 through 697 removed outlier: 6.572A pdb=" N ALA A 696 " --> pdb=" O ILE C 783 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 706 through 710 Processing sheet with id=AB5, first strand: chain 'A' and resid 713 through 723 removed outlier: 3.511A pdb=" N MET A1045 " --> pdb=" O VAL A1060 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N TYR A1062 " --> pdb=" O HIS A1043 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N HIS A1043 " --> pdb=" O TYR A1062 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 728 through 731 removed outlier: 4.494A pdb=" N LYS A 728 " --> pdb=" O LEU A 856 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1115 through 1117 Processing sheet with id=AB8, first strand: chain 'A' and resid 1089 through 1092 Processing sheet with id=AB9, first strand: chain 'B' and resid 23 through 27 removed outlier: 7.437A pdb=" N ASN B 58 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N TYR B 264 " --> pdb=" O ASN B 58 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ALA B 259 " --> pdb=" O THR B 90 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N THR B 90 " --> pdb=" O ALA B 259 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N SER B 200 " --> pdb=" O PRO B 220 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 39 through 40 removed outlier: 5.916A pdb=" N ASP C 569 " --> pdb=" O ILE C 582 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU C 319 " --> pdb=" O ASN C 535 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N ASN C 537 " --> pdb=" O GLU C 319 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE C 321 " --> pdb=" O ASN C 537 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 44 through 52 removed outlier: 7.639A pdb=" N THR B 269 " --> pdb=" O ASP B 285 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ASP B 285 " --> pdb=" O THR B 269 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU B 271 " --> pdb=" O ALA B 283 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ALA B 283 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LYS B 273 " --> pdb=" O THR B 281 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 79 through 80 removed outlier: 6.706A pdb=" N ARG B 97 " --> pdb=" O ASN B 116 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ASN B 116 " --> pdb=" O ARG B 97 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 306 through 314 removed outlier: 6.939A pdb=" N VAL B 590 " --> pdb=" O THR B 310 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ASN B 312 " --> pdb=" O GLY B 588 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLY B 588 " --> pdb=" O ASN B 312 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLY B 589 " --> pdb=" O GLN B 608 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 349 through 353 Processing sheet with id=AC6, first strand: chain 'B' and resid 356 through 357 removed outlier: 6.727A pdb=" N CYS B 356 " --> pdb=" O CYS B 520 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 447 through 449 Processing sheet with id=AC8, first strand: chain 'B' and resid 468 through 469 Processing sheet with id=AC9, first strand: chain 'B' and resid 649 through 650 removed outlier: 6.033A pdb=" N GLU B 649 " --> pdb=" O ALA B 689 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N THR B 691 " --> pdb=" O GLU B 649 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA B 667 " --> pdb=" O PRO B 660 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 706 through 710 removed outlier: 3.829A pdb=" N ALA B1073 " --> pdb=" O PHE B1090 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N PHE B1090 " --> pdb=" O ALA B1073 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 713 through 723 removed outlier: 3.579A pdb=" N MET B1045 " --> pdb=" O VAL B1060 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N TYR B1062 " --> pdb=" O HIS B1043 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N HIS B1043 " --> pdb=" O TYR B1062 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 728 through 731 removed outlier: 4.464A pdb=" N LYS B 728 " --> pdb=" O LEU B 856 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1115 through 1117 Processing sheet with id=AD5, first strand: chain 'C' and resid 23 through 27 removed outlier: 7.373A pdb=" N ASN C 58 " --> pdb=" O TYR C 264 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N TYR C 264 " --> pdb=" O ASN C 58 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ALA C 259 " --> pdb=" O THR C 90 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N THR C 90 " --> pdb=" O ALA C 259 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N SER C 200 " --> pdb=" O PRO C 220 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 44 through 52 removed outlier: 7.665A pdb=" N THR C 269 " --> pdb=" O ASP C 285 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ASP C 285 " --> pdb=" O THR C 269 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU C 271 " --> pdb=" O ALA C 283 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ALA C 283 " --> pdb=" O LEU C 271 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LYS C 273 " --> pdb=" O THR C 281 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 79 through 80 removed outlier: 6.484A pdb=" N ARG C 97 " --> pdb=" O ASN C 116 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ASN C 116 " --> pdb=" O ARG C 97 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 306 through 314 removed outlier: 6.967A pdb=" N VAL C 590 " --> pdb=" O THR C 310 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ASN C 312 " --> pdb=" O GLY C 588 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLY C 588 " --> pdb=" O ASN C 312 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLY C 589 " --> pdb=" O GLN C 608 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 349 through 353 Processing sheet with id=AE1, first strand: chain 'C' and resid 356 through 357 removed outlier: 6.545A pdb=" N CYS C 356 " --> pdb=" O CYS C 520 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 447 through 449 Processing sheet with id=AE3, first strand: chain 'C' and resid 468 through 469 Processing sheet with id=AE4, first strand: chain 'C' and resid 649 through 650 removed outlier: 6.062A pdb=" N GLU C 649 " --> pdb=" O ALA C 689 " (cutoff:3.500A) removed outlier: 8.561A pdb=" N THR C 691 " --> pdb=" O GLU C 649 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA C 667 " --> pdb=" O PRO C 660 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 706 through 710 Processing sheet with id=AE6, first strand: chain 'C' and resid 713 through 723 removed outlier: 3.517A pdb=" N MET C1045 " --> pdb=" O VAL C1060 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N TYR C1062 " --> pdb=" O HIS C1043 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N HIS C1043 " --> pdb=" O TYR C1062 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 728 through 731 removed outlier: 4.499A pdb=" N LYS C 728 " --> pdb=" O LEU C 856 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1115 through 1117 Processing sheet with id=AE9, first strand: chain 'C' and resid 1089 through 1092 1065 hydrogen bonds defined for protein. 2874 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.81 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7999 1.34 - 1.47: 6429 1.47 - 1.59: 11080 1.59 - 1.72: 1 1.72 - 1.84: 135 Bond restraints: 25644 Sorted by residual: bond pdb=" N VAL A 610 " pdb=" CA VAL A 610 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.11e-02 8.12e+03 1.07e+01 bond pdb=" N VAL A 615 " pdb=" CA VAL A 615 " ideal model delta sigma weight residual 1.461 1.496 -0.034 1.23e-02 6.61e+03 7.83e+00 bond pdb=" N ASN A 611 " pdb=" CA ASN A 611 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.33e-02 5.65e+03 5.75e+00 bond pdb=" CB ASN C1130 " pdb=" CG ASN C1130 " ideal model delta sigma weight residual 1.516 1.575 -0.059 2.50e-02 1.60e+03 5.64e+00 bond pdb=" CA ASP C 359 " pdb=" CB ASP C 359 " ideal model delta sigma weight residual 1.531 1.602 -0.071 3.28e-02 9.30e+02 4.74e+00 ... (remaining 25639 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 34200 2.41 - 4.82: 599 4.82 - 7.22: 89 7.22 - 9.63: 15 9.63 - 12.04: 5 Bond angle restraints: 34908 Sorted by residual: angle pdb=" N VAL B 125 " pdb=" CA VAL B 125 " pdb=" C VAL B 125 " ideal model delta sigma weight residual 112.43 105.93 6.50 9.20e-01 1.18e+00 4.99e+01 angle pdb=" C ASN C 712 " pdb=" N PHE C 713 " pdb=" CA PHE C 713 " ideal model delta sigma weight residual 121.54 131.77 -10.23 1.91e+00 2.74e-01 2.87e+01 angle pdb=" N ILE C 839 " pdb=" CA ILE C 839 " pdb=" C ILE C 839 " ideal model delta sigma weight residual 113.53 108.56 4.97 9.80e-01 1.04e+00 2.57e+01 angle pdb=" N ILE B 839 " pdb=" CA ILE B 839 " pdb=" C ILE B 839 " ideal model delta sigma weight residual 113.53 108.59 4.94 9.80e-01 1.04e+00 2.55e+01 angle pdb=" CG ARG B 504 " pdb=" CD ARG B 504 " pdb=" NE ARG B 504 " ideal model delta sigma weight residual 112.00 122.55 -10.55 2.20e+00 2.07e-01 2.30e+01 ... (remaining 34903 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 14887 17.78 - 35.56: 607 35.56 - 53.35: 88 53.35 - 71.13: 18 71.13 - 88.91: 12 Dihedral angle restraints: 15612 sinusoidal: 6387 harmonic: 9225 Sorted by residual: dihedral pdb=" CB CYS B 612 " pdb=" SG CYS B 612 " pdb=" SG CYS B 644 " pdb=" CB CYS B 644 " ideal model delta sinusoidal sigma weight residual -86.00 -35.38 -50.62 1 1.00e+01 1.00e-02 3.51e+01 dihedral pdb=" CA PHE A 795 " pdb=" C PHE A 795 " pdb=" N ASN A 796 " pdb=" CA ASN A 796 " ideal model delta harmonic sigma weight residual 180.00 154.75 25.25 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA THR C 711 " pdb=" C THR C 711 " pdb=" N ASN C 712 " pdb=" CA ASN C 712 " ideal model delta harmonic sigma weight residual 180.00 154.87 25.13 0 5.00e+00 4.00e-02 2.53e+01 ... (remaining 15609 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.223: 4016 0.223 - 0.446: 8 0.446 - 0.669: 1 0.669 - 0.892: 0 0.892 - 1.115: 1 Chirality restraints: 4026 Sorted by residual: chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 796 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.28 -1.12 2.00e-01 2.50e+01 3.11e+01 chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN C 712 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-01 2.50e+01 8.14e+00 chirality pdb=" CG LEU B 911 " pdb=" CB LEU B 911 " pdb=" CD1 LEU B 911 " pdb=" CD2 LEU B 911 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.23e+00 ... (remaining 4023 not shown) Planarity restraints: 4509 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 712 " 0.059 2.00e-02 2.50e+03 5.66e-02 4.00e+01 pdb=" CG ASN C 712 " -0.068 2.00e-02 2.50e+03 pdb=" OD1 ASN C 712 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN C 712 " -0.065 2.00e-02 2.50e+03 pdb=" C1 NAG R 1 " 0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 796 " -0.057 2.00e-02 2.50e+03 5.49e-02 3.77e+01 pdb=" CG ASN A 796 " 0.071 2.00e-02 2.50e+03 pdb=" OD1 ASN A 796 " -0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN A 796 " 0.059 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 796 " -0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" CG ASN A 796 " 0.056 2.00e-02 2.50e+03 pdb=" OD1 ASN A 796 " -0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN A 796 " -0.018 2.00e-02 2.50e+03 ... (remaining 4506 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 5779 2.80 - 3.32: 21341 3.32 - 3.85: 39712 3.85 - 4.37: 45987 4.37 - 4.90: 82567 Nonbonded interactions: 195386 Sorted by model distance: nonbonded pdb=" OD1 ASP C 359 " pdb=" OG SER C 361 " model vdw 2.269 3.040 nonbonded pdb=" O THR A 388 " pdb=" OG1 THR A 518 " model vdw 2.278 3.040 nonbonded pdb=" O THR C 388 " pdb=" OG1 THR C 518 " model vdw 2.284 3.040 nonbonded pdb=" NH1 ARG C 323 " pdb=" O THR C 526 " model vdw 2.290 3.120 nonbonded pdb=" OD1 ASP A 359 " pdb=" OG SER A 361 " model vdw 2.293 3.040 ... (remaining 195381 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'I' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.020 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: 0.040 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 23.130 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 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 : 0.004 0.071 25709 Z= 0.195 Angle : 0.826 17.367 35062 Z= 0.436 Chirality : 0.058 1.115 4026 Planarity : 0.006 0.064 4497 Dihedral : 10.161 88.910 9555 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.14), residues: 3126 helix: 1.88 (0.19), residues: 660 sheet: 0.45 (0.19), residues: 675 loop : -1.33 (0.13), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 314 TYR 0.027 0.002 TYR C 195 PHE 0.033 0.002 PHE A 372 TRP 0.021 0.002 TRP A 881 HIS 0.004 0.001 HIS C1078 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.19 (25644) covalent geometry : angle 0.80122 / 0.43 (34908) SS BOND : bond 0.00304 / 0.19 ( 41) SS BOND : angle 1.70495 / 1.22 ( 82) hydrogen bonds : bond 0.07451 / 4.72 ( 1065) hydrogen bonds : angle 5.92443 / 4.06 ( 2874) link_BETA1-4 : bond 0.00939 / 0.64 ( 12) link_BETA1-4 : angle 1.87865 / 1.16 ( 36) link_NAG-ASN : bond 0.00997 / 0.68 ( 12) link_NAG-ASN : angle 5.60486 / 3.27 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 191 average time/residue: 0.4810 time to fit residues: 111.0660 Evaluate side-chains 104 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 950 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.0670 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 4.9990 overall best weight: 3.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 ASN ** B 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 757 GLN C 383 ASN C 400 ASN C 608 GLN C 750 GLN C 757 GLN C 799 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.109539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.065799 restraints weight = 54515.996| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 3.28 r_work: 0.2791 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 25709 Z= 0.262 Angle : 0.648 10.269 35062 Z= 0.336 Chirality : 0.048 0.328 4026 Planarity : 0.005 0.041 4497 Dihedral : 4.790 43.504 3905 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.80 % Allowed : 4.76 % Favored : 94.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.14), residues: 3126 helix: 2.27 (0.20), residues: 675 sheet: 0.49 (0.19), residues: 714 loop : -1.37 (0.13), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 760 TYR 0.026 0.002 TYR A 375 PHE 0.041 0.002 PHE A 152 TRP 0.018 0.002 TRP B1097 HIS 0.006 0.001 HIS A1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00632 / 0.26 (25644) covalent geometry : angle 0.63465 / 0.33 (34908) SS BOND : bond 0.00776 / 0.40 ( 41) SS BOND : angle 1.49958 / 1.07 ( 82) hydrogen bonds : bond 0.06470 / 4.17 ( 1065) hydrogen bonds : angle 5.53177 / 3.78 ( 2874) link_BETA1-4 : bond 0.00322 / 0.22 ( 12) link_BETA1-4 : angle 1.62913 / 1.11 ( 36) link_NAG-ASN : bond 0.00517 / 0.39 ( 12) link_NAG-ASN : angle 3.22573 / 2.05 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 ILE cc_start: 0.8471 (mp) cc_final: 0.8021 (tp) REVERT: A 195 TYR cc_start: 0.8282 (m-80) cc_final: 0.8073 (m-80) REVERT: A 198 ILE cc_start: 0.8208 (pt) cc_final: 0.7946 (pp) REVERT: B 309 GLN cc_start: 0.8026 (tp-100) cc_final: 0.7770 (tp-100) REVERT: B 989 ASP cc_start: 0.8848 (m-30) cc_final: 0.8609 (t70) REVERT: C 989 ASP cc_start: 0.8575 (m-30) cc_final: 0.8256 (t0) outliers start: 22 outliers final: 11 residues processed: 102 average time/residue: 0.4425 time to fit residues: 56.0369 Evaluate side-chains 88 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 560 PHE Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 959 LYS Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 935 SER Chi-restraints excluded: chain C residue 1127 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: [23, 291, 257, 136, 293, 26, 67, 307, 37, 234, 118] chunk 23 optimal weight: 0.9990 chunk 291 optimal weight: 0.7980 chunk 257 optimal weight: 7.9990 chunk 136 optimal weight: 9.9990 chunk 293 optimal weight: 0.6980 chunk 26 optimal weight: 9.9990 chunk 67 optimal weight: 0.8980 chunk 307 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 234 optimal weight: 2.9990 chunk 118 optimal weight: 8.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 234 GLN A 608 GLN B 670 GLN C 234 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.110688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.068300 restraints weight = 54822.094| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 3.26 r_work: 0.2843 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 25709 Z= 0.119 Angle : 0.525 8.699 35062 Z= 0.269 Chirality : 0.044 0.353 4026 Planarity : 0.004 0.038 4497 Dihedral : 4.362 43.416 3903 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.87 % Allowed : 5.63 % Favored : 93.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.15), residues: 3126 helix: 2.89 (0.20), residues: 660 sheet: 0.60 (0.19), residues: 696 loop : -1.18 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 323 TYR 0.017 0.001 TYR A 360 PHE 0.012 0.001 PHE B 560 TRP 0.008 0.001 TRP C 99 HIS 0.004 0.001 HIS B1078 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (25644) covalent geometry : angle 0.51742 / 0.27 (34908) SS BOND : bond 0.00244 / 0.16 ( 41) SS BOND : angle 1.00132 / 0.72 ( 82) hydrogen bonds : bond 0.04823 / 3.09 ( 1065) hydrogen bonds : angle 5.20908 / 3.55 ( 2874) link_BETA1-4 : bond 0.00441 / 0.30 ( 12) link_BETA1-4 : angle 1.17927 / 0.78 ( 36) link_NAG-ASN : bond 0.00668 / 0.47 ( 12) link_NAG-ASN : angle 2.24357 / 1.46 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 TYR cc_start: 0.8292 (m-80) cc_final: 0.8084 (m-80) REVERT: A 198 ILE cc_start: 0.8126 (OUTLIER) cc_final: 0.7861 (pp) REVERT: A 409 GLN cc_start: 0.8068 (mm-40) cc_final: 0.7817 (mm-40) REVERT: A 740 ASP cc_start: 0.8366 (t0) cc_final: 0.7831 (p0) REVERT: A 989 ASP cc_start: 0.8734 (OUTLIER) cc_final: 0.8482 (t70) REVERT: B 670 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.8123 (pp30) REVERT: B 989 ASP cc_start: 0.8740 (m-30) cc_final: 0.8498 (t70) REVERT: C 234 GLN cc_start: 0.7440 (OUTLIER) cc_final: 0.6862 (pp30) REVERT: C 928 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8393 (mtpt) REVERT: C 1033 LYS cc_start: 0.9516 (mmtp) cc_final: 0.9244 (mmtm) outliers start: 24 outliers final: 12 residues processed: 110 average time/residue: 0.4800 time to fit residues: 64.3001 Evaluate side-chains 99 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 560 PHE Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 733 CYS Chi-restraints excluded: chain A residue 989 ASP Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 670 GLN Chi-restraints excluded: chain B residue 1095 THR Chi-restraints excluded: chain C residue 234 GLN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 895 MET Chi-restraints excluded: chain C residue 928 LYS Chi-restraints excluded: chain C residue 935 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: [232, 144, 74, 309, 203, 299, 48, 287, 43, 126, 165] chunk 232 optimal weight: 0.9990 chunk 144 optimal weight: 20.0000 chunk 74 optimal weight: 0.9980 chunk 309 optimal weight: 2.9990 chunk 203 optimal weight: 0.9980 chunk 299 optimal weight: 0.3980 chunk 48 optimal weight: 2.9990 chunk 287 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 chunk 126 optimal weight: 1.9990 chunk 165 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.110176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.067578 restraints weight = 54714.248| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 3.28 r_work: 0.2839 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 25709 Z= 0.119 Angle : 0.511 10.258 35062 Z= 0.261 Chirality : 0.043 0.206 4026 Planarity : 0.004 0.037 4497 Dihedral : 4.138 39.557 3903 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.98 % Allowed : 6.50 % Favored : 92.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.15), residues: 3126 helix: 3.24 (0.20), residues: 642 sheet: 0.76 (0.19), residues: 687 loop : -1.09 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 323 TYR 0.015 0.001 TYR B1062 PHE 0.032 0.001 PHE A 152 TRP 0.007 0.001 TRP C 431 HIS 0.003 0.000 HIS B1078 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (25644) covalent geometry : angle 0.50404 / 0.26 (34908) SS BOND : bond 0.00238 / 0.16 ( 41) SS BOND : angle 0.96946 / 0.70 ( 82) hydrogen bonds : bond 0.04678 / 2.99 ( 1065) hydrogen bonds : angle 5.11207 / 3.47 ( 2874) link_BETA1-4 : bond 0.00251 / 0.16 ( 12) link_BETA1-4 : angle 1.19113 / 0.78 ( 36) link_NAG-ASN : bond 0.00565 / 0.40 ( 12) link_NAG-ASN : angle 2.02108 / 1.33 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 90 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ILE cc_start: 0.8421 (mp) cc_final: 0.8151 (tp) REVERT: A 198 ILE cc_start: 0.8133 (pt) cc_final: 0.7875 (pp) REVERT: A 409 GLN cc_start: 0.8114 (mm-40) cc_final: 0.7877 (mm-40) REVERT: A 740 ASP cc_start: 0.8428 (t0) cc_final: 0.7970 (p0) REVERT: A 989 ASP cc_start: 0.8727 (OUTLIER) cc_final: 0.8330 (t70) REVERT: B 989 ASP cc_start: 0.8737 (OUTLIER) cc_final: 0.8498 (t70) REVERT: C 928 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8400 (mtpt) REVERT: C 1087 GLU cc_start: 0.8861 (pm20) cc_final: 0.8626 (pm20) outliers start: 27 outliers final: 16 residues processed: 108 average time/residue: 0.4754 time to fit residues: 62.9546 Evaluate side-chains 101 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 733 CYS Chi-restraints excluded: chain A residue 989 ASP Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 989 ASP Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 560 PHE Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 895 MET Chi-restraints excluded: chain C residue 928 LYS Chi-restraints excluded: chain C residue 935 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: [156, 249, 286, 240, 253, 295, 117, 15, 111, 159, 73] chunk 156 optimal weight: 0.9980 chunk 249 optimal weight: 9.9990 chunk 286 optimal weight: 1.9990 chunk 240 optimal weight: 2.9990 chunk 253 optimal weight: 9.9990 chunk 295 optimal weight: 0.0370 chunk 117 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 chunk 159 optimal weight: 0.4980 chunk 73 optimal weight: 6.9990 overall best weight: 1.3062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 309 GLN B 445 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.109880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.067612 restraints weight = 54636.617| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 3.24 r_work: 0.2823 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25709 Z= 0.130 Angle : 0.512 11.006 35062 Z= 0.262 Chirality : 0.043 0.196 4026 Planarity : 0.004 0.036 4497 Dihedral : 3.996 36.257 3903 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.94 % Allowed : 7.08 % Favored : 91.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.15), residues: 3126 helix: 3.30 (0.20), residues: 642 sheet: 0.67 (0.19), residues: 708 loop : -1.07 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 760 TYR 0.015 0.001 TYR A1062 PHE 0.036 0.001 PHE B 152 TRP 0.007 0.001 TRP C 431 HIS 0.003 0.001 HIS A1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (25644) covalent geometry : angle 0.50616 / 0.26 (34908) SS BOND : bond 0.00242 / 0.16 ( 41) SS BOND : angle 0.99457 / 0.72 ( 82) hydrogen bonds : bond 0.04777 / 3.06 ( 1065) hydrogen bonds : angle 5.03713 / 3.43 ( 2874) link_BETA1-4 : bond 0.00257 / 0.15 ( 12) link_BETA1-4 : angle 1.12672 / 0.74 ( 36) link_NAG-ASN : bond 0.00517 / 0.37 ( 12) link_NAG-ASN : angle 1.88555 / 1.24 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ILE cc_start: 0.8090 (pt) cc_final: 0.7826 (pp) REVERT: A 740 ASP cc_start: 0.8525 (t0) cc_final: 0.8124 (p0) REVERT: A 989 ASP cc_start: 0.8683 (OUTLIER) cc_final: 0.8290 (t70) REVERT: B 96 ILE cc_start: 0.8486 (mp) cc_final: 0.8145 (tp) REVERT: B 989 ASP cc_start: 0.8716 (OUTLIER) cc_final: 0.8469 (t70) REVERT: C 50 ASP cc_start: 0.7912 (t70) cc_final: 0.7702 (t70) REVERT: C 928 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8371 (mtpt) REVERT: C 1033 LYS cc_start: 0.9532 (mmtp) cc_final: 0.9252 (mmtm) REVERT: C 1087 GLU cc_start: 0.8862 (pm20) cc_final: 0.8636 (pm20) outliers start: 26 outliers final: 19 residues processed: 114 average time/residue: 0.4840 time to fit residues: 67.3444 Evaluate side-chains 103 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 733 CYS Chi-restraints excluded: chain A residue 989 ASP Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 989 ASP Chi-restraints excluded: chain B residue 1095 THR Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 560 PHE Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 895 MET Chi-restraints excluded: chain C residue 928 LYS Chi-restraints excluded: chain C residue 935 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: [288, 152, 148, 160, 263, 248, 173, 274, 297, 242, 146] chunk 288 optimal weight: 3.9990 chunk 152 optimal weight: 5.9990 chunk 148 optimal weight: 9.9990 chunk 160 optimal weight: 7.9990 chunk 263 optimal weight: 0.9980 chunk 248 optimal weight: 4.9990 chunk 173 optimal weight: 0.7980 chunk 274 optimal weight: 5.9990 chunk 297 optimal weight: 2.9990 chunk 242 optimal weight: 0.9980 chunk 146 optimal weight: 4.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 482 ASN B 799 GLN C 482 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.108393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.065847 restraints weight = 54914.309| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 3.27 r_work: 0.2788 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 25709 Z= 0.178 Angle : 0.541 10.795 35062 Z= 0.279 Chirality : 0.044 0.188 4026 Planarity : 0.004 0.038 4497 Dihedral : 4.077 35.080 3903 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.31 % Allowed : 7.59 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.15), residues: 3126 helix: 3.25 (0.20), residues: 642 sheet: 0.66 (0.19), residues: 693 loop : -1.03 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 760 TYR 0.017 0.001 TYR A1062 PHE 0.041 0.001 PHE A 152 TRP 0.007 0.001 TRP A 431 HIS 0.004 0.001 HIS A1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 (25644) covalent geometry : angle 0.53466 / 0.28 (34908) SS BOND : bond 0.00277 / 0.17 ( 41) SS BOND : angle 1.10918 / 0.80 ( 82) hydrogen bonds : bond 0.05370 / 3.45 ( 1065) hydrogen bonds : angle 5.14824 / 3.50 ( 2874) link_BETA1-4 : bond 0.00210 / 0.12 ( 12) link_BETA1-4 : angle 1.15451 / 0.76 ( 36) link_NAG-ASN : bond 0.00540 / 0.39 ( 12) link_NAG-ASN : angle 1.90376 / 1.25 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 84 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 ILE cc_start: 0.8138 (OUTLIER) cc_final: 0.7871 (pp) REVERT: A 740 ASP cc_start: 0.8598 (t0) cc_final: 0.8222 (p0) REVERT: A 989 ASP cc_start: 0.8758 (OUTLIER) cc_final: 0.8387 (t70) REVERT: B 96 ILE cc_start: 0.8493 (mp) cc_final: 0.8172 (tp) REVERT: B 989 ASP cc_start: 0.8804 (OUTLIER) cc_final: 0.8569 (t70) REVERT: C 50 ASP cc_start: 0.7941 (t70) cc_final: 0.7727 (t70) REVERT: C 928 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8510 (mtpt) REVERT: C 1033 LYS cc_start: 0.9543 (mmtp) cc_final: 0.9264 (mmtm) REVERT: C 1087 GLU cc_start: 0.8891 (pm20) cc_final: 0.8664 (pm20) outliers start: 36 outliers final: 20 residues processed: 110 average time/residue: 0.4473 time to fit residues: 60.9762 Evaluate side-chains 103 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 79 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 733 CYS Chi-restraints excluded: chain A residue 989 ASP Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 989 ASP Chi-restraints excluded: chain B residue 1095 THR Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 786 THR Chi-restraints excluded: chain C residue 895 MET Chi-restraints excluded: chain C residue 928 LYS Chi-restraints excluded: chain C residue 935 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: [58, 112, 168, 238, 299, 66, 164, 37, 2, 162, 305] chunk 58 optimal weight: 2.9990 chunk 112 optimal weight: 8.9990 chunk 168 optimal weight: 1.9990 chunk 238 optimal weight: 8.9990 chunk 299 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 164 optimal weight: 0.9980 chunk 37 optimal weight: 9.9990 chunk 2 optimal weight: 0.9980 chunk 162 optimal weight: 0.3980 chunk 305 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 950 ASN B 482 ASN B 608 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.109467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.067357 restraints weight = 54527.137| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 3.23 r_work: 0.2826 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25709 Z= 0.113 Angle : 0.507 9.923 35062 Z= 0.259 Chirality : 0.043 0.349 4026 Planarity : 0.004 0.037 4497 Dihedral : 3.947 34.588 3903 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.84 % Allowed : 8.06 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.15), residues: 3126 helix: 3.18 (0.20), residues: 660 sheet: 0.82 (0.19), residues: 696 loop : -1.03 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 323 TYR 0.015 0.001 TYR C 360 PHE 0.019 0.001 PHE B 152 TRP 0.007 0.001 TRP A 431 HIS 0.003 0.000 HIS B1078 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (25644) covalent geometry : angle 0.50145 / 0.26 (34908) SS BOND : bond 0.00240 / 0.16 ( 41) SS BOND : angle 0.98995 / 0.74 ( 82) hydrogen bonds : bond 0.04580 / 2.93 ( 1065) hydrogen bonds : angle 4.98444 / 3.39 ( 2874) link_BETA1-4 : bond 0.00277 / 0.18 ( 12) link_BETA1-4 : angle 1.01706 / 0.66 ( 36) link_NAG-ASN : bond 0.00512 / 0.36 ( 12) link_NAG-ASN : angle 1.72021 / 1.14 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 ILE cc_start: 0.8080 (OUTLIER) cc_final: 0.7813 (pp) REVERT: A 740 ASP cc_start: 0.8573 (t0) cc_final: 0.8300 (p0) REVERT: A 989 ASP cc_start: 0.8666 (OUTLIER) cc_final: 0.8305 (t70) REVERT: B 96 ILE cc_start: 0.8485 (mp) cc_final: 0.8173 (tp) REVERT: B 989 ASP cc_start: 0.8735 (OUTLIER) cc_final: 0.8526 (t70) REVERT: C 50 ASP cc_start: 0.7894 (t70) cc_final: 0.7679 (t70) REVERT: C 740 ASP cc_start: 0.8060 (t0) cc_final: 0.7727 (p0) REVERT: C 928 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8477 (mtpt) REVERT: C 1033 LYS cc_start: 0.9542 (mmtp) cc_final: 0.9265 (mmtm) REVERT: C 1087 GLU cc_start: 0.8878 (pm20) cc_final: 0.8666 (pm20) outliers start: 23 outliers final: 15 residues processed: 107 average time/residue: 0.4601 time to fit residues: 60.6555 Evaluate side-chains 102 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 733 CYS Chi-restraints excluded: chain A residue 989 ASP Chi-restraints excluded: chain A residue 1131 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 989 ASP Chi-restraints excluded: chain B residue 1095 THR Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 786 THR Chi-restraints excluded: chain C residue 928 LYS Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 935 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: [41, 283, 56, 280, 79, 48, 14, 74, 153, 85, 278] chunk 41 optimal weight: 20.0000 chunk 283 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 280 optimal weight: 0.0040 chunk 79 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 chunk 153 optimal weight: 6.9990 chunk 85 optimal weight: 0.8980 chunk 278 optimal weight: 0.9980 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.110001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.067991 restraints weight = 54626.605| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 3.23 r_work: 0.2843 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 25709 Z= 0.100 Angle : 0.500 11.054 35062 Z= 0.253 Chirality : 0.043 0.297 4026 Planarity : 0.004 0.037 4497 Dihedral : 3.824 33.728 3903 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.84 % Allowed : 8.46 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.15), residues: 3126 helix: 3.26 (0.20), residues: 660 sheet: 0.76 (0.19), residues: 714 loop : -0.97 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 323 TYR 0.014 0.001 TYR B1062 PHE 0.036 0.001 PHE C 152 TRP 0.007 0.001 TRP A 431 HIS 0.002 0.000 HIS B1078 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (25644) covalent geometry : angle 0.49537 / 0.25 (34908) SS BOND : bond 0.00223 / 0.14 ( 41) SS BOND : angle 0.92505 / 0.69 ( 82) hydrogen bonds : bond 0.04271 / 2.73 ( 1065) hydrogen bonds : angle 4.89302 / 3.33 ( 2874) link_BETA1-4 : bond 0.00317 / 0.20 ( 12) link_BETA1-4 : angle 1.01038 / 0.65 ( 36) link_NAG-ASN : bond 0.00469 / 0.33 ( 12) link_NAG-ASN : angle 1.64003 / 1.09 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 TYR cc_start: 0.8304 (m-80) cc_final: 0.7642 (t80) REVERT: A 198 ILE cc_start: 0.8115 (OUTLIER) cc_final: 0.7850 (pp) REVERT: A 740 ASP cc_start: 0.8616 (t0) cc_final: 0.8393 (p0) REVERT: A 989 ASP cc_start: 0.8661 (OUTLIER) cc_final: 0.8279 (t70) REVERT: B 96 ILE cc_start: 0.8496 (mp) cc_final: 0.8172 (tp) REVERT: B 989 ASP cc_start: 0.8737 (m-30) cc_final: 0.8508 (t70) REVERT: C 50 ASP cc_start: 0.7897 (t70) cc_final: 0.7678 (t70) REVERT: C 211 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7799 (mm) REVERT: C 389 ASN cc_start: 0.8615 (m-40) cc_final: 0.8192 (m-40) REVERT: C 740 ASP cc_start: 0.8098 (t0) cc_final: 0.7687 (p0) REVERT: C 928 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8484 (mtpt) REVERT: C 1033 LYS cc_start: 0.9540 (mmtp) cc_final: 0.9259 (mmtm) REVERT: C 1087 GLU cc_start: 0.8868 (pm20) cc_final: 0.8666 (pm20) outliers start: 23 outliers final: 17 residues processed: 110 average time/residue: 0.4493 time to fit residues: 61.4153 Evaluate side-chains 106 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 989 ASP Chi-restraints excluded: chain A residue 1131 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 1095 THR Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 786 THR Chi-restraints excluded: chain C residue 928 LYS Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 935 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: [78, 31, 30, 183, 251, 63, 169, 255, 45, 181, 254] chunk 78 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 0.0000 chunk 183 optimal weight: 3.9990 chunk 251 optimal weight: 10.0000 chunk 63 optimal weight: 0.9980 chunk 169 optimal weight: 0.8980 chunk 255 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 181 optimal weight: 8.9990 chunk 254 optimal weight: 5.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 551 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.108601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.066229 restraints weight = 54981.115| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 3.26 r_work: 0.2812 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 25709 Z= 0.149 Angle : 0.531 12.966 35062 Z= 0.270 Chirality : 0.044 0.285 4026 Planarity : 0.004 0.037 4497 Dihedral : 3.902 33.082 3903 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.87 % Allowed : 8.64 % Favored : 90.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.15), residues: 3126 helix: 3.39 (0.20), residues: 642 sheet: 0.78 (0.19), residues: 690 loop : -1.00 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 760 TYR 0.016 0.001 TYR A1062 PHE 0.011 0.001 PHE C 451 TRP 0.008 0.001 TRP C 99 HIS 0.003 0.001 HIS A1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (25644) covalent geometry : angle 0.52537 / 0.27 (34908) SS BOND : bond 0.00369 / 0.24 ( 41) SS BOND : angle 1.08826 / 0.82 ( 82) hydrogen bonds : bond 0.04957 / 3.18 ( 1065) hydrogen bonds : angle 4.99392 / 3.39 ( 2874) link_BETA1-4 : bond 0.00210 / 0.12 ( 12) link_BETA1-4 : angle 1.04340 / 0.68 ( 36) link_NAG-ASN : bond 0.00465 / 0.33 ( 12) link_NAG-ASN : angle 1.73754 / 1.14 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 TYR cc_start: 0.8353 (m-80) cc_final: 0.7654 (t80) REVERT: A 198 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7911 (pp) REVERT: A 989 ASP cc_start: 0.8720 (OUTLIER) cc_final: 0.8348 (t70) REVERT: B 96 ILE cc_start: 0.8540 (mp) cc_final: 0.8226 (tp) REVERT: B 989 ASP cc_start: 0.8793 (OUTLIER) cc_final: 0.8558 (t70) REVERT: C 50 ASP cc_start: 0.7928 (t70) cc_final: 0.7704 (t70) REVERT: C 211 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7813 (mm) REVERT: C 740 ASP cc_start: 0.8167 (t0) cc_final: 0.7752 (p0) REVERT: C 928 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8510 (mtpt) REVERT: C 1033 LYS cc_start: 0.9547 (mmtp) cc_final: 0.9276 (mmtm) outliers start: 24 outliers final: 19 residues processed: 110 average time/residue: 0.4528 time to fit residues: 61.4280 Evaluate side-chains 111 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 989 ASP Chi-restraints excluded: chain A residue 1131 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 989 ASP Chi-restraints excluded: chain B residue 1095 THR Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 786 THR Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 928 LYS Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 935 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: [169, 214, 57, 103, 216, 143, 96, 58, 236, 115, 154] chunk 169 optimal weight: 0.9990 chunk 214 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 216 optimal weight: 4.9990 chunk 143 optimal weight: 10.0000 chunk 96 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 chunk 236 optimal weight: 9.9990 chunk 115 optimal weight: 0.8980 chunk 154 optimal weight: 6.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.108597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.066358 restraints weight = 54814.250| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 3.25 r_work: 0.2816 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 25709 Z= 0.142 Angle : 0.537 13.862 35062 Z= 0.272 Chirality : 0.044 0.270 4026 Planarity : 0.004 0.036 4497 Dihedral : 3.917 33.379 3903 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.87 % Allowed : 8.71 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.15), residues: 3126 helix: 3.20 (0.20), residues: 660 sheet: 0.80 (0.19), residues: 687 loop : -0.98 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1086 TYR 0.015 0.001 TYR A1062 PHE 0.039 0.001 PHE C 152 TRP 0.007 0.001 TRP A 431 HIS 0.003 0.001 HIS A1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 (25644) covalent geometry : angle 0.53179 / 0.27 (34908) SS BOND : bond 0.00250 / 0.16 ( 41) SS BOND : angle 1.10404 / 0.84 ( 82) hydrogen bonds : bond 0.04851 / 3.10 ( 1065) hydrogen bonds : angle 4.95460 / 3.37 ( 2874) link_BETA1-4 : bond 0.00249 / 0.15 ( 12) link_BETA1-4 : angle 0.99729 / 0.65 ( 36) link_NAG-ASN : bond 0.00476 / 0.33 ( 12) link_NAG-ASN : angle 1.70832 / 1.13 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6252 Ramachandran restraints generated. 3126 Oldfield, 0 Emsley, 3126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 TYR cc_start: 0.8363 (m-80) cc_final: 0.7692 (t80) REVERT: A 198 ILE cc_start: 0.8185 (OUTLIER) cc_final: 0.7914 (pp) REVERT: A 989 ASP cc_start: 0.8709 (OUTLIER) cc_final: 0.8350 (t70) REVERT: B 96 ILE cc_start: 0.8537 (mp) cc_final: 0.8222 (tp) REVERT: B 453 LYS cc_start: 0.8724 (mmpt) cc_final: 0.7934 (pttt) REVERT: B 989 ASP cc_start: 0.8774 (OUTLIER) cc_final: 0.8562 (t70) REVERT: C 124 LYS cc_start: 0.7418 (mmmt) cc_final: 0.6914 (tppt) REVERT: C 211 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7840 (mm) REVERT: C 740 ASP cc_start: 0.8181 (t0) cc_final: 0.7780 (p0) REVERT: C 928 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8512 (mtpt) REVERT: C 1033 LYS cc_start: 0.9547 (mmtp) cc_final: 0.9276 (mmtm) outliers start: 24 outliers final: 17 residues processed: 110 average time/residue: 0.4630 time to fit residues: 62.6297 Evaluate side-chains 104 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 989 ASP Chi-restraints excluded: chain A residue 1131 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 989 ASP Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 786 THR Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 928 LYS Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 935 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: [137, 30, 9, 43, 301, 272, 219, 279, 63, 111, 88] chunk 137 optimal weight: 8.9990 chunk 30 optimal weight: 0.8980 chunk 9 optimal weight: 7.9990 chunk 43 optimal weight: 10.0000 chunk 301 optimal weight: 0.3980 chunk 272 optimal weight: 0.9990 chunk 219 optimal weight: 0.7980 chunk 279 optimal weight: 0.4980 chunk 63 optimal weight: 0.0970 chunk 111 optimal weight: 10.0000 chunk 88 optimal weight: 0.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 705 ASN C 705 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.110232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.067923 restraints weight = 54434.334| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 3.27 r_work: 0.2863 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 25709 Z= 0.095 Angle : 0.513 13.521 35062 Z= 0.257 Chirality : 0.043 0.269 4026 Planarity : 0.004 0.037 4497 Dihedral : 3.747 33.195 3903 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.69 % Allowed : 9.04 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.15), residues: 3126 helix: 3.17 (0.20), residues: 678 sheet: 0.74 (0.19), residues: 705 loop : -0.95 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 629 TYR 0.015 0.001 TYR A 360 PHE 0.011 0.001 PHE A 87 TRP 0.011 0.001 TRP C 99 HIS 0.002 0.000 HIS C1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.09 (25644) covalent geometry : angle 0.50900 / 0.26 (34908) SS BOND : bond 0.00226 / 0.15 ( 41) SS BOND : angle 0.85536 / 0.63 ( 82) hydrogen bonds : bond 0.03957 / 2.52 ( 1065) hydrogen bonds : angle 4.78872 / 3.26 ( 2874) link_BETA1-4 : bond 0.00344 / 0.22 ( 12) link_BETA1-4 : angle 0.92532 / 0.59 ( 36) link_NAG-ASN : bond 0.00452 / 0.31 ( 12) link_NAG-ASN : angle 1.53028 / 1.02 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7378.75 seconds wall clock time: 126 minutes 28.43 seconds (7588.43 seconds total)